BIOLOGY

John W. Kimball
Tufts University & Harvard University
Tufts University & Harvard University
Biology

John W. Kimball
This text is disseminated via the Open Education Resource (OER) LibreTexts Project (https://LibreTexts.org) and like the hundreds
of other texts available within this powerful platform, it is freely available for reading, printing and "consuming." Most, but not all,
pages in the library have licenses that may allow individuals to make changes, save, and print this book. Carefully
consult the applicable license(s) before pursuing such effects.
Instructors can adopt existing LibreTexts texts or Remix them to quickly build course-specific resources to meet the needs of their
students. Unlike traditional textbooks, LibreTexts’ web based origins allow powerful integration of advanced features and new
technologies to support learning.

The LibreTexts mission is to unite students, faculty and scholars in a cooperative effort to develop an easy-to-use online platform
for the construction, customization, and dissemination of OER content to reduce the burdens of unreasonable textbook costs to our
students and society. The LibreTexts project is a multi-institutional collaborative venture to develop the next generation of open-
access texts to improve postsecondary education at all levels of higher learning by developing an Open Access Resource
environment. The project currently consists of 14 independently operating and interconnected libraries that are constantly being
optimized by students, faculty, and outside experts to supplant conventional paper-based books. These free textbook alternatives are
organized within a central environment that is both vertically (from advance to basic level) and horizontally (across different fields)
integrated.
The LibreTexts libraries are Powered by NICE CXOne and are supported by the Department of Education Open Textbook Pilot
Project, the UC Davis Office of the Provost, the UC Davis Library, the California State University Affordable Learning Solutions
Program, and Merlot. This material is based upon work supported by the National Science Foundation under Grant No. 1246120,
1525057, and 1413739.
Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not
necessarily reflect the views of the National Science Foundation nor the US Department of Education.
Have questions or comments? For information about adoptions or adaptions contact [email protected]. More information on our
activities can be found via Facebook (https://facebook.com/Libretexts), Twitter (https://twitter.com/libretexts), or our blog
(http://Blog.Libretexts.org).
This text was compiled on 05/01/2023
TABLE OF CONTENTS
About this Book
Licensing

Unit 1: The Chemical Basis of Life

1.1: Mixtures and Compounds
1.2: Elements and Atoms
1.3: Electronegativity and types of Chemical Bonds
1.4: Noncovalent Bonding
1.5: Hydrogen Bonds
1.6: Acids and Bases
1.7: Molecular Weight and the Mole
1.8: pH

Unit 2: The Molecules of Life

2.1: Organic Molecules
2.2: Hydrocarbons
2.3: Fats
2.4: Phospholipids
2.5: Cholesterol
2.6: Carbohydrates
2.7: Amino Acids
2.8: Enantiomers
2.9: Polypeptides
2.10: Proteins
2.11: Rules of Protein Structure
2.12: Glycoproteins
2.13: Nucleotides
2.14: Proteomics

Unit 3: The Cellular Basis of Life

3.1: Animal Cells
3.2: Cell Membranes
3.3: The Nucleus
3.4: Ribosomes
3.5: Endoplasmic Reticulum
3.6: Golgi Apparatus
3.7: Centrosomes and Centrioles
3.8: Lysosomes and Peroxisomes
3.9: Protein Kinesis
3.10: The Proteasome
3.11: The Cytoskeleton
3.12: Cilia
3.13: Animal Tissues
3.14: Adipose Tissue
3.15: Junctions between Cells
3.16: Plant Cells

1 https://bio.libretexts.org/@go/page/25004
 3.17: Chloroplasts
3.18: Chlorophylls and Carotenoids
3.19: Plant Tissues
3.20: Apoptosis
3.21: Collagens
3.22: Chromatophores
3.23: Diffusion, Active Transport and Membrane Channels
3.24: Endocytosis
3.25: Exocytosis

Unit 4: Cell Metabolism

4.1: Enzymes
4.2: ATP
4.3: NAD and NADP
4.4: Glycolysis
4.5: Cellular Respiration
4.6: ATP Synthase
4.7: Photosynthesis - Pathway of Carbon Fixation
4.8: Photosynthesis - The Role of Light
4.9: Photosynthesis - Dicovering the Secrets
4.10: Chemiosmosis
4.11: Metabolism
4.12: Intermediary Metabolism
4.13: G Proteins
4.14: Secondary Messengers
4.15: Bioluminescence

Unit 5: DNA
5.1: Transformation in Bacteria
5.2: The Hershey - Chase Experiments
5.3: The Double Helix of DNA
5.4: Base Pairing in DNA and RNA
5.5: DNA Replication
5.6: The Meselson - Stahl Experiment
5.7: Restriction Enzymes
5.8: DNA Sequencing by the Dideoxy Method
5.9: Genome Sizes
5.10: The Human Genome Projects
5.11: The Human and Chimpanzee Genomes
5.12: Pyrosequencing
5.13: DNA Repair
5.14: Harlequin Chromosomes
5.15: Metagenomics - Exploring the Microbial World

Unit 6: Gene Expression

6.1: One Gene - One Enzyme Theory
6.2: The Transcription of DNA into RNA
6.3: Genetic Code
6.4: The Translation of RNA into Proteins
6.5: RNA Editing
6.6: Expressed Sequence Tags

2 https://bio.libretexts.org/@go/page/25004
 6.7: Ribosomal RNA (rRNA) Gene Cluster

Unit 7: Cell Division

7.1: Chromosomes
7.2: The Cell Cycle
7.3: Mitosis
7.4: Polyploidy
7.5: Endoreplication
7.6: Sex Chromosomes
7.7: Meiosis

Unit 8: The Genetic Consequences of Meiosis

8.1: Mendel's Monohybrid Crosses
8.2: Crossing Over and Genetic Recombination in Meiosis
8.3: The Evidence of Creighton and McClintock
8.4: Genetic linkage and Genetic Maps
8.5: Gene Mapping with Three-point Crosses
8.6: Quantitative Trait Loci
8.7: Mapping the Genes of T2
8.8: rII Locus of T4

Unit 9: Regulation of Gene Expression

9.1: Regulation of Gene Expression in Bacteria
9.2: The Tryptophan Repressor
9.3: Regulation of Gene Expression in Eukaryotes
9.4: Steroid Response Elements
9.5: Epigenetics
9.6: Visualization of Transcription and Translation in Bacteria
9.7: Footprinting
9.8: Chromatin Immunoprecipitation
9.9: Isolating Transcription Factors
9.10: Palindromes
9.11: Cell-speci c gene expression
9.12: Imprinted Genes
9.13: Ribozymes

Unit 10: Mutation

10.1: Mutations - Causes and Signi cance
10.2: Testing for Mutagenic Chemicals in Bacteria and Mice
10.3: Radiation and its effect on DNA
10.4: Transposons - "jumping genes"

Unit 11: Genomics

11.1: Recombinant DNA and Gene Cloning
11.2: Polymerase Chain Reaction
11.3: Gene Therapy - Methods and Prospects
11.4: Recent Advances in Gene Therapy
11.5: Transgenic Animals
11.6: Transgenic Plants
11.7: Restriction Fragment Length Polymorphisms

3 https://bio.libretexts.org/@go/page/25004
 11.8: Gel Blotting
11.9: Genetic Screening for Phenylketonuria
11.10: Antisense RNA
11.11: Antisense Oligodeoxynucleotides and their Therapeutic Potential
11.12: Forward and Reverse genetics
11.13: Metagenomics

Unit 12: Cancer

12.1: Cancer in General
12.2: Cancer Cells in Culture
12.3: Oncogenes
12.4: Tumor Suppressor Genes
12.5: BCL-2
12.6: Burkitt's Lymphoma
12.7: Chronic Myelogenous Leukemia (CML)
12.8: Fighting Cancer with Inhibitors of Angiogenesis
12.9: Immunotherapy of Cancer
12.10: Cancer- The Causes and Prevention of Cancer
12.11: Estimating Cancer Risks
12.12: The LD50 test
12.13: Dioxin
12.14: Magnetic Fields and Cancer

Unit 13: Aging

13.1: Aging
13.2: Telomeres

Unit 14: Embryonic Development and its Regulation

14.1: Embryonic Development
14.2: Frog Embryology
14.3: Cleavage
14.4: The Organizer
14.5: Segmentation - Organizing the Embryo
14.6: Homeobox Genes
14.7: Stem Cells
14.8: Embryonic Stem Cells
14.9: Germline vs. Soma
14.10: Regeneration

Unit 15: The Anatomy and Physiology of Animals

15.1: Nutrition
15.1A: The Human Gastrointestinal Tract
15.1B: Metabolism
15.1C: Nutrition
15.1D: Recommended Dietary Allowances
15.2: Gas Exchange
15.2A: Human Respiratory System
15.2B: Control of Breathing
15.2C: Vertebrate Lungs
15.2D: Tracheal Breathing

4 https://bio.libretexts.org/@go/page/25004
15.3: Circulatory Systems
15.3A: Anatomy of Human Circulatory System
15.3B: How the Human Circulatory System Works
15.3C: The Heartbeat
15.3D: The Lymphatic System
15.3E: Blood
15.3F: Blood Groups
15.3G: The Transport of Heat
15.3H: Blood Clotting
15.3I: Sickle-Cell Disease
15.3J: Serine Proteases
15.3K: Animal Circulatory Systems
15.4: Immune System
15.4.1: 15.4T Allergies
15.4A: Clonal Selection and Immunological Memory
15.4B: Antibody-Antigen Binding
15.4C: B Cells and T Cells
15.4D: Antigen Receptors
15.4E: Histocompatibility Molecules
15.4F: Antigen Receptor Diversity
15.4G: Anatomy of the Immune System
15.4H: T Helper cells
15.4I: Cytotoxic T lymphocytes (CTL)
15.4J: Cell-Mediated Immunity
15.4K: Organ Transplants
15.4L: Bone Marrow Transplants
15.4M: Antigen Presentation
15.4N: The Immunological Synapse
15.4O: Dendritic Cells
15.4P: Passive Immunity
15.4Q: Innate Immunity
15.4R: The Complement System
15.4S: In ammation
15.4U: Asthma
15.4V: AIDS
15.4W: Vaccines
15.5: Excretion
15.5A: Human Kidneys
15.5B: Vertebrate Kidneys
15.5C: Urea Cycle
15.6: Hormones
15.6.1: Human Hormones
15.6.1.1: Thyroid and Parathyroids
15.6.1.2: Hormones of the Gut
15.6.1.3: Hormones of the Pancreas
15.6.1.4: Hormones of the Pituitary
15.6.1.5: Hormones of the Hypothalamus
15.6.1.6: Adrenal Glands
15.6.1.7: Sex Hormones
15.6.1.8: Progesterone
15.6.1.9: Melatonin and the Pineal Gland

5 https://bio.libretexts.org/@go/page/25004
 15.6.1.10: Hormones of Kidney, Skin and Heart
15.6.1.11: Leptin - the Fat Hormone
15.6.1.12: Hormones of the Liver
15.6.1.13: Melanocyte Stimulating Hormone (MSH)
15.6.2: Insect Hormones
15.7: Sexual Reproduction
15.7A: Sexual Reproduction
15.7B: Asexual Reproduction in Animals
15.7C: Birth Control
15.7D: Prenatal Screening
15.7E: Extraembryonic Membranes and the Physiology of the Placenta
15.7F: Genetic Mosaics
15.7G: Human Cloning
15.8: Nervous System
15.8A: Neurons
15.8B: Synapses
15.8C: The Human Central Nervous System
15.8D: The Peripheral Nervous System
15.8E: Drugs and the Nervous System
15.8F: Nitric Oxide (NO)
15.8G: Prion Diseases
15.9: Senses
15.9A: Mechanoreceptors
15.9B: Hearing
15.9C: Vision
15.9D: Processing Visual Information
15.9E: Vision in Arthropods
15.9F: Heat, Cold, and Pain Receptors
15.9G: Taste
15.9H: Olfaction - The Sense of Smell
15.9I: Electric Organs and Electroreceptors
15.9J: Magnetoreceptors
15.10: Muscles
15.10A: Bones
15.10B: Muscles
15.10C: Testing the Sliding-Filament Hypothesis
15.11: Behavior
15.11.1: Innate Behavior
15.11.2: Taxis
15.11.3: Learned Behavior
15.11.4: Long-Term Potentiation (LTP)
15.11.5: Honeybee Navigation
15.11.6: Avoiding Predation
15.11.7: Pheromones
15.11.8: Circadian Rhythms in Drosophila and Mammals

Unit 16: The Anatomy and Physiology of Plants

16.1: Plant Anatomy
16.1.1: Plant Tissues
16.1.2: Roots

6 https://bio.libretexts.org/@go/page/25004
 16.1.3: Stems
16.1.4: The Leaf
16.1.5: Arabidopsis Thaliana
16.2: Plant Physiology
16.2A: Xylem
16.2B: Phloem
16.2C: Transpiration
16.2D: Gas Exchange in Plants
16.2E: Photorespiration and C4 Plants
16.2F: Tropisms
16.3: Reproduction in Plants
16.3A: Alternation of Generations in Plants
16.3B: Moss Life Cycle
16.3C: Fern Life Cycle
16.3D: Angiosperm Life Cycle
16.3E: Asexual Reproduction in Plants
16.3E: Self-incompatibility - How Plants Avoid Inbreeding
16.3F: Transgenic Plants
16.4: Plant Development - Fundamentals
16.4A: Plant Growth
16.4B: Germination of Seeds
16.4C: Etiolation
16.4D: Flowering
16.4E: Photoperiodism and Phytochrome
16.5: Plant Development - Hormones
16.5A: Abscisic acid (ABA)
16.5B: Auxin
16.5C: Cytokinins
16.5D: Ethylene
16.5E: Gibberellins
16.5F: Strigolactones

Unit 17: Ecology

17.1: Energy Flow through the Biosphere
17.1A: Ecosystem Productivity
17.1B: Food Chains and Food Webs
17.1C: Biomes
17.1D: Freshwater Ecosystems
17.1E: Marine Ecosystems
17.1F: Biomagni cation of Pesticides
17.2: Cycles of Matter in the Biosphere
17.2A: Carbon Cycle
17.2B: Nitrogen Cycle
17.2C: Symbiotic Nitrogen Fixation
17.2D: Soil
17.2E: Sewage Treatment
17.2F: Chlorination and the Law of Unintended Consequences
17.2G: Air Pollution
17.2H: Acid Rain
17.2I: Ozone

7 https://bio.libretexts.org/@go/page/25004
 17.3: The Growth of Populations
17.3A: The Human Population
17.3B: Principles of Population Growth
17.4: Interactions between Species
17.4A: Symbiosis
17.4B: Insecticides
17.4C: Biological Control of Pests

Unit 18: Evolution

18.1: Evolution and Adaptation
18.2: Speciation
18.3: The Evolution of Body Form in Animals
18.4: Recapitulation
18.5: Mutation and Evolution
18.6: The Hardy-Weinberg Equilibrium
18.7: Polymorphisms
18.8: Kin Selection
18.9: The Origin of Life
18.10: Mars
18.11: Endosymbiosis
18.12: Geologic Eras

Unit 19: The Diversity of Life

19.1: Eukaryotic Life
19.1.1: Taxonomy
19.1.2: Protists
19.1.3: Ciliates
19.1.4: Volvox
19.1.5: Diversity and Evolutionary Relationships of the Plants
19.1.6: Arabidopsis Thaliana - A Model Organism
19.1.7: Fungi
19.1.8: Yeast
19.1.9: Barcoding
19.1.10: Invertebrates
19.1.11: Drosophila Melanogaster
19.1.12: Caenorhabditis Elegans
19.1.13: Vertebrates
19.1.14: Zebra sh
19.1.15: Monotremes
19.2: Microbes
19.2A: Bacteria
19.2B: Archaea
19.2C: Antibiotics
19.2D: E. coli
19.2E: Anthrax
19.2F: Bacillus Thuringiensis
19.2G: The Rapid Identi cation of Microorganisms
19.3: Viruses
19.3A: Viruses
19.3B: In uenza

8 https://bio.libretexts.org/@go/page/25004
 19.3C: φX174
19.3D: Smallpox
19.3E: Retroviruses

Unit 20: General Science

20.1: Epidemiology
20.2: Types of Clinical Studies
20.3: Scienti c Methods
20.4: Scienti c Papers
20.5: Statistical Methods
20.6: Drugs

Index
Glossary

Detailed Licensing

9 https://bio.libretexts.org/@go/page/25004
About this Book
It has always seemed to me that the many parts that make up the subject of biology are related to each other more like the nodes of
a web than as a linear collection of independent topics. So I believe that the power of hypertext will be better suited to learning
about biology than is the linear structure of a printed textbook. Another disadvantage of printed textbooks is the inevitable delay
between the time that new advances in biology are reported and the time that they can become incorporated in a printed book (often
several years). Material here can be updated promptly. So although some of this information has been drawn from the sixth edition
of the author's text Biology published in 1994 by Wm. C. Brown, every effort has been made to adapt the material to the
opportunities provided by an online text.

1 https://bio.libretexts.org/@go/page/31346
Licensing
A detailed breakdown of this resource's licensing can be found in Back Matter/Detailed Licensing.

1 https://bio.libretexts.org/@go/page/97921
 CHAPTER OVERVIEW
Unit 1: The Chemical Basis of Life
The following pages examine some of the principles of chemistry upon which an understanding of modern biology depends.
1.1: Mixtures and Compounds
1.2: Elements and Atoms
1.3: Electronegativity and types of Chemical Bonds
1.4: Noncovalent Bonding
1.5: Hydrogen Bonds
1.6: Acids and Bases
1.7: Molecular Weight and the Mole
1.8: pH

This page titled Unit 1: The Chemical Basis of Life is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1
1.1: Mixtures and Compounds
Mixtures are heterogeneous forms of matter. Mixtures are composed of variable proportions of molecules and atoms.

The composition of a mixture is variable with each components retaining its characteristic properties. Its components are easily
separated. Examples of Mixtures: soil, ocean water and other solutions, air, the cytosol of a cell
n contrast, compounds are homogeneous forms of matter. Their constituent elements (atoms and/or ions) are always present in
fixed proportions . Properties of compounds include
The relative proportions of the elements in a compound are fixed.
The components of a compound do not retain their individual properties. Both sodium and chlorine are poisonous; their
compound, table salt (NaCl) is absolutely essential to life.
It takes large inputs of energy to separate the components of a compound.

Examples of Compounds
water (H2O)
table salt (NaCl)
sucrose (table sugar, C12H22O11)

Separating the Components of a Mixture

Most laboratory work in biology requires the use of techniques to separate the components of mixtures. This is done by exploiting
some property that distinguishes the components, such as their relative
size
density
solubility
electrical charge

Dialysis
Dialysis is the separation of small solute molecules or ions (e.g., glucose, Na+, Cl-) from macromolecules (e.g., starch) by virtue of
their differing rates of diffusion through a differentially permeable membrane.

Figure 1.1.1 : Small-molecule dialysis using dialysis tubing. (CC-SA-BY-3.0; Potcherboy).

As shown in Figure 1.1.1, the cellophane used to construct a bag is perforated with tiny pores that permit ions and small molecules
to pass through, but exclude molecules with molecular weights greater than about 12,000. If a cellophane bag is mixed with a
mixture of sugar and starch and place it in salt water, the sugar molecules (teal dots) will diffuse out into the water until

1.1.1 https://bio.libretexts.org/@go/page/3741
equilibrium is reached; i.e., until their concentrations are equal on both sides of the membrane. Similarly, the salt (red dots) will
diffuse into the bag. However, because of their large size, all the starch (big blue disks) will be retained within the tubing.

Chromatography
Chromatography is the term used for several techniques for separating the components of a mixture. The different types of
chromatography techniques used are: paper chromatography, exclusion chromatography, and affinity chromatography.
Paper chromatography technique provides an easy way to separate the components of a mixture. A drop of mixture is placed in one
corner of a square of absorbent paper.
One edge of the paper is immersed in a solvent. (a)
The solvent migrates up the sheet by capillary attraction.
As it does so, the substances in the drop are carried along at different rates. (b)
Each compound migrates at a rate that reflects
the size of its molecule and
its solubility in the solvent.
After a second run at right angles to the first (often using a different solvent), the various substances will be spread out at
distinct spots across the sheet, forming a chromatogram. (c)
The identity of each spot can be determined by comparing its position with the position occupied by known substances under
the same conditions.
In many cases, a fragment of the paper can be cut away from the sheet and chemical analysis run on the tiny amount of
substance in it.

Figure 1.1.2: Paper chromatography

Autoradiography
If the mixture contains molecules that have been labeled with a radioactive isotope, these can be located by placing the
chromatogram next to a sheet of X-ray film. The location of dark spots on the developed film (because of radiation emitted by the
isotope) can be correlated with the position of the substances on the chromatogram.

1.1.2 https://bio.libretexts.org/@go/page/3741
The above figures (courtesy of Dr. James A. Bassham) show autoradiograms of the type that were essential in working out the dark
reactions of photosynthesis. The dark spots show the radioactive compounds produced after 10 secs (left) and 2 minutes (right) of
photosynthesis by the green alga Scenedesmus. The alga was supplied with carbon dioxide labeled with 14C, a radioactive isotope
of carbon.
At 10 seconds, most of the radioactivity is found in 3-phosphoglyceric acid ("P-Glyceric").
At 2 minutes, phosphorylated 6-carbon sugars (glucose and fructose) have been synthesized as well as a number of amino acids.
The small rectangle and circle (lower right-hand corners) mark the spots where the cell extract was applied.

Exclusion chromatography
One of the most common problems in biochemical research is to separate the many components — usually
macromolecules — in cell extracts and the like. Methods for separating the components of a mixture exploit such
differences as size, electrical charge, and solubility in different solvents. of the molecules in it. One example:
Electrophoresis which separates such macromolecules as proteins and DNA by their charge (and sometimes size as
well).
Exclusion chromatography separates molecules on the basis of size. A column is filled with semi-solid beads of a
polymeric gel that will admit ions and small molecules (blue) into their interior but not large ones (shown in red).
When a mixture of molecules and ions dissolved in a solvent is applied to the top of the column, the smaller
molecules (and ions) are distributed through a larger volume of solvent than is available to the large molecules.
Consequently, the large molecules move more rapidly through the column, and in this way the mixture can be
separated (fractionated) into its components. The porosity of the gel can be adjusted to exclude all molecules above a
certain size. Sephadex and sepharose are trade names for gels that are available commercially in a broad range of
porosities.

Affinity chromatography
The goal of affinity chromatography is to separate all the molecules of a particular specificity
from the whole gamut of molecules in a mixture such as a blood serum. For example, the
antibodies in a serum sample specific for a particular antigenic determinant can be isolated by
the use of affinity chromatography.
The following steps are performed to achieve that:
Step 1
An immunoadsorbent is prepared. This consists of a solid matrix to which the antigen
(shown in blue) has been coupled (usually covalently). Agarose, sephadex, derivatives of
cellulose, or other polymers can be used as the matrix.
Step 2
The serum is passed over the immunoadsorbent. As long as the capacity of the column is not
exceeded, those antibodies in the mixture specific for the antigen (shown in red) will bind (noncovalently) and be retained.
Antibodies of other specificities (green) and other serum proteins (yellow) will pass through unimpeded.
Step 3
Elution. A reagent is passed into the column to release the antibodies from the immunoadsorbent. Buffers containing a high
concentration of salts and/or low pH are often used to disrupt the noncovalent interactions between antibodies and antigen. A
denaturing agent, such as 8 M urea, will also break the interaction by altering the configuration of the antigen-binding site of the
antibody molecule.
Another, gentler, approach is to elute with a soluble form of the antigen. These compete with the immunoadsorbent for the antigen-
binding sites of the antibodies and release the antibodies to the fluid phase.
Step 4
Dialysis. The eluate is then dialyzed against, for example, buffered saline in order to remove the reagent used for elution.

1.1.3 https://bio.libretexts.org/@go/page/3741
Electrophoresis
Electrophoresis uses a direct electric current to separate the components of a mixture by the differing electrical charge.

Example of Electrophoresis
Proteins in blood serum can be separated by electrophoresis.

A drop of serum is applied in a band to a thin sheet of supporting material, like paper, that has been soaked in a slightly-alkaline
salt solution.
At pH 8.6, which is commonly used, all the proteins are negatively charged, but some more strongly than others.
A direct current can flow through the paper because of the conductivity of the buffer with which it is moistened.
As the current flows, the serum proteins move toward the positive electrode.
The stronger the negative charge on a protein, the faster it migrates.
After a time (typically 20 min), the current is turned off and the proteins stained to make them visible (most are otherwise
colorless).
The separated proteins appear as distinct bands.
The most prominent of these and the one that moves closest to the positive electrode is serum albumin.
The other proteins are the various serum globulins.

Pure Substances
Some of the pure substances isolated from mixtures cannot be further broken down. Oxygen (O2) is an example. It is one of the
elements; the fundamental building blocks of matter. Most pure substances are compounds. Table salt, sodium chloride (NaCl), is
an example; water (H2O) is another. If we pass an electrical current through molten NaCl, two new substances will be formed:
sodium, a shiny metal so reactive that it must be stored out of contact with the air
chlorine, a yellowish poisonous gas.
In this operation, a compound has been decomposed into its constitutive elements. Note the differences between separating the
components of a mixture and those of a compound. The decomposition of NaCl required a large input of energy since the strong
ionic bonds holding the Na and Cl atoms together must be broken. The ratio of the weights of the two products are always 23 parts
of sodium to 35.5 parts of chlorine. This reflects the invariance of the ratio (1:1 in this case) of the number of atoms in a compound
and the relative weights (23:35.5) of the atoms in table salt. The properties of the components of the compound are not the same as
those of the compound itself. Both sodium and chlorine are hazardous to life; their compound, sodium chloride, is a vital ingredient
of all animal diets.

This page titled 1.1: Mixtures and Compounds is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1.1.4 https://bio.libretexts.org/@go/page/3741
 1.2: Elements and Atoms
Elements
Elements consist of only one kind of atom and cannot be decomposed into simpler substances. Our planet is made up of some 90
elements. (Tiny amounts — sometimes only a few atoms — of additional elements have been made in nuclear physics laboratories,
but they play no role in our story). Of these 90, only 25 or so are used to build living things. The table shows the 11 most prevalent
elements in the lithosphere (the earth's crust) and in the human body.
Living matter
uses only a fraction of the elements available to it
but, as the table shows, the relative proportions of those it does acquire from its
surroundings are quite different from the proportions in the environment
So,
the composition of living things is not simply a reflection of the elements available to
them
For example, hydrogen, carbon, and nitrogen together represent less than 1% of the
atoms found in the earth's crust but some 74% of the atoms in living matter.
one of the properties of life is to take up certain elements that are scarce in the nonliving
world and concentrate them within living cells.
Some sea animals accumulate elements like vanadium and iodine within their cells to
concentrations a thousand or more times as great as in the surrounding sea water. It has
even been proposed that uranium be "mined" from the sea by extracting it from certain
algae that can take up uranium from sea water and concentrate it within their cells.
There is still some uncertainty about the exact number of elements required by living things.
Some elements, e.g., aluminum, are found in tiny amounts in living tissue, but whether they
are playing an essential role or are simply an accidental acquisition (aluminum probably is) is sometimes difficult to determine.

Atoms
Each element is made up of one kind of atom. We can define an atom as the smallest part of an element that can enter into
combination with other elements.

Structure of the atom

Each atom consists of a small, dense, positively-charged nucleus surrounded by much lighter, negatively-charged electrons. The
nucleus of the simplest atom, the hydrogen atom (H), consists of a single positively-charged proton. Because of its single proton,
the atom of hydrogen is assigned an atomic number of 1 and a single electron. The charge of the electron is the same magnitude
as that of the proton, so the atom as a whole is electrically neutral. Its proton accounts for almost all the weight of the atom.
The nucleus of the atom of the element helium (He) has two protons (hence helium has an atomic number of 2) and two
neutrons. Neutrons have the same weight as protons but no electrical charge. The helium atom has two electrons so that, once
again, the atom as a whole is neutral.
The structure of each of the other kinds of atoms follows the same plan. From Lithium (At. No. = 3) to uranium (At. No. = 92), the
atoms of each element can be listed in order of increasing atomic number. There are no gaps in the list. Each element has a unique
atomic number and its atoms have one more proton and one more electron than the atoms of the element that precedes it in the list.

Electrons
Ele
mber Atomic
Element
Number Element Energy Levels or "shells"
ctro
K L M N O
ns
are 1 Hydrogen (H) 1
con

1.2.1 https://bio.libretexts.org/@go/page/3742
 fine
mber Atomic
Element
Number Element Energy Levels or "shells"
d to
2 Helium (He) 2
rela
tive 3 Lithium (Li) 2 1
ly 4 Beryllium (Be) 2 2
disc
5 Boron (B) 2 3
rete
regi 6 Carbon (C) 2 4
ons 7 Nitrogen (N) 2 5
aro
8 Oxygen (O) 2 6
und
the 9 Fluorine (F) 2 7
nuc 10 Neon (Ne) 2 8
leus
. 11 Sodium (Na) 2 8 1

The 12 Magnesium (Mg) 2 8 2

two
13 Aluminum (Al) 2 8 3
elec
tron 14 Silicon (Si) 2 8 4
s of 15 Phosphorus (P) 2 8 5
heli
16 Sulfur (S) 2 8 6
um,
for 17 Chlorine (Cl) 2 8 7
exa 18 Argon (Ar) 2 8 8
mpl
19 Potassium (K) 2 8 8 1
e,
are 20 Calcium (Ca) 2 8 8 2
con 21 Scandium (Sc) 2 8 9 2
fine
22 Titanium (Ti) 2 8 10 2
d to
a 23 Vanadium (V) 2 8 11 2
sph 24 Chromium (Cr) 2 8 13 1
eric
25 Manganese (Mn) 2 8 13 2
al
zon 26 Iron (Fe) 2 8 14 2
e 27 Cobalt (Co) 2 8 15 2
surr
oun 28 Nickel (Ni) 2 8 16 2

din 29 Copper (Cu) 2 8 18 1

g
30 Zinc (Zn) 2 8 18 2
the
nuc 31 Gallium (Ga) 2 8 18 3
leus 32 Germanium (Ge) 2 8 18 4
call
33 Arsenic (As) 2 8 18 5
ed
the 34 Selenium (Se) 2 8 18 6
K 35 Bromine (Br) 2 8 18 7
she
36 Krypton (Kr) 2 8 18 8
ll or
K Molybdenum
42 2 8 18 13 1
ene (Mo)
rgy 48 Cadmium (Cd) 2 8 18 18 2

1.2.2 https://bio.libretexts.org/@go/page/3742
 lev
mber Atomic
Element
Number Element Energy Levels or "shells"
el.
50 Tin (Sn) 2 8 18 18 4
Lit
53 Iodine (I) 2 8 18 18 7
hiu
m
(At. No. = 3) has three electrons, two in the K shell and one located farther from the nucleus in the L shell. Being farther away
from the opposite (+) charges of the nucleus, this third electron is held less tightly.
Each of the following elements, in order of increasing atomic number, adds one more electron to the L shell until we reach neon
(At. No. = 10) which has eight electrons in the L shell.
Sodium places its eleventh electron in a still higher energy level, the M shell.
From sodium to argon, this shell is gradually filled with electrons until, once again, a maximum of eight is reached.
Note that after the K shell with its maximum of two electrons, the maximum number of electrons in any other outermost shell is
eight.
As we shall see, the chemical properties of each element are strongly influenced by the number of electrons in its outermost
energy level (shell).
This table shows the electronic structure of the atoms of elements 1 – 36 with those that have been demonstrated to be used by
living things shown in red. Four elements of still higher atomic numbers that have been shown to be used by living things are also
included.

The electronic structure of an atom plays the major role in its chemistry.
The pattern of electrons in an atom — especially those in the outermost shell — determines
the valence of the atom; that is, the ratios with which it interacts with other atoms, and to a large degree,
the electronegativity of the atom; that is, the strength with which it attracts other electrons.
Elements with the same number of electrons in their outermost shell show similar chemical properties.
Example 1: Fluorine, chlorine, bromine, and iodine each have 7 electrons in their outermost shell. These so-called halogens are
also quite similar in their chemical behavior. When dissolved in water, for example, they all produce germicidal solutions.
Example 2: Those elements with 1, 2, or 3 electrons in their outermost shell are the metals.
Example 3: Those elements with 4, 5, 6, or 7 in their outermost shell are the nonmetals.
Example 4: Helium (with its 2), neon, argon, and krypton (each with 8) have "filled" their outermost shells. They are the so-
called inert or "noble" gases. They have no chemistry at all. Under normal conditions they do not interact with other atoms. So, it is
the number and arrangement of the electrons in the atoms of an element that establish the chemical behavior of that element.
This is how it works:
The atoms of an element interact with other atoms in such ways and ratios that they can "fill" their outermost shell with 8 electrons
(2 for hydrogen). They may do this by
acquiring more electrons from another atom
losing electrons to another atom
sharing electrons with another atom
The number of electrons that an atom must acquire, or lose, or share to reach a stable configuration of 8 (2 for hydrogen) is called
its valence.
Hydrogen, lithium, sodium, and potassium atoms all have a single electron in their outermost shell. Fluorine, chlorine, bromine,
and iodine atoms all have 7. Any atom of the first group will interact with a single atom of any of the second group forming, HCl,
NaCl, KI, etc. The result of all of these interactions is a pair of atoms each with an outermost shell like that of one of the inert
gases: 2 for hydrogen, 8 for the others.
The elements with 2 electrons in their outermost shell interact with chlorine and the other halogens to form, e.g., BeCl2, MgCl2,
CaCl2. Again, the result is a pair of atoms each with a stable octet of electrons in its outermost shell.

1.2.3 https://bio.libretexts.org/@go/page/3742
The elements with 3 electrons in their outermost shell will interact with chlorine in a ratio of 1:3, forming BCl3, AlCl3.
Carbon atoms, with their 4 electrons in the L shell interact with chlorine to form CCl4.
Nitrogen, with its 5 outermost electrons, interacts with hydrogen atoms in a ratio of 1:3, forming ammonia (NH3).
Oxygen and sulfur, with their 6 outermost electrons react with hydrogen to form water (H2O) and hydrogen sulfide (H2S).
What determines whether a pair of atoms swap or share electrons?
The answer is their relative electronegativities. If two atoms differ greatly in their affinity for electrons; that is, in their
electronegativity, then the strongly electronegative atom will take the electron away from the weakly electronegative one.
Example: Na (weakly electronegative) gives up its single electron to an atom of chlorine (strongly electronegative) to form NaCl.
The sodium atom now has only 10 electrons but still 11 protons so there is a net positive charge of one on the atom. Similarly,
chlorine now has one more electron than proton so its now has a net negative charge of 1. Electrically charged atoms are called
ions. The mutual attraction of opposite electrical charges holds the ions together by ionic bonds.
Example: Carbon and hydrogen are both only weakly electronegative so neither can remove electrons from the other. Instead they
achieve a stable configuration by sharing their outermost electrons forming covalent bonds of CH4.

Isotopes
The number of protons in the nucleus of its atoms, which is its atomic number, defines each element. However, the nuclei of a
given element may have varying numbers of neutrons. Because neutrons have weight (about the same as that of protons), such
atoms differ in the atomic weight.
Atoms of the same element that differ in their atomic weight are called isotopes.
Atomic weights are expressed in terms of a standard atom: the isotope of carbon that has 6 protons and 6 neutrons in its nucleus.
This atom is designated carbon-12 or 12C. It is arbitrarily assigned an atomic weight of 12 daltons (named after John Dalton, the
pioneer in the study of atomic weights). Thus a dalton is 1/12 the weight of an atom of 12C. Both protons and neutrons have
weights very close to 1 dalton each. Carbon-12 is the most common isotope of carbon. Carbon-13 (13C) with 6 protons and 7
neutrons, and carbon-14 (14C) with 6 protons and 8 neutrons are found in much smaller quantities.

Isotopes as "tracers"
One can prepare, for example, a carbon compound used by living things that has many of its normal 12C atoms replaced by 14C
atoms. Carbon-14 happens to be radioactive. By tracing the fate of radioactivity within the organism, one can learn the normal
pathway of this carbon compound in that organism. Thus 14C serves as an isotopic "label" or "tracer".
The basis of this technique is that the weight of the nucleus of an atom has little or no effect on the chemical properties of that
atom. The chemistry of an element and the atoms of which it is made — whatever their atomic weight — is a function of the
atomic number of that element. As long as the atom had 6 protons, it is an atom of carbon irrespective of the number of neutrons.
Thus while 6 protons and 8 neutrons produce an isotope of carbon, 14C, 7 protons and 7 neutrons produce a totally-different
element, nitrogen-14.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and made
possible by funding from The Saylor Foundation.

This page titled 1.2: Elements and Atoms is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1.2.4 https://bio.libretexts.org/@go/page/3742
1.3: Electronegativity and types of Chemical Bonds
Electronegativity
The electronegativity of an atom is a measure of its affinity for electrons. The atoms of the various elements differ in their affinity
for electrons.

Figure 1.3.1
This image distorts the conventional periodic table of the elements so that the greater the electronegativity of an atom, the higher its
position in the table. Although fluorine (F) is the most electronegative element, it is the electronegativity of runner-up oxygen (O)
that is exploited by life. The shuttling of electrons between carbon (C) and oxygen (O) atoms powers life.
1. Moving electrons against the gradient (O to C) — as occurs in photosynthesis — requires energy (and stores it).
2. Moving electrons down the gradient (C to O) — as occurs in cellular respiration — releases energy.
The relative electronegativity of two interacting atoms also plays a major part in determining what kind of chemical bond forms
between them.

Chemical Bonds
Three main types of chemical bonds:Ionic Bond, Covalent Bond, Polar Covalent Bond.

Ionic Bond
Example of an ionic bond is : Sodium (Na) and Chlorine (Cl) = Ionic Bond. There is a large difference in
electronegativity between Na and Cl atoms, so
the chlorine atom takes an electron from the sodium atom
converting the atoms into ions (Na+) and (Cl−)
These are held together by their opposite electrical charge forming ionic bonds
Each sodium ion is held by 6 chloride ions while each chloride ion is, in turn, held by 6 sodium ions
Result: a crystal lattice (not molecules) of common table salt (NaCl)

Covalent Bond
Example of a covalent bond is: Carbon (C) and Hydrogen (H) = Covalent Bond. There is only a small difference in
electronegativity between the C and H atoms, so
the two atoms share the electrons
Result: a covalent bond (depicted as C:H or C-H)
The atoms are held together by their mutual affinity for their shared electrons
An array of atoms held together by covalent bonds forms a true molecule

Polar Covalent Bond

Example of a polar covalent bond is: Hydrogen (H) and Oxygen (O) = Polar Covalent Bond. There is a moderate difference in
electronegativity, causing the oxygen atom to pull the electron of the hydrogen atom closer to itself. This results in a polar

1.3.1 https://bio.libretexts.org/@go/page/3743
covalent bond. Oxygen does this with 2 hydrogen atoms to form a molecule of water
Molecules, like water, with polar covalent bonds are themselves polar; that is, have partial electrical charges across the molecule
and may be attracted to each other (as occurs with water molecules). These species are good solvents for polar and/or hydrophilic
compounds may form hydrogen bonds.

This page titled 1.3: Electronegativity and types of Chemical Bonds is shared under a CC BY 3.0 license and was authored, remixed, and/or
curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is
available upon request.

1.3.2 https://bio.libretexts.org/@go/page/3743
1.4: Noncovalent Bonding
Noncovalent Bonding
Noncovalent bonding does not involve sharing of electrons. Instead it:
holds the two strands of the DNA double helix together (hydrogen bonds)
folds polypeptides into such secondary structures as the alpha helix and the beta conformation
enables enzymes to bind to their substrate
enables antibodies to bind to their antigen
enables transcription factors to bind to each other
enables transcription factors to bind to DNA
enables proteins (e.g. some hormones) to bind to their receptor
permits the assembly of such macromolecular machinery as
ribosomes
actin filaments
microtubules
and many more
There are three principle kinds of noncovalent forces:
ionic interactions
hydrophobic interactions
hydrogen bonds

Ionic Interactions
At any given pH, proteins have charged groups that may participate in binding them to each other or to other types of molecules.
For example, as the figure shows, negatively-charged carboxyl groups on aspartic acid (Asp) and glutamic acid (Glu) residues may
be attracted by the positively-charged free amino groups on lysine (Lys) and arginine (Arg) residues.
Ionic interactions are highly sensitive to
changes in pH.
As the pH drops,
H+ bind to the carboxyl groups (COO-) of aspartic acid (Asp) and glutamic acid (Glu),
neutralizing their negative charge, and
H+ bind to the unoccupied pair of electrons on the N atom of the amino (NH2) groups of lysine
(Lys) and arginine (Arg) giving them a positive charge
The result: Not only does the net charge on the molecule change (it becomes more positive) but
many of the opportunities that its R groups have for ionic (electrostatic) interactions with other
molecules and ions are altered.
As the pH rises,
H+ are removed from the COOH groups of Asp and Glu, giving them a negative charge (COO−), and
H+ are removed from the NH3+ groups of Lys and Arg removing their positive charge
The result: Again the net charge on the molecule changes (it becomes more negative) and, again, many of the opportunities its R
groups have for electrostatic interactions with other molecules or ions are altered.
salt concentration
Increasing salt concentration reduces the strength of ionic binding by providing competing ions for the charged residues.

Hydrophobic Interactions
The side chains (R groups) of such amino acids as phenylalanine and leucine are nonpolar and hence interact poorly with polar
molecules like water. For this reason, most of the nonpolar residues in globular proteins are directed toward the interior of the

1.4.1 https://bio.libretexts.org/@go/page/3744
molecule whereas such polar groups as aspartic acid and lysine are on the surface exposed to the
solvent. When nonpolar residues are exposed at the surface of two different molecules, it is energetically
more favorable for their two "oily" nonpolar surfaces to approach each other closely displacing the polar
water molecules from between them.
The strength of hydrophobic interactions is not appreciably affected by changes in pH or in salt
concentration.

Hydrogen Bonds
Hydrogen bonds can form whenever
a strongly electronegative atom (e.g., oxygen, nitrogen) approaches
a hydrogen atom which is covalently attached to a second strongly-electronegative atom
Some common examples:
between the −C=O group and the H-N− group of nearby peptide bonds in proteins giving rise to the alpha helix and beta
configuration

Between −C=O groups and hydroxyl (H-O−) groups in

serine and threonine residues of proteins and

sugars
Noncovalent interactions are individually weak but collectively strong.
All three forms of noncovalent interactions are individually weak (on the order of 5 kcal/mole) as compared with a covalent bond
(with its 90–100 kcal/mole of bond energy). And what strength these interactions do have requires that the interacting groups can
approach each other closely (an angstrom or less). So we can conclude that all the examples given at the top of the page require:
a substantial number of noncovalent interactions working together to hold the structures together
a surface topography that enables substantial areas of two interacting surfaces to approach each other closely; that is, they must
fit each other

This page titled 1.4: Noncovalent Bonding is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1.4.2 https://bio.libretexts.org/@go/page/3744
1.5: Hydrogen Bonds
Hydrogen Bonds
Polar molecules, such as water molecules, have a weak, partial negative charge at one region of the molecule (the oxygen atom in
water) and a partial positive charge elsewhere (the hydrogen atoms in water). Thus when water molecules are close together, their
positive and negative regions are attracted to the oppositely-charged regions of nearby molecules. The force of attraction, shown
here as a dotted line, is called a hydrogen bond. Each water molecule is hydrogen bonded to four others.

The hydrogen bonds that form between water molecules account for some of the essential — and unique — properties of water.
The attraction created by hydrogen bonds keeps water liquid over a wider range of temperature than is found for any other
molecule its size.
The energy required to break multiple hydrogen bonds causes water to have a high heat of vaporization; that is, a large amount
of energy is needed to convert liquid water, where the molecules are attracted through their hydrogen bonds, to water vapor,
where they are not.
Two outcomes of this:
The evaporation of sweat, used by many mammals to cool themselves, cools by the large amount of heat needed to break the
hydrogen bonds between water molecules.
Reduction of temperature extremes near large bodies of water like the ocean.
The hydrogen bond has only 5% or so of the strength of a covalent bond. However, when many hydrogen bonds can form between
two molecules (or parts of the same molecule), the resulting union can be sufficiently strong as to be quite stable.
Multiple hydrogen bonds
hold the two strands of the DNA double helix together
hold polypeptides together in such secondary structures as the alpha helix and the beta conformation
help enzymes bind to their substrate
help antibodies bind to their antigen
help transcription factors bind to each other
help transcription factors bind to DNA

This page titled 1.5: Hydrogen Bonds is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1.5.1 https://bio.libretexts.org/@go/page/3745
1.6: Acids and Bases
Acids
Acids are substances that donate protons (hydrogen ions, H+) to bases.

Bases
Bases are substances that accept protons from acids.

Example of Acid and Base formation

Hydrogen chloride (HCl) is a gas. Its two atoms are held together by a shared pair of electrons. However, the
chlorine atom is so much more electronegative than hydrogen, that the bond between them is polar
covalent.
When hydrogen chloride is bubbled through water, the nucleus of the hydrogen atom leaves and takes up
residence at one of the unshared pairs of electrons in the water molecule. However, its electron remains
behind still attached to the chlorine atom. "1" This ionization produces:
a chloride ion (Cl−)
a hydronium ion (H3O+). "2"
The resulting mixture is called hydrochloric acid.
Now let us bubble ammonia gas (NH3) through the hydrochloric acid. Ammonia molecules have one pair of
unshared electrons and these have a greater affinity for a proton than do the unshared electrons in the water
molecule. Consequently, the proton shifts again ("3") to form a new ion, the ammonium ion (NH4+) and
water ("4").
Because both the HCl molecule and the hydronium ion are proton donors, they meet the definition of an acid.
The water molecule in the first example and the ammonia in the second example accept protons; therefore
each is a base.
While HCl is found in living systems (e.g., the gastric juice secreted by the stomach), the most common acids
in biology are those containing the carboxyl group ("5").
The proton of the carboxyl group is easily removed forming the carboxyl ion ("6").
Acetic acid (CH3COOH) is a common example of a carboxylic acid. When mixed with water, some of the protons on its -COOH
group are attracted to the unshared electron pairs of water molecules. Hydronium ions (H3O+) and acetate ions (CH3COO−) result.
Vinegar is a dilute solution of acetic acid.
Ammonia is also found (in low concentrations) in living matter. But the most common bases are those molecules that contain an
amino group ("7"). The unshared pair of electrons serves as a proton acceptor, as it does in the ammonia molecule.
Bicarbonate ions ("8") also serve as an important base in living tissue.

This page titled 1.6: Acids and Bases is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1.6.1 https://bio.libretexts.org/@go/page/3746
1.7: Molecular Weight and the Mole
Molecular Weight
The weight of a molecule is the sum of the weights of the atoms of which it is made. The unit of weight is the dalton, one-twelfth
the weight of an atom of 12C. Thus the molecular weight (MW) of water is 18 daltons. (We shall ignore the tiny error introduced
by the presence of traces of other isotopes - 17O, 18O, and 2H among the predominant 1H and 16O atoms.)
Why is it important to know the molecular weight of a compound?
For an example, let us assume that you want to study the response of honeybees to solutions of various kinds of sugars. One way to
do this would be to make up several different solutions and see which one the bees prefer to harvest.
You might offer the bees the choice between, say, a 35% solution of sucrose (common table sugar) and a 35% solution of glucose
(a natural component of honey). This would involve, in each case, dissolving 350 parts by weight (e.g., grams) of sugar in 650 parts
(g) of water, thus producing 1000 g of each solution. But there is a problem with this approach. The willingness of the honeybee to
respond to the presence of sugar dissolved in water is dependent on the number of sugar molecules in a given volume of the
solution.
The sucrose molecule (MW = 342) is almost twice as heavy as the glucose molecule (MW = 180). So a 35% solution of glucose
would contain almost twice as many molecules as a 35% solution of sucrose. To correct the problem, you should make the solution
with the weights of sucrose and glucose in a ratio of 342:180. Then you would have the same concentration of molecules in each;
that is, drop for drop, each solution would contain the same number of molecules.

Mole
A mole is the quantity of a substance whose weight in grams is equal to the molecular weight of the substance. If you weight out
exactly 342 grams (g) of sucrose, you will have weighed out 1 mole of it. Thus 1 mole of glucose weighs 180 g. Furthermore, if
you dissolve 1 mole of a substance in enough water to make 1 liter (L) of solution, you have made a 1-molar (1 M) solution.
A 1 M solution of these sugars would probably be too strong for the experiment with the bees. It might be better to make up a liter
of each solution containing 34.2 g and 18.0 g respectively. Such solutions would be designated one-tenth molar (0.1 M) solutions.
Drop for drop, these two solutions would still contain exactly the same number of molecules because they are of the same
molarity.

 Avogadro's Number
How many molecules are there in a mole?
Solution
The number is approximately 6 x 1023. This number is called Avogadro's number after the chemist who first attempted to
determine it.
Avogadro's number applies to a mole of any substance: molecule or ion. Thus we can properly refer to a mole of hydrogen ions
(1 g).

This page titled 1.7: Molecular Weight and the Mole is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1.7.1 https://bio.libretexts.org/@go/page/3747
1.8: pH
pH is a measure of the concentration of hydrogens ions (= H+) (= protons) in a solution. Numerically it is the negative logarithm
of that concentration expressed in moles per liter (M).
Pure water spontaneously dissociates into ions, forming a 10-7 M solution of H+ (and OH-). The negative of this logarithm is 7, so
the pH of pure water is 7.

Solutions with a higher concentration of H+ than occurs in pure water have pH values below 7 and are acidic. Solutions containing
molecules or ions that reduce the concentration of H+ below that of pure water have pH values above 7 and are basic or alkaline.
Is pH important? Yes!
The properties of most proteins, enzymes for example, are sensitive to pH.
As the pH drops,
H+ bind to the carboxyl groups (COO-) of aspartic acid (Asp) and glutamic acid (Glu), neutralizing their negative charge, and
H+ bind to the unoccupied pair of electrons on the N atom of the amino (NH2 ) groups of lysine (Lys) and arginine (Arg) giving
them a positive charge.
The result: Not only does the net charge on the molecule change (it becomes more positive) but many of the opportunities that its
R groups have for ionic interactions with other molecules and ions are altered.
As the pH rises,
H+ are removed from the COOH groups of Asp and Glu, giving them a negative charge (COO-), and
H+ are removed from the NH3+ groups of Lys and Arg removing their positive charge.
The result: Again the net charge on the molecule changes (it becomes more negative) and, again, many of the opportunities its R
groups have for ionic interactions with other molecules or ions are altered.
The pH of the cytosol within a human cell is about 7.4. BUT, this value masks the pH differences that are found in various
compartments within the cell. For example,
The interior of lysosomes is much more acidic (as low as pH 4) than the cytosol, and the enzymes within work best at these low
pH values.
The pH differential created within chloroplasts by the energy of the sun is harnessed to synthesize ATP which, in turn, powers
the synthesis of food.
The pH differential created within mitochondria during the respiration of food is harnessed to the synthesis of ATP which, in
turn, powers most of the energy-consuming activities of the cell such as locomotion and biosynthesis of cell components.

This page titled 1.8: pH is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source content
that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1.8.1 https://bio.libretexts.org/@go/page/3748
 CHAPTER OVERVIEW
Unit 2: The Molecules of Life
2.1: Organic Molecules
2.2: Hydrocarbons
2.3: Fats
2.4: Phospholipids
2.5: Cholesterol
2.6: Carbohydrates
2.7: Amino Acids
2.8: Enantiomers
2.9: Polypeptides
2.10: Proteins
2.11: Rules of Protein Structure
2.12: Glycoproteins
2.13: Nucleotides
2.14: Proteomics

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.
Thumbnail: Cellulose molecular structure (CC BY-SA 3.0 Unported; Pintor4257 via Wikipedia)

This page titled Unit 2: The Molecules of Life is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1
2.1: Organic Molecules
Functional groups
The various functional groups include:
hydroxyl group (-OH)
carboxyl group [-COOH]
carbonyl group (-C=O)
amino group -NH2

Organic Molecules
Various organic molecules formed by these groups are as follows:

Alcohols
Organic molecules with a hydroxyl group (-OH).
Methanol [CH3OH] and ethanol (beverage alcohol)[CH3CH2OH] are common examples.
Sugars are also alcohols.

Carboxylic Acids
Contain one or more carboxyl groups [-COOH].
Many of the intermediates in the breakdown of foodstuffs by cellular respiration are
carboxylic acids.

Aldehydes
Contain a carbon atom to which is attached one hydrogen atom and — by a double bond —
one oxygen atom.
Formaldehyde [HCHO] is a powerful disinfectant and preservative (it denatures proteins).
Acetaldehyde is produced during the conversion of pyruvic acid to ethanol when yeast
ferment sugars. The converse is also true — acetaldehyde is produced in the liver as it
metabolizes ingested ethanol (and may be the prime culprit in a "hangover").
Phosphoglyceraldehyde is an intermediate in glycolysis and the "dark reaction" of
photosynthesis

Ethers
Formed when two carbon atoms are linked by an oxygen atom.
Diethyl ether is a commonly-used anesthetic.

Esters
The removal of a molecule of water between the -OH group of an alcohol and the -OH group
of a
carboxylic acid (-COOH) [shown in the diagram] or
phosphoric acid
produces an ester.
Fats are triesters of three fatty acids and glycerol (the alcohol).
Phospholipids are also esters.
Nucleotides are esters of nucleosides and phosphoric acid.
The nucleotides of DNA and RNA are linked by a double ester linkage called a phosphodiester bond.

2.1.1 https://bio.libretexts.org/@go/page/3779
Ketones
Organic molecules with a carbonyl group (-C=O) between two hydrocarbon portions.
Ketones are synthesized in the liver, usually from fatty acids.
When glucose metabolism is suppressed, during starvation or in diabetics, fatty acids are used as a source of energy. But instead of
entering the citric acid cycle, the acetyl-CoA produced from them is converted into the ketone acetoacetate. Some of this is then
converted into acetone (which can be smelled on the breath of patients whose diabetes is out of control).

Amines
Organic molecules with an amino group, -NH2. Some examples:
all the amino acids (lysine has two of them).
the thyroid hormones thyroxine (T4) and triiodothyronine (T3)
Many neurotransmitters:
adrenaline and noradrenaline
dopamine
serotonin (5-hydroxytryptamine)
histamine

Amides
Amides are organic molecules containing a carbonyl group (-C=O) attached to a nitrogen atom. The peptide bond between the
amino acids linked in a polypeptide is also called an amide bond.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and made
possible by funding from The Saylor Foundation.

This page titled 2.1: Organic Molecules is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

2.1.2 https://bio.libretexts.org/@go/page/3779
2.2: Hydrocarbons
Hydrocarbons are organic molecules that consist exclusively, or primarily, of carbon and hydrogen atoms. They come in two
flavors: (1) aliphatic hydrocarbons that consist of linear chains of carbon atoms and (2) aromatic hydrocarbons that which consist
of closed rings of carbon atoms.

Aliphatic Hydrocarbons

The simplest is methane, CH4. Next is ethane, C2H6.

The fatty acids in fats are aliphatic hydrocarbons. If a chain holds all the hydrogen atoms it can, the molecule is said to be
saturated. The fatty acids in tristearin are all saturated.
If two adjacent carbon atoms each lose a hydrogen atom, a double bond forms between them. Such a molecule is said to be
unsaturated.
Example : Ethylene H2C=CH2
The fatty acids in trilinolein and linolenic acid are examples of unsaturated fatty acids

Aromatic Hydrocarbons
The building block of aromatic hydrocarbons is the benzene ring. The arrangement of atoms is shown on the left. The version in the
center is often used to simplify diagrams of molecular structures. The three double bonds are not restricted to the positions shown
but are free to pass around the ring. This is sometimes indicated by drawing the benzene ring as it is on the far right.

Some examples of biological molecules that incorporate the benzene ring:

the amino acids tyrosine and phenylalanine
cholesterol and its various derivatives, such as the sex hormones: estrogens and testosterone
the herbicide, 2,4-D

2.2.1 https://bio.libretexts.org/@go/page/3780
The carotenoid, beta-carotene, is a hydrocarbon that has both aliphatic and aromatic portions.

This page titled 2.2: Hydrocarbons is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

2.2.2 https://bio.libretexts.org/@go/page/3780
2.3: Fats
Fat molecules are made up of four parts: a molecule of glycerol (on the right) and three molecules of fatty acids. Each fatty acid
consists of a hydrocarbon chain with a carboxyl group at one end. The glycerol molecule has three hydroxyl groups, each able to
interact with the carboxyl group of a fatty acid. Removal of a water molecule at each of the three positions forms a triglyceride.
The three fatty acids in a single fat molecule may be all alike (as shown here for tristearin) or they may be different. They may
contain as few as 4 carbon atoms or as many as 24.

Figure 3.0.1: tristearin

Because fatty acids are synthesized from fragments containing two carbon atoms, the number of carbon atoms in the chain is
almost always an even number. In animal fats, 16-carbon (palmitic acid) and 18-carbon (stearic acid - shown here) fatty acids are
the most common.

Unsaturated Fats
Some fatty acids have one or more double bonds between their carbon atoms. They are called unsaturated because they could hold
more hydrogen atoms than they do. Monounsaturated fats have a single double bond in their fatty acids and polyunsaturated
fats, such as trilinolein shown here, have two or more.

Figure 3.0.2: trilinolein

Double bonds are rigid and those in natural fats introduce a kink in the molecule. This prevents the fatty acids from packing close
together and as a result, unsaturated fats have a lower melting point than do saturated fats. Because most of them are liquid at room
temperature, we call them oils. Corn oil, canola oil, cottonseed oil, peanut oil, and olive oil are common examples. As this list
suggests, plant fats tend to be unsaturated (therefore "oils"). Fats from such animals as cattle tend to be saturated.

Trans Fatty Acids

The most abundant (and least expensive) source of fat is from plant oils but many cooking applications, particularly baked
products, need solid fats. The food industry uses hydrogenated oils for things like shortening and margarine. In hydrogenation,
plant oils are exposed to hydrogen at a high temperature and in the presence of a catalyst.

2.3.1 https://bio.libretexts.org/@go/page/3781
 Figure 3.0.3: Trans vs. Cis fatty acid
Two things result:(1) some double bonds are converted into single bonds and (2) other double bonds are converted from cis to
trans configuration. Both these effects straighten out the molecules so they can lie closer together and become solid rather than
liquid.

Omega fatty acids

One system for naming unsaturated fatty acids is to indicate the position of the first double bond counting from the opposite end
from the carboxyl group. That terminal carbon atom (shown here in blue) is called the omega carbon atom. Thus a
monounsaturated fatty acid with its single double bond after carbon #3 (counting from and including the omega carbon) is called an
omega-3 fatty acid. But so is a polyunsaturated fatty acid, such as linolenic acid (shown here), if its first double bond is in that
position.

Figure 3.0.4: Linolenic Acid

Some studies have suggested that omega-3 fatty acids help protect against cardiovascular disease. For this reason, a Dietary
Reference Intake (DRI) of 1.1 grams/day for women (1.6 for men) was established in September 2002.

This page titled 2.3: Fats is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source content
that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

2.3.2 https://bio.libretexts.org/@go/page/3781
2.4: Phospholipids
Phospholipids are fat derivatives in which one fatty acid has been replaced by a phosphate group and one of several nitrogen-
containing molecules.

Example 2.4.1: Phosphatidyl ethanolamine (also known as cephalin)

The hydrocarbon chains are hydrophobic (as in all fats). However, the charges on the phosphate and amino groups (in red) make
that portion of the molecule hydrophilic. The result is an amphiphilic molecule.

Phospholipids like phosphatidyl ethanolamine are major constituents of cell membranes. These molecules form a phospholipid
bilayer with their hydrophilic (polar) heads facing their aqueous surroundings (e.g., the cytosol) and their hydrophobic tails facing
each other.

This page titled 2.4: Phospholipids is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

2.4.1 https://bio.libretexts.org/@go/page/3782
2.5: Cholesterol
The cholesterol molecule is a steroid that is essential to life. It has also been responsible for 17 Nobel Prizes, countless pages of
reports in scientific journals and the popular press, and mounting anxiety on the part of health-conscious people. The human body
contains about 100 g of cholesterol. Most of this is incorporated in the membranes from which cells are constructed and is an
indispensable component of them. The insulating layers of myelin wound around neurons are especially rich in cholesterol.

H
H

H H
HO

The structure of Cholesterol

Uses of Cholesterol
Cholesterol is starting ingredient for the synthesis of the steroid hormones including progesterone, estrogens, androgens (e.g.,
testosterone), glucocorticoids (e.g., cortisol), and mineralocorticoids (e.g., aldosterone). Cholesterol is also the precursor from
which the body synthesizes vitamin D.
Another major use of cholesterol is the synthesis of bile acids. These are synthesized in the liver from cholesterol and are secreted
in the bile. They are essential for the absorption of fat from the contents of the intestine. A clue to the importance of cholesterol is
that more than 90% of the bile acids are not lost in the feces but are reabsorbed from the lower intestine and recycled to the liver.
There is some loss, however, and to compensate for this and to meet other needs, the liver synthesizes some 1500–2000 mg of new
cholesterol each day. It synthesizes cholesterol from the products of fat metabolism.
There is also an unceasing transport of cholesterol in the blood between the liver and all the other tissues. Most of this cholesterol
travels as low density lipoproteins (LDLs). Each LDL particle is a sphere filled with ~1,500 molecules of cholesterol complexed
with fatty acids and coated with a layer of phospholipids and a single molecule of a protein called apolipoprotein B (apoB). Cells
that need cholesterol trap and ingest LDLs by receptor-mediated endocytosis.

Problems caused by cholesterol

Cholesterol can also create problems.
High levels of LDL cholesterol lead to the development of atherosclerosis: cholesterol-rich deposits (plaques) that form on the
inside of blood vessels and predispose to heart attacks.
Cholesterol in the bile can crystallize to form gall stones that may block the bile ducts.

Typical lipid values in humans

The level of cholesterol in the blood is measured in milligrams per deciliter (mg/dl), which is equivalent to parts per 100,000. The
levels range from less than 50 in infants to an average of 215 in adults and to 1,200 or more in individuals suffering from a rare,
inherited disorder called familial hypercholesterolemia. For those of us in the normal range, approximately two-thirds of our
cholesterol is transported as LDLs. Most of the rest is carried by so-called high density lipoproteins (HDLs).
Because of their relationship to cardiovascular disease, the analysis of serum lipids has become an important health measure. The
table shows the range of typical values as well as the values above (or below) which the subject may be at increased risk of
developing atherosclerosis.

LIPID Typical values (mg/dl) Desirable (mg/dl)

Cholesterol (total) 170–210 <200

2.5.1 https://bio.libretexts.org/@go/page/3783
 LIPID Typical values (mg/dl) Desirable (mg/dl)

LDL cholesterol 60–140 <130

HDL cholesterol 35–85 >40

Triglycerides 40–150 <135

Total cholesterol is the sum of

HDL cholesterol
LDL cholesterol and
20% of the triglyceride value
Note that
high LDL values are bad, but
high HDL values are good (because HDL cholesterol transports cholesterol from the tissues back to the liver where it is
secreted in the bile).
Using the various values, one can calculate a
cardiac risk ratio = total cholesterol divided by HDL cholesterol
A cardiac risk ratio greater than 7 is considered a warning.
In May of 2001, a panel of the National Institutes of Health recommended a more aggressive attack on reducing cholesterol levels
in the U.S. population. In addition to a better diet and more exercise, they urged that many more people at risk of developing heart
disease, such as
smokers
diabetics
people with high blood pressure and/or
obesity
be put on cholesterol-lowering drugs.
There are several types:
drugs that interfere with the ability of the liver to synthesize cholesterol by blocking the action of the enzyme HMG-CoA
reductase. These are the "statins", e.g., lovastatin (Mevacor®), pravastatin (Pravachol®), atorvastatin (Lipitor®).
insoluble powders ("colestipol", "cholestyramine") that bind to bile acids in the intestine so that instead of being reabsorbed
they are eliminated in the feces. In compensation, the liver increases its consumption of blood-borne cholesterol. The main
drawback to these drugs is that they are gritty powders and must be consumed in rather large amounts.
nicotinic acid (niacin);
"fibric acids" such as gemfibrozil and clofibrate.
Careful attention to diet may by itself lead to a reduction in cholesterol levels. In one study, men with high (>265 mg/dl) levels
were able to lower these an average of 3.5% (10 mg/dl) by diet alone. Their diets were low in fat as well as low in cholesterol, and
it was not — and still is not — clear as to what aspect of the diet contributed to the modest reduction. Cholesterol is made from fat
and lowering the proportion of fat in the diet will probably help. Favoring unsaturated fats over saturated fats appears to be
beneficial. There is little evidence that lowering one's intake of cholesterol is, by itself, useful. An average intake of cholesterol of
300–500 mg per day is joined in the intestine by several times that amount that has been synthesized by the liver and appears to
have little or no effect on blood levels of cholesterol. So when choosing between the pat of butter and the pat of margarine, it is not
the 30-odd mg of cholesterol in the butter (vs. 0 in the margarine) but its high content of saturated fat (over 3 times that in the
margarine) that is probably significant.

This page titled 2.5: Cholesterol is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

2.5.2 https://bio.libretexts.org/@go/page/3783
2.6: Carbohydrates
Carbohydrates have the general molecular formula CH2O, and thus were once thought to represent "hydrated carbon". However,
the arrangement of atoms in carbohydrates has little to do with water molecules. Starch and cellulose are two common
carbohydrates. Both are macromolecules with molecular weights in the hundreds of thousands. Both are polymers (hence
"polysaccharides"); that is, each is built from repeating units, monomers, much as a chain is built from its links. The monomers of
both starch and cellulose are the same: units of the sugar glucose.

Monosaccharides
Three common sugars share the same molecular formula: C6H12O6. Because of their six carbon atoms, each is a hexose.

They are:
glucose, "blood sugar", the immediate source of energy for cellular respiration
galactose, a sugar in milk (and yogurt)
fructose, a sugar found in honey
Although all three share the same molecular formula (C6H12O6), the arrangement of atoms differs in each case. Substances such
as these three, which have identical molecular formulas but different structural formulas, are known as structural isomers.
Glucose, galactose, and fructose are "single" sugars or monosaccharides. Two monosaccharides can be linked together to form a
"double" sugar or disaccharide.

Disaccharides
Three common disaccharides:
sucrose — common table sugar = glucose + fructose
lactose — major sugar in milk = glucose + galactose
maltose — product of starch digestion = glucose + glucose
Although the process of linking the two monomers is rather complex, the end result in each case is the loss of a hydrogen atom (H)
from one of the monosaccharides and a hydroxyl group (OH) from the other. The resulting linkage between the sugars is called a
glycosidic bond. The molecular formula of each of these disaccharides is

C12 H22 O11 = 2 C6 H12 O6 − H2 O (2.6.1)

All sugars are very soluble in water because of their many hydroxyl groups. Although not as concentrated a fuel as fats, sugars are
the most important source of energy for many cells. Carbohydrates provide the bulk of the calories (4 kcal/gram) in most diets, and
starches provide the bulk of that. Starches are polysaccharides.

Polysaccharides
There are three primary polysaccharide polymer systems of interest: Starches, Glycogen and Cellulose.

Starches
Starches are polymers of glucose. Two types are found:
amylose consists of linear, unbranched chains of several hundred glucose residues
(units). The glucose residues are linked by a glycosidic bond between their #1 and #4
carbon atoms.
amylopectin differs from amylose in being highly branched. At approximately every
thirtieth residue along the chain, a short side chain is attached by a glycosidic bond to the #6 carbon atom (the carbon above the

2.6.1 https://bio.libretexts.org/@go/page/3784
 ring). The total number of glucose residues in a molecule of amylopectin is several thousand.

Potato starch Amylase

Figure 2.6.3: This electron micrograph (courtesy of R. D. Preston) shows the cellulose fibrils in the cell wall of a green alga. These
long, rigid fibrils are a clear reflection of the nature of the cellulose molecules of which they are composed.

This page titled 2.6: Carbohydrates is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

2.6.2 https://bio.libretexts.org/@go/page/3784
2.7: Amino Acids
Amino acids are the building blocks (monomers) of proteins. 20 different amino acids are used to synthesize proteins. The shape
and other properties of each protein is dictated by the precise sequence of amino acids in it.

Each amino acid consists of an alpha carbon atom to which is attached

a hydrogen atom
an amino group (hence "amino" acid)
a carboxyl group (-COOH). This gives up a proton and is thus an acid (hence amino "acid")
one of 20 different "R" groups. It is the structure of the R group that determines which of the 20 it is and its special properties.
The amino acid shown here is Alanine
Table 2.7.1: Types of Amino Acids. For each amino acid both three-letter and single letter codes are given
Alanine Ala A hydrophobic

free amino group makes it basic

Arginine Ala Arg A R
and hydrophilic
carbohydrate can be covalently
AsparagineAla Asn A N
linked ("N-linked) to its -NH
free carboxyl group makes it
Aspartic acid
Ala Asp A D
acidic and hydrophilic
oxidation of their sulfhydryl (-SH)
Cysteine Ala Cys A C
groups link 2 Cys (S-S)
free carboxyl group makes it
Glutamic acid
Ala Glu A E
acidic and hydrophilic

GlutamineAla Gln A Q moderately hydrophilic

so small it is amphiphilic (can

Glycine Ala Gly A G
exist in any surroundings)

Histidine Ala His A H basic and hydrophilic

Isoleucine Ala Ile A I hydrophobic

Leucine Ala Leu A L hydrophobic

Lysine Ala Lys A K strongly basic and hydrophilic

MethionineAla Met A M hydrophobic

Ala
Phenylalanine Phe A F very hydrophobic

Proline Ala Pro A P causes kinks in the chain

carbohydrate can be covalently

Serine Ala Ser A S
linked ("O-linked") to its -OH
carbohydrate can be covalently
Threonine Ala Thr A T
linked ("O-linked") to its -OH

TryptophanAla Trp A W scarce in most plant proteins

a phosphate or sulfate group can

Tyrosine Ala Tyr A Y
be covalently attached to its -OH

2.7.1 https://bio.libretexts.org/@go/page/3785
 Alanine Ala A hydrophobic

Valine Ala Val A V hydrophobic

The Essential Amino Acids

Humans must include adequate amounts of 9 amino acids in their diet.
Histidine
Isoleucine
Leucine
Lysine
Methionine (and/or cysteine)
Phenylalanine (and/or tyrosine)
Threonine
Tryptophan
Valine
These "essential" amino acids cannot be synthesized from other precursors. However, cysteine can partially meet the need for
methionine (they both contain sulfur), and tyrosine can partially substitute for phenylalanine. Two of the essential amino acids,
lysine and tryptophan, are poorly represented in most plant proteins. Thus strict vegetarians should ensure that their diet contains
sufficient amounts of these two amino acids. 19 of the 20 amino acids listed above can exist in two forms in three dimensions.

This page titled 2.7: Amino Acids is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

2.7.2 https://bio.libretexts.org/@go/page/3785
2.8: Enantiomers
In three-dimensional (3D) space, the four covalent bonds of carbon atoms point toward the corners of a regular tetrahedron. The
molecule represented to the below is methane (C H ). 4

Figure 2.8.1: 3-D representation of methane. Image used wtih permission (public domain; credit Ben Mills)
Whenever a carbon atom has four different structures bonded to it, two different molecules can be formed.

Figure 2.8.2: Basic Amino Acid Structure. Photo Credit: Credit: Yassine Mrabet

 Example 2.8.1: Alanine

The amino acid alanine.

Bonded to its alpha carbon atom are four different groups:

a carboxyl group (COO−)
an amino group (NH3+)
a methyl group (CH3)(its R group)
a hydrogen atom
If you orient the molecule so that you look along it from the COO− group to the NH3+ group, the methyl (R) group can
extend out to the left, forming L-alanine (shown on the left) or to the right, forming D-alanine (on the right). Although they
share the same chemical formula, they are not interchangeable any more than a left-hand glove is interchangeable with right-
hand glove.

19 of the 20 amino acids used to synthesize proteins can exist as L- or D- enantiomorphs. The exception is glycine, which has two
(indistinguishable) hydrogen atoms attached to its alpha carbon. L amino acids are used exclusively for protein synthesis by all life
on our planet. (Some D amino acids are used for other purposes).

2.8.1 https://bio.libretexts.org/@go/page/3786
 Figure 2.8.3: Two enantiomers of a generic chiral amino acid.
Does chirality really matter? Yes. The function of a protein is determined by its shape. A protein with a D amino acid instead of L
will have its R group sticking out in the wrong direction (Figure 2.8.3).
Many other kinds of organic molecules exist as enantiomers. Usually only one form is active in biological systems. For example, if
one form binds to a receptor protein on the surface of a cell, the other probably cannot. With their protein catalysts (enzymes), cells
usually synthesize only one form. However, chemical synthesis in the laboratory or pharmaceutical factory usually produces equal
amounts of the two enantiomers — called a racemic mixture.

 Example 2.8.2: Albuterol

The drug albuterol (e.g., Proventil®) contains equal amounts of two enantiomers. Only one of them is effective, and the other
may be responsible for the occasional unpleasant side-effects associated with the drug (which is used to dilate the bronchi, e.g,
during an attack of asthma). The active form can now be synthesized pure, and — called levalbuterol (Xopenex®) — is
available by prescription.

Two enantiomers of albuterol: (R)-(−)-salbutamol (top) and (S)-(+)-salbutamol (bottom)

Enantiomers are also called optical isomers because their solutions rotate the plane of polarized light passing through them. If one
enantiomer rotates light in the clockwise direction, a solution of the other enantiomer will rotate it in the opposite direction.

This page titled 2.8: Enantiomers is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

2.8.2 https://bio.libretexts.org/@go/page/3786
2.9: Polypeptides

Figure 2.9.2: A longer peptide.

The sequence of amino acids in a polypeptide is dictated by the codons in the messenger RNA (mRNA) molecules from which the
polypeptide was translated. The sequence of codons in the mRNA was, in turn, dictated by the sequence of codons in the DNA
from which the mRNA was transcribed. Proteins are made up of one or more polypeptide molecules.

This page titled 2.9: Polypeptides is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

2.9.1 https://bio.libretexts.org/@go/page/3787
2.10: Proteins
Proteins are macromolecules. They are constructed from one or more unbranched chains of amino acids; that is, they are polymers.
An average eukaryotic protein contains around 500 amino acids but some are much smaller (the smallest are often called peptides)
and some much larger (the largest to date is titin a protein found in skeletal and cardiac muscle; one version contains 34,350 amino
acids in a single chain!).
Every function in the living cell depends on proteins.
Motion and locomotion of cells and organisms depends on proteins. [Examples: Muscles, Cilia and Flagella]
The catalysis of all biochemical reactions is done by enzymes, which contain protein.
The structure of cells, and the extracellular matrix in which they are embedded, is largely made of protein. [Examples:
Collagens] (Plants and many microbes depend more on carbohydrates, e.g., cellulose, for support, but these are synthesized by
enzymes.)
The transport of materials in body fluids depends of proteins.
The receptors for hormones and other signaling molecules are proteins.
Proteins are an essential nutrient for heterotrophs.
The transcription factors that turn genes on and off to guide the differentiation of the cell and its later responsiveness to signals
reaching it are proteins.
and many more — proteins are truly the physical basis of life.
The protein represented here displays many of the features of proteins. Let's examine some of
them as you scroll down the image. The protein consists of two polypeptide chains, a long one
on the left of 346 amino acids — it is called the heavy chain — and a short one on the right of
99 amino acids. The heavy chain is shown as consisting of 5 main regions or domains:
three extracellular domains, designated here as N (includes the N-terminal), C1, and C2;
a transmembrane domain where the polypeptide chain passes through the plasma membrane
of the cell;
a cytoplasmic domain (with the C terminal) within the cytoplasm of the cell.

Figure 2.10.X: Structure of the prototypic cyclotide kalata B1 (public domain: KalataB1).

Inteins
Another, very rare, post-translational modification is the later removal of a section of the polypeptide and the splicing together
(with a peptide bond) of the remaining N-terminal and C-terminal segments. The portion removed is called an intein (a "protein
intron"), and the ligated segments are called exteins ("protein exons"). Genes encoding inteins have been discovered in a variety of
organisms, including
some "true" bacteria such as
Bacillus subtilis
several mycobacteria
several blue-green algae (cyanobacteria)

2.10.1 https://bio.libretexts.org/@go/page/3788
 some Archaea such as
Methanococcus jannaschii
Aeropyrum pernix
and a few unicellular eukaryotes, e.g., budding yeast (Saccharomyces cerevisiae).
None has been found in the genomes of multicellular eukaryotes like Drosophila, C. elegans, or the green plant Arabidopsis.

How proteins get their shape

The function of a protein is determined by its shape. The shape of a protein is determined by its primary structure(sequence of
amino acids). The sequence of amino acids in a protein is determined by the sequence of nucleotides in the gene (DNA) encoding
it. The function of a protein (except when it is serving as food) is absolutely dependent on its three-dimensional structure. A
number of agents can disrupt this structure thus denaturing the protein.
changes in pH (alters electrostatic interactions between charged amino acids)
changes in salt concentration (does the same)
changes in temperature (higher temperatures reduce the strength of hydrogen bonds)
presence of reducing agents (break S-S bonds between cysteines)
None of these agents breaks peptide bonds, so the primary structure of a protein remains intact when it is denatured. When a
protein is denatured, it loses its function.

 Example 2.10.1
A denatured enzyme ceases to function.
A denatured antibody no longer can bind its antigen.

Often when a protein has been gently denatured and then is returned to normal physiological conditions of temperature, pH, salt
concentration, etc., it spontaneously regains its function (e.g. enzymatic activity or ability to bind its antigen). This tells us
The protein has spontaneously resumed its native three-dimensional shape.
Its ability to do so is intrinsic; no outside agent was needed to get it to refold properly.
However, there are:
enzymes that add sugars to certain amino acids, and these may be essential for proper folding;
proteins, called molecular chaperones, that may enable a newly-synthesized protein to acquire its final shape faster and more
reliably than it otherwise would.

2.10.2 https://bio.libretexts.org/@go/page/3788
Chaperones
Although the three-dimensional (tertiary) structure of a protein is determined by its primary structure, it may need assistance in
achieving its final shape.
As a polypeptide is being synthesized, it emerges (N-terminal first) from the ribosome and the folding process begins.
However, the emerging polypeptide finds itself surrounded by the watery cytosol and many other proteins.
As hydrophobic amino acids appear, they must find other hydrophobic amino acids to associate with. Ideally, these should be
their own, but there is the danger that they could associate with nearby proteins instead — leading to aggregation and a failure
to form the proper tertiary structure.
To avoid this problem, the cells of all organisms contain molecular chaperones that stabilize newly-formed polypeptides while they
fold into their proper structure. The chaperones use the energy of ATP to do this work.

Chaperonins
Some proteins are so complex that a subset of molecular chaperones — called chaperonins — is needed. Chaperonins are hollow
cylinders into which the newly-synthesized protein fits while it folds. The inner wall of the cylinder is lined with hydrophobic
amino acids which stabilize the hydrophobic regions of the polypeptide chain while it folds safely away from the
watery cytosol and
other proteins outside.
Chaperonins also use ATP as the energy source to drive the folding process.
As mentioned above, high temperatures can denature proteins, and when a cell is exposed to high temperatures, several types of
molecular chaperones swing into action. For this reason, these chaperones are also called heat-shock proteins (HSPs). Not only do
molecular chaperones assist in the folding of newly-synthesized proteins, but some of them can also unfold aggregated proteins and
then refold the protein properly. Protein aggregation is the cause of disorders such as Alzheimer's disease, Huntington's disease, and
prion diseases (e.g., "mad-cow" disease). Perhaps some day ways will be found to treat these diseases by increasing the efficiency
of disaggregating chaperones.
Despite the importance of chaperones, the rule still holds: the final shape of a protein is determined by only one thing: the precise
sequence of amino acids in the protein. And the sequence of amino acids in every protein is dictated by the sequence of
nucleotides in the gene encoding that protein. So the function of each of the thousands of proteins in an organism is specified by
one or more genes.

Primary Structure
The primary structure of a protein is its linear sequence of amino acids and the location of any disulfide
(-S-S-) bridges. Note the amino terminal or "N-terminal" (NH3+) at one end; carboxyl terminal
("C-terminal") (COO-) at the other.

Secondary Structure
Most proteins contain one or more stretches of amino acids that take on a characteristic structure in 3-D space. The most common
of these are the alpha helix and the beta conformation.

Alpha Helix
The R groups of the amino acids all extend to the outside.
The helix makes a complete turn every 3.6 amino acids.
The helix is right-handed; it twists in a clockwise direction.
The carbonyl group (-C=O) of each peptide bond extends parallel to the axis of the helix and points directly at the
-N-H group of the peptide bond 4 amino acids below it in the helix. A hydrogen bond forms between them [-N-
H·····O=C-]

Beta Conformation
consists of pairs of chains lying side-by-side and
stabilized by hydrogen bonds between the carbonyl oxygen atom on one chain and the -NH group on the adjacent chain.
The chains are often "anti-parallel"; the N-terminal to C-terminal direction of one being the reverse of the other.

2.10.3 https://bio.libretexts.org/@go/page/3788
Tertiary Structure
Tertiary structure refers to the three-dimensional structure of the entire polypeptide chain.
The images (courtesy of Dr. D. R. Davies) represent the tertiary structure of the antigen-
binding portion of an antibody molecule. Each circle represents an alpha carbon in one of the
two polypeptide chains that make up this protein. (The filled circles at the top are amino
acids that bind to the antigen.) Most of the secondary structure of this protein consists of
beta conformation, which is particularly easy to see on the right side of the image.
Do try to fuse these two images into a stereoscopic (3D) view. I find that it works best when my eyes are about 18" from the screen
and I try to relax so that my eyes are directed at a point behind the screen.
Where the entire protein or parts of a protein are exposed to water (e.g., in blood or the cytosol), hydrophilic R groups — including
R groups with sugars attached , are found at the surface; hydrophobic R groups are buried in the interior.

Importance of Tertiary structure

The function of a protein (except as food) depends on its tertiary structure. If this is disrupted, the protein is said to be denatured,
and it loses its activity. Examples:
denatured enzymes lose their catalytic power
denatured antibodies can no longer bind antigen
A mutation in the gene encoding a protein is a frequent cause of altered tertiary structure.
Curiously, tiny amounts of the mutant version can trigger the alpha-to-beta conversion in the normal protein. Thus the mutant
version can be infectious. There have been several cases in Europe of people ill with Creutzfeldt-Jakob disease that may have
acquired it from ingesting tiny amounts of the mutant protein in their beef.
A number of other proteins altered by a point mutation in the gene encoding them, e.g.,
fibrinogen
lysozyme
transthyretin (a serum protein that transports thyroxin and retinol (vitamin A) in the blood)
can form insoluble amyloid deposits in humans.
The many hydrogen bonds that can form between the polypeptide backbones in the beta conformation suggests that this is a stable
secondary structure potentially available to many proteins and so a tendency to form insoluble aggregates is as well. Avoidance of
amyloid formation may account for the large investment in the cell in
chaperones
proteasomes
as well as the crucial importance of particular amino acid side chains in maintaining a globular, and hence soluble, tertiary
structure.

Protein Domains
The tertiary structure of many proteins is built from several domains. Often each domain has a
separate function to perform for the protein, such as:
binding a small ligand (e.g., a peptide in the molecule shown here)
spanning the plasma membrane (transmembrane proteins)
containing the catalytic site (enzymes)
DNA-binding (in transcription factors)
providing a surface to bind specifically to another protein
In some (but not all) cases, each domain in a protein is encoded by a separate exon in the gene
encoding that protein. In the histocompatibility molecule shown here ,
three domains α1, α2, and α3 are each encoded by its own exon.
Two additional domains a transmembrane domain and a cytoplasmic domainare also encoded by
separate exons.

2.10.4 https://bio.libretexts.org/@go/page/3788
 (β2-microglobulin, "β2m", is NOT a domain of this molecule. It is a separate molecule that binds to the three alpha domains
(red line and circle) by noncovalent forces only. The complex of these two proteins is an example of quaternary structure.)
This image (courtesy of P. J. Bjorkman from Nature 329:506, 1987) is a schematic representation of the extracellular portion of
HLA-A2, a human class I histocompatibility molecule. It also illustrates two common examples of secondary structure: the
stretches of beta conformation are represented by the broad green arrows (pointing N -> C terminal); regions of alpha helix are
shown as helical ribbons. The pairs of purple spheres represent the disulfide bridges. A correspondence between exons and
domains is more likely to be seen in recently-evolved proteins. Presumably, "exon shuffling" during evolution has enabled
organisms to manufacture new proteins, with new functions, by adding exons from other parts of the genome to encode new
domains (rather like Lego® pieces).

Quaternary Structure
Complexes of 2 or more polypeptide chains held together by noncovalent forces (usually) but in precise ratios and with a precise 3-
D configuration. The noncovalent association of a molecule of beta-2 microglobulin with the heavy chain of each class I
histocompatibility molecule is an example.

Protein Kinesis
All proteins are synthesized by ribosomes using the information encoded in molecules of messenger RNA (mRNA). The various
destinations for proteins occur in two major sets:
one set for those proteins synthesized by ribosomes that remain suspended in the cytosol, and
a second set for proteins synthesized by ribosomes that are attached to the membranes of the endoplasmic reticulum (ER)
forming "rough endoplasmic reticulum" (RER).
Some of the important destinations for proteins are:
the cytosol
the nucleus
mitochondria
chloroplasts
peroxisomes

This page titled 2.10: Proteins is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

2.10.5 https://bio.libretexts.org/@go/page/3788
2.11: Rules of Protein Structure
The function of a protein is determined by its shape. The shape of a protein is determined by its primary structure (sequence of
amino acids). The sequence of amino acids in a protein is determined by the sequence of nucleotides in the gene (DNA) encoding
it. The function of a protein (except when it is serving as food) is absolutely dependent on its three-dimensional structure. A
number of agents can disrupt this structure thus denaturing the protein.
changes in pH (alters electrostatic interactions between charged amino acids)
changes in salt concentration (does the same)
changes in temperature (higher temperatures reduce the strength of hydrogen bonds)
presence of reducing agents (break S-S bonds between cysteines)

Figure 2.11.1: The denaturation (unfolding) and renaturation (refolding) of a protein is depicted. The red boxes represent stabilizing
interactions, such as disulfide linkages, hydrogen bonding, and/or ionic bonds.
Often when a protein has been gently denatured and then is returned to normal physiological conditions of temperature, pH, salt
concentration, etc., it spontaneously regains its function (e.g. enzymatic activity or ability to bind its antigen). This tells us that the
protein has spontaneously resumed its native three-dimensional shape. Moreover, this ability is intrinsic; no outside agent was
needed to get it to refold properly.
However, there are enzymes that add sugars to certain amino acids, and these may be essential for proper folding. These proteins,
called molecular chaperones, enable a newly-synthesized protein to acquire its final shape faster and more reliably than it
otherwise would.

Chaperones
Although the three-dimensional (tertiary) structure of a protein is determined by its primary structure, it may need assistance in
achieving its final shape.
As a polypeptide is being synthesized, it emerges (N-terminal first) from the ribosome and the folding process begins.
However, the emerging polypeptide finds itself surrounded by the watery cytosol and many other proteins.
As hydrophobic amino acids appear, they must find other hydrophobic amino acids to associate with. Ideally, these should be
their own, but there is the danger that they could associate with nearby proteins instead — leading to aggregation and a failure
to form the proper tertiary structure.

2.11.1 https://bio.libretexts.org/@go/page/3789
 Chaperonin

Figure 11.2: Structure of the HSP90AA1 protein. from Wikipedia (CC_SA-BY-3.0 by Emw)
Despite the importance of chaperones, the rule still holds: the final shape of a protein is determined by only one thing: the precise
sequence of amino acids in the protein. And the sequence of amino acids in every protein is dictated by the sequence of
nucleotides in the gene encoding that protein. So the function of each of the thousands of proteins in an organism is specified by
one or more genes.

This page titled 2.11: Rules of Protein Structure is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

2.11.2 https://bio.libretexts.org/@go/page/3789
2.12: Glycoproteins
Glycoproteins have carbohydrate attached to them — a process called glycosylation. The attachment is a covalent linkage to:
the hydroxyl (-OH) group of the R group of serine or threonine - called "O-linked" in both cases or to
the amino group (-NH2) in the R group of asparagine - called "N-linked"
The carbohydrate consists of short, usually branched, chains of
plain sugars (e.g., glucose, galactose)
amino sugars (sugars with an amino group, e.g., N-acetylglucosamine), and
acidic sugars (sugars with a carboxyl group, e.g., sialic acid)
Sugars are very hydrophilic thanks to their many -OH groups. Their presence
makes glycoproteins far more hydrophilic than they would be otherwise and
are often essential for the proper folding of the protein into its tertiary structure
Most of the proteins exposed to the watery surroundings at the surface of cells are glycoproteins.
This image shows the primary structure of glycophorin A, a glycoprotein that spans the
plasma membrane ("Lipid bilayer") of human red blood cells. Each RBC has some
500,000 copies of the molecule embedded in its plasma membrane.
Fifteen carbohydrate chains are "O-linked" to serine (Ser) and threonine (Thr) residues
One carbohydrate chain is "N-linked" to the asparagine (Asn) at position 26
Two polymorphic versions of glycophorin A, which differ only at residues 1 and 5, occur
in humans. These give rise to the MN blood groups
The M allele encodes Ser at position 1 (Ser-1) and Gly at position 5 (Gly-5)
The N allele encodes Leu-1 and Glu-5

Genotype to Phenotype
Individuals who inherit two N alleles (are homozygous) have blood group N.
Individuals who are homozygous for the M allele have blood group M.
Heterozygous individuals produce both proteins and have blood group MN.
Glycophorin A is the most important attachment site by which the parasite Plasmodium falciparum invades human red blood cells.

This page titled 2.12: Glycoproteins is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

2.12.1 https://bio.libretexts.org/@go/page/3790
2.13: Nucleotides
Nucleic acids are linear, unbranched polymers of nucleotides. Nucleotides consist of three parts.

A five-carbon sugar (hence a pentose). Two kinds are found:

deoxyribose, which has a hydrogen atom attached to its #2 carbon atom (designated 2'), and
ribose, which has a hydroxyl group there.
Deoxyribose-containing nucleotides, the deoxyribonucleotides, are the monomers of deoxyribonucleic acids (DNA). Ribose-
containing nucleotides, the ribonucleotides, are the monomers of ribonucleic acids (RNA).

The Purines The Pyrimidines

A nitrogen-containing ring structure called a nucleobase (or simply a base). The nucleobase is attached to the 1' carbon atom of the
pentose. In DNA, four different nucleobases are found:
two purines, called adenine (A) and guanine (G)
two pyrimidines, called thymine (T) and cytosine (C)
RNA contains:
The same purines, adenine (A) and guanine (G).
RNA also uses the pyrimidine cytosine (C), but instead of thymine, it uses the pyrimidine uracil (U).

Nucleoside
The combination of a nucleobase and a pentose is called a nucleoside.

2.13.1 https://bio.libretexts.org/@go/page/3791
One (as shown in the first figure), two, or three phosphate groups. These are attached to the 5' carbon atom of the pentose. The
product in each case is called a nucleotide. Both DNA and RNA are assembled from nucleoside triphosphates.
For DNA, these are dATP, dGTP, dCTP, and dTTP.
For RNA, these are ATP, GTP, CTP, and UTP.
In both cases, as each nucleotide is attached, the second and third phosphates are removed.
Table 2.13.1: The nucleosides and their mono-, di-, and triphosphates
Nucleobase Nucleoside Nucleotides

Adenine (A) Deoxyadenosine dAMP dADP dATP

Guanine (G) Deoxyguanosine dGMP dGDP dGTP

DNA
Cytosine (C) Deoxycytidine dCMP dCDP dCTP

Thymine (T) Deoxythymidine dTMP dTDP dTTP

Adenine (A) Adenosine AMP ADP ATP

Guanine (G) Guanosine GMP GDP GTP

RNA
Cytosine (C) Cytidine CMP CDP CTP

Uracil (U) Uridine UMP UDP UTP

This page titled 2.13: Nucleotides is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

2.13.2 https://bio.libretexts.org/@go/page/3791
2.14: Proteomics
Genome
One complete set of genes in an organism (a haploid set).
Except for occasional unrepaired damage to its DNA (= mutations), the genome is fixed.

Transcriptome
The most common definition: All the messenger RNA (mRNA) molecules transcribed from the genome.
Varies with the differentiated state of the cell and the activity of the transcription factors that turn gene transcription on (and off).
Speaking strictly, one would define the transcriptome as all the RNA molecules — which includes a wide variety of untranslated,
nonprotein-encoding RNA — transcribed from the DNA of the genome. It is now thought that ~75% of our DNA is transcribed
into RNA although only 1.5% of this is messenger RNA for protein synthesis.

Metabolome
All the metabolic machinery, e.g.,
enzymes
coenzymes
small metabolites, like
the intermediates in glycolysis and cellular respiration
nucleotides
present in a cell at a given time.
Varies with the differentiated state of the cell and its current activities.

Proteome
The proteome is the protein complement of the genome. It is quite a bit more complicated than the genome because a single gene
can give rise to a number of different proteins through
alternative splicing of the pre-messenger RNAs (pre-mRNAs)
RNA editing of the pre-messenger RNAs
attachment of carbohydrate residues to form glycoproteins
addition of phosphate groups to some of the amino acids in the protein
While we humans probably have only some 21 thousand genes, we probably make at least 10 times that number of different
proteins. The great majority of our genes produce pre-mRNAs that are alternatively-spliced.
The study of proteomics is important because proteins are responsible for both the structure and the functions of all living things.
Genes are simply the instructions for making proteins. It is proteins that make life.
The set of proteins within a cell varies
from one differentiated cell type to another (e.g. red blood cell vs lymphocyte) and
from moment to moment, depending on the activities of the cell, e.g.,
getting ready to duplicate its genome;
repairing damage to its DNA;
responding to a newly-available nutrient or cytokine;
responding to the arrival of a hormone

This page titled 2.14: Proteomics is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

2.14.1 https://bio.libretexts.org/@go/page/3792
 CHAPTER OVERVIEW
Unit 3: The Cellular Basis of Life
3.1: Animal Cells
3.2: Cell Membranes
3.3: The Nucleus
3.4: Ribosomes
3.5: Endoplasmic Reticulum
3.6: Golgi Apparatus
3.7: Centrosomes and Centrioles
3.8: Lysosomes and Peroxisomes
3.9: Protein Kinesis
3.10: The Proteasome
3.11: The Cytoskeleton
3.12: Cilia
3.13: Animal Tissues
3.14: Adipose Tissue
3.15: Junctions between Cells
3.16: Plant Cells
3.17: Chloroplasts
3.18: Chlorophylls and Carotenoids
3.19: Plant Tissues
3.20: Apoptosis
3.21: Collagens
3.22: Chromatophores
3.23: Diffusion, Active Transport and Membrane Channels
3.24: Endocytosis
3.25: Exocytosis

Thumbnail: A diagram of a typical prokaryotic cell. (Public Domain; LadyofHats).

This page titled Unit 3: The Cellular Basis of Life is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1
3.1: Animal Cells
This schematic represents an idealized animal cell, e.g., a liver cell. The columns to the left and right of the labels contain links to
discussions of the particular structures.

Intermediate filaments
Pinocytotic vesicle
Plasma membrane
Actin filaments
Peroxisome
Glycogen granules
Vacuole
Smooth endoplasmic reticulum
Lysosome
Microtubules
Nucleolus
Ribosomes
Centrioles
Mitochondrion
Nucleus
Rough endoplasmic reticulum
Nuclear envelope
Golgi apparatus Cytosol

This page titled 3.1: Animal Cells is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.1.1 https://bio.libretexts.org/@go/page/3965
3.2: Cell Membranes
One universal feature of all cells is an outer limiting membrane called the plasma membrane. In addition, all eukaryotic cells
contain elaborate systems of internal membranes which set up various membrane-enclosed compartments within the cell. Cell
membranes are built from lipids and proteins.

The Plasma Membrane

The plasma membrane serves as the interface between the machinery in the interior of the cell and the extracellular fluid (ECF) that
bathes all cells. The lipids in the plasma membrane are chiefly phospholipids like phosphatidyl ethanolamine. Phospholipids are
amphiphilic with the hydrocarbon tail of the molecule being hydrophobic; its polar head hydrophilic. As the plasma membrane
faces watery solutions on both sides, its phospholipids accommodate this by forming a phospholipid bilayer with the hydrophobic
tails facing each other. Substantial amounts of cholesterol are tucked within the hydrocarbon tails (not shown).

Figure 3.2.1: A detailed diagram of the cell membrane

Integral Membrane Proteins

Many of the proteins associated with the plasma membrane are tightly bound to it. Some are attached to lipids in the bilayer. In
others — the transmembrane proteins — the polypeptide chain actually traverses the lipid bilayer (Figure 3.2.2). The figure
shows a transmembrane protein that passes just once through the bilayer and another that passes through it 7 times. All G-protein-
coupled receptors (e.g., receptors of peptide hormones, and odors) each span the plasma membrane 7 times.

Figure 3.2.2: Schematic representation of transmembrane proteins: 1. a single transmembrane α-helix (bitopic membrane protein)
2. a polytopic transmembrane α-helical protein 3. a polytopic transmembrane β-sheet protein
In all these cases, the portion within the lipid bilayer consists primarily of hydrophobic amino acids. These are usually arranged in
an alpha helix so that the polar -C=O and -NH groups at the peptide bonds can interact with each other rather than with their
hydrophobic surroundings. Those portions of the polypeptide that project out from the bilayer tend to have a high percentage of
hydrophilic amino acids. Furthermore, those that project into the aqueous surroundings of the cell are usually glycoproteins, with
many hydrophilic sugar residues attached to the part of the polypeptide exposed at the surface of the cell. Some transmembrane
proteins that span the bilayer several times form a hydrophilic channel through which certain ions and molecules can enter (or
leave) the cell.

Peripheral Membrane Proteins

These are more loosely associated with the membrane. They are usually attached noncovalently to the protruding portions of
integral membrane proteins (Figure 3.2.3). Membrane proteins are often restricted in their movements. A lipid bilayer is really a
film of oil. Thus we might expect that structures immersed in it would be relatively free to float about. For some membrane
proteins, this is the case. For others, however, their mobility is limited:
Some of the proteins exposed at the interior face of the plasma membrane are tethered to cytoskeletal elements like actin
microfilaments.

3.2.1 https://bio.libretexts.org/@go/page/3966
 Some proteins are the exterior face of the plasma membrane are anchored to components of the extracellular matrix like
collagen.
Integral membrane proteins cannot pass through the tight junctions found between some kinds of cells (e.g., epithelial cells).

Figure 3.2.3: Schematic representation of peripheral membrane proteins

This page titled 3.2: Cell Membranes is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.2.2 https://bio.libretexts.org/@go/page/3966
3.3: The Nucleus
The nucleus is the hallmark of eukaryotic cells; the very term eukaryotic means having a "true nucleus".

The Nuclear Envelope

The nucleus is enveloped by a pair of membranes enclosing a lumen that is continuous with that of the endoplasmic reticulum. The
inner membrane is stabilized by a meshwork of intermediate filament proteins called lamins. The nuclear envelope is perforated by
thousands of nuclear pore complexes (NPCs) that control the passage of molecules in and out of the nucleus.

Chromatin
The nucleus contains the chromosomes of the cell. Each chromosome consists of a single molecule of DNA
complexed with an equal mass of proteins. Collectively, the DNA of the nucleus with its associated proteins is called
chromatin.
Most of the protein consists of multiple copies of 5 kinds of histones. These are basic proteins, bristling with
positively charged arginine and lysine residues. (Both Arg and Lys have a free amino group on their R group, which
attracts protons (H+) giving them a positive charge.) Just the choice of amino acids you would make to bind tightly
to the negatively-charged phosphate groups of DNA.
Chromatin also contains small amounts of a wide variety of nonhistone proteins. Most of these are transcription
factors (e.g., the steroid receptors) and their association with the DNA is more transient.
The image on the right shows the 5 histones separated by electrophoresis. These 5 proteins vary little from one cell
type to another or even from one species to another. However, the many nonhistone proteins in chromatin (also
shown on the right) do vary from one cell type to another and from one species to another. (Courtesy of Gary S.
Stein and Janet Swinehart Stein, University of Florida.)
Two copies of each of four kinds of histones H2A, H2B, H3, H4 form a core of protein, the nucleosome core. Around this is
wrapped about 147 base pairs of DNA. From 20–60 bp of DNA link one nucleosome to the next. Each linker region is occupied by
a single molecule of histone 1 (H1). This region is longer (50–150 bp) adjacent to the promoters of genes which presumably makes
more room for the binding of transcription factors.

Nucleosomes Nucleosome Schematics

The binding of histones to DNA does not depend on particular nucleotide sequences in the DNA but does depend critically on the
amino acid sequence of the histone. Histones are some of the most conserved molecules during the course of evolution. Histone H4
in the calf differs from H4 in the pea plant at only 2 amino acids residues in the chain of 102. The above electron micrograph
(courtesy of David E. Olins and Ada L. Olins) for nucleosomes shows chromatin from the nucleus of a chicken red blood cell
(birds, unlike most mammals, retain the nucleus in their mature red blood cells). The arrows point to the nucleosomes. You can see
why the arrangement of nucleosomes has been likened to "beads on a string".
The formation of nucleosomes helps somewhat, but not nearly enough, to make the DNA sufficiently compact to fit in the nucleus.
In order to fit 46 DNA molecules (in humans), totaling over 2 meters in length, into a nucleus that may be only 10 µm across
requires more extensive folding and compaction. Interactions between the exposed "tails" of the core histones causes nucleosomes
to associate into a compact fiber 30 nm in diameter. These fibers are then folded into more complex structures whose precise
configuration is uncertain and which probably changes with the level of activity of the genes in the region.

Histone Modifications
Although their amino acid sequence (primary structure) is unvarying, individual histone molecules do vary in structure as a result
of chemical modifications that occur later to individual amino acids. These include adding:

3.3.1 https://bio.libretexts.org/@go/page/3967
 acetyl groups (CH3CO−) to lysines
phosphate groups to serines and threonines
methyl groups to lysines and arginines
Although 75–80% of the histone molecule is incorporated in the core, the remainder — at the N-terminal — dangles out from the
core as a "tail" (not shown in the figure). Most of the chemical modifications occur on these tails, especially of H3 and H4. Most of
theses changes are reversible. For example, acetyl groups are added by enzymes called histone acetyltransferases (HATs)(not to
be confused with the "HAT" medium used to make monoclonal antibodies) and are also removed by histone deacetylases
(HDACs). More often than not, acetylation of histones occurs in regions of chromatin that become active in gene transcription.
This makes a kind of intuitive sense as adding acetyl groups neutralizes the positive charges on Lys thus reducing the strength of
the association between the highly-negative DNA and the highly-positive histones.
However, there is surely more to the story. Acetylation of Lys-16 on H4 ("H4K16ac") prevents the interaction of their "tails"
needed to form the compact 30-nm structure of inactive chromatin and thus is associated with active genes (note that this case
involves interrupting protein-protein not protein-DNA interactions). Methylation, which also neutralizes the charge on lysines (and
arginines), can either stimulate or inhibit gene transcription in that region.
Adding 3 methyl groups to lysine-4 and/or lysine-36 in H3 (H3K4me3 and H3K36me3 respectively) is associated with active
gene transcription while
trimethylation of lysine-9 and/or lysine-27 in H3 (H3K9me3 and H3K27me3 respectively) is associated with inactive genes.
(These include those imprinted genes that have been permanently inactivated in somatic cells.)
And adding phosphates causes the chromosomes to become more — not less — compact as they get ready for mitosis and
meiosis.
In any case, it is now clear that histones are a dynamic component of chromatin and not simply inert DNA-packing material.

Histone Variants
We have genes for 8 different varieties of histone 1 (H1). Which variety is found at a particular linker depends on such factors as
the type of cell, where it is in the cell cycle, and its stage of differentiation. In some cases, at least, a particular variant of H1
associates with certain transcription factors to bind to the enhancer of specific genes turning off expression of those genes.
Some other examples of histone variants:
H3 is replaced by CENP-A ("centromere protein A") at the nucleosomes near centromeres. Failure to substitute CENP-A for
H3 in this regions blocks centromere structure and function.
H2A is replaced by the variant H2A.Z at gene promoters and enhancers.
All the "standard" histones are replaced by variants as sperm develop.
In general, the "standard" histones are incorporated into the nucleosomes as new DNA is synthesized during S phase of the cell
cycle. Later, some are replaced by variant histones as conditions in the cell dictate.

Chromosome Territories
During interphase, little can be seen of chromatin structure (except for special cases like the polytene chromosomes of Drosophila
and some other flies). Although each chromosome is greatly elongated, it tends to occupy a discrete region within the nucleus
called its territory. This can be demonstrated by:
directing a tiny laser beam at a small portion of the nucleus. If all the chromosomes were intertwined, one would expect that all
would receive some damage. That does not occur — only one or two chromosomes are damaged.
Fluorescent stains specific for a particular chromosome stain only two regions in the nucleus — revealing the territory of the
two homologs.

"Kissing" Chromosomes
Portions of one chromosome can loop out of its territory and interact with part of a different chromosome looping out from its
territory. These are "kissing" chromosomes. The examples that have been found so far indicate that these interactions are another
way of coordinating the activity of genes residing on different chromosomes.

3.3.2 https://bio.libretexts.org/@go/page/3967
 The human genome contains many genes — scattered along different chromosomes — that are turned on by the arrival of a
single signal. Among the many genes activated by estrogen, are TIFF1 on chromosome 21 and GREB1 on chromosome 2.
Using FISH analysis, researchers at the University of California in San Diego showed that within a little as 2 minutes after
exposing cells to estrogen, the TIFF1 and GREB1 loci move from their respective chromosome territories and "kiss".

In the mouse, naive helper T cells — awaiting a signal to direct them to become either Th1 cells or Th2 cells have
the part of chromosome 10 carrying the gene for interferon-gamma (a Th1 cytokine) kissing
the part of chromosome 11 carrying the genes for IL-4 and IL-5 (Th2 cytokines).
When the cell receives the signals committing it to one path or the other, the two regions separate, the appropriate one going to
a region of active transcription; the other to a region of heterochromatin.

And still another example (in this case, two loci far apart on the same chromosome "kiss"):
In the head region of the Drosophila larva, expression of the homeobox (HOX) genes Antp and Abd-B is shut down. FISH analysis
shows that these two loci — 10,000,000 base pairs apart on chromosome III — are brought together in the nucleus bound by
proteins that prevent their transcription.

Euchromatin versus Heterochromatin

The density of the chromatin that makes up each chromosome (that is, how tightly it is packed) varies along the length of the
chromosome. Dense regions are called heterochromatin and less dense regions are called euchromatin. Heterochromatin is found in
parts of the chromosome where there are few or no genes, such as
centromeres and
telomeres. This heterochromatin is found in all types of cells in the organism.
is also found in gene-rich regions of the chromosome but where the genes are inactive; that is, not transcribed. The location of
this heterochromatin varies from one type of differentiated cell to another (as we would expect — a liver cell, for example,
should shut down expression of genes that are not needed for its functions.
is densely-packed.
is greatly enriched with transposons and other types of DNA that does not contribute to the proteome.
is replicated late in S phase of the cell cycle.
has reduced crossing over in meiosis.
is localized near the inner surface of the nuclear envelope, in most animal cells.
The histones in the nucleosomes of heterochromatin show characteristic modifications:
decreased acetylation;
increased methylation of lysine-9 in histone H3 (H3K9), which now provides a binding site for heterochromatin protein 1
(HP1), which blocks access by the transcription factors needed for gene transcription
increased methylation of lysine-27 in histone H3 (H3K27)

Euchromatin
is found in parts of the chromosome that contain many active genes.
is loosely-packed in loops of 30-nm fibers.
separated from adjacent heterochromatin by insulators.
In animal cells, euchromatin and thus active gene transcription occurs near the center of the nucleus.
The genes in euchromatin show
decreased methylation of the cytosines in CpG sites of the gene's promoter(s)
increased acetylation of nearby histones
decreased methylation of lysine-9 and lysine-27 in histone H3

Nucleosomes and Transcription

Transcription factors cannot bind to their promoter if the promoter is blocked by a nucleosome. One of the first functions of the
assembling transcription factors is to either expel the nucleosome from the site where transcription begins or at least to slide the

3.3.3 https://bio.libretexts.org/@go/page/3967
nucleosomes along the DNA molecule. Either action exposes the gene's promoter so that the transcription factors can then bind to
it.
The actual transcription of protein-coding genes is done by RNA polymerase II (Pol II or RNAP II). In order for it to travel along
the DNA to be transcribed, a complex of proteins removes the nucleosomes in front of it and then replaces them after Pol II has
transcribed that portion of DNA and moved on.

Nucleosomes and DNA Replication

As is the case in transcription, the DNA helix must open to allow DNA replication to proceed. This, too, requires that the
nucleosomes preceding the replication fork be removed and then quickly reassembled as the leading and lagging strands are
synthesized.

The Nucleolus
During the period between cell divisions, when the chromosomes are in their extended state, one or more of them (10 in human
cells) have loops extending into a spherical mass called the nucleolus. Here are synthesized three (of the four) kinds of RNA
molecules (28S, 18S, 5.8S) used in the assembly of the large and small subunits of ribosomes.
28S, 18S, and 5.8S ribosomal RNA is transcribed (by RNA polymerase I) from hundreds to thousands of tandemly-arranged rDNA
genes distributed (in humans) on 10 different chromosomes. The rDNA-containing regions of these 10 chromosomes cluster
together in the nucleolus.
(In yeast, the 5S rRNA molecules — as well as transfer RNA molecules — are also synthesized (by RNA polymerase III) in the
nucleolus.)
Once formed, rRNA molecules associate with the dozens of different ribosomal proteins used in the assembly of the large and
small subunits of the ribosome.
But proteins are synthesized in the cytosol — and all the ribosomes are needed in the cytosol to do their work — so there must be a
mechanism for the transport of these large structures in and out of the nucleus. This is one of the functions of the nuclear pore
complexes.

Nuclear Pore Complexes (NPCs)

The nuclear envelope is perforated with thousands of pores. Each is constructed from multiple copies of
several dozen different proteins called nucleoporins.
The entire assembly forms an aqueous channel connecting the cytosol with the interior of the nucleus
("nucleoplasm"). When materials are to be transported through the pore, it opens up to form a channel
some 27–41 nm wide — large enough to get such large assemblies as ribosomal subunits through.
Transport through the nuclear pore complexes is active; that is, it requires
energy
many different carrier molecules each specialized to transport a particular cargo
docking molecules in the NPC (represented here as colored rods and disks)

Import into the nucleus

Proteins are synthesized in the cytosol and those needed by the nucleus must be imported into it through the NPCs. They include:
all the histones needed to make the nucleosomes
all the ribosomal proteins needed for the assembly of ribosomes
all the transcription factors (e.g., the steroid receptors) needed to turn genes on (and off)
all the splicing factors needed to process pre-mRNA into mature mRNA molecules; that is, to cut out intron regions and splice
the exon regions.
Probably all of these proteins has a characteristic sequence of amino acids — called a nuclear localization sequence (NLS) — that
target them for entry.

3.3.4 https://bio.libretexts.org/@go/page/3967
Export from the nucleus
Molecules and macromolecular assemblies exported from the nucleus include:
the ribosomal subunits containing both rRNA and proteins
messenger RNA (mRNA) molecules (accompanied by proteins)
transfer RNA (tRNA) molecules (also accompanied by proteins)
transcription factors that are returned to the cytosol to await reuse
Both the RNA and protein molecules contain a characteristic nuclear export sequence (NES) needed to ensure their association
with the right carrier molecules to take them out to the cytosol.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and made
possible by funding from The Saylor Foundation.

This page titled 3.3: The Nucleus is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.3.5 https://bio.libretexts.org/@go/page/3967
3.4: Ribosomes
Ribosomes are the protein-synthesizing machines of the cell. They translate the information encoded in messenger RNA (mRNA)
into a polypeptide.

Shape, size and function

Ribosomes are roughly spherical with a diameter of ~20 nm, they can be seen only with the electron microscope. Figure 3.4.1 is an
electron micrograph showing clusters of ribosomes. These clusters, called polysomes, are held together by messenger RNA
(mRNA). They can make up 25% of the dry weight of cells (e.g., pancreas cells) and specialize in protein synthesis. A single
pancreas cell can synthesize 5 million molecules of protein per minute.

Figure 3.4.1 : An electron micrograph of polysomes held together with mRNA. Image courtesy of Alexander Rich.
In eukaryotes, ribosomes that synthesize proteins for use within the cytosol (e.g., enzymes of glycolysis) are suspended in the
cytosol. The specific ribosomes that synthesize proteins destined for secretion (by exocytosis), the plasma membrane (e.g., cell
surface receptors), and lysosomes. These ribosomes are attached to the cytosolic face of the membranes of the endoplasmic
reticulum. As the polypeptide is synthesized, it is extruded into the interior (lumen) of the endoplasmic reticulum. Then, before
these proteins reach their final destinations, they undergo a series of processing steps in the Golgi apparatus.
Ribosomes that synthesize 13 of the proteins destined for the inner membrane of mitochondria are found within the mitochondrion
itself and are quite different in structure from the others. The ribosomes of bacteria, eukaryotes, and mitochondria differ in many
details of their structure (Table 3.4.1). However, despite these differences, the basic operations of bacterial, eukaryotic, and
mitochondrial ribosomes are very similar.
Table 3.4.1 : Comparison of Ribosome Structure in Bacteria, Eukaryotes, and Human Mitochondria
Bacterial (70S) Eukaryotic (80S) Mitochondrial (55S)

Large Subunit 50S 60S 39S

23S (2904 nts) 28S (4700 nts) 16S (1560 nts)

rRNAs
5S (120 nts) 5S (120 nts)
(1 of each)
5.8S (160 nts)

Proteins 35 47 50

Small Subunit 30S 40S 28S

rRNA 16S (1542 nts) 18S (1900 nts) 12S (950 nts)

Proteins 20 33 30

S values are the sedimentation coefficient: a measure of the rate at which the particles are spun down in the ultracentrifuge. S values are not
additive. nts = nucleotides.

This page titled 3.4: Ribosomes is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.4.1 https://bio.libretexts.org/@go/page/3968
3.5: Endoplasmic Reticulum
The endoplasmic reticulum (ER) is a system of membrane-enclosed sacs and tubules in the cell. Their lumens are probably all
interconnected, and their membranes are continuous with the outer membrane of the nuclear envelope. All the materials within the
system are separated from the cytosol by a membrane. The endoplasmic reticulum is the site where the cell manufactures most of
the membranes of the cell (plasma membrane, Golgi apparatus, lysosomes, nuclear envelope), lipids (including lipids for
membranes, e.g., of the mitochondria, that are not made by the ER), and transmembrane proteins and secreted proteins. The ER
comes in two versions: the rough endoplasmic reticulum (RER) and the smooth endoplasmic reticulum (SER).

Rough Endoplasmic Reticulum (RER)

The RER is typically arranged as interconnecting stacks of disc-like sacs. The cytosolic surface of the RER is studded with
ribosomes engaged in protein synthesis. As the messenger RNA is translated by the ribosome, the growing polypeptide chain is
inserted into the membrane of the RER. Proteins destined to be secreted by the cell or shipped into the lumen of certain other
organelles like the Golgi apparatus and lysosomes pass all the way through into the lumen of the RER. Transmembrane proteins
destined for the plasma membrane or the membrane of those organelles are retained within the membrane of the RER.

Figure 3.5.1 : This electron micrograph (courtesy of Keith Porter) shows the RER in a bat pancreas cell. The clearer areas are the
lumens.
In either case, the portion of the protein within the lumen of the RER is subject to extensive glycosylation (primarily N-linked) in
Figure 3.5.1. The RER takes up a large proportion of the cytoplasm of cells specialized for protein synthesis such as cells secreting
digestive enzymes (e.g. the pancreas cell above) and antibody-secreting plasma cells

Smooth Endoplasmic Reticulum (SER)

The SER differs from the RER in lacking attached ribosomes and usually being tubular rather than disc-like. A major function of
the SER is the synthesis of lipids from which various cell membranes are made and like steroids, they are secreted from the cell.
The SER represents only a small portion of the ER is most cells, e.g. serving as transport vesicles for the transport of protein to the
Golgi apparatus. However, it is a prominent constituent of some cells, especially the cells of the adrenal cortex (which secrete
steroid hormones), the cells of the liver (hepatocytes) where it synthesis lipids for secretion of lipoproteins, and the sarcoplasmic
reticulum of muscle cells is SER.

This page titled 3.5: Endoplasmic Reticulum is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.5.1 https://bio.libretexts.org/@go/page/3969
3.6: Golgi Apparatus
The Golgi apparatus is a cell structure mainly devoted to processing the proteins synthesized in the endoplasmic reticulum (ER).
Some of these will eventually end up as integral membrane proteins embedded in the plasma membrane. Other proteins moving
through the Golgi will end up in lysosomes or be secreted by exocytosis (e.g., digestive enzymes). The major processing activity is
glycosylation: the adding of sugar molecules to form glycoproteins. In some cells, e.g., mucus-secreting cells in epithelia, the
amount of carbohydrate so far exceeds that of the protein that the product is called a mucopolysaccharide (also known as a
proteoglycan). In plant cells, the Golgi secretes the cell plate and cell wall.
Small peptides, e.g., some hormones and neurotransmitters, are typically too small to be synthesized directly by ribosomes.
Instead, the ribosomes on the ER synthesize a large precursor protein that is later cut up into small peptide fragments as it traverses
the Golgi. For example, proopiomelanocortin (POMC) is a polypeptide of 241 amino acids from which is cut ACTH, alpha and
beta MSH, beta- endorphin, and others. POMC is cleaved to give rise to multiple peptide hormones.
α-MSH produced by neurons in the arcuate nucleus has important roles in the regulation of appetite and sexual behavior, while
α-MSH secreted from the intermediate lobe of the pituitary regulates the production of melanin.
ACTH is a peptide hormone that regulates the secretion of glucocorticoids from the adrenal cortex.
β-Endorphin and [Met]enkephalin are endogenous opioid peptides with widespread actions in the brain.

Figure 3.6.1 : Proopiomelanocortin (POMC) and Melanocortin Peptides.

The Golgi consists of a stack of membrane-bounded cisternae located between the endoplasmic reticulum and the cell surface
(Figure 3.6.2). Many different enzymes (proteins) are present in the Golgi to perform its various synthetic activities. So there must
be mechanisms to sort out the processed proteins and send them on to their destinations while reclaiming processing proteins (e.g.,
glycosylases) for reuse.

Figure 3.6.2 : Golgi apparatus in a bat cell (Courtesy of Keith R. Porter)

The Outbound Path (Membrane Fission)

Two mechanisms appear to participate in the migration of proteins from the endoplasmic reticulum through the Golgi apparatus.
Mechanism 1: Transition vesicles pinch off from the surface of the endoplasmic reticulum carrying integral membrane
proteins, soluble proteins awaiting processing, and processing enzymes. Pinching off requires that the vesicle be coated with
COPII (Coat Protein II). The transition vesicles move toward the cis Golgi on microtubules. As they do so, their COPII coat is

3.6.1 https://bio.libretexts.org/@go/page/3970
 removed and they may fuse together forming larger vesicles; these fuse with the cis Golgi. Sugars are added to proteins in small
packets so many glycoproteins have to undergo a large number of sequential steps of glycosylation, each requiring its own
enzymes. These steps take place as shuttle vesicles carry the proteins from cis to medial to the trans Golgi compartments. At
the outer face of the trans Golgi, vesicles pinch off and carry their completed products to their various destinations.
Mechanism 2: In addition to the pinching off and fusing of shuttle vesicles, the cisternae of the Golgi actually migrate
themselves, that is, the cis Golgi gradually migrates up the stack becoming a medial and finally a trans Golgi (Figure 3.6.3).

Figure 3.6.3

The Inbound Path (Membrane Fusion)

The movement of cisternal contents through the stack means that essential processing enzymes are also moving away from their
proper site of action. Using a variety of signals, the Golgi separates the products from the processing enzymes that made them and
returns the enzymes back to the endoplasmic reticulum. This transport is also done by pinching off vesicles, but the inbound
vesicles are coated with COPI (coat protein I). A vesicle recognize its correct target by involving pairs of complementary
integral membrane proteins:
v-SNAREs = "vesicle SNAREs" — on the vesicle surface
t-SNAREs = "target SNAREs" — on the surface of the target membrane
v-SNAREs and t-SNAREs bind specifically to each other thanks to the complementary structure of their surface domains. Binding
is followed by fusion of the two membranes (Figure 3.6.4).

Figure 3.6.4

 The Golgi is Not a Static Organelle

The Golgi breaks up and disappears at the onset of mitosis. By telophase of mitosis, the Golgi reappears. How it is recreated is
still uncertain.

This page titled 3.6: Golgi Apparatus is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.6.2 https://bio.libretexts.org/@go/page/3970
3.7: Centrosomes and Centrioles
Centrioles
Centrioles are built from a cylindrical array of 9 microtubules, each of which has attached to it 2 partial microtubules. Figure
3.7.1 is an electron micrograph showing a cross section of a centriole with its array of nine triplets of microtubules.

Figure 3.7.1 : Cross Section of a Centriole (courtesy of E. deHarven). The magnification is approximately 305,000.
When a cell enters the cell cycle and passes through S phase, each centriole is duplicated. A "daughter" centriole grows out of the
side of each parent ("mother") centriole. Thus centriole replication — like DNA replication (which is occurring at the same time)
— is semiconservative.
Functional microtubules grow out only from the "mother".
When stem cells divide, one daughter cell remains a stem cell; the other goes on to differentiate. In two animal systems that
have been examined (mouse glial cells and Drosophila male germline cells), the cell that receives the old ("mother") centriole
remains a stem cell while the one that receives what had been the original "daughter" centriole goes on to differentiate. (You can
read about these findings in Wang, X., et. al., Nature, 15 October 2009.)
Centrioles are a key feature of eukaryotic cells and presumably arose with the first eukaryotes. A few groups have since lost their
centrioles including most fungi (but not the primitive chytrids), "higher" plants (but not the more primitive mosses, ferns, and
cycads with their motile sperm) and animal eggs lose their centriole during meiosis and must have it restored by the sperm that
fertilizes it
In nondividing cells, the mother centriole can attach to the inner side of the plasma membrane forming a basal body. In almost all
types of cell, the basal body forms a nonmotile primary cilium. In cells with a flagellum, e.g. sperm, the flagellum develops from a
single basal body. (While sperm cells have a basal body, eggs have none. So the sperm's basal body is absolutely essential for
forming a centrosome which will form a spindle enabling the first division of the zygote to take place.)
In ciliated cells such as the columnar epithelial cells of the lungs and ciliated protozoans like the paramecium, many basal bodies
form, each producing a beating cilium. Most of their centrioles are produced by repeated duplication of the daughter centriole of
centrosome and are temporarily assembled in a special organelle called the deuterosome (not to be confused with deuterostome).
Centrioles organize the centrosome in which they are embedded.

Centrosomes
The centrosome is located in the cytoplasm usually close to the nucleus. It consists of two centrioles — oriented at right angles to
each other — embedded in a mass of amorphous material containing more than 100 different proteins.It is duplicated during S
phase of the cell cycle. Just before mitosis, the two centrosomes move apart until they are on opposite sides of the nucleus. As
mitosis proceeds, microtubules grow out from each centrosome with their plus ends growing toward the metaphase plate. These
clusters of microtubules are called spindle fibers. Figure 3.7.2 shows microtubules growing in-vitro from an isolated centrosome.
The centrosome was supplied with a mixture of alpha and beta tubulin monomers spontaneously assembled into microtubules only
in the presence of centrosomes.

3.7.1 https://bio.libretexts.org/@go/page/3971
 Figure 3.7.2 : Centrosome (Courtesy Tim Hutchison)
Spindle fibers have three destinations:
1. Some attach to one kinetochore of a dyad with those growing from the opposite centrosome binding to the other kinetochore of
that dyad.
2. Some bind to the arms of the chromosomes.
3. Still others continue growing from the two centrosomes until they extend between each other in a region of overlap.

Figure 3.7.3 : Chromosome assembly at metaphase

All three groups of spindle fibers participate in
the assembly of the chromosomes at the metaphase plate at metaphase.
1. Microtubules attached to opposite sides of the dyad shrink or grow until they are of equal length.
2. Microtubules motors attached to the kinetochores move them
toward the minus end of shrinking microtubules (a dynein);
toward the plus end of lengthening microtubules (a kinesin).
3. The chromosome arms use a different kinesin to move to the metaphase plate.
the separation of the chromosomes at anaphase.
1. The sister kinetochores separate and, carrying their attached chromatid,
2. move along the microtubules powered by minus-end motors, dyneins, while the microtubules themselves shorten (probably
at both ends).
3. The overlapping spindle fibers move past each other (pushing the poles farther apart) powered by plus-end motors, the
"bipolar" kinesins.
4. In this way the sister chromatids end up at opposite poles.

Functions of Centrosomes
In addition to their role in spindle formation, centrosomes play other important roles in animal cells:
Formation of the network of microtubules that participate in making the cytoskeleton.
Signaling that it is o.k. to proceed to cytokinesis. Destruction of both centrosomes with a laser beam prevents cytokinesis even
if mitosis has been completed normally.
Signaling that it is o.k. for the daughter cells to begin another round of the cell cycle; specifically to duplicate their
chromosomes in the next S phase. Destruction of one centrosome with a laser beam still permits cytokinesis but the daughter
cells fail to enter a new S phase.
Segregating signaling molecules (e.g., mRNAs) so that they pass into only one of the two daughter cells produced by mitosis. In
this way, the two daughter cells can enter different pathways of differentiation even though they contain identical genomes.

3.7.2 https://bio.libretexts.org/@go/page/3971
 In at least some developing neurons, the position of the centrosome establishes the point at which the axon will grow out.

 Centrosomes and Cancer

Cancer cells often have more than the normal number of centrosomes. They also are aneuploid (have abnormal numbers of
chromosomes), and considering the role of centrosomes in chromosome movement, it is tempting to think that the two
phenomena are related. Mutations in the tumor suppressor gene p53 seem to predispose the cell to excess replication of the
centrosomes. Chromosome movement in mitosis also involves polymerization and depolymerization of microtubules.
Because the hallmark of cancer cells is uncontrolled mitosis, both vincristine and Taxol are used as anticancer drugs.
Vincristine, a drug found in the Madagascar periwinkle (a wildflower), binds to tubulin dimers preventing the assembly of
microtubules. This halts cells in metaphase of mitosis and Taxol, a drug found in the bark of the Pacific yew, prevents
depolymerization of the microtubules of the spindle fiber. This, in turn, stops chromosome movement, and thus prevents the
completion of mitosis.

This page titled 3.7: Centrosomes and Centrioles is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.7.3 https://bio.libretexts.org/@go/page/3971
3.8: Lysosomes and Peroxisomes
A cell is composed of many different organelles and microbodies (or cytosomes) is a type of organelle that is found in the cells of
plants, protozoa, and animals. Organelles in the microbody family include peroxisomes, glyoxysomes, glycosomes and
hydrogenosomes.

Lysosomes
Lysosomes are roughly spherical bodies enclosed by a single membrane. They are manufactured by the Golgi apparatus (Figure
3.8.1) and contain over 50 different kinds of hydrolytic enzymes including proteases, lipases, nucleases, and polysaccharidases.

The pH within the lysosome is about pH 5, substantially less than that of the cytosol (~pH 7.2). All the enzymes in the lysosome
work best at an acid pH, which reduces the risk of their digesting their own cell if they should escape from the lysosome.

Figure 3.8.1 : Lysosome manufacturing process The lysosome is shown in purple, as an endpoint in Endocytotic sorting. AP2 is
necessary for vesicle formation, whereas the Mannose-6-receptor is necessary for sorting Hydrolase into the Lysosome's lumen.
Image used wtih permission (CC BY-SA; Matthew R G Russell).
Materials within the cell scheduled for digestion are first deposited within lysosomes. These may be:
other organelles, such as mitochondria, that have ceased functioning properly and have been engulfed in autophagosomes
food molecules or, in some cases, food particles taken into the cell by endocytosis
foreign particles like bacteria that are engulfed by neutrophils
antigens that are taken up by
"professional" antigen-presenting cells like dendritic cells (by phagocytosis) and
B cells (by binding to their antigen receptors (BCRs) followed by receptor-mediated endocytosis.

At one time, it was thought that lysosomes were responsible for killing cells scheduled to be removed from a tissue; for
example, the resorption of its tail as the tadpole metamorphoses into a frog. This is incorrect. These examples of programmed
cell death (PCD) or apoptosis take place by an entirely different mechanism.

In some cells, lysosomes have a secretory function — releasing their contents by exocytosis.
Cytotoxic T cells (CTL) secrete perforin from lysosomes.

3.8.1 https://bio.libretexts.org/@go/page/3972
 Mast cells secrete some of their many mediators of inflammation from modified lysosomes.
Melanocytes secrete melanin from modified lysosomes.
The exocytosis of lysosomes provides the additional membrane needed to quickly seal wounds in the plasma membrane.

 Lysosomal Storage Diseases

Lysosomal storage diseases are caused by the accumulation of macromolecules (proteins, polysaccharides, lipids) in the
lysosomes because of a genetic failure to manufacture an enzyme needed for their breakdown. Neurons of the central nervous
system are particularly susceptible to damage. Most of these diseases are caused by the inheritance of two defective alleles of
the gene encoding one of the hydrolytic enzymes. Examples include:
Tay-Sachs disease and Gaucher's disease — both caused by a failure to produce an enzyme needed to break down
sphingolipids (fatty acid derivatives found in all cell membranes).
Mucopolysaccharidosis I (MPS-I). Caused by a failure to synthesize an enzyme (α-L-iduronidase) needed to break down
proteoglycans like heparan sulfate. In April 2003, the U.S. Food and Drug Administration approved a synthetic version of
the enzyme, laronidase (Aldurazyme®), as a possible treatment. This enzyme (containing 628 amino acids) is manufactured
by recombinant DNA technology.
However, one lysosomal storage disease, I-cell disease ("inclusion-cell disease"), is caused by a failure to "tag" (by
phosphorylation) all the hydrolytic enzymes that are supposed to be transported from the Golgi apparatus to the lysosomes.
Lacking the mannose 6-phosphate (M6P) tag, they are secreted from the cell instead. The result: all the macromolecules
incorporated in lysosomes remain undegraded forming "inclusion bodies" in the cell.

Peroxisomes
Peroxisomes, also called microbodies, are about the size of lysosomes (0.5–1.5 µm) and like them are enclosed by a single
membrane. They also resemble lysosomes in being filled with enzymes. However, peroxisomes bud off from the endoplasmic
reticulum, not the Golgi apparatus (the source of lysosomes) and the enzymes and other proteins destined for peroxisomes are
synthesized in the cytosol. Each contains a peroxisomal targeting signal (PTS) that binds to a receptor molecule that takes the
protein into the peroxisome and then returns for another load. Two peroxisomal targeting signals have been identified: a 9-amino
acid sequence at the N-terminal of the protein and a tripeptide at the C-terminal. Each has its own receptor to take it to the
peroxisome.
Functions of the peroxisomes in the human liver inlcude:
Breakdown (by oxidation) of excess fatty acids.
Breakdown of hydrogen peroxide (H2O2), a potentially dangerous product of fatty-acid oxidation. It is catalyzed by the enzyme
catalase.
Participates in the synthesis of cholesterol. One of the enzymes involved, HMG-CoA reductase, is the target of the popular
cholesterol-lowering "statins".
Participates in the synthesis of bile acids.
Participates in the synthesis of the lipids used to make myelin.
Breakdown of excess purines (AMP, GMP) to uric acid.
Peroxisomes are also present in plant cells where they participate is such functions as symbiotic nitrogen fixation and
photorespiration.

 Peroxisome Disorders

A variety of rare inherited disorders of peroxisome function occur in humans. Most involve mutant versions of one or another
of the enzymes found within peroxisomes. For example: X-linked adrenoleukodystrophy (X-ALD) results from a failure to
metabolize fatty acids properly. One result is deterioration of the myelin sheaths of neurons. The disorder occurs in young boys
because the gene is X-linked. An attempt to find an effective treatment was the subject of the 1992 film Lorenzo's Oil. A few
diseases result from failure to produce functional peroxisomes. For example: Zellweger syndrome results from the inheritance
of two mutant genes for one of the receptors (PXR1) needed to import proteins into the peroxisome.

3.8.2 https://bio.libretexts.org/@go/page/3972
This page titled 3.8: Lysosomes and Peroxisomes is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.8.3 https://bio.libretexts.org/@go/page/3972
3.9: Protein Kinesis
Proteins are the major building blocks of life. Eukaryotic cells synthesize proteins for thousands of different functions. Some
examples:
to build the components of the cytosol (e.g. microtubules, glycolytic enzymes);
to build the receptors and other molecules exposed at the surface of the cell embedded in the plasma membrane;
to supply some of the components of the mitochondria and (in plant cells) chloroplasts;
proteins secreted from the cell to supply the needs of other cells and tissues (e.g. collagens to support cells, hormones to signal
them).
All proteins are synthesized by ribosomes using the information encoded in molecules of messenger RNA (mRNA). This process
is called translation and is described in Gene Translation: RNA -> Protein. Our task here is to explore the ways that these proteins
are delivered to their proper destinations.
The various destinations for proteins occur in two major sets: (1) one set for those proteins synthesized by ribosomes that remain
suspended in the cytosol, and (2) a second set for proteins synthesized by ribosomes that are attached to the membranes of the
endoplasmic reticulum (ER) forming "rough endoplasmic reticulum" (RER). This electron micrograph (courtesy of Keith Porter)
shows the RER in a bat pancreas cell. The clearer areas are the lumens. So the first decision that must be made as a ribosome
begins to translate a mRNA into a polypeptide is whether to remain free in the cytosol or to bind to the ER.

Pathways Through the Endoplasmic Reticulum (ER)

The decision to enter the ER is dictated by the presence of a signal sequence on the growing polypeptide. The signal sequence
consists of the first portion of the elongating polypeptide chain (so the signal sequence occurs at the amino terminal of the
polypeptide). Typical signal sequences contain 15–30 amino acids. The precise amino acid sequence varies surprisingly from one
protein to the next, but all signal sequences include many hydrophobic amino acids.
If a signal sequence is present,
translation ceases after it has been synthesized.
The signal sequence is recognized by and is bound by a signal recognition particle (SRP).
The complex of ribosome with its nascent polypeptide and the SRP binds to a receptor on the surface (facing the cytosol) of the
ER.
The SRP leaves and translation recommences.
The growing polypeptide chain is extruded through a pore in the ER membrane and into the lumen of the ER.
The signal sequence is usually clipped off the polypeptide unless the polypeptide is to be retained as an integral membrane
protein.
Other proteins, called molecular chaperones, present in the lumen of the ER, bind the growing polypeptide chain and assist it
to fold into its correct tertiary structure.
Sugar residues may be added to the protein. The process is called glycosylation and often is essential for proper folding of the
final product, a glycoprotein.

 Note

The 1999 Nobel Prize in Physiology or Medicine was awarded to Dr. Günter Blobel for his discovery of the signal sequence
and other intrinsic signals that enable proteins to reach their proper destinations.

Destinations of proteins synthesized within the ER

3.9.1 https://bio.libretexts.org/@go/page/3974
 Figure 3.9.1: Glycosylation
There are two options.
1. proteins glycosylated with residues of mannose-6-phosphate will leave the Golgi in transport vesicles that eventually fuse with
lysosomes (path 2 in fig. 3.9.1).
2. proteins that do not receive this marker, leave in transport vesicles that eventually fuse with the plasma membrane (path 1 in
fig. 3.9.1). These are integral membrane proteins that become exposed at the surface of the cell (forming receptors and the like)
and proteins in solution within the transport vesicle. These are discharged from the cell. This secretory process is called
exocytosis.

The Signal Recognition Particle (SRP)

The signal recognition particle in mammalian cells is made from:
a single small (7S) molecule of RNA
six different molecules of protein
It contains binding sites for the signal sequence, the ribosome, and an SRP receptor, also called the docking protein, on the cytosol
face of the membranes of the ER.

Destinations of Proteins Synthesized By Free Ribosomes

Ribosomes synthesizing a protein without a signal sequence do not bind to the ER and continue synthesis until the polypeptide is
completed. Chaperones are also present in the cytosol that help the protein assume its final three-dimensional configuration. Some
of the important destinations for these proteins are:
The cytosol itself. Such proteins as the enzymes of glycolysis, tubulins for making microtubules, and actin for making
microfilaments are simply released from the ribosome and go to work.
The nucleus. Many proteins — histones, transcription factors, and ribosomal proteins are notable examples — must move
from the cytosol into the interior of the nucleus. They are targeted to the nucleus by their nuclear localization sequence, a
sequence of 7–41 amino acids of which the basic amino acids lysine and arginine are characteristic members. These proteins are
actively transported through pores in the nuclear envelope into the interior.
Mitochondria. Although the mitochondrion has its own genome and protein-synthesizing machinery, most of the proteins used
by mitochondria are Proteins destined for mitochondrion contain a characteristic signal sequence. This is recognized and bound
by a chaperone called mitochondrial stimulation factor (MSF). MSF targets the protein to a receptor embedded in the outer
membrane of the mitochondrion. Other factors and receptors shepherd proteins through the intermembrane space to the inner
mitochondrial membrane (e.g. some proteins of the electron transport chain) and the matrix.
encoded by genes in the nucleus of the cell
synthesized in the cytosol
must be imported into the mitochondrion.
Chloroplasts. Chloroplasts, like mitochondria, have their own genome and their own protein-synthesizing machinery. But also
like mitochondria, most of the proteins used in chloroplasts are encoded by genes in the nucleus of the cell, are synthesized by
ribosomes in the cytosol, and must then be imported into the chloroplast. Proteins destined for chloroplasts are recognized by

3.9.2 https://bio.libretexts.org/@go/page/3974
 their characteristic transit sequence. Chaperones are also needed to get them to their final destination: stroma, thylakoid
membrane, etc.
Peroxisomes. Proteins destined for peroxisomes are synthesized with a peroxisomal targeting signal (PTS) that binds to a
receptor molecule that takes the protein into the peroxisome and then returns for another load.
Two peroxisomal targeting signals have been identified:
Each has its own receptor to take it to the peroxisome.
a 9-amino acid sequence at the N-terminal of the protein
a tripeptide at the C-terminal.

This page titled 3.9: Protein Kinesis is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.9.3 https://bio.libretexts.org/@go/page/3974
3.10: The Proteasome
Protein degradation is as essential to the cell as protein synthesis. For example, to supply amino acids for fresh protein synthesis,
to remove excess enzymes, and to remove transcription factors that are no longer needed. There are two major intracellular devices
in which damaged or unneeded proteins are broken down. They are lysosomes and proteasomes

Lysosomes
Lysosomes deal primarily with extracellular proteins, e.g., plasma proteins, that are taken into the cell, e.g., by endocytosis. They
are cell-surface membrane proteins that are used in receptor-mediated endocytosis. The proteins (and other macromolecules) are
engulfed by autophagosomes.

Figure 3.10.1: Structure of Lysosome. of lumoreno (via Wikipedia)

Proteasomes
Proteasomes deal primarily with endogenous proteins; that is, proteins that were synthesized within the cell such as transcription
factors, cyclins (which must be destroyed to prepare for the next step in the cell cycle) and proteins encoded by viruses and other
intracellular pathogens. Proteasomes also address proteins that are folded incorrectly because of translation errors, or they are
encoded by faulty genes or they have been damaged by other molecules in the cytosol. Structure of the Proteasome in the Core
Particle (CP) and the Regulatory Particle (RP) as shown in Figure 3.10.2.

Figure 3.10.2: Simplified scheme of the proteosome complex.

The core particle is made of 2 copies of each of 14 different proteins that are assembled in groups of 7 forming a ring. The 4 rings
are stacked on each other (like 4 doughnuts) along a common center (Figure 3.10.3).

3.10.1 https://bio.libretexts.org/@go/page/3975
 Figure 3.10.3: (left) Cartoon representation of a proteasome. Its active sites are sheltered inside the tube (blue). The caps (red; in
this case, 11S regulatory particles) on the ends regulate entry into the destruction chamber, where the protein is degraded. (right)
view through the poor. Images used with permission from Wikipedia (CC-SA-BY.3.0; Thomas Splettstoesser).
There are two identical RPs, one at each end of the core particle. Each is made of 19 different proteins (none of them the same as
those in the CP). 6 of these are ATPases and some of the subunits have sites that recognize the protein ubiquitin. Ubiquitin is a
small protein (76 amino acids) that is conserved throughout all the kingdoms of life (Figure 3.10.4) and is virtually identical in
sequence whether in bacteria, yeast, or mammals. Ubiquitin is used by all these creatures to target proteins for destruction (hence
the name based off of the "ubiquitous" term).

Figure 3.10.4: Cartoon representation of ubiquitin protein, highlighting the secondary structure. from Wikipedia (CC-SA-BY-3.0;
Rogerdodd).

The Process
Proteins destined for destruction are conjugated to a molecule of ubiquitin which binds to the terminal amino group of a lysine
residue. Additional molecules of ubiquitin bind to the first forming a chain and this complex then binds to ubiquitin-recognizing
site(s) on the regulatory particle. The protein is unfolded by the ATPases using the energy of ATP, which is translocated into the
central cavity of the core particle. Several active sites on the inner surface of the two middle "doughnuts" break various specific
peptide bonds of the chain, which produces a set of peptides averaging about 8 amino acids long. These leave the core particle by
an unknown route where they may be further broken down into individual amino acids by peptidases in the cytosol. However, in
mammals, they may be incorporated in a class I histocompatibility molecule to be presented to the immune system as a potential
antigen. The regulatory particle releases the ubiquitins for reuse

Antigen Processing by Proteasomes

In mammals, activation of the immune system leads to the release of the cytokine interferon-gamma. This causes three of the
subunits in the core particle to be replaced by substitute subunits; the peptides generated in this altered proteasome are picked up by
TAP (= transporter associated with antigen processing) proteins and transported from the cytosol into the endoplasmic reticulum
where each enters the groove at the surface of a class I histocompatibility molecule. This complex then moves through the Golgi
apparatus and is inserted in the plasma membrane where it can be "recognized" by CD8+ T cells. It is probably no coincidence that
the genes encoding the three substitute core particle subunits, TAP and all the MHC (major histocompatibility complex)
molecules are clustered together on the same chromosome (#6 in humans).

3.10.2 https://bio.libretexts.org/@go/page/3975
This page titled 3.10: The Proteasome is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.10.3 https://bio.libretexts.org/@go/page/3975
3.11: The Cytoskeleton
Cells contain elaborate arrays of protein fibers that serve such functions as establishing cell shape, providing mechanical strength,
and locomotion. These fibers participate in chromosome separation in mitosis and meiosis and intracellular transport of organelles.
The cytoskeleton is made up of three kinds of protein filaments: Actin filaments (also called microfilaments), Intermediate
filaments, and Microtubules.

Actin Filaments
Monomers of the protein actin polymerize to form long, thin fibers. These are about 8 nm in diameter and, being the thinnest of the
cytoskeletal filaments, are also called microfilaments (in skeletal muscle fibers they are called "thin" filaments). Some functions of
actin filaments are:
form a band just beneath the plasma membrane that
provides mechanical strength to the cell
links transmembrane proteins (e.g., cell surface receptors) to cytoplasmic proteins
pinches dividing animal cells apart during cytokinesis
generate cytoplasmic streaming in some cells
generate locomotion in cells such as white blood cells and the amoeba
interact with myosin ("thick") filaments in skeletal muscle fibers to provide the force of muscular contraction

Intermediate Filaments
These cytoplasmic fibers average 10 nm in diameter (and thus are "intermediate" in size between actin filaments (8 nm) and
microtubules (25 nm) (as well as of the thick filaments of skeletal muscle fibers). There are several types of intermediate filament,
each constructed from one or more proteins characteristic of it.
keratins are found in epithelial cells and also form hair and nails;
nuclear lamins form a meshwork that stabilizes the inner membrane of the nuclear envelope;
neurofilaments strengthen the long axons of neurons;
vimentins provide mechanical strength to muscle (and other) cells.
Despite their chemical diversity, intermediate filaments play similar roles in the cell: providing a supporting framework within the
cell. For example, the nucleus in epithelial cells is held within the cell by a basketlike network of intermediate filaments made of
keratins.

Figure 3.11.1 Intermediate Filaments courtesy Mary Osborn. A fluorescent stain has been used to show the intermediate filaments
of keratin in two epithelial cells. Note the basketlike arrangement of filaments around each nucleus.
Different kinds of epithelia use different keratins to build their intermediate filaments. Over 20 different kinds of keratins have been
found, although each kind of epithelial cell may use no more than 2 of them. Up to 85% of the dry weight of squamous epithelial
cells can consist of keratins.

3.11.1 https://bio.libretexts.org/@go/page/3988
Microtubules
Microtubules are straight, hollow cylinders whose wall is made up of a ring of 13 "protofilaments" and have a diameter of about 25
nm. They are variable in length but can grow 1000 times as long as they are wide. They are built by the assembly of dimers of
alpha tubulin and beta tubulin. Microtubules are found in both animal and plant cells. In plant cells, microtubules are created at
many sites scattered through the cell. In animal cells, the microtubules originate at the centrosome. The attached end is called the
minus end; the other end is the plus end.
Microtubules grow at the plus end by the polymerization of tubulin dimers (powered by the hydrolysis of GTP), and shrink by the
release of tubulin dimers (depolymerization) at the same end. They participate in a wide variety of cell activities. Most involve
motion. The motion is provided by protein "motors" that use the energy of ATP to move along the microtubule.

Microtubule motors
There are two major groups of microtubule motors kinesins (most of these move toward the plus end of the microtubules) and
dyneins (which move toward the minus end)

 Examples
The rapid transport of organelles, like vesicles and mitochondria, along the axons of neurons takes place along
microtubules with their plus ends pointed toward the end of the axon. The motors are kinesins.
The migration of chromosomes in mitosis and meiosis takes place on microtubules that make up the spindle fibers. Both
kinesins and dyneins are used as motors

Cilia and Flagella

Cilia and flagella are built from arrays of microtubules.

This page titled 3.11: The Cytoskeleton is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.11.2 https://bio.libretexts.org/@go/page/3988
3.12: Cilia
These whiplike appendages extend from the surface of many types of eukaryotic cells. If there are many of them, they are called
cilia. If only one, or a few, they are flagella. Flagella also tend to be longer than cilia but are otherwise similar in construction.

Function of Cilia and Flagella

Cilia and flagella move liquid past the surface of the cell. For single cells, such as sperm, this enables them to swim. For cells
anchored in a tissue, like the epithelial cells lining our air passages, this moves liquid over the surface of the cell (e.g., driving
particle-laden mucus toward the throat). Both cilia and flagella consist of:
a cylindrical array of 9 filaments consisting of:
a complete microtubule (the A-microtubule) extending into the tip of the cilium. When a cilium is being disassembled,
protein complexes move down from the tip of the cilium traveling along A-microtubules.
a partial microtubule (the B-microtubule) that doesn't extend as far into the tip. When the cilium is growing, its protein
components move up toward the tip of the cilium traveling along B-microtubules.
cross-bridges of the motor protein dynein that extend from the complete microtubule of one filament to the partial
microtubule of the adjacent filament.
a pair of single microtubules running up through the center of the bundle, producing the "9+2" arrangement.
The entire assembly is sheathed in a membrane that is an extension of the plasma membrane.

Figure 3.12.1 : Cilia courtesy of Peter Satir

This electron micrograph (Figure 3.12.1) shows a cilium in cross section. Each cilium (and flagellum) grows out from, and remains
attached to, a basal body embedded in the cytoplasm. Basal bodies are identical to centrioles and are, in fact, produced by them.
For example, one of the centrioles in developing sperm cells — after it has completed its role in the distribution of chromosomes
during meiosis — becomes a basal body and produces the flagellum

The Sliding-Filament Model of Bending

Motion of cilia and flagella is created by the microtubules sliding past one another. This requires motor molecules of dynein,
which link adjacent microtubules together, and the energy of ATP. Dynein powers the sliding of the microtubules against one
another — first on one side, then on the other. The bending of cilia (and flagella) has many parallels to the contraction of skeletal
muscle fibers.

Testing the Model

Remember, the partial microtubules do not extend as far into the tip as the complete microtubules. So if a slice is made a short
distance back from the tip:
A straight cilium should show the complete pattern (center of diagram).
In a bent cilium, approximately half the filaments on the upper side should be retracted because of the greater arc on the convex
side. So the partial microtubules would disappear being drawn below the plane of the slice. As seen here, bending to the left
causes the partial microtubules 4, 5, 6, 7, and 8 to disappear.
When the cilium bends the other way, the partial microtubules on the opposite side disappear while they reappear on what is
now the lower or concave side.
Electron micrographs (made by Peter Satir) have verified this model precisely.

3.12.1 https://bio.libretexts.org/@go/page/3989
 Figure 3.12.1 : Cilia Model courtesy Peter Satir

Other Parallels
There are other parallels between the sliding filaments of skeletal muscle and the sliding microtubules of cilia. Both are powered by
ATP. Both motors —dynein in cilia, myosin in skeletal muscle — are ATPases and both are regulated by calcium ions.

The Primary Cilium

Motile, "9+2", cilia are found only on certain cells in the vertebrate body, e.g., the epithelia lining the airways. But almost every
cell in mammals has — or had — a single primary cilium. The primary cilium grows out of the older of the two centrioles that the
cell inherited following mitosis. The primary cilium does not beat because it lacks the central pair of microtubules; that is, it is
"9+0". Where functions have been identified, they all involve sensory reception. Some examples are as follows:
Mechanoreceptors: A primary cilium extends from the apical surface of the epithelial cells lining the kidney tubules and
monitors the flow of fluid through the tubules. Inherited defects in the formation of these cilia cause polycystic kidney disease.
Chemoreceptors: We detect odors by receptors on the primary cilium of olfactory neurons. Many types of cells detect
extracellular signaling molecules, e.g., nutrients, growth factors, hormones, with receptors localized on their primary cilium.
These signals may be transduced into the nucleus where they alter gene expression.
Photoreceptors: The outer segment of the rods in the vertebrate retina is also derived from a primary cilium.

This page titled 3.12: Cilia is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source content
that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.12.2 https://bio.libretexts.org/@go/page/3989
3.13: Animal Tissues
The development of a fertilized egg into a newborn child requires an average of 41 rounds of mitosis (2 = 2.2 × 10 ). During
41 12

this period, the cells produced by mitosis enter different pathways of differentiation; some becoming blood cells, some muscle
cells, and so on. There are more than 100 visibly-distinguishable kinds of differentiated cells in the vertebrate animal. These are
organized into tissues; the tissues into organs. Groups of organs make up the various systems — digestive, excretory, etc. — of the
body (Figure 3.13.1 and Table 3.13.1).

Figure 3.13.1 : Animal Tissues

The actual number of differentiated cell types is surely much larger than 100. All lymphocytes, for example, look alike but actually
represent a variety of different functional types, e.g., B cells, T cells of various subsets. The neurons of the central nervous system
must exist in a thousand or more different functional types, each representing the result of a particular pathway of differentiation.
This page will give a brief introduction to the major types of animal tissues.
Table 3.13.1 : Classification of Animal Tissues
Linings and Coverings Simple Epithelia

Classifying or Naming Epithelia Stratified Epithelia

Epithelial Tissues
Exocrine Glands
Glands
Endocrine Glands
Lymph
Fluid Connective Tissues
Blood
Loose Connective Tissues
Connective Tissues Connective Tissues Proper Loose Connective Tissues and Inflammation
Dense Connective Tissues
Osseous Tissue
Supportive Connective Tissues
Cartilage

Non-striated Smooth muscle

Muscle Tissues Skeletal Muscle
Striated
Cardiac Muscle

Neurons Multipolar Neurons in CNS

Nervous Tissues Nerves Nerves of the PNS

Receptors Miessner's and Pacinian Corpuscles

3.13.1 https://bio.libretexts.org/@go/page/3990
Epithelial
Epithelial tissue is made of closely-packed cells arranged in flat sheets. Epithelia form the surface of the skin, line the various
cavities and tubes of the body, and cover the internal organs. Epithelia that form the interface between the internal and external
environments. Skin as well as the lining of the mouth and nasal cavity. These are derived from ectoderm. Inner lining of the GI
tract, lungs, urinary bladder, exocrine glands, vagina and more. These are derived from endoderm.
The apical surface of these epithelial cells is exposed to the "external environment", the lumen of the organ or the air.
Mesothelia. These are derived from mesoderm.
pleura — the outer covering of the lungs and the inner lining of the thoracic (chest) cavity.
peritoneum — the outer covering of all the abdominal organs and the inner lining of the abdominal cavity.
pericardium — the outer lining of the heart.
Endothelia. These are derived from mesoderm. The inner lining of the heart, all blood and lymphatic vessels.
The basolateral surface of all epithelia is exposed to the internal environment - extracellular fluid (ECF). The entire sheet of
epithelial cells is attached to a layer of extracellular matrix that is called the basement membrane or, better (because it is not a
membrane in the biological sense), the basal lamina.
The function of epithelia always reflects the fact that they are boundaries between masses of cells and a cavity or space. Some
examples include:
The epithelium of the skin protects the underlying tissues from mechanical damage, ultraviolet light, dehydration and invasion
by bacteria
The columnar epithelium of the intestine secretes digestive enzymes into the intestine and absorbs the products of digestion
from it.
An epithelium also lines our air passages and the alveoli of the lungs. It secretes mucus which keeps it from drying out and
traps inhaled dust particles. Most of its cells have cilia on their apical surface that propel the mucus with its load of foreign
matter back up to the throat.

Muscle
Three kinds of muscle are found in vertebrates. Skeletal muscle is made of long fibers whose contraction provides the force of
locomotion and other voluntary body movements. Smooth muscle lines the walls of the hollow structures of the body, such as the
intestine, urinary bladder, uterus, and blood vessels. Its contraction, which is involuntary, reduces the size of these hollow organs.
The heart is made of cardiac muscle.

Connective
The cells of connective tissue are embedded in a great amount of extracellular material. This matrix is secreted by the cells. It
consists of protein fibers embedded in an amorphous mixture of protein-polysaccharide ("proteoglycan") molecules. Supporting
connective tissue gives strength, support, and protection to the soft parts of the body.
cartilage. Example: the outer ear
bone. The matrix of bone contains collagen fibers and mineral deposits. The most abundant mineral is calcium phosphate,
although magnesium, carbonate, and fluoride ions are also present.
Dense connective tissue is often called fibrous connective tissue and include Tendons and Ligaments. Tendons connect muscle to
bone with a The matrix is principally Type I collagen, and the fibers are all oriented parallel to each other. Tendons are strong but
not elastic. Ligaments attach one bone to another and contain both collagen and also the protein elastin. Elastin permits ligaments
to be stretched.
Loose connective tissue is distributed throughout the body. It serves as a packing and binding material for most of our organs.
Sheets of loose connective tissue that bind muscles and other structures together are called fascia. Collagen, elastin, and other
proteins are found in the matrix of loose connective tissue. Both dense and loose connective tissue are derived from cells called
fibroblasts, which secrete the extracellular matrix.

3.13.2 https://bio.libretexts.org/@go/page/3990
Adipose Tissue
Adipose tissue is "fat". There are two kinds found in mammals: white adipose tissue (WAT) and brown adipose tissue (BAT). The
WAT in which the cells, called adipocytes, have become almost filled with oil, which is confined within a single membrane-
enclosed droplet. Virtually all of the "fat" in adult humans is white adipose tissue. BAT in which the adipocytes contain many small
droplets of oil as well as many mitochondria. White adipose tissue and brown adipose tissue differ in function as well as cellular
structure. These differences are described elsehwhere.
New adipocytes in white adipose tissue are formed throughout life from a pool of precursor cells. These are needed to replace those
that die (after an average life span of 10 years). Whether the total number of these adipocytes increases in humans becoming fatter
as adults is still uncertain. If not, why do so many of us get fatter as we age? Because of the increased size of individual adipocytes
as they become filled with oil. The adipocytes of white adipose tissue secrete several hormones, including leptin and adiponectin.

Nerve
Nerve tissue is composed of nerve cells called neurons and glial cells. Neurons are specialized for the conduction of nerve
impulses; a typical neuron consists of a cell body which contains the nucleus; a number of short fibers — dendrites — extending
from the cell body and a single long fiber, the axon. The nerve impulse is conducted along the axon. The tips of axons meet other
neurons at junctions called synapses, muscles (called neuromuscular junctions) and glands.

Glia
Glial cells surround neurons. Once thought to be simply support for neurons (glia = glue), they turn out to serve several important
functions. There are three types:
Schwann cells. These produce the myelin sheath that surrounds many axons in the peripheral nervous system.
Oligodendrocytes. These produce the myelin sheath that surrounds many axons in the central nervous system (brain and spinal
cord).
Astrocytes. These, often star-shaped cells are clustered around synapses and the nodes of Ranvier where they perform a variety
of functions such as:
modulating the activity of neurons
supplying neurons with materials (e.g. glucose and lactate) as well as some signaling molecules
regulating the flow of blood to their region of the brain. It is primarily the metabolic activity of astrocytes that is being
measured in brain imaging by positron-emission tomography (PET) and functional magnetic resonance imaging (fMRI).
pruning away (by phagocytosis) weak synapses
In addition, the central nervous system contains many microglia — mobile cells (macrophages) that respond to damage (e.g., from
an infection) by engulfing cell debris and secreting inflammatory cytokines like tumor necrosis factor (TNF-α) and interleukin-1
(IL-1). Microglia are also active in the healthy brain, at least in young mice where, like astrocytes, they engulf synapses thus
reducing the number of synapses in the developing brain.

Blood
The bone marrow is the source of all the cells of the blood. These include red blood cells (RBCs or erythrocytes), five kinds of
white blood cells (WBCs or leukocytes), and platelets (or thrombocytes).

This page titled 3.13: Animal Tissues is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.13.3 https://bio.libretexts.org/@go/page/3990
3.14: Adipose Tissue
Two kinds of adipose tissue are found in mammals: white adipose tissue (WAT) and brown adipose tissue (BAT). White adipose
tissue is the most common and is the fat that so many of us complain of acquiring. Brown adipose tissue is present in small
mammals (e.g., mice) and in newborn humans. Most of it disappears in adult humans.The cells in both types of fat are called
adipocytes although they differ in origin, structure, and function in the two types of tissue.
Table 3.14.1: Two classifications of Adipocytes
WAT Adipocytes BAT Adipocytes

a narrow rim of cytoplasm with its nucleus

pressed near the margin of the cell Cytoplasm throughout the cell with a central nucleus and
surrounding

a single large membrane-enclosed lipid droplet many small lipid droplets

few mitochondria many mitochondria (providing the brown color)

modest blood supply rich blood supply

serves as a depot of stored energy function is to generate heat

New adipocytes in white adipose tissue are formed throughout life from a pool of precursor cells. These are needed to replace those
that die (after an average life span of 10 years). Whether the total number of these adipocytes increases in humans becoming fatter
as adults is still uncertain. If not, why do so many of us get fatter as we age? Because of the increased size of individual adipocytes
as they become filled with oil.
The adipocytes of white adipose tissue secrete several hormones, including leptin, asprosin (which, during fasting, causes a rapid
release of blood sugar (glucose) from the liver) and adiponectin. In addition to serving as a major source of energy reserves, white
adipose tissue also provides some mechanical protection and insulation to the body. Obesity is the excessive accumulation of white
adipose tissue.
Brown adipose tissue provides a vital source of heat to maintain body temperature in small mammals (with their high surface to
volume ratio) and infants (who usually cannot shiver when they are cold).

Adipose tissue activation mechanism

Brown adipose tissue is activated by the following mechanism when the body temperature drops:

Figure 3.14.1 Adipose tissue activation process

Cold activates the sympathetic nervous system.
Noradrenaline is released by the postganglionic neurons.
The noradrenaline binds to G-protein-coupled receptors on the adipocytes surface.
The second messenger cAMP is generated and moves into the nucleus where
it binds to the promoter of the gene encoding an enzyme that converts thyroxine (T4) to triiodothyronine (T3).
T3 enters the nucleus and bind to the promoter of the gene encoding uncoupling protein1 (UCP1).
UCP1 inserts into the inner membrane of the mitochondria where
it allows the protons that have been pumped out into the intermembrane space by the electron transport chain
to return to the matrix without having to pass through ATP synthase.
So instead of cellular respiration (of fatty acids and glucose) generating ATP, it generates heat.

3.14.1 https://bio.libretexts.org/@go/page/3991
WAT can Acquire the Properties of BAT
In mice and perhaps in humans, skeletal muscles that have undergone a period of vigorous exercise secrete a protein hormone
called irisin. Irisin acts on white adipose tissue to give it the properties of brown adipose tissue:
an increase in the number of mitochondria and lipid droplets;
a marked increase in the synthesis of UCP1;
an increase in the rate of cellular respiration but with the energy released as heat rather than fueling the synthesis of ATP.
These brown-like fat cells derived from white fat cells have been called "beige" or "brite" cells. Lean adult humans have deposits
of beige cells in the neck and upper chest regions. When they are exposed to cold, their beige cells are activated. Obese people have
few or no beige cells. Probably their layers of white adipose tissue provide such good insulation that they are in less danger of heat
loss.

This page titled 3.14: Adipose Tissue is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.14.2 https://bio.libretexts.org/@go/page/3991
3.15: Junctions between Cells
In many animal tissues (e.g., connective tissue), each cell is separated from the next by an extracellular coating or matrix. However,
in some tissues (e.g., epithelia), the plasma membranes of adjacent cells are pressed together. Four kinds of junctions occur in
vertebrates:
1. Tight junctions
2. Adherens junctions
3. Gap junctions
4. Desmosomes
In many plant tissues, it turns out that the plasma membrane of each cell is continuous with that of the adjacent cells. The
membranes contact each other through openings in the cell wall called Plasmodesmata.

Tight Junctions
Epithelia are sheets of cells that provide the interface between masses of cells and a cavity or space (a lumen). The portion of the
cell exposed to the lumen is called its apical surface. The rest of the cell (i.e., its sides and base) make up the basolateral surface.
Tight junctions seal adjacent epithelial cells in a narrow band just beneath their apical surface. They consist of a network of
claudins and other proteins. Tight junctions perform two vital functions:
1. They limit the passage of molecules and ions through the space between cells. So most materials must actually enter the cells
(by diffusion or active transport) in order to pass through the tissue. This pathway provides tighter control over what substances
are allowed through.
2. They block the movement of integral membrane proteins (red and green ovals) between the apical and basolateral surfaces of
the cell. Thus the special functions of each surface, for example receptor-mediated endocytosis at the apical surface and
exocytosis at the basolateral surface can be preserved.

Figure 3.15.1: Tight Junction

 The Epithelia of the Human Lung

A report by Vermeer, et al., in the 20 March 2003 issue of Nature provides a striking example of the role of tight junctions. The
epithelial cells of the human lung express
a growth stimulant, called heregulin, on their apical surface and
its receptors on the basolateral surface. (These receptors also respond to epidermal growth factor (EGF), and mutant
versions have been implicated in cancer.
As long as the sheet of cells is intact, there is no stimulation of its receptors by heregulin thanks to the seal provided by tight
junctions. However, if the sheet of cells becomes broken, heregulin can reach its receptors. The result is an autocrine
stimulation of mitosis leading to healing of the wound. Several disorders of the lung the chronic bronchitis of cigarette
smokers, asthma, cystic fibrosis increase the permeability of the airway epithelium. The resulting opportunity for autocrine
stimulation may account for the proliferation (piling up) of the epithelial cells characteristic of these disorders.

Adherens Junctions
Adherens junctions provide strong mechanical attachments between adjacent cells. They hold cardiac muscle cells tightly together
as the heart expands and contracts and hold epithelial cells together. Adherens junctions seem to be responsible for contact
inhibition and some are present in narrow bands connecting adjacent cells. Others are present in discrete patches holding the cells
together . Adherens junctions are built from cadherins that are transmembrane proteins (Figure 3.15.2; red labeled) whose

3.15.1 https://bio.libretexts.org/@go/page/3993
extracellular segments bind to each other and whose intracellular segments bind to catenins (Figure 3.15.2; yellow labeled), which
are connected to actin filaments

Figure 3.15.2: Adheren Junctions

Human synthesize some 80 different types of cadherins. In most cases, a cell expressing one type of cadherin will only form
adherens junctions with another cell expressing the same type. This is because molecules of cadherin tend to form homodimers, not
heterodimers. Inherited mutations in a gene encoding a cadherin can cause stomach cancer. Mutations in a gene (APC), whose
protein normally interacts with catenins, are a common cause of colon cancer. Loss of functioning adherens junctions may
accelerate the edema associated with sepsis and tumor metastasis.

Gap Junctions
Gap junctions are intercellular channels some 1.5–2 nm in diameter. These permit the free passage between the cells of ions and
small molecules (up to a molecular weight of about 1000 daltons). They are cylinders constructed from 6 copies of transmembrane
proteins called connexins. Because ions can flow through them, gap junctions permit changes in membrane potential to pass from
cell to cell.

Figure 3.15.3: The diagram shows a gap junction and its main element. connexon. together with the structure of the connexin. (CC-
BY-SA-3.0; Mariana Ruiz)
Examples of gap junctions include:
The action potential in heart (cardiac) muscle flows from cell to cell through the heart providing the rhythmic contraction of the
heartbeat.
At some so-called electrical synapses in the brain, gap junctions permit the arrival of an action potential at the synaptic
terminals to be transmitted across to the postsynaptic cell without the delay needed for release of a neurotransmitter.
As the time of birth approaches, gap junctions between the smooth muscle cells of the uterus enable coordinated, powerful
contractions to begin.
Several inherited disorders of humans such as certain congenital heart defects and certain cases of congenital deafness have been
found to be caused by mutant genes encoding connexins.

Desmosomes
Desmosomes are localized patches that hold two cells tightly together. They are common in epithelia (e.g., the skin). Desmosomes
are attached to intermediate filaments of keratin in the cytoplasm. Pemphigus is an autoimmune disease in which the patient has

3.15.2 https://bio.libretexts.org/@go/page/3993
developed antibodies against proteins (cadherins) in desmosomes. The loosening of the adhesion between adjacent epithelial cells
causes blistering. Carcinomas are cancers of epithelia. However, the cells of carcinomas no longer have desmosomes. This may
partially account for their ability to metastasize.

Hemidesmosomes
These are similar to desmosomes but attach epithelial cells to the basal lamina ("basement membrane") instead of to each other.
Pemphigoid is an autoimmune disease in which the patient develops antibodies against proteins (integrins) in hemidesmosomes.
This, too, causes severe blistering of epithelia.

Plasmodesmata
Although each plant cell is encased in a boxlike cell wall, it turns out that communication between cells is just as easy, if not easier,
than between animal cells (Figure 3.15.4). Fine strands of cytoplasm, called plasmodesmata, extend through pores in the cell wall
connecting the cytoplasm of each cell with that of its neighbors.

Figure 3.15.4: A diagram showing the different routes through which water can travel through a plant. Plasmodesmata allow
molecules to travel between plant cells through the symplastic pathway. Image used wtih permission from Wikipedia (public
domain; Jackacon).
Plasmodesmata provide an easy route for the movement of ions, small molecules like sugars and amino acids, and even
macromolecules like RNA and proteins, between cells. The larger molecules pass through with the aid of actin filaments.
Plasmodesmata are sheathed by a plasma membrane that is simply an extension of the plasma membrane of the adjoining cells.
This raises the intriguing question of whether a plant tissue is really made up of separate cells or is, instead, a syncytium: a single,
multinucleated cell distributed throughout hundreds of tiny compartments.

This page titled 3.15: Junctions between Cells is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.15.3 https://bio.libretexts.org/@go/page/3993
3.16: Plant Cells
Plant cells are eukaryotic and have many of the structures found in animal cells.
Plasma membrane
Nucleus and nucleolus
Mitochondria
Ribosomes
Endoplasmic reticulum
Golgi apparatus
Peroxisomes (the crystal in the electron micrograph is enclosed within a peroxisome)
Microtubules
Plant cells differ from animal cells as they lack centioles and intermediate filament; they also do not have plastids and a cell wall
and large vacuoles.

Figure 3.16.1 Sunflower leaf micrograph courtesy of H. J. Arnott and Kenneth M. Smith

Plastids
Chloroplasts are the most familiar plastids. They are usually disk-shaped and about 5-8 µm in diameter and 2-4 µm thick. A typical
plant cell has 20-40 of them. Chloroplasts are green because they contain chlorophylls — the pigments that harvest the light used in
photosynthesis. Chloroplasts are probably the descendants of cyanobacteria that took up residence in the ancestor of the plants.
Plant cells that are not engaged in photosynthesis also have plastids that serve other functions such as storing starch (when they are
called leucoplasts) and storing the carotenoids that give flowers and fruits their color (when they are called chromoplasts)

The Cell Wall

The rigid cell wall of plants is made of fibrils of cellulose embedded in a matrix of several other kinds of polymers such as pectin
and lignin. The linear nature of cellulose molecules and the many opportunities for side-to-side intermolecular hydrogen bonding
provide just what one would want to build long and stiff fibrils.
Primary cell walls: The cell walls of parenchyma and meristems are uniform in thickness and are primary cell walls. Although
each cell appears encased within a box, in fact primary cell walls are perforated permitting plasmodesmata to connect adjacent
cells.
Secondary cell walls: The cells of sclerenchyma, collenchyma and xylem have secondary deposits of lignified cellulose which
provide mechanical strength to the tissue.

Vacuoles
Vacuoles are enclosed by a single membrane. Young plant cells often contain many small vacuoles, but as the cells mature, these
unite to form a large central vacuole. Vacuoles serve several functions such as:
storing foods (e.g., proteins in seeds)
storing wastes
storing malic acid in CAM plants

3.16.1 https://bio.libretexts.org/@go/page/3994
 storing various ions (e.g., calcium, sodium, iron) which, among other functions, helps to
maintain turgor in the cell.
Plant cells avoid bursting in hypotonic surroundings by their strong cell walls. These allow the build-up of turgor within the cell.
Loss of turgor causes wilting.

Plasmolysis
When a freshwater (or terrestrial) plant is placed in sea water, its cells quickly lose turgor and the plant wilts. This is because sea
water is hypertonic to the cytoplasm. As water diffuses from the cytoplasm into the sea water, the cells shrink — drawing their
plasma membrane away from the cell wall.

Figure 3.16.2: Plasmolyzed cell of freshwater plant Elodea

This page titled 3.16: Plant Cells is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.16.2 https://bio.libretexts.org/@go/page/3994
3.17: Chloroplasts
A typical plant cell (e.g., in the palisade layer of a leaf) might contain as many as 50 chloroplasts.

Figure 3.17.1 Typical Chloroplast

The chloroplast is made up of 3 types of membrane:
A smooth outer membrane which is freely permeable to molecules.
A smooth inner membrane which contains many transporters: integral membrane proteins that regulate the passage in an out
of the chloroplast of
small molecules like sugars
proteins synthesized in the cytoplasm of the cell but used within the chloroplast
A system of thylakoid membranes

Thylakoids
The thylakoid membranes enclose a lumen: a system of vesicles (that may all be interconnected). At various places within the
chloroplast these are stacked in arrays called grana (resembling a stack of coins). Four types of protein assemblies are embedded in
the thylakoid membranes: These carry out the so-called light reactions of photosynthesis including:
1. Photosystem I which includes chlorophyll and carotenoid molecules
2. Photosystem II which also contains chlorophyll and carotenoid molecules
3. Cytochromes b and f
4. ATP synthase
The thylakoid membranes are surrounded by a fluid stroma, which contains all the enzymes, e.g., RUBISCO, needed to carry out
the "dark" reactions of photosynthesis; that is, the conversion of CO2 into organic molecules like glucose. A number of identical
molecules of DNA, each of which carries the complete chloroplast genome. The genes encode some — but not all of the molecules
needed for chloroplast function. The others are
transcribed from genes in the nucleus of the cell
translated in the cytoplasm and
transported into the chloroplast.

Figure 3.17.2 Chloroplast from a corn cell courtesy of Dr. L. K. Shumway

3.17.1 https://bio.libretexts.org/@go/page/3995
 Figure 3.17.3 Inner surface of thylakoid courtesy of Kenneth R. Miller
The electron micrograph in Figure 3.17.3 shows the inner surface of a thylakoid membrane. Each particle may represent one
photosystem II complex. In the functioning chloroplast, these particles may not be as highly ordered as seen here.

This page titled 3.17: Chloroplasts is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.17.2 https://bio.libretexts.org/@go/page/3995
3.18: Chlorophylls and Carotenoids
Chlorophylls
Two types of chlorophyll are found in plants and the green algae: chlorophyll a and chlorophyll b. The difference in their
structures is shown in the above figure (red disks).

Figure 3.18.1 Chlorophyll

In the chloroplast, both types are associated with integral membrane proteins in the thylakoid membrane. Note the system of
alternating single and double bonds (white bars) that run around the porphyrin ring. Although I am forced to draw the single and
double bonds in fixed positions, actually the "extra" electrons responsible for the double bonds are not fixed between any particular
pair of carbon atoms but instead are free to migrate around the ring. This property enables these molecules to absorb light. Both
chlorophylls absorb light most strongly in the red and violet parts of the spectrum. Green light is absorbed poorly. Thus when white
light shines on chlorophyll-containing structures like leaves, green light is transmitted and reflected and the structures appear green.

Carotenoids
Chloroplasts also contain carotenoids. These are also pigments with colors ranging from red to yellow. Carotenoids absorb light
most strongly in the blue portion of the spectrum. They thus enable the chloroplast to trap a larger fraction of the radiant energy
falling on it. Carotenoids are often the major pigments in flowers and fruits. The red of a ripe tomato and the orange of a carrot are
produced by their carotenoids. In leaves, the carotenoids are usually masked by the chlorophylls. In the autumn, as the quantity of
chlorophyll in the leaf declines, the carotenoids become visible and produce the yellows and reds of autumn foliage.

Figure 3.18.2 Carotenoids

Figure 3.18.2 shows the structure of beta-carotene, one of the most abundant carotenoids. Note again the system of alternating
single and double bonds that in this molecule runs along the hydrocarbon chain that connects the two benzene rings. As in
chlorophyll, the electrons of the double bonds actually migrate though the chain and also make this molecule an efficient absorber
of light. Many animals use ingested beta-carotene as a precursor for the synthesis of vitamin A.

This page titled 3.18: Chlorophylls and Carotenoids is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.18.1 https://bio.libretexts.org/@go/page/3996
3.19: Plant Tissues
A mature vascular plant (any plant other than mosses and liverworts), contains several types of differentiated cells. These are
grouped together in tissues. Some tissues contain only one type of cell. Others consist of several cells.

Meristematic
The main function of meristematic tissue is mitosis. The cells are small, thin-walled, with no central vacuole and no specialized
features. Meristematic tissue is located in the apical meristems at the growing points of roots and stems, the secondary meristems
(lateral buds) at the nodes of stems (where branching occurs), and meristematic tissue, called the cambium, that is found within
mature stems and roots. The cells produced in the meristems soon become differentiated into one or another of several types.

Protective
Protective tissue covers the surface of leaves and the living cells of roots and stems. Its cells are flattened with their top and bottom
surfaces parallel. The upper and lower epidermis of the leaf are examples of protective tissue.

Parenchyma
The cells of parenchyma are large, thin-walled, and usually have a large central vacuole. They are often partially separated from
each other and are usually stuffed with plastids. In areas not exposed to light, colorless plastids predominate and food storage is the
main function. The cells of the white potato are parenchyma cells. Where light is present, e.g., in leaves, chloroplasts predominate
and photosynthesis is the main function.

Sclerenchyma
The walls of these cells are very thick and built up in a uniform layer around the entire margin of the cell. Often, the cell dies after
its cell wall is fully formed. Sclerenchyma cells are usually found associated with other cells types and give them mechanical
support. Sclerenchyma is found in stems and also in leaf veins. Sclerenchyma also makes up the hard outer covering of seeds and
nuts.

Collenchyma
Collenchyma cells have thick walls that are especially thick at their corners. These cells provide mechanical support for the plant.
They are most often found in areas that are growing rapidly and need to be strengthened. The petiole ("stalk") of leaves is usually
reinforced with collenchyma.

Xylem
Xylem conducts water and dissolved minerals from the roots to all the other parts of the plant. In angiosperms, most of the water
travels in the xylem vessels. These are thick-walled tubes that can extend vertically through several feet of xylem tissue. Their
diameter may be as large as 0.7 mm. Their walls are thickened with secondary deposits of cellulose and are usually further
strengthened by impregnation with lignin. The secondary walls of the xylem vessels are deposited in spirals and rings and are
usually perforated by pits.
Xylem vessels arise from individual cylindrical cells oriented end to end. At maturity the end walls of these cells dissolve away,
and the cytoplasmic contents die. The result is the xylem vessel, a continuous nonliving duct. Xylem also contains tracheids.
These are individual cells tapered at each end so the tapered end of one cell overlaps that of the adjacent cell. Like xylem vessels,
they have thick, lignified walls and, at maturity, no cytoplasm. Their walls are perforated so that water can flow from one tracheid
to the next. The xylem of ferns and conifers contains only tracheids. In woody plants, the older xylem ceases to participate in water
transport and simply serves to give strength to the trunk. Wood is xylem. When counting the annual rings of a tree, one is counting
rings of xylem.

Phloem
The main components of phloem are sieve elements and companion cells. Sieve elements are so-named because their end walls
are perforated. This allows cytoplasmic connections between vertically-stacked cells. The result is a sieve tube that conducts the
products of photosynthesis — sugars and amino acids — from the place where they are manufactured (a "source"), e.g., leaves, to
the places ("sinks") where they are consumed or stored; such as

3.19.1 https://bio.libretexts.org/@go/page/3997
 roots
growing tips of stems and leaves
flowers
fruits, tubers, corms, etc.
Sieve elements have no nucleus and only a sparse collection of other organelles. They depend on the adjacent companion cells for
many functions.
Companion cells move sugars, amino acids and a variety of macromolecules into and out of the sieve elements. In "source" tissue,
such as a leaf, the companion cells use transmembrane proteins to take up — by active transport — sugars and other organic
molecules from the cells manufacturing them. Water follows by osmosis. These materials then move into adjacent sieve elements
through plasmodesmata. The pressure created by osmosis drives the flow of materials through the sieve tubes.
In "sink" tissue, the sugars and other organic molecules leave the sieve elements through plasmodesmata connecting the sieve
elements to their companion cells and then pass on to the cells of their destination. Again, water follows by osmosis where it may
leave the plant by transpiration or
increase the volume of the cells or
move into the xylem for recycling through the plant

This page titled 3.19: Plant Tissues is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.19.2 https://bio.libretexts.org/@go/page/3997
3.20: Apoptosis
Apoptosis is a process of programmed cell death that occurs in multicellular organisms. There are two ways in which cells die: (1)
They are killed by injurious agents or (2) they are induced to commit suicide.

Death by injury
Cells that are damaged by injury, such as by mechanical damage or exposure to toxic chemicals undergo a characteristic series of
changes. They (and their organelles like mitochondria) swell (because the ability of the plasma membrane to control the passage of
ions and water is disrupted). The cell contents leak out, leading to inflammation of surrounding tissues.

Death by Suicide
Cells that are induced to commit suicide:
shrink
develop bubble-like blebs on their surface
have the chromatin (DNA and protein) in their nucleus degraded
have their mitochondria break down with the release of cytochrome c
break into small, membrane-wrapped, fragments
release (at least in mammalian cells) ATP and UTP
These nucleotides bind to receptors on wandering phagocytic cells like macrophages and dendritic cells and attract them to the
dying cells (a "find-me" signal")
The phospholipid phosphatidylserine, which is normally hidden in the inner layer of the plasma membrane, is exposed on the
surface
This "eat me" signal is bound by other receptors on the phagocytes which then engulf the cell fragments
The phagocytic cells secrete cytokines that inhibit inflammation (e.g., IL-10 and TGF-β)
The pattern of events in death by suicide is so orderly that the process is often called programmed cell death or PCD. The cellular
machinery of programmed cell death turns out to be as intrinsic to the cell as, say, mitosis. Programmed cell death is also called
apoptosis. (There is no consensus yet on how to pronounce it; some say APE oh TOE sis; some say uh POP tuh sis.)

Why should a cell commit suicide?

There are two different reasons.
1. Programmed cell death is as needed for proper development as mitosis is.
Examples:
The resorption of the tadpole tail at the time of its metamorphosis into a frog occurs by apoptosis.
The formation of the fingers and toes of the fetus requires the removal, by apoptosis, of the tissue between them.
The sloughing off of the inner lining of the uterus (the endometrium) at the start of menstruation occurs by apoptosis.
The formation of the proper connections (synapses) between neurons in the brain requires that surplus cells be eliminated by
apoptosis.
The elimination of T cells that might otherwise mount an autoimmune attack on the body occurs by apoptosis.
During the pupal stage of insects that undergo complete metamorphosis, most of the cells of the larva die by apoptosis thus
providing the nutrients for the development of the structures of the adult.
2. Programmed cell death is needed to destroy cells that represent a threat to the integrity of the organism.
Examples:

Cells infected with viruses

One of the methods by which cytotoxic T lymphocytes (CTLs) kill virus-infected cells is by inducing apoptosis and some
viruses mount countermeasures to thwart it.
Cells of the immune system
As cell-mediated immune responses wane, the effector cells must be removed to prevent them from attacking body constituents.
CTLs induce apoptosis in each other and even in themselves. Defects in the apoptotic machinery is associated with autoimmune

3.20.1 https://bio.libretexts.org/@go/page/3998
 diseases such as systemic lupus erythematosus and rheumatoid arthritis.
Cells with DNA damage
Damage to its genome can cause a cell
to disrupt proper embryonic development leading to birth defects
to become cancerous.
Cells respond to DNA damage by increasing their production of p53. p53 is a potent inducer of apoptosis. Is it any wonder that
mutations in the p53 gene, producing a defective protein, are so often found in cancer cells (that represent a lethal threat to the
organism if permitted to live)?
Cancer cells
Radiation and chemicals used in cancer therapy induce apoptosis in some types of cancer cells.

What makes a cell decide to commit suicide?

The balance between the withdrawal of positive signals; that is, signals needed for continued survival, and the receipt of negative
signals.
Withdrawal of positive signals
The continued survival of most cells requires that they receive continuous stimulation from other cells and, for many, continued
adhesion to the surface on which they are growing. Some examples of positive signals: growth factors for neurons and Interleukin-
2 (IL-2), an essential factor for the mitosis of lymphocytes
Receipt of negative signals
increased levels of oxidants within the cell
damage to DNA by these oxidants or other agents like ultraviolet light, X-rays and chemotherapeutic drugs
accumulation of proteins that failed to fold properly into their proper tertiary structure
molecules that bind to specific receptors on the cell surface and signal the cell to begin the apoptosis program. These death
activators include:
Tumor necrosis factor-alpha (TNF-α) that binds to the TNF receptor
Lymphotoxin (also known as TNF-β) that also binds to the TNF receptor
Fas ligand (FasL), a molecule that binds to a cell-surface receptor named Fas (also called CD95)

The Mechanisms of Apoptosis

There are 3 different mechanisms by which a cell commits suicide by apoptosis.
1. Generated by signals arising within the cell
2. Triggered by death activators binding to receptors at the cell surface:
TNF-α
Lymphotoxin
Fas ligand (FasL)
3. Triggered by dangerous reactive oxygen species

Apoptosis triggered by internal signals

Figure 3.20.1 Apoptosis by internal trigger

In a healthy cell, the outer membranes of its mitochondria display the protein Bcl-2 on their surface. Bcl-2 inhibits apoptosis.

3.20.2 https://bio.libretexts.org/@go/page/3998
 Internal damage to the cell
causes a related protein, Bax, to migrate to the surface of the mitochondrion where it inhibits the protective effect of Bcl-2
and inserts itself into the outer mitochondrial membrane punching holes in it and causing
cytochrome c to leak out.
The released cytochrome c binds to the protein Apaf-1 ("apoptotic protease activating factor-1").
Using the energy provided by ATP, these complexes aggregate to form apoptosomes. The apoptosomes bind to and activate
caspase-9. Caspase-9 is one of a family of over a dozen caspases. They are all proteases. They get their name because they
cleave proteins — mostly each other — at aspartic acid (Asp) residues.
Caspase-9 cleaves and, in so doing, activates other caspases (caspase-3 and -7).
The activation of these "executioner" caspases creates an expanding cascade of proteolytic activity (rather like that in blood
clotting and complement activation) which leads to
digestion of structural proteins in the cytoplasm,
degradation of chromosomal DNA
phagocytosis of the cell

Apoptosis triggered by external signals

Figure 3.20.2 Apoptosis by external trigger

Fas and the TNF receptor are integral membrane proteins with their receptor domains exposed at the surface of the cell
Binding of the complementary death activator (FasL and TNF respectively) transmits a signal to the cytoplasm that leads to
the activation of caspase 8
Caspase 8 (like caspase 9) initiates a cascade of caspase activation leading to phagocytosis of the cell.
Example: When cytotoxic T cells recognize (bind to) their target,
They produce more FasL at their surface.
This binds with the Fas on the surface of the target cell leading to its death by apoptosis.
The early steps in apoptosis are reversible — at least in C. elegans. In some cases, final destruction of the cell is guaranteed
only with its engulfment by a phagocyte.

Apoptosis-Inducing Factor (AIF)

Neurons, and perhaps other cells, have another way to self-destruct that — unlike the two paths described above — does not use
caspases. Apoptosis-inducing factor (AIF) is a protein that is normally located in the intermembrane space of mitochondria. When
the cell receives a signal telling it that it is time to die, AIF is released from the mitochondria (like the release of cytochrome c in
the first pathway). It migrates into the nucleus and binds to DNA, which triggers the destruction of the DNA and cell death.

Apoptosis and Cancer

Some viruses associated with cancers use tricks to prevent apoptosis of the cells they have transformed.
Several human papilloma viruses (HPV) have been implicated in causing cervical cancer. One of them produces a protein
(E6) that binds and inactivates the apoptosis promoter p53.
Epstein-Barr Virus (EBV), the cause of mononucleosis and associated with some lymphomas
produces a protein similar to Bcl-2

3.20.3 https://bio.libretexts.org/@go/page/3998
 produces another protein that causes the cell to increase its own production of Bcl-2. Both these actions make the cell more
resistant to apoptosis (thus enabling a cancer cell to continue to proliferate).
Even cancer cells produced without the participation of viruses may have tricks to avoid apoptosis.
Some B-cell leukemias and lymphomas express high levels of Bcl-2, thus blocking apoptotic signals they may receive. The
high levels result from a translocation of the BCL-2 gene into an enhancer region for antibody production.
Melanoma (the most dangerous type of skin cancer) cells avoid apoptosis by inhibiting the expression of the gene encoding
Apaf-1.
Some cancer cells, especially lung and colon cancer cells, secrete elevated levels of a soluble "decoy" molecule that binds to
FasL, plugging it up so it cannot bind Fas. Thus, cytotoxic T cells (CTL) cannot kill the cancer cells by the mechanism shown
above.
Other cancer cells express high levels of FasL, and can kill any cytotoxic T cells (CTL) that try to kill them because CTL also
express Fas (but are protected from their own FasL).

Apoptosis in the Immune System

The immune response to a foreign invader involves the proliferation of lymphocytes — T and/or B cells. When their job is done,
they must be removed leaving only a small population of memory cells. This is done by apoptosis. Very rarely humans are
encountered with genetic defects in apoptosis. The most common one is a mutation in the gene for Fas, but mutations in the gene
for FasL or even one of the caspases are occasionally seen. In all cases, the genetic problem produces autoimmune
lymphoproliferative syndrome or ALPS.
Features
an accumulation of lymphocytes in the lymph nodes and spleen greatly enlarging them.
the appearance of clones that are autoreactive; that is, attack "self" components producing such autoimmune disorders as
hemolytic anemia
thrombocytopenia
the appearance of lymphoma — a cancerous clone of lymphocytes.
In most patients with ALPS, the mutation is present in the germline; that is, every cell in their body carries it. In a few cases,
however, the mutation is somatic; that is, has occurred in a precursor cell in the bone marrow. These later patients are genetic
mosaics — with some lymphocytes that undergo apoptosis normally and others that do not. The latter tend to out-compete the
former and grow to become the major population in the lymph nodes and blood.

Apoptosis and Organ Transplants

For many years it has been known that certain parts of the body such as the anterior chamber of the eye and the testes are
"immunologically privileged sites". Antigens within these sites fail to elicit an immune response. It turns out that cells in these sites
differ from the other cells of the body in that they express high levels of FasL at all times. Thus antigen-reactive T cells, which
express Fas, would be killed when they enter these sites. (This is the reverse of the mechanism described above.)
This finding raises the possibility of a new way of preventing graft rejection. If at least some of the cells on a transplanted kidney,
liver, heart, etc. could be made to express high levels of FasL, that might protect the graft from attack by the T cells of the host's
cell-mediated immune system. If so, then the present need for treatment with immunosuppressive drugs for the rest of the
transplant recipient's life would be reduced or eliminated. So far, the results in animal experiments have been mixed. Allografts
engineered to express FasL have shown increased survival for kidneys, but not for hearts or islets of Langerhans.

Apoptosis in Plants
Plants, too, can turn on a system of programmed cell death; for example, in an attempt to halt the spread of virus infection. The
mechanism differs from that in animals although it, too, involves a protease that — like caspases — cleaves other proteins at Asp
(and Asn) residues. Activation of this enzyme destroys the central vacuole, which is followed by disintegration of the rest of the
cell.

This page titled 3.20: Apoptosis is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.20.4 https://bio.libretexts.org/@go/page/3998
3.21: Collagens
Collagens are insoluble, extracellular glycoproteins found in all animals. They are the most abundant proteins in the human body
and are essential structural components of all connective tissues such as cartilage, bone, tendons, ligaments, fascia, skin. Gelatin is
solubilized collagen. 29 types of collagens have been found in humans and the major ones are:
Type I. The chief component of tendons, ligaments, and bones.
Type II. Represents more than 50% of the protein in cartilage and is the major component of the vitreous body of the eye. It is
also used to build the notochord of vertebrate embryos.
Type III. Strengthens the walls of hollow structures like arteries, the intestine, and the uterus.
Type IV. Forms the basal lamina of epithelia. (The basal lamina is often called the basement membrane, but is not related to
lipid bilayer membranes.) A meshwork of Type IV collagens provides the filter for the blood capillaries and the glomeruli of
the kidneys.
The other 25 types are probably equally important, but they are much less abundant.

Collagens Structure
The basic unit of collagens is a polypeptide consisting of the repeating sequence
n
where X is often proline (Pro) and Y is often hydroxyproline (proline to which an -OH group is added after synthesis of the
polypeptide). The resulting molecule twists into an elongated, left-handed helix (NOT an alpha helix).
A single collagen molecule, tropocollagen, is used to make up larger collagen aggregates, such as fibrils. It is approximately 300
nm long and 1.5 nm in diameter, and it is made up of three polypeptide strands (called alpha peptides, see step 2), each of which
has the conformation of a left-handed helix (Figure 3.21.1). These three left-handed helices are twisted together into a right-handed
triple helix or "super helix", a cooperative quaternary structure stabilized by many hydrogen bonds.

Figure 3.21.1 : Tropocollagen molecule: three left-handed procollagens (red, green, blue) join to form a right handed triple helical
tropocollagen. Image usd with permision (CC-SA-BY-3.0: Vossman and JWSchmidt)
When synthesized, the N- terminal and C- terminal of the polypeptide have globular domains, which keep the molecule soluble. As
they pass through the endoplasmic reticulum (ER) and Golgi apparatus,
The molecules are glycosylated.
Hydroxyl (-OH) groups are added to the "Y" amino acid.
S-S bonds link three chains covalently.
The three molecules twist together to form a triple helix.
In some collagens (e.g., Type II), the three molecules are identical (the product of a single gene). In other collagens (e.g., Type I),
two polypeptides of one kind (gene product) assemble with a second, quite similar, polypeptide, that is the product of a second
gene.

Figure 3.21.2: Collagen courtesy of Dr. Jerome Gross

3.21.1 https://bio.libretexts.org/@go/page/3999
When the triple helix is secreted from the cell (usually by a fibroblast), the globular ends are cleaved off. The resulting linear,
insoluble molecules assemble into collagen fibers. They assemble in a staggered pattern that gives rise to the striations seen in the
above electron micrograph. Type IV collagens are an exception; they form a meshwork rather than striated fibers.

Inherited Diseases Caused by Mutant Collagen Genes

Brittle-bone disease ("osteogenesis imperfecta"): Caused by a mutation in one or the other of the two genes whose products
are used to make Type I collagen. Like all the inherited collagen diseases, this one is inherited as a dominant trait. The reason:
even though one collagen allele is normal, the assembly of the normal gene product with the mutant product produces defective
collagen fibers. Bone marrow stem cells from patients with this disease have had their mutant gene knocked out by gene
targeting and gained the ability to make good collagen and bone (when the cells were placed in immunodeficient mice). So this
disease now seems to be a promising candidate for gene therapy.
Forms of dwarfism: Caused by mutations in a Type II collagen gene.
Rubber-man syndrome: Caused by a mutations in a Type I collagen gene. The subject has hyperextensible joints, tendons,
and skin. (This inherited disorder represents one type of Ehlers-Danlos syndrome.)
Ehlers-Danlos syndrome: It is caused by mutations in the gene for Type III collagen. Patients are at risk of rupture of major
arteries or the intestine.
Alport's syndrome: Most cases involve mutations in the gene on the X chromosome for one of the chains of Type IV collagen.
So it shows the typical pattern of X-linked inheritance. Other cases are caused by two mutant autosomal genes for another of
the Type IV collagen chains. Patients usually have damage to their glomeruli, leading to blood in their urine and, often, become
deaf as well.
Herniated discs between the vertebrae?: A study in Finland has found that some families that share a tendency to develop
herniated discs (leading to sciatica) have an inherited point mutation in the gene (COL9A2) encoding one of the alpha chains in
collagen IX. This collagen is one component of the extracellular matrix in the padding (discs) between our vertebrae.

Other Collagen Diseases

Scurvy: Caused by a deficiency of vitamin C. The sufferer is unable to add hydroxyl (-OH) groups to proline to convert it into
hydroxyproline.
Goodpasture's Syndrome: Some people develop antibodies against an epitope on their Type IV collagen molecules. These
attach to the basal lamina of epithelial cells and "fix" complement which damages the basal lamina. So Goodpasture's syndrome
is an example of an autoimmune disorder.

Figure 3.21.2: Goodpasture's syndrome courtesy of Dr. Frank J. Dixon

The basal lamina of the lung epithelia and the glomeruli of the kidney are especially likely to be affected. In this photo (courtesy of
Dr. Frank J. Dixon), a fluorescent antibody against human IgG shows the autoantibodies coating the basement membranes of the
glomeruli in a patient with Goodpasture's syndrome.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.
Wikipedia

3.21.2 https://bio.libretexts.org/@go/page/3999
This page titled 3.21: Collagens is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.21.3 https://bio.libretexts.org/@go/page/3999
3.22: Chromatophores
Chromatophores are irregularly shaped, pigment-containing cells. If the pigment is melanin, they are called melanophores.
Chromatophores are common in crustaceans, cephalopod mollusks, lizards and amphibians, and some fishes.

Figure 3.22.1: Chromatophores in the skin of a squid. (CC-By-Sa-2.0 Minette)

Chromatophores are often used for camouflage. Figure 3.22.1 shows a winter flounder resting on a checkerboard pattern. The
chromatophores of cephalopods change size (expand and contract) as a result of activity of muscle fibers and the motor neurons
that terminate at them. In crustaceans and amphibians, the chromatophores have a fixed shape. Color change comes about through
the dispersal (darkening) or aggregation (lightening) of granules within the cell. This is under hormonal control.

Figure 3.22.2: Chromatopores of a Flounder courtesy of the Field Museum of Natural History

This page titled 3.22: Chromatophores is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.22.1 https://bio.libretexts.org/@go/page/4000
3.23: Diffusion, Active Transport and Membrane Channels
Transport Across Cell Membranes
All cells acquire the molecules and ions they need from their surrounding extracellular fluid (ECF). There is an unceasing traffic
of molecules and ions in and out of the cell through its plasma membrane (Examples: glucose, N a , C a ). In eukaryotic cells,
+ 2+

there is also transport in and out of membrane-bounded intracellular compartments such as the nucleus, endoplasmic reticulum, and
mitochondria (Examples: proteins, mRNA, C a , and ATP).
2+

The following problems can occur during transport:

1. Relative concentrations
Molecules and ions move spontaneously down their concentration gradient (i.e., from a region of higher to a region of lower
concentration) by diffusion. Molecules and ions can be moved against their concentration gradient, but this process, called active
transport, requires the expenditure of energy (usually from ATP).
2. Lipid bilayers are impermeable to most essential molecules and ions.
The lipid bilayer is permeable to water molecules and a few other small, uncharged, molecules like oxygen (O2) and carbon
dioxide (CO2). These diffuse freely in and out of the cell. The diffusion of water through the plasma membrane is of such
importance to the cell that it is given a special name - osmosis. Lipid bilayers are not permeable to ions such as K+, Na+, Ca2+
(called cations because when subjected to an electric field they migrate toward the cathode [the negatively-charged electrode]) and
Cl-, HCO3- (called anions because they migrate toward the anode [the positively-charged electrode]). They are also not permeable
to small hydrophilic molecules like glucose and macromolecules like proteins and RNA. The cells solve the problem of
transporting ions and small molecules across their membranes with the help of the following two mechanisms:
Facilitated diffusion: Transmembrane proteins create a water-filled pore through which ions and some small hydrophilic
molecules can pass by diffusion. The channels can be opened (or closed) according to the needs of the cell.
Active transport: Transmembrane proteins, called transporters, use the energy of ATP to force ions or small molecules through
the membrane against their concentration gradient.

Facilitated Diffusion of Ions

Facilitated diffusion of ions takes place through proteins, or assemblies of proteins, embedded in the plasma membrane. These
transmembrane proteins form a water-filled channel through which the ion can pass down its concentration gradient. The
transmembrane channels that permit facilitated diffusion can be opened or closed. They are said to be "gated"; some types of
gated ion channels:
ligand-gated
mechanically-gated
voltage-gated
light-gated

Ligand-gated ion channels

Many ion channels open or close in response to binding a small signaling molecule or "ligand". Some ion channels are gated by
extracellular ligands; some by intracellular ligands. In both cases, the ligand is not the substance that is transported when the
channel opens.
External ligands
External ligands (shown here in green) bind to a site on the extracellular side of the channel.

Figure 3.23.1 External Ligands

3.23.1 https://bio.libretexts.org/@go/page/4070
Examples:
Acetylcholine (ACh). The binding of the neurotransmitter acetylcholine at certain synapses opens channels that admit Na+ and
initiate a nerve impulse or muscle contraction.
Gamma amino butyric acid (GABA). Binding of GABA at certain synapses — designated GABAA — in the central nervous
system admits Cl- ions into the cell and inhibits the creation of a nerve impulse
Internal ligands
Internal ligands bind to a site on the channel protein exposed to the cytosol. Examples:
"Second messengers", like cyclic AMP (cAMP) and cyclic GMP (cGMP), regulate channels involved in the initiation of
impulses in neurons responding to odors and light respectively.
ATP is needed to open the channel that allows chloride (Cl-) and bicarbonate (HCO3-) ions out of the cell. This channel is
defective in patients with cystic fibrosis. Although the energy liberated by the hydrolysis of ATP is needed to open the channel,
this is not an example of active transport; the ions diffuse through the open channel following their concentration gradient.

Mechanically-gated ion channels

Sound waves bending the cilia-like projections on the hair cells of the inner ear open up ion channels leading to the creation of
nerve impulses that the brain interprets as sound. Mechanical deformation of the cells of stretch receptors opens ion channels
leading to the creation of nerve impulses.

Voltage-gated ion channels

In so-called "excitable" cells like neurons and muscle cells, some channels open or close in response to changes in the charge
(measured in volts) across the plasma membrane. For example, as an impulse passes down a neuron, the reduction in the voltage
opens sodium channels in the adjacent portion of the membrane. This allows the influx of N a into the neuron and thus the
+

continuation of the nerve impulse. Some 7000 sodium ions pass through each channel during the brief period (about 1 millisecond)
that it remains open. This was learned by use of the patch clamp technique.
The Patch Clamp Technique
The properties of ion channels can be studied by means of the patch clamp technique. A very fine pipette (with an opening of about
0.5 µm) is pressed against the plasma membrane of either an intact cell or the plasma membrane can be pulled away from the cell
and the preparation placed in a test solution of desired composition. Current flow through a single ion channel can then be
measured.

Figure 3.23.2 The Patch Clamp

Such measurements reveal that each channel is either fully open or fully closed; that is, facilitated diffusion through a single
channel is "all-or-none". This technique has provided so much valuable information about ion channels that its inventors, Erwin
Neher and Bert Sakmann, were awarded a Nobel Prize in 1991.

Facilitated Diffusion of Molecules

Some small, hydrophilic organic molecules, like sugars, can pass through cell membranes by facilitated diffusion. Once again, the
process requires transmembrane proteins. In some cases, these — like ion channels — form water-filled pores that enable the
molecule to pass in (or out) of the membrane following its concentration gradient.
Example:

3.23.2 https://bio.libretexts.org/@go/page/4070
Maltoporin. This homotrimer in the outer membrane of E. coli forms pores that allow the disaccharide maltose and a few related
molecules to diffuse into the cell.
Example: The plasma membrane of human red blood cells contain transmembrane proteins that permit the diffusion of glucose
from the blood into the cell.
Note that in all cases of facilitated diffusion through channels, the channels are selective; that is, the structure of the protein admits
only certain types of molecules through. Whether all cases of facilitated diffusion of small molecules use channels is yet to be
proven. Perhaps some molecules are passed through the membrane by a conformational change in the shape of the transmembrane
protein when it binds the molecule to be transported.
In either case, the interaction between the molecule being transported and its transporter resembles in many ways the interaction
between an enzyme and its substrate.

Active Transport
Active transport is the pumping of molecules or ions through a membrane against their concentration gradient. It requires a
transmembrane protein (usually a complex of them) called a transporter and energy. The source of this energy is ATP.
The energy of ATP may be used directly or indirectly.
Direct Active Transport. Some transporters bind ATP directly and use the energy of its hydrolysis to drive active transport.
Indirect Active Transport. Other transporters use the energy already stored in the gradient of a directly-pumped ion. Direct
active transport of the ion establishes a concentration gradient. When this is relieved by facilitated diffusion, the energy released
can be harnessed to the pumping of some other ion or molecule.

Direct Active Transport

The Na+/K+ ATPase
The cytosol of animal cells contains a concentration of potassium ions (K+) as much as 20 times higher than that in the
extracellular fluid. Conversely, the extracellular fluid contains a concentration of sodium ions (Na+) as much as 10 times greater
than that within the cell. These concentration gradients are established by the active transport of both ions. And, in fact, the same
transporter, called the Na+/K+ ATPase, does both jobs. It uses the energy from the hydrolysis of ATP to
actively transport 3 Na+ ions out of the cell
for each 2 K+ ions pumped into the cell.
This accomplishes several vital functions:
It helps establish a net charge across the plasma membrane with the interior of the cell being negatively charged with respect to
the exterior. This resting potential prepares nerve and muscle cells for the propagation of action potentials leading to nerve
impulses and muscle contraction.
The accumulation of sodium ions outside of the cell draws water out of the cell and thus enables it to maintain osmotic balance
(otherwise it would swell and burst from the inward diffusion of water).
The gradient of sodium ions is harnessed to provide the energy to run several types of indirect pumps.
The crucial roles of the Na+/K+ ATPase are reflected in the fact that almost one-third of all the energy generated by the
mitochondria in animal cells is used just to run this pump.

The H+/K+ ATPase

The parietal cells of your stomach use this pump to secrete gastric juice. These cells transport protons (H+) from a concentration of
about 4 x 10-8 M within the cell to a concentration of about 0.15 M in the gastric juice (giving it a pH close to 1). Small wonder
that parietal cells are stuffed with mitochondria and uses huge amounts of ATP as they carry out this three-million fold
concentration of protons.

The Ca2+ ATPases

A Ca2+ ATPase is located in the plasma membrane of all eukaryotic cells. It uses the energy provided by one molecule of ATP to
pump one Ca2+ ion out of the cell. The activity of these pumps helps to maintain the ~20,000-fold concentration gradient of Ca2+
between the cytosol (~ 100 nM) and the ECF (~ 20 mM). In resting skeletal muscle, there is a much higher concentration of

2+ 2+

3.23.3 https://bio.libretexts.org/@go/page/4070
calcium ions (Ca2+) in the sarcoplasmic reticulum than in the cytosol. Activation of the muscle fiber allows some of this Ca2+ to
pass by facilitated diffusion into the cytosol where it triggers contraction.
After contraction, this Ca2+ is pumped back into the sarcoplasmic reticulum. This is done by another Ca2+ ATPase that uses the
energy from each molecule of ATP to pump 2 Ca2+ ions.
Pumps 1. - 3. are designated P-type ion transporters because they use the same basic mechanism: a conformational change in the
proteins as they are reversibly phosphorylated by ATP. And all three pumps can be made to run backward. That is, if the pumped
ions are allowed to diffuse back through the membrane complex, ATP can be synthesized from ADP and inorganic phosphate.

ABC Transporters
ABC ("ATP-Binding Cassette") transporters are transmembrane proteins that
expose a ligand-binding domain at one surface and a
ATP-binding domain at the other surface.
The ligand-binding domain is usually restricted to a single type of molecule.
The ATP bound to its domain provides the energy to pump the ligand across the membrane.
The human genome contains 48 genes for ABC transporters. Some examples:
CFTR — the cystic fibrosis transmembrane conductance regulator
TAP, the transporter associated with antigen processing
The transporter that liver cells use to pump the salts of bile acids out into the bile.
ABC transporters that pump chemotherapeutic drugs out of cancer cells thus reducing their effectiveness.
ABC transporters must have evolved early in the history of life. The ATP-binding domains in archaea, eubacteria, and eukaryotes
all share a homologous structure, the ATP-binding "cassette".

Indirect Active Transport

Indirect active transport uses the downhill flow of an ion to pump some other molecule or ion against its gradient. The driving ion
is usually sodium (Na+) with its gradient established by the Na+/K+ ATPase.

Symport Pumps
In this type of indirect active transport, the driving ion (Na+) and the pumped molecule pass through the membrane pump in the
same direction. Examples:
The Na+/glucose transporter. This transmembrane protein allows sodium ions and glucose to enter the cell together. The
sodium ions flow down their concentration gradient while the glucose molecules are pumped up theirs. Later the sodium is
pumped back out of the cell by the Na+/K+ ATPase. The Na+/glucose transporter is used to actively transport glucose out of the
intestine and also out of the kidney tubules and back into the blood.
All the amino acids can be actively transported, for example out of the kidney tubules and into the blood, by sodium-driven
symport pumps.
Sodium-driven symport pumps also return neurotransmitters to the presynaptic neuron.
The Na+/iodide transporter. This symporter pumps iodide ions into the cells of the thyroid gland (for the manufacture of
thyroxine) and also into the cells of the mammary gland (to supply the baby's need for iodide).
The permease encoded by the lac operon of E. coli that transports lactose into the cell.

Antiport Pumps
In antiport pumps, the driving ion (again, usually sodium) diffuses through the pump in one direction providing the energy for the
active transport of some other molecule or ion in the opposite direction. Example:
Ca2+ ions are pumped out of cells by sodium-driven antiport pumps. Antiport pumps in the vacuole of some plants harness the
outward facilitated diffusion of protons (themselves pumped into the vacuole by a H+ ATPase) to the active inward transport of
sodium ions. This sodium/proton antiport pump enables the plant to sequester sodium ions in its vacuole. Transgenic tomato plants
that overexpress this sodium/proton antiport pump are able to thrive in saline soils too salty for conventional tomatoes. Antiport
pumps to the active inward transport of nitrate ions (NO3−)

3.23.4 https://bio.libretexts.org/@go/page/4070
Some inherited ion-channel diseases
A growing number of human diseases have been discovered to be caused by inherited mutations in genes encoding channels.
Examples:
Chloride-channel diseases
cystic fibrosis
inherited tendency to kidney stones (caused by a different kind of chloride channel than the one involved in cystic fibrosis)
Potassium-channel diseases
the majority of cases of long QT syndrome, an inherited disorder of the heartbeat
a rare, inherited tendency to epileptic seizures in the newborn
several types of inherited deafness
Sodium-channel diseases
inherited tendency to certain types of muscle spasms
Liddle's syndrome. Inadequate sodium transport out of the kidneys, because of a mutant sodium channel, leads to elevated
osmotic pressure of the blood and resulting hypertension (high blood pressure)

Osmosis
Osmosis is a special term used for the diffusion of water through cell membranes. Although water is a polar molecule, it is able to
pass through the lipid bilayer of the plasma membrane. Aquaporins — transmembrane proteins that form hydrophilic channels —
greatly accelerate the process, but even without these, water is still able to get through. Water passes by diffusion from a region of
higher to a region of lower concentration. Note that this refers to the concentration of water, NOT the concentration of any solutes
present in the water. Water is never transported actively; that is, it never moves against its concentration gradient. However, the
concentration of water can be altered by the active transport of solutes and in this way the movement of water in and out of the cell
can be controlled. Example: the reabsorption of water from the kidney tubules back into the blood depends on the water following
behind the active transport of N a .
+

Figure 3.23.3: Osmosis effect on blood cells in different solutions. (Public domain; Ladyofhats).
Hypotonic solutions: If the concentration of water in the medium surrounding a cell is greater than that of the cytosol, the
medium is said to be hypotonic. Water enters the cell by osmosis. A red blood cell placed in a hypotonic solution (e.g., pure
water) bursts immediately ("hemolysis") from the influx of water. Plant cells and bacterial cells avoid bursting in hypotonic
surroundings by their strong cell walls. These allow the buildup of turgor within the cell. When the turgor pressure equals the
osmotic pressure, osmosis ceases.
Isotonic solutions: When red blood cells are placed in a 0.9% salt solution, they neither gain nor lose water by osmosis. Such a
solution is said to be isotonic. The extracellular fluid (ECF) of mammalian cells is isotonic to their cytoplasm. This balance
must be actively maintained because of the large number of organic molecules dissolved in the cytosol but not present in the
ECF. These organic molecules exert an osmotic effect that, if not compensated for, would cause the cell to take in so much
water that it would swell and might even burst. This fate is avoided by pumping sodium ions out of the cell with the Na+/K+
ATPase.
Hypertonic solutions: If red cells are placed in sea water (about 3% salt), they lose water by osmosis and the cells shrivel up.
Sea water is hypertonic to their cytosol. Similarly, if a plant tissue is placed in sea water, the cell contents shrink away from the
rigid cell wall. This is called plasmolysis. Sea water is also hypertonic to the ECF of most marine vertebrates. To avoid fatal
dehydration, these animals (e.g., bony fishes like the cod) must continuously drink sea water and then desalt it by pumping ions
out of their gills by active transport.

3.23.5 https://bio.libretexts.org/@go/page/4070
Marine birds, which may pass long periods of time away from fresh water, and sea turtles use a similar device. They, too, drink salt
water to take care of their water needs and use metabolic energy to desalt it. In the herring gull, shown here, the salt is extracted by
two glands in the head and released (in a very concentrated solution — it is saltier than the blood) to the outside through the
nostrils. Marine snakes use a similar desalting mechanism.

Figure 3.23.4: herring gull salt glands

This page titled 3.23: Diffusion, Active Transport and Membrane Channels is shared under a CC BY 3.0 license and was authored, remixed,
and/or curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history
is available upon request.

3.23.6 https://bio.libretexts.org/@go/page/4070
3.24: Endocytosis
In endocytosis, the cell engulfs some of its extracellular fluid (ECF) including material dissolved or suspended in it. A portion of
the plasma membrane is invaginated, coated with molecules of the protein clathrin, and pinched off forming a membrane-bounded
vesicle called an endosome (Figure 3.24.1).

Figure 3.24.1 : Endocytosis (IPA: [ɛndəʊsaɪˈtəʊsɪs]) is a process whereby cells absorb material (molecules such as proteins) from
the outside by engulfing it with their cell membrane. It is used by all cells of the body because most substances important to them
are polar and consist of big molecules, and thus cannot pass through the hydrophobic plasma membrane. (Public Domain; Mariana
Ruiz Villarreal LadyofHats)

Phagocytosis
Phagocytosis ("cell eating") results in the ingestion of particulate matter (e.g., bacteria) from the ECF. The endosome is so large
that it is called a phagosome or vacuole. Phagocytosis occurs only in certain specialized cells (e.g., neutrophils, macrophages, the
amoeba) and occurs sporadically.

Figure 3.24.2 : guinea pig Phagocyte courtesy of Dr. Robert J. North

This electron micrograph shows a guinea pig phagocyte ingesting polystyrene beads. Several beads are already enclosed in
phagosomes while the others are in the process of being engulfed. In due course, phagosomes deliver their contents to lysosomes.
The membranes of the two organelles fuse. Once inside the lysosome, the contents of the phagosome, e.g. ingested bacteria, are
destroyed by the degradative enzymes of the lysosome.

Games parasites play

Phagocytic cells, like macrophages and neutrophils, are an early line of defense against invading bacteria. However, some bacteria
have evolved mechanisms to avoid destruction even after they have been engulfed by phagocytes.
Examples:
Salmonella enterica is a bacterium that causes food poisoning in humans. Once engulfed by phagocytosis, it secretes a protein
that prevents the fusion of its phagosome with a lysosome.
Mycobacteria (e.g., the tubercle bacillus that causes tuberculosis) use a different trick.
When the phagosome is first pinched off from the plasma membrane, it is coated with a protein called "TACO" (for
tryptophan-aspartate-containing coat protein).
This must be removed before the phagosome can fuse with a lysosome.

3.24.1 https://bio.libretexts.org/@go/page/4071
 Mycobacteria taken into a phagosome are able, in some way, to keep the TACO coat from being removed.
Thus there is no fusion with lysosomes and the mycobacteria can continue to live in this protected intracellular location.
Some intracellular parasites exploit receptor-mediated endocytosis to sneak their way into their host cell. They have evolved
surface molecules that serve as decoy ligands for receptors on the target cell surface. Binding to these receptors tricks the cell into
engulfing the parasite.
Examples:
Epstein-Barr Virus (EBV). This virus causes mononucleosis and is a contributing factor in the development of Burkitt's
lymphoma, a cancer of B lymphocytes. It binds to a receptor present on the surface of B cells.
Influenza virus. The hemagglutinin on the surface of the virus binds to carbohydrate on the surface of the target cell tricking
the cell into engulfing it.
Listeria monocytogenes. This food-borne bacterium can be dangerous to people with defective immune systems as well as to
pregnant women and their newborn babies. It has two kinds of surface molecules each a ligand for a different receptor on the
target cell surface.
Streptococcus pneumoniae. Epithelial cells like those in the nasopharynx have receptors that are responsible for transporting
IgA and IgM antibodies from the blood to the apical surface of the cell. The pneumococcus piggybacks on this receptor on its
return trip into the cell. This is the organism that led to the discovery that genes are DNA.

Pinocytosis
In pinocytosis ("cell drinking"), the drop engulfed is relatively small (Figure 3.24.1 ). Pinocytosis occurs in almost all cells and
continuously.

Figure 3.24.3 : Pinocytosis courtesy Fawcett, The Cell: Its Organelles and Inclusions, W. B. Saunders Co., 1966
This electron micrograph shows a section of the wall of a capillary (the smallest of the blood vessels). On the right is the interior or
lumen of the capillary. In the middle is the tissue space separating the capillary wall from a nearby muscle cell (left). The small
inpocketings of the plasma membrane are clearly seen (arrows). Most of these are open to the tissue space but some can also be
seen on the other side of the cell apparently engulfing fluid from within the capillary. Perhaps most of the vesicles facing the tissue
space are not taking up material by endocytosis but are instead discharging material by exocytosis. If so, the pinocytic vesicles
formed at one surface of the cell may, after being detached, move through the cell to the opposite surface and there discharge their
contents. In this way materials can be moved efficiently through the capillary wall. The pinocytosis vesicles in this image represent
a subtype called caveolae. In addition to their function in endo- and exocytosis, they also can serve as a reservoir of plasma

3.24.2 https://bio.libretexts.org/@go/page/4071
membrane. When a cell expands (e.g., by osmotic swelling) or is stretched, the caveolae flatten out providing more plasma
membrane.
A cell sipping away at the ECF by pinocytosis acquires a representative sample of the molecules and ions dissolved in the ECF. But
cells also have a much more elegant method for picking up critical components of the ECF that may be in scant supply as we shall
now see.

Receptor-Mediated Endocytosis
Some of the integral membrane proteins that a cell displays at its surface are receptors for particular components of the ECF
(Figure 3.24.1c). For example, iron is transported in the blood complexed to a protein called transferrin. Cells have receptors for
transferrin on their surface. When these receptors encounter a molecule of transferrin, they bind tightly to it. The complex of
transferrin and its receptor is then engulfed by endocytosis. Ultimately, the iron is released into the cytosol. The strong affinity of
the transferrin receptor for transferrin (its ligand) ensures that the cell will get all the iron it needs even if transferrin represents
only a small fraction of the protein molecules present in the ECF. Receptor-mediated endocytosis is many thousand times more
efficient than simple pinocytosis in enabling the cell to acquire the macromolecules it needs.

Low-Density Lipoprotein (LDL) Receptor

Cells take up cholesterol by receptor-mediated endocytosis. Cholesterol is an essential component of all cell membranes. Most cells
can, as needed, either synthesize cholesterol or acquire it from the ECF. Human cells get much of their cholesterol from the liver
and, if your diet is not strictly "100% cholesterol-free", by absorption from the intestine.
Cholesterol is a hydrophobic molecule and quite insoluble in water. Thus it cannot pass from the liver and/or the intestine to the
cells simply dissolved in blood and ECF. Instead it is carried in tiny droplets of lipoprotein. The most abundant cholesterol carriers
in humans are the low-density lipoproteins or LDLs.
LDL particles are spheres covered with a single layer of phospholipid molecules with their hydrophilic heads exposed to the watery
fluid (e.g., blood) and their hydrophobic tails directed into the interior. Some 1,500 molecules of cholesterol (each bound to a fatty
acid) occupy the hydrophobic interior of LDL particles. One molecule of a protein called apolipoprotein B (apoB) is exposed at
the surface of each LDL particle.

Figure 3.24.4 : LDL Receptor

The first step in acquiring LDL particles is for them to bind to LDL receptors exposed at the cell surface. These transmembrane
proteins have a site that recognizes and binds to the apolipoprotein B on the surface of the LDL. The portion of the plasma
membrane with bound LDL is internalized by endocytosis. A drop in the pH (from ~7 to ~5) causes the LDL to separate from its
receptor. The vesicle then pinches apart into two smaller vesicles: one containing free LDLs; the other containing now-empty
receptors. The vesicle with the LDLs fuses with a lysosome to form a secondary lysosome. The enzymes of the lysosome then
release free cholesterol into the cytosol. The vesicle with unoccupied receptors returns to and fuses with the plasma membrane,
turning inside out as it does so (exocytosis). In this way the LDL receptors are returned to the cell surface for reuse.

3.24.3 https://bio.libretexts.org/@go/page/4071
People who inherit two defective (mutant) genes for the LDL receptor have receptors that function poorly or not at all. This creates
excessively high levels of LDL in their blood and predisposes them to atherosclerosis and heart attacks. The ailment is called
familial (because it is inherited) hypercholesterolemia.
Mutations in APOB, the apoB gene, cause another form of inherited hypercholesterolemia.
Other small hydrophobic molecules are also transported in the blood while bound to soluble proteins:
the retinoid vitamin A (retinol) bound to the retinol-binding protein
the steroids
25[OH] vitamin D3 bound to the vitamin D binding protein
cortisol bound to the corticosteroid binding globulin
testosterone and estrogens bound to the sex hormone binding globulin
There is growing evidence that, like cholesterol, they are taken into the cell by receptor-mediated endocytosis.
Endocytosis removes portions of the plasma membrane and takes them inside the cell. To keep in balance, membrane must be
returned to the plasma membrane. This occurs by exocytosis.

This page titled 3.24: Endocytosis is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.24.4 https://bio.libretexts.org/@go/page/4071
3.25: Exocytosis
Exocytosis is the reverse of endocytosis and that is just as well. In 30 minutes an active cell like a macrophage can endocytose an
amount of plasma membrane equal to its complete plasma membrane. The electron micrograph in Figure 3.25.1 shows a guinea pig
phagocyte ingesting polystyrene beads. Several beads are already enclosed in vacuoles while the others are in the process of being
engulfed. So the cell must have a mechanism to restore the normal amount of plasma membrane. Exocytosis is that mechanism.

Figure 3.25.1: Guinea pig Phagocyte courtesy Dr. Robert J. North

The Secretion Mechanism

Membrane-enclosed vesicles move to the cell surface where they fuse with the plasma membrane. This restores the normal amount
of plasma membrane and any molecules dissolved in the fluid contents of these vesicles are discharged into the extracellular fluid -
this is called secretion (e.g., the various components of the extracellular matrix are secreted by exocytosis). Any integral
membrane proteins exposed to the interior surface of the vesicles will now be displayed at the cell surface because the vesicles
turn inside out as they fuse with the plasma membrane. Thus exocytosis does not simply replace plasma membrane, but ensures
that the plasma membrane will display its characteristic cell-surface proteins.

Figure 3.25.2: Exocytosis/ Endocytosis

Exocytic vesicles are created from several sources. Some are simply endosomes traversing the cell and others are pinched off from
endosomes before they fuse with lysosomes. Others bud off from the endoplasmic reticulum and Golgi apparatus taking their
products to the surface of the cell. The exocytosis of lysosomes supplies the membrane needed to repair wounds in the plasma
membrane.
Some cells specialize in secretion. In cells that secrete large amounts of protein, for example, the protein accumulates in specialized
secretory granules formed by the Golgi apparatus. These move to the cell surface and discharge their contents to the outside. For
example, exocrine cells in the pancreas synthesize and secrete pancreatic digestive enzymes. The electron micrograph in Figure
3.25.4 shows four cells in the pancreas of a bat. The lumen where their apical surfaces meet leads eventually to the pancreatic duct
draining into the small intestine. The spherical bodies (budded off from the Golgi apparatus) contain precursors of digestive
enzymes. One is discharging its contents into the lumen by exocytosis (red arrow).

Figure 3.25.4: Pancreas cells of a bat courtesy Fawcett, The Cell: Its Organelles and Inclusions, W. B. Saunders Co., 1966

3.25.1 https://bio.libretexts.org/@go/page/4072
The cells lining our intestine synthesize tiny droplets of fat and discharge them into the lacteals by exocytosis.

The Kiss-and-Run Mechanism

The process described above involves the fusion of the exocytotic vesicle with the plasma membrane. In some cells, such as at
synapses, a second type of exocytosis also takes place: (1) the vesicles make a brief contact at the plasma membrane, (2) release
their contents (neurotransmitters in this case) to the exterior and (3) retreat back into the cytosol. This "kiss-and-run" version of
exocytosis does not restore plasma membrane to the cell.

The Exosome Mechanism

A third type of exocytosis is found in some cells and involves endosomes themselves invaginating their membrane. As the
invaginations break off they produce vesicles within vesicles, called multivesicular bodies. When these fuse with the cell's plasma
membrane, these tiny (40–100 nm) internal vesicles — called exosomes — are secreted. Exosomes are produced in abundance by
dendritic cells and B-cells and enhance their antigen-presenting function.

Figure 3.25.5: Exosomes

This page titled 3.25: Exocytosis is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

3.25.2 https://bio.libretexts.org/@go/page/4072
 CHAPTER OVERVIEW
Unit 4: Cell Metabolism
Metabolism is the set of life-sustaining chemical transformations within the cells of living organisms. The three main purposes of
metabolism are the conversion of food/fuel to energy to run cellular processes, the conversion of food/fuel to building blocks for
proteins, lipids, nucleic acids, and some carbohydrates, and the elimination of nitrogenous wastes. These enzyme-catalyzed
reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments.
4.1: Enzymes
4.2: ATP
4.3: NAD and NADP
4.4: Glycolysis
4.5: Cellular Respiration
4.6: ATP Synthase
4.7: Photosynthesis - Pathway of Carbon Fixation
4.8: Photosynthesis - The Role of Light
4.9: Photosynthesis - Dicovering the Secrets
4.10: Chemiosmosis
4.11: Metabolism
4.12: Intermediary Metabolism
4.13: G Proteins
4.14: Secondary Messengers
4.15: Bioluminescence

This page titled Unit 4: Cell Metabolism is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1
4.1: Enzymes
Enzymes are catalysts. Most are proteins. (A few ribonucleoprotein enzymes have been discovered and, for some of these, the
catalytic activity is in the RNA part rather than the protein part. Link to discussion of these ribozymes). Enzymes bind temporarily
to one or more of the reactants — the substrate(s) — of the reaction they catalyze. In doing so, they lower the amount of
activation energy needed and thus speed up the reaction.

Figure 4.1.1 : Activation Energy

Examples:
Catalase catalyzes the decomposition of hydrogen peroxide into water and oxygen.
2 H2 O2 → 2 H2 O + O2 (4.1.1)

One molecule of catalase can break 40 million molecules of hydrogen peroxide each second.
Carbonic anhydrase is found in red blood cells where it catalyzes the reaction.
+ −
C O2 + H2 O ⇌ H + HC O (4.1.2)
3

It enables red blood cells to transport carbon dioxide from the tissues to the lungs. One molecule of carbonic anhydrase can
process one million molecules of CO2 each second.
Acetylcholinesterase catalyzes the breakdown of the neurotransmitter acetylcholine at several types of synapses as well as at
the neuromuscular junction — the specialized synapse that triggers the contraction of skeletal muscle. One molecule of
acetylcholinesterase breaks down 25,000 molecules of acetylcholine each second. This speed makes possible the rapid
"resetting" of the synapse for transmission of another nerve impulse.
Enzyme activity can be analyzed quantitatively. To do its work, an enzyme must unite — even if ever so briefly — with at least one
of the reactants. In most cases, the forces that hold the substrate in the active site of the enzyme are noncovalent, an assortment of
hydrogen bonds, ionic interactions, and hydrophobic interactions.
Most of these interactions are weak and especially so if the atoms involved are farther than about one angstrom from each other. So
successful binding of the substrate in the active site of the enzyme requires that the two molecules be able to approach each other
closely over a fairly broad surface. Thus the analogy that a substrate molecule binds its enzyme like a key in a lock. This
requirement for complementarity in the configuration of substrate and enzyme explains the remarkable specificity of most
enzymes. Generally, a given enzyme is able to catalyze only a single chemical reaction or, at most, a few reactions involving
substrates sharing the same general structure.

Competitive inhibition
The necessity for a close, if brief, fit between enzyme and substrate explains the phenomenon of competitive inhibition. One of the
enzymes needed for the release of energy within the cell is succinic dehydrogenase. It catalyzes the oxidation (by the removal of
two hydrogen atoms) of succinic acid. If one adds malonic acid to cells, or to a test tube mixture of succinic acid and the enzyme,
the action of the enzyme is strongly inhibited. This is because the structure of malonic acid allows it to bind to the same site on the
enzyme. But there is no oxidation so no speedy release of products. The inhibition is called competitive because if you increase the
ratio of succinic to malonic acid in the mixture, you will gradually restore the rate of catalysis. At a 50:1 ratio, the two molecules
compete on roughly equal terms for the binding (=catalytic) site on the enzyme.

Enzyme cofactors
Many enzymes require the presence of an additional nonprotein - a cofactor.
Some of these are metal ions such as Zn2+ (the cofactor for carbonic anhydrase), Cu2+, Mn2+, K+, and Na+.

4.1.1 https://bio.libretexts.org/@go/page/4626
 Some cofactors are small organic molecules called coenzymes. The B vitamins thiamine (B1), riboflavin (B2) and nicotinamide
are precursors of coenzymes.
Coenzymes may be covalently bound to the protein part (called the apoenzyme) of enzymes as a prosthetic group. Others bind
more loosely and, in fact, may bind only transiently to the enzyme as it performs its catalytic act.

 Lysozyme: a model of enzyme action

A number of lysozymes are found in nature; in human tears and egg white, for examples. The enzyme is antibacterial because
it degrades the polysaccharide that is found in the cell walls of many bacteria. It does this by catalyzing the insertion of a water
molecule at forming a glycosidic bond. This hydrolysis breaks the chain at that point.
The bacterial polysaccharide consists of long chains of alternating amino sugars:
N-acetylglucosamine (NAG)
N-acetylmuramic acid (NAM)
These hexose units resemble glucose except for the presence of the side chains containing amino groups.
Lysozyme is a globular protein with a deep cleft across part of its surface. Six hexoses of the substrate fit into this cleft. With
so many oxygen atoms in sugars, as many as 14 hydrogen bonds form between the six amino sugars and certain amino acid R
groups such as Arg-114, Asn-37, Asn-44, Trp-62, Trp-63, and Asp-101. Some hydrogen bonds also form with the C=O
groups of several peptide bonds. In addition, hydrophobic interactions may help hold the substrate in position.
X-ray crystallography has shown that as lysozyme and its substrate unite, each is slightly deformed. The fourth hexose in the
chain (ring #4) becomes twisted out of its normal position. This imposes a strain on the C-O bond on the ring-4 side of the
oxygen bridge between rings 4 and 5. It is just at this point that the polysaccharide is broken. A molecule of water is inserted
between these two hexoses, which breaks the chain. Here, then, is a structural view of what it means to lower activation energy.
The energy needed to break this covalent bond is lower now that the atoms connected by the bond have been distorted from
their normal position.
As for lysozyme itself, binding of the substrate induces a small (~0.75Å) movement of certain amino acid residues so the cleft
closes slightly over its substrate. So the "lock" as well as the "key" changes shape as the two are brought together. (This is
sometimes called "induced fit".)
The amino acid residues in the vicinity of rings 4 and 5 provide a plausible mechanism for completing the catalytic act.
Residue 35, glutamic acid (Glu-35), is about 3Å from the -O- bridge that is to be broken. The free carboxyl group of glutamic
acid is a hydrogen ion donor and available to transfer H+ to the oxygen atom. This would break the already-strained bond
between the oxygen atom and the carbon atom of ring 4.
Now having lost an electron, the carbon atom acquires a positive charge. Ionized carbon is normally very unstable, but the
attraction of the negatively-charged carboxyl ion of Asp-52 could stabilize it long enough for an -OH ion (from a
spontaneously dissociated water molecule) to unite with the carbon. Even at pH 7, water spontaneously dissociates to produce
H+ and OH- ions. The hydrogen ion (H+) left over can replace that lost by Glu-35. In either case, the chain is broken, the two
fragments separate from the enzyme, and the enzyme is free to attach to a new location on the bacterial cell wall and continue
its work of digesting it.

Factors Affecting Enzyme Action

The activity of enzymes is strongly affected by changes in pH and temperature. Each enzyme works best at a certain pH (left
graph) and temperature (right graph), its activity decreasing at values above and below that point. This is not surprising considering
the importance of tertiary structure (i.e. shape) in enzyme function and noncovalent forces, e.g., ionic interactions and hydrogen
bonds, in determining that shape. Examples:
the protease pepsin works best as a pH of 1–2 (found in the stomach)
the protease trypsin is inactive at such a low pH but very active at a pH of 8 (found in the small intestine as the bicarbonate of
the pancreatic fluid neutralizes the arriving stomach contents).
Changes in pH alter the state of ionization of charged amino acids (e.g., Asp, Lys) that may play a crucial role in substrate binding
and/or the catalytic action itself. Without the unionized -COOH group of Glu-35 and the ionized -COO- of Asp-52, the catalytic

4.1.2 https://bio.libretexts.org/@go/page/4626
action of lysozyme would cease. Hydrogen bonds are easily disrupted by increasing temperature. This, in turn, may disrupt the
shape of the enzyme so that its affinity for its substrate diminishes.

Regulation of Enzyme Activity

Several mechanisms work to make enzyme activity within the cell efficient and well-coordinated.

Anchoring enzymes in membranes

Many enzymes are inserted into cell membranes, for examples,
the plasma membrane
the membranes of mitochondria and chloroplasts
the endoplasmic reticulum
the nuclear envelope
These are locked into spatial relationships that enable them to interact efficiently.

Inactive precursors
Enzymes, such as proteases, that can attack the cell itself are inhibited while within the cell that synthesizes them. For example,
pepsin is synthesized within the chief cells (in gastric glands) as an inactive precursor, pepsinogen. Only when exposed to the low
pH outside the cell is the inhibiting portion of the molecule removed and active pepsin produced.

Feedback Inhibition

Figure 4.1.1 : Feedback Inhibition

If the product of a series of enzymatic reactions, e.g., an amino acid, begins to accumulate within the cell, it may specifically inhibit
the action of the first enzyme involved in its synthesis (red bar). Thus further production of the enzyme is halted.

Precursor Activation
The accumulation of a substance within a cell may specifically activate (blue arrow) an enzyme that sets in motion a sequence of
reactions for which that substance is the initial substrate. This reduces the concentration of the initial substrate.

Figure 4.1.3 Precursor Activation

In the case if feedback inhibition and precursor activation, the activity of the enzyme is being regulated by a molecule which is not
its substrate. In these cases, the regulator molecule binds to the enzyme at a different site than the one to which the substrate binds.
When the regulator binds to its site, it alters the shape of the enzyme so that its activity is changed. This is called an allosteric
effect. In feedback inhibition, the allosteric effect lowers the affinity of the enzyme for its substrate and in precursor activation, the
regulator molecule increases the affinity of the enzyme in the series for its substrate.

Regulation of Enzyme Synthesis

The four mechanisms described above regulate the activity of enzymes already present within the cell. What about enzymes that
are not needed or are needed but not present? Here, too, control mechanisms are at work that regulate the rate at which new
enzymes are synthesized. Most of these controls work by turning on or off — the transcription of genes.
If, for example, ample quantities of an amino acid are already available to the cell from its extracellular fluid, synthesis of the
enzymes that would enable the cell to produce that amino acid for itself is shut down. Conversely, if a new substrate is made

4.1.3 https://bio.libretexts.org/@go/page/4626
available to the cell, it may induce the synthesis of the enzymes needed to cope with it. Yeast cells, for example, do not ordinarily
metabolize lactose, and no lactase can be detected in them. However, if grown in a medium containing lactose, they soon begin
synthesizing lactase — by transcribing and translating the necessary gene(s) — and so can begin to metabolize the sugar. E. coli
also has a mechanism which regulates enzyme synthesis by controlling translation of a needed messenger RNA.

This page titled 4.1: Enzymes is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

4.1.4 https://bio.libretexts.org/@go/page/4626
4.2: ATP
ATP (Adenosine triphosphate) is a nucleotide that performs many essential roles in the cell.
It is the major energy currency of the cell, providing the energy for most of the energy-consuming activities of the cell.
It is one of the monomers used in the synthesis of RNA and, after conversion to deoxyATP (dATP), DNA.
It regulates many biochemical pathways.

Energy
When the third phosphate group of ATP is removed by hydrolysis, a substantial amount of free energy is released. The exact
amount depends on the conditions, but we shall use a value of 7.3 kcal per mole.
ATP + H O → ADP + Pi (4.2.1)
2

where ADP is adenosine diphosphate and Pi is inorganic phosphate.

Figure 4.2.1 : ATP

Because of the substantial amount of energy that is liberated when it is broken, the bond between the second and third phosphates
is commonly described as a "high-energy" bond and is depicted in the figure by a wavy red line. (The bond between the first and
second phosphates is also "high-energy".) (But please note that the term is not being used in the same sense as the term "bond
energy". In fact, these bonds are actually weak bonds with low bond energies.)
Cells contain a wide variety of enzymes — called ATPases — that catalyze the hydrolysis of ATP and couple the energy released
to particular energy-consuming reactions in the cell (see examples below).

Synthesis of ATP
ADP + Pi → ATP + H2O
requires energy: 7.3 kcal/mole
occurs in the cytosol by glycolysis
occurs in mitochondria by cellular respiration
occurs in chloroplasts by photosynthesis

Consumption of ATP
ATP powers most of the energy-consuming activities of cells, such as:
Most anabolic reactions such as
joining transfer RNAs to amino acids for assembly into proteins
synthesis of nucleoside triphosphates for assembly into DNA and RNA
synthesis of polysaccharides
synthesis of fats
active transport of molecules and ions
nerve impulses
maintenance of cell volume by osmosis
adding phosphate groups (phosphorylation) to many different proteins, e.g., to alter their activity in cell signaling
muscle contraction

4.2.1 https://bio.libretexts.org/@go/page/4628
 beating of cilia and flagella (including sperm)
bioluminescence

Extracellular ATP
In mammals, ATP also functions outside of cells. Its release
from damaged cells can elicit inflammation and pain
from the carotid body signals a shortage of oxygen in the blood
from taste receptor cells triggers action potentials in the sensory nerves leading back to the brain
from the stretched wall of the urinary bladder signals when the bladder needs emptying

This page titled 4.2: ATP is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source content
that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

4.2.2 https://bio.libretexts.org/@go/page/4628
4.3: NAD and NADP
Nicotinamide adenine dinucleotide (NAD) and its relative nicotinamide adenine dinucleotide phosphate (NADP) are two of the
most important coenzymes in the cell. NADP is simply NAD with a third phosphate group attached as shown at the bottom of the
figure.

Figure 4.3.1 : NAD and NADP

Because of the positive charge on the nitrogen atom in the nicotinamide ring (upper right), the oxidized forms of these important
redox reagents are often depicted as NAD+ and NADP+ respectively.
In cells, most oxidations are accomplished by the removal of hydrogen atoms. Both of these coenzymes play crucial roles in this.
Each molecule of NAD+ (or NADP+) can acquire two electrons; that is, be reduced by two electrons. However, only one proton
accompanies the reduction. The other proton produced as two hydrogen atoms are removed from the molecule being oxidized is
liberated into the surrounding medium. For NAD, the reaction is thus:
+ +
NAD + 2 H ⟶ NADH + H (4.3.1)

NAD and NADP uses

NAD participates in many redox reactions in cells, including those in glycolysis and most of those in the citric acid cycle of cellular
respiration.
NADP is the reducing agent produced by the light reactions of photosynthesis and is consumed in the Calvin cycle of
photosynthesis and used in many other anabolic reactions in both plants and animals.
Under the conditions existing in a normal cell, the hydrogen atoms shown in red are dissociated from these acidic substances.

This page titled 4.3: NAD and NADP is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

4.3.1 https://bio.libretexts.org/@go/page/4629
4.4: Glycolysis
Glycolysis is the anaerobic catabolism of glucose and occurs in virtually all cells (Figure 4.4.1). In eukaryotes, it occurs in the
cytosol, where it converts a molecule of glucose into 2 molecules of pyruvic acid.
+ +
C6 H12 O6 + 2N AD → 2 C3 H4 O3 + 2N ADH + 2 H (4.4.1)

The free energy stored in 2 molecules of pyruvic acid is somewhat less than that in the original glucose molecule;some of this
difference is captured in 2 molecules of ATP.

Figure 4.4.1 : Glycolysis

The Fates of Pyruvic Acid

In Yeasts, Pyruvic acid is decarboxylated and reduced by NADH to form a molecule of carbon dioxide and one of ethanol.
+ +
C3 H4 O3 + N ADH + H → C O2 + C2 H5 OH + N AD (4.4.2)

This accounts for the bubbles and alcohol in, for examples, beer and champagne via a process called alcoholic fermentation. The
process is energetically wasteful because so much of the free energy of glucose (some 95%) remains in the alcohol (a good fuel).
In Red Blood Cells and active Muscles, Pyruvic acid is reduced by NADH forming a molecule of lactic acid.
+ +
C3 H4 O3 + N ADH + H → C3 H6 O3 + N AD (4.4.3)

The process is called lactic acid fermentation. The process is energetically wasteful because so much free energy remains in the
lactic acid molecule. (It can also be debilitating because of the drop in pH as the lactic acid produced in overworked muscles is
transported out into the blood.)
In Mitochondria, Pyruvic acid is oxidized completely to form carbon dioxide and water via a process called cellular respiration.
Approximately 40% of the energy in the original glucose molecule is trapped in molecules of ATP.

This page titled 4.4: Glycolysis is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

4.4.1 https://bio.libretexts.org/@go/page/4630
4.5: Cellular Respiration
Cellular respiration is the process of oxidizing food molecules, like glucose, to carbon dioxide and water.
C6 H12 O6 + 6 O2 + 6 H2 O → 12 H2 O + 6C O2 (4.5.1)

The energy released is trapped in the form of ATP for use by all the energy-consuming activities of the cell. The process occurs in
two phases:
glycolysis, the breakdown of glucose to pyruvic acid
the complete oxidation of pyruvic acid to carbon dioxide and water
In eukaryotes, glycolysis occurs in the cytosol and the remaining processes take place in mitochondria.

Mitochondria
Mitochondria are membrane-enclosed organelles distributed through the cytosol of most eukaryotic cells. Their number within the
cell ranges from a few hundred to, in very active cells, thousands. Their main function is the conversion of the potential energy of
food molecules into ATP.

Figure 4.5.1 : (left) Mitochondria (right) Mitochondrion from bat pancreas cell courtesy Keith R. Porter
Mitochondria have:
an outer membrane that encloses the entire structure
an inner membrane that encloses a fluid-filled matrix
between the two is the intermembrane space
the inner membrane is elaborately folded with shelflike cristae projecting into the matrix.
a small number (some 5–10) circular molecules of DNA
This electron micrograph in Figure 4.5.1, shows a single mitochondrion from a bat pancreas cell. Note the double membrane and
the way the inner membrane is folded into cristae. The dark, membrane-bounded objects above the mitochondrion are lysosomes.
The number of mitochondria in a cell can increase either by their fission (e.g. following mitosis) or decrease by their fusing
together. Defects in either process can produce serious, even fatal, illness.

The Outer Membrane

The outer membrane contains many complexes of integral membrane proteins that form channels through which a variety of
molecules and ions move in and out of the mitochondrion.

The Inner Membrane

The inner membrane contains 5 complexes of integral membrane proteins:
NADH dehydrogenase (Complex I)
succinate dehydrogenase (Complex II)
cytochrome c reductase (Complex III; also known as the cytochrome b-c1 complex)

4.5.1 https://bio.libretexts.org/@go/page/4631
 cytochrome c oxidase (Complex IV)
ATP synthase (Complex V)

The Matrix
The matrix contains a complex mixture of soluble enzymes that catalyze the respiration of pyruvic acid and other small organic
molecules. Here pyruvic acid is
oxidized by NAD+ producing NADH + H+
decarboxylated producing a molecule of
carbon dioxide (CO2) and
a 2-carbon fragment of acetate bound to coenzyme A forming acetyl-CoA

The Citric Acid Cycle

This 2-carbon fragment is donated to a molecule of oxaloacetic acid. The resulting molecule of citric acid (which gives its name
to the process) undergoes the series of enzymatic steps shown in the diagram. The final step regenerates a molecule of oxaloacetic
acid and the cycle is ready to turn again.

Figure 4.5.2 : The Citric Acid Cycle

A brief summary of the cycle is as follows:
Each of the 3 carbon atoms present in the pyruvate that entered the mitochondrion leaves as a molecule of carbon dioxide
(CO2).
At 4 steps, a pair of electrons (2e-) is removed and transferred to NAD+ reducing it to NADH + H+.
At one step, a pair of electrons is removed from succinic acid and reduces the prosthetic group flavin adenine dinucleotide
(FAD) to FADH2.
The electrons of NADH and FADH2 are transferred to the electron transport chain.

The Electron Transport Chain

The electron transport chain consists of 3 complexes of integral membrane proteins
the NADH dehydrogenase complex (I)
the cytochrome c reductase complex (III)
the cytochrome c oxidase complex (IV)
and two freely-diffusible molecules ubiquinone, cytochrome c, that shuttle electrons from one complex to the next.

4.5.2 https://bio.libretexts.org/@go/page/4631
 Figure 4.5.4 Electron Transport Chain
The electron transport chain accomplishes:
The stepwise transfer of electrons from NADH (and FADH2) to oxygen molecules to form (with the aid of protons) water
molecules (H2O). Cytochrome c can only transfer one electron at a time, so cytochrome c oxidase must wait until it has
accumulated 4 of them before it can react with oxygen.
Harnessing the energy released by this transfer to the pumping of protons (H+) from the matrix to the intermembrane space.
Approximately 20 protons are pumped into the intermembrane space as the 4 electrons needed to reduce oxygen to water pass
through the respiratory chain.
The gradient of protons formed across the inner membrane by this process of active transport forms a miniature battery.
The protons can flow back down this gradient only by reentering the matrix through ATP synthase, another complex (complex
V) of 16 integral membrane proteins in the inner membrane. The process is called chemiosmosis.

Chemiosmosis in mitochondria

Fig.4.5.5 Chemiosmosis in Mitochondria

The energy released as electrons pass down the gradient from NADH to oxygen is harnessed by three enzyme complexes of the
respiratory chain (I, III, and IV) to pump protons (H+) against their concentration gradient from the matrix of the mitochondrion
into the intermembrane space.
As their concentration increases there (which is the same as saying that the pH decreases), a strong diffusion gradient is set up. The
only exit for these protons is through the ATP synthase complex. As in chloroplasts, the energy released as these protons flow
down their gradient is harnessed to the synthesis of ATP. The process is called chemiosmosis and is an example of facilitated
diffusion. One-half of the 1997 Nobel Prize in Chemistry was awarded to Paul D. Boyer and John E. Walker for their discovery of
how ATP synthase works.

How many ATPs?

It is tempting to try to view the synthesis of ATP as a simple matter of stoichiometry (the fixed ratios of reactants to products in a
chemical reaction). But (with 3 exceptions) it is not. Most of the ATP is generated by the proton gradient that develops across the
inner mitochondrial membrane. The number of protons pumped out as electrons drop from NADH through the respiratory chain to

4.5.3 https://bio.libretexts.org/@go/page/4631
oxygen is theoretically large enough to generate, as they return through ATP synthase, 3 ATPs per electron pair (but only 2 ATPs
for each pair donated by FADH2).
With 12 pairs of electrons removed from each glucose molecule,
10 by NAD+ (so 10x3=30); and
2 by FADH2 (so 2x2=4),
this could generate 34 ATPs. Add to this the 4 ATPs that are generated by the 3 exceptions and one arrives at 38. However, the
energy stored in the proton gradient is also used for the active transport of several molecules and ions through the inner
mitochondrial membrane into the matrix. NADH is also used as reducing agent for many cellular reactions. So the actual yield of
ATP as mitochondria respire varies with conditions and probably seldom exceeds 30.

The three exceptions

A stoichiometric production of ATP does occur at:
one step in the citric acid cycle yielding 2 ATPs for each glucose molecule. This step is the conversion of alpha-ketoglutaric
acid to succinic acid.
at two steps in glycolysis yielding 2 ATPs for each glucose molecule.

Mitochondrial DNA (mtDNA)

The human mitochondrion contains 5–10 identical, circular molecules of DNA. Each consists of 16,569 base pairs carrying the
information for 37 genes which encode:
2 different molecules of ribosomal RNA (rRNA)
22 different molecules of transfer RNA (tRNA) (at least one for each amino acid)
13 polypeptides
The rRNA and tRNA molecules are used in the machinery that synthesizes the 13 polypeptides.
The 13 polypeptides participate in building several protein complexes embedded in the inner mitochondrial membrane.
7 subunits that make up the mitochondrial NADH dehydrogenase (complex I)
cytochrome b, a subunit of cytochrome c reductase (complex III)
3 subunits of cytochrome c oxidase (complex IV)
2 subunits of ATP synthase (complex V)
Each of these protein complexes also requires subunits that are encoded by nuclear genes, synthesized in the cytosol, and imported
from the cytosol into the mitochondrion. Nuclear genes also encode ~1,000 other proteins that must be imported into the
mitochondrion.

Mutations in mtDNA cause human diseases

Mutations in 12 of the 13 polypeptide-encoding mitochondrial genes have been found to cause human disease. Although many
different organs may be affected, disorders of the muscles and brain are the most common. Perhaps this reflects the great demand
for energy of both these organs. (Although representing only ~2% of our body weight, the brain consumes ~20% of the energy
produced when we are at rest.)
Some of these disorders are inherited in the germline. In every case, the mutant gene is received from the mother because none of
the mitochondria in sperm survives in the fertilized egg. Other disorders are somatic; that is, the mutation occurs in the somatic
tissues of the individual.

 Example: Exercise Intolerance

A number of humans who suffer from easily-fatigued muscles turn out to have a mutations in their cytochrome b gene.
Curiously, only the mitochondria in their muscles have the mutation; the mtDNA of their other tissues is normal. Presumably,
very early in their embryonic development, a mutation occurred in a cytochrome b gene in the mitochondrion of a cell destined
to produce their muscles.

4.5.4 https://bio.libretexts.org/@go/page/4631
The severity of mitochondrial diseases varies greatly. The reason for this is probably the extensive mixing of mutant DNA and
normal DNA in the mitochondria as they fuse with one another. A mixture of both is called heteroplasmy. The higher the ratio of
mutant to normal, the greater the severity of the disease. In fact by chance alone, cells can on occasion end up with all their
mitochondria carrying all-mutant genomes — a condition called homoplasmy (a phenomenon resembling genetic drift).

Mitochondrial Replacement Techniques

As I noted above, only mothers can pass mutant mtDNA on to their offspring. Two techniques are under intense investigation,
either of which could enable a mother to have children free of defective mitochondria. Mutations in some 228 nuclear genes have
also been implicated in human mitochondrial diseases, but mitochondrial replacement techniques will not be able to help with
these.

Why do mitochondria have their own genome?

Many of the features of the mitochondrial genetic system resemble those found in bacteria. This has strengthened the theory that
mitochondria are the evolutionary descendants of a bacterium that established an endosymbiotic relationship with the ancestors of
eukaryotic cells early in the history of life on earth. However, many of the genes needed for mitochondrial function have since
moved to the nuclear genome. The recent sequencing of the complete genome of Rickettsia prowazekii has revealed a number of
genes closely related to those found in mitochondria. Perhaps rickettsias are the closest living descendants of the endosymbionts
that became the mitochondria of eukaryotes.

This page titled 4.5: Cellular Respiration is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

4.5.5 https://bio.libretexts.org/@go/page/4631
4.6: ATP Synthase
ATP synthase is a huge molecular complex (>500,000 daltons) embedded in the inner membrane of mitochondria. Its function is to
convert the energy of protons (H+) moving down their concentration gradient into the synthesis of ATP. 3 to 4 protons moving
through this machine is enough to convert a molecule of ADP and Pi (inorganic phosphate) into a molecule of ATP. One ATP
synthase complex can generate >100 molecules of ATP each second.

Figure 4.6.1 : ATP Synthase

ATP synthase can be separated into 2 parts:
Fo - the portion embedded in the inner mitochondrial membrane
F1-ATPase — the portion projecting into the matrix of the mitochondrion
This is why the intact ATP synthase is also called the FoF1-ATPase.
When the F1-ATPase is isolated in vitro, it catalyzes the hydrolysis of ATP to ADP and Pi (which is why it is called the F1-
ATPase). While it is doing so, the central portion of Fo attached to the stalk rotates rapidly in a counter-clockwise direction (as
viewed from above).
In the intact mitochondrion, the protons that have accumulated in the intermembrane space enter the Fo complex and exit from it
into the matrix. The energy they give up as they travel down their concentration gradient rotates Fo and its stalk (at ~6000 rpm) in a
clockwise direction. As it does so, it induces repeating conformational changes in the head proteins that enable them to convert
ADP and Pi into ATP. (In the figure, two of the three dimers that make up the head proteins have been pulled aside to reveal the
stalk inserted in their center.)
In both these cases, the machine is converting chemical energy from the hydrolysis of ATP in the in vitro case and the flow of
protons down their concentration gradient in the intact mitochondrion into mechanical energy — the turning of the motor. But this
remarkable device can be made to do the reverse, converting mechanical energy (turning of the motor) into chemical energy.

A group of Japanese scientists interested in nano-machines have succeeded in attaching magnetic beads to the stalks of the F1-
ATPase isolated in vitro. Then using a rotating magnetic field they were able to make the stalks rotate. When rotated in a
clockwise direction, the F1-ATPase synthesized ATP from ADP and Pi in the surrounding medium — at a rate of about 5
molecules per second! (When rotating the stalks in the counter-clockwise direction, or not rotating them at all, ATP was
hydrolyzed into ADP and Pi.)
Their achievement was reported in Itoh, H., et al., Nature, 29 January 2004.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 4.6: ATP Synthase is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

4.6.1 https://bio.libretexts.org/@go/page/4632
4.7: Photosynthesis - Pathway of Carbon Fixation
Photosynthesis is the synthesis of organic molecules using the energy of light. For the sugar glucose (one of the most abundant
products of photosynthesis) the equation is:
6 CO + 12 H O ⟶ C H O +6 H O+6 O (4.7.1)
2 2 6 12 6 2 2

Light provides the energy to transfer electrons from water to nicotinamide adenine dinucleotide phosphate (NADP ) forming +

NADPH and to generate ATP. Both ATP and NADPH provide the energy and electrons to reduce carbon dioxide (CO ) to organic
2

molecules.

The Steps that lead to Photosynthesis

Figure 4.7.1 : The steps in the fixation of carbon dioxide during photosynthesis
CO2 combines with the phosphorylated 5-carbon sugar ribulose bisphosphate.
This reaction is catalyzed by the enzyme ribulose bisphosphate carboxylase oxygenase (RUBISCO)(an enzyme which can
fairly claim to be the most abundant protein on earth).
The resulting 6-carbon compound breaks down into two molecules of 3-phosphoglyceric acid (PGA).
The PGA molecules are further phosphorylated (by ATP) and are reduced (by NADPH) to form phosphoglyceraldehyde
(PGAL).
Phosphoglyceraldehyde serves as the starting material for the synthesis of glucose and fructose.
Glucose and fructose make the disaccharide sucrose, which travels in solution to other parts of the plant (e.g., fruit, roots).
Glucose is also the monomer used in the synthesis of the polysaccharides starch and cellulose.
The Figure 4.7.1 shows the steps in the fixation of carbon dioxide during photosynthesis. All of these reactions occur in the stroma
of the chloroplast. These steps were worked out by Melvin Calvin and his colleagues at the University of California and, for this
reason, are named the Calvin cycle.

Calvin's Experiment

Figure 4.7.2 Apparatus used for Calvin's experiment courtesy of Dr. James A. Bassham

4.7.1 https://bio.libretexts.org/@go/page/4633
The experimental apparatus is shown above. After various intervals of illumination, a suspension of unicellular algae is inactivated
and the contents of the cells extracted. The compounds in a drop of the extract are then separated by paper chromatography.
The identity of each substance may be determined simply by comparing its position with the positions occupied by known
substances under the same conditions. Or, a fragment containing the spot can be cut from the sheet and chemically analyzed.
To determine which, if any, of the substances separated on the chromatogram are radioactive, a sheet of X-ray film is placed next to
the chromatogram. If dark spots appear on the film (because of radiation emitted by the 14C atoms), their position can be correlated
with the positions of the chemicals in the chromatogram. Using this technique of autoradiography, Calvin found that 14C turned
up in glucose molecules within 30 seconds after the start of photosynthesis. When he permitted photosynthesis to proceed for only
5 seconds, however, the radioactivity was concentrated in several other, smaller, molecules.

Figure 4.7.3 Chromatogram of Calvin's experiment courtesy of Dr. James A. Bassham

The dark spots show the radioactive compounds produced after 10 secs (left) and 2 minutes (right) of photosynthesis by the green
alga Scenedesmus. The alga was supplied with carbon dioxide labeled with 14C, a radioactive isotope of carbon. At 10 seconds,
most of the radioactivity is found in 3-phosphoglyceric acid ("P-Glyceric"). At 2 minutes, phosphorylated 6-carbon sugars (glucose
and fructose) have been synthesized as well as a number of amino acids. The small rectangle and circle (lower right-hand corners)
mark the spots where the cell extract was applied.

This page titled 4.7: Photosynthesis - Pathway of Carbon Fixation is shared under a CC BY 3.0 license and was authored, remixed, and/or curated
by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available
upon request.

4.7.2 https://bio.libretexts.org/@go/page/4633
4.8: Photosynthesis - The Role of Light
The heart of photosynthesis as it occurs in most autotrophs consists of two key processes:
the removal of hydrogen (H) atoms from water molecules
the reduction of carbon dioxide (CO2) by these hydrogen atoms to form organic molecules.
The second process involves a cyclic series of reactions named (after its discoverer) the Calvin Cycle.
The electrons (e−) and protons (H+) that make up hydrogen atoms are stripped away separately from water molecules.
− +
2H O⟶ 4e +4 H +O (4.8.1)
2 2

The electrons serve two functions:

They reduce NADP+ to NADPH for use in the Calvin Cycle.
They set up an electrochemical charge that provides the energy for pumping protons from the stroma of the chloroplast into
the interior of the thylakoid.
The protons also serve two functions:
They participate in the reduction of NADP+ to NADPH.
As they flow back out from the interior of the thylakoid (by facilitated diffusion), passing down their concentration gradient),
the energy they give up is harnessed to the conversion of ADP to ATP.
Because it is drive by light, this process is called photophosphorylation.
ADP + Pi ⟶ ATP (4.8.2)

The ATP provides the second essential ingredient for running the Calvin Cycle.
The removal of electrons from water molecules and their transfer to NADP+ requires energy. The electrons are moving from a
redox potential of about +0.82 volt in water to −0.32 volt in NADPH. Thus enough energy must be available to move them against
a total potential of 1.14 volts. Where does the needed energy come from? The answer: Light.

The Thylakoid Membrane

Chloroplasts contain a system of thylakoid membranes surrounded by a fluid stroma. Six different complexes of integral
membrane proteins are embedded in the thylakoid membrane. The exact structure of these complexes differs from group to group
(e.g., plant vs. alga) and even within a group (e.g., illuminated in air or underwater). They are as follows:

Photosystem I
The structure of photosystem I in a cyanobacterium ("blue-green alga") has been completely worked out. It probably closely
resembles that of plants as well. It is a homotrimer with each subunit in the trimer containing:
12 different protein molecules bound to
96 molecules of chlorophyll a
2 molecules of the reaction center chlorophyll P700
4 accessory molecules closely associated with them
90 molecules that serve as antenna pigments
22 carotenoid molecules
4 lipid molecules
3 clusters of Fe4S4
2 phylloquinones

Photosystem II
Photosystem II is also a complex of
> 20 different protein molecules bound to
50 or more chlorophyll a molecules
2 molecules of the reaction center chlorophyll P680

4.8.1 https://bio.libretexts.org/@go/page/4634
 2 accessory molecules close to them
2 molecules of pheophytin (chlorophyll without the Mg++)
the remaining molecules of chlorophyll a serve as antenna pigments.
some half dozen carotenoid molecules. These also serve as antenna pigments.
2 molecules of plastoquinone

Light-Harvesting Complexes (LHC)

LHC-I associated with photosystem I
LHC-II associated with photosystem II
These LHCs also act as antenna pigments harvesting light and passing its energy on to their respective photosystems.
The LHC-II of spinach is a homotrimer, with each monomer containing
a single polypeptide
8 molecules of chlorophyll a
6 molecules of chlorophyll b
4 carotenoid molecules

Cytochromes b6 and f
ATP synthase

How the System Works

Figure 4.8.1 : Photosystems

Light is absorbed by the antenna pigments of photosystems II and I.
The absorbed energy is transferred to the reaction center chlorophylls, P680 in photosystem II, P700 in photosystem I.
Absorption of 1 photon of light by Photosystem II removes 1 electron from P680.
With its resulting positive charge, P680 is sufficiently electronegative that it can remove 1 electron from a molecule of water.
When these steps have occurred 4 times, requiring 2 molecules of water, 1 molecule of oxygen and 4 protons (H+) are released
The electrons are transferred (by way of plastoquinone — PQ in the figure) to the cytochrome b6/f complex where they
provide the energy for chemiosmosis.
Activation of P700 in photosystem I enables it to pick up electrons from the cytochrome b6/f complex (by way of plastocyanin
— PC in the figure) and raise them to a sufficiently high redox potential that, after passing through ferredoxin (Fd in the
figure),
they can reduce NADP+ to NADPH.
The sawtooth shifts in redox potential as electrons pass from P680 to NADP+ have caused this system to be called the Z-Scheme
(although as I have drawn the diagram, it looks more like an "N"). It is also called noncyclic photophosphorylation because it
produces ATP in a one-way process (unlike cyclic photophosphorylation and pseudocyclic photophosphorylation described below).

4.8.2 https://bio.libretexts.org/@go/page/4634
Chemiosmosis in Chloroplasts
The energy released as electrons pass down the gradient between photosystem II and plastocyanin (PC) is harnessed by the
cytochrome b6/f complex to pump protons (H+) against their concentration gradient from the stroma of the chloroplast into the
interior of the thylakoid (an example of active transport). As their concentration increases inside (which is the same as saying that
the pH of the interior decreases), a strong diffusion gradient is set up. The only exit for these protons is through the ATP synthase
complex. As in mitochondria, the energy released as these protons flow down their gradient is harnessed to the synthesis of ATP.
The process is called chemiosmosis and is an example of facilitated diffusion.

Figure 4.8.2 : Chemiosmosis in Chloroplasts

Cyclic Photophosphorylation
Each CO2 taken up by the Calvin cycle) requires 2 NADPH molecules and 3 ATP molecules
Each molecule of oxygen released by the light reactions supplies the 4 electrons needed to make 2 NADPH molecules.
The chemiosmosis driven by these 4 electrons as they pass through the cytochrome b6/f complex liberates only enough energy
to pump 12 protons into the interior of the thylakoid.
But in order to make 3 molecules of ATP, the ATPase in chloroplasts appears to have 14 protons (H+) pass through it.
So there appears to be a deficit of 2 protons.
How is this deficit to be made up?
One likely answer: cyclic photophosphorylation.
In cyclic photophosphorylation,
the electrons expelled by the energy of light absorbed by photosystem I pass, as normal, to ferredoxin (Fd).
But instead of going on to make NADPH,
they pass to plastoquinone (PQ) and on back into the cytochrome b6/f complex.
Here the energy each electron liberates pumps 2 protons (H+) into the interior of the
thylakoid — enough to make up the deficit left by noncyclic photophosphorylation.
This process is truly cyclic because no outside source of electrons is required. Like the photocell in a light meter, photosystem I is
simply using light to create a flow of current. The only difference is that instead of using the current to move the needle on a light
meter, the chloroplast uses the current to help synthesize ATP.

Pseudocyclic Photophosphorylation
Another way to make up the deficit is by a process called pseudocyclic photophosphorylation in which some of the electrons
passing to ferredoxin then reduce molecular oxygen back to H2O instead of reducing NADP+ to NADPH.
At first glance, this might seem a fruitless undoing of all the hard work of photosynthesis. But look again. Although the electrons
cycle from water to ferredoxin and back again, part of their pathway is through the chemiosmosis-generating stem of cytochrome
b6/f. Here, then, is another way that simply by turning on a light, enough energy is imparted to electrons that they can bring about
the synthesis of ATP.

4.8.3 https://bio.libretexts.org/@go/page/4634
Antenna Pigments
Chlorophylls a and b differ slightly in the wavelengths of light that they absorb best (although both absorb red and blue much better
than yellow and green). Carotenoids help fill in the gap by strongly absorbing green light. The entire complex ensures that most of
the energy of light will be trapped and passed on to the reaction center chlorophylls.

This page titled 4.8: Photosynthesis - The Role of Light is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

4.8.4 https://bio.libretexts.org/@go/page/4634
4.9: Photosynthesis - Dicovering the Secrets
This chapter talks about various scientists and their path towards discovering photosynthesis.

van Helmont
Perhaps the first experiment designed to explore the nature of photosynthesis was that reported by the Dutch physician van
Helmont in 1648. Some years earlier, van Helmont had placed in a large pot exactly 200 pounds (91 kg) of soil that had been
thoroughly dried in an oven. Then he moistened the soil with rain water and planted a 5-pound (2.3 kg) willow shoot in it. He then
placed the pot in the ground and covered its rim with a perforated iron plate. The perforations allowed water and air to reach the
soil but lessened the chance that dirt or other debris would be blown into the pot from the outside.
For five years, van Helmont kept his plant watered with rain water or distilled water. At the end of that time, he carefully removed
the young tree and found that it had gained 164 pound, 3 ounces (74.5 kg). (This figure did not include the weight of the leaves that
had been shed during the previous four autumns.) He then redried the soil and found that it weighed only 2 ounces (57 g) less that
the original 200 pounds (91 kg). Faced with these experimental facts, van Helmont theorized that the increase in weight of the
willow arose from the water alone. He did not consider the possibility that gases in the air might be involved.

Joseph Priestley
The first evidence that gases participate in photosynthesis was reported by Joseph Priestley in 1772. He knew that if a burning
candle is placed in a sealed chamber, the candle soon goes out. If a mouse is then placed in the chamber, it soon suffocates because
the process of combustion has used up all the oxygen in the air — the gas on which animal respiration depends. However, Priestley
discovered that if a plant is placed in an atmosphere lacking oxygen, it soon replenishes the oxygen, and a mouse can survive in the
resulting mixture. Priestley thought (erroneously) that it was simply the growth of the plant that accounted for this.

Ingen-Housz
It was another Dutch physician, Ingen-Housz, who discovered in 1778 that the effect observed by Priestley occurred only when the
plant was illuminated. A plant kept in the dark in a sealed chamber consumes oxygen just as a mouse (or candle) does.
Ingen-Housz also demonstrated that only green parts of plants liberated oxygen during photosynthesis. Nongreen plant structure,
such as woody stems, roots, flowers, and fruits actually consume oxygen in the process of respiration. We now know that this is
because photosynthesis can go on only in the presence of the green pigment chlorophyll.

Jean Senebier
The growth of plants is accompanied by an increase in their carbon content. A Swiss minister, Jean Senebier, discovered that the
source of this carbon is carbon dioxide and that the release of oxygen during photosynthesis accompanies the uptake of carbon
dioxide. Senebier concluded (erroneously as it turned out) that in photosynthesis carbon dioxide is decomposed, with the carbon
becoming incorporated in the organic matter of the plant and the oxygen being released.
CO2 + H2O → (CH2O) + O2
(The parentheses around the CH2O signify that no specific molecule is being indicated but, instead, the ratio of atoms in some
carbohydrate, e.g., glucose, C6H12O6.) The equation also indicates that the ratio of carbon dioxide consumed to oxygen release is
1:1, a finding that was carefully demonstrated in the years following Senebier's work. Using glucose as the carbohydrate product,
we can write the equation for photosynthesis as
6CO2 + 6H2O → C6H12O6 + 6O2

F. F. Blackman

4.9.1 https://bio.libretexts.org/@go/page/4635
 Figure 4.9.1 : (left) Elodea experiment by Blackman (right) Blackman experiment graphic interpretation
The above equation shows the relationship between the substances used in and produced by the process. It tells us nothing about
the intermediate steps. That photosynthesis does involve at least two quite distinct processes became apparent from the experiments
of the British plant physiologist F. F. Blackman. His results can easily be duplicated by using the setup in Figure 4.9.1. The green
water plant Elodea (available wherever aquarium supplies are sold) is the test organism. When a sprig is placed upside down in a
dilute solution of NaHCO3 (which serves as a source of CO2) and illuminated with a flood lamp, oxygen bubbles are soon given off
from the cut portion of the stem. One then counts the number of bubbles given off in a fixed interval of time at each of several light
intensities. Plotting these data produces a graph like the one in Figure 4.9.2.
Since the rate of photosynthesis does not continue to increase indefinitely with increased illumination, Blackman concluded that at
least two distinct processes are involved: one, a reaction that requires light and the other, a reaction that does not. This latter is
called a "dark" reaction although it can go on in the light. Blackman theorized that at moderate light intensities, the "light" reaction
limits or "paces" the entire process. In other words, at these intensities the dark reaction is capable of handling all the intermediate
substances produced by the light reaction. With increasing light intensities, however, a point is eventually reached when the dark
reaction is working at maximum capacity. Any further illumination is ineffective, and the process reaches a steady rate.
This interpretation is strengthened by repeating the experiment as a somewhat higher temperature. Most chemical reactions proceed
more rapidly at higher temperatures (up to a point). At 35°C, the rate of photosynthesis does not level off until greater light
intensities are present. This suggest that the dark reaction is now working faster. The fact that at low light intensities the rate of
photosynthesis is no greater at 35°C than at 20°C also supports the idea that it is a light reaction that is limiting the process in this
range. Light reactions depend, not on temperature, but simply on the intensity of illumination.
The increased rate of photosynthesis with increased temperature does not occur if the supply of CO2 is limited. As the figure
shows, the overall rate of photosynthesis reaches a steady value at lower light intensities if the amount of CO2 available is limited.
Thus CO2 concentration must be added as a third factor regulating the rate at which photosynthesis occurs. As a practical matter,
however, the concentration available to terrestrial plants is simply that found in the atmosphere: 0.035%.

Van Niel
It was the American microbiologist Van Niel who first glimpsed the role that light plays in photosynthesis. He studied
photosynthesis in purple sulfur bacteria. These microorganisms synthesize glucose from CO2 as do green plants, and they need
light to do so. Water, however, is not the starting material. Instead they use hydrogen sulfide (H2S). Furthermore, no oxygen is
liberated during this photosynthesis but rather elemental sulfur. Van Niel reasoned that the action of light caused a decomposition
of H2S into hydrogen and sulfur atoms. Then, in a series of dark reactions, the hydrogen atoms were used to reduce CO2 to
carbohydrate:
CO + 2 H S → (CH O) + H O + 2 S (4.9.1)
2 2 2 2

4.9.2 https://bio.libretexts.org/@go/page/4635
Van Niel envisioned a parallel to the process of photosynthesis as it occurs in green plants. There the energy of light causes water to
break up into hydrogen and oxygen. The hydrogen atoms are then used to reduce CO2 in a series of dark reactions:
CO + 2 H O → (CH O) + H O + O (4.9.2)
2 2 2 2 2

If this theory is correct, then it follows that all of the oxygen released during photosynthesis comes from water just as all the sulfur
produced by the purple sulfur bacteria comes from H2S. This conclusion directly contradicts Senebier's theory that the oxygen
liberated in photosynthesis comes from the carbon dioxide. If Van Niel's theory is correct, then the equation for photosynthesis
would have to be rewritten:
6 CO + 12 H O → C H O +6 H O+6 O (4.9.3)
2 2 6 12 6 2 2

In science, a theory should be testable. By deduction, one can make a prediction of how a particular experiment will come out if the
theory is sound. In this case, the crucial experiments needed to test the two theories had to await the time when the growth of
atomic research made it possible to produce isotopes other than those found naturally or in greater concentrations than are found
naturally.

Samuel Ruben
In air, water and other natural materials containing oxygen, 99.76% of the oxygen atoms are 16O and only 0.20% of them are the
heavier isotope 18O. In 1941, Samuel Ruben and his coworkers at the University of California were able to prepare specially
"labeled" water in which the 0.85% of the molecules contained 18O atoms. When this water was supplied to a suspension of
photosynthesizing algae, the proportion of 18O in the oxygen gas that was evolved was 0.85%, the same as that of the water
supplied, and not simply the 0.20% found in all natural samples of oxygen (and its compounds like CO2).

% 18O FOUND IN

EXPERIMENT H2O CO2 O2

1. START 0.85 0.20 —

FINISH 0.85 0.61* 0.86

2. START 0.20 0.68 —

FINISH 0.20 0.57 0.20

* A non-biochemical exchange of oxygen atoms between the water and the bicarbonate ions used as a source of CO2 explains the
uptake of the isotope by CO2 in the first experiment.
These results clearly demonstrated that Senebier's interpretation was in error. If all the oxygen liberated during photosynthesis
comes from the carbon dioxide, we would expect the oxygen evolved in Ruben's experiment to contain simply the 0.20% found
naturally. If, on the other hand, both the carbon dioxide and the water contribute to the oxygen released, we would expect its
isotopic composition to have been some intermediate figure. In fact, the isotopic composition of the evolved oxygen was the same
as that of the water used.
Ruben and his colleagues also prepared a source of carbon dioxide that was enriched in 18O atoms. When algae carried out
photosynthesis using this material and natural water, the oxygen that was given off was not enriched in 18O. It contained simply
the 0.20% 18O found in the natural water used. The heavy atoms presumably became incorporated in the other two products
(carbohydrate and by-product water).
These experiments lent great support to Van Niel's idea that one function of light in photosynthesis was the separation of the
hydrogen and oxygen atoms of water molecules. But there remained to work out just how the hydrogen atoms were made available
to the dark reactions.

This page titled 4.9: Photosynthesis - Dicovering the Secrets is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by
John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

4.9.3 https://bio.libretexts.org/@go/page/4635
4.10: Chemiosmosis
Several kinds of evidence support the chemiosmotic theory of ATP synthesis in chloroplasts. When isolated chloroplasts are
illuminated, the medium in which they are suspended becomes alkaline — as we would predict if protons were being removed
from the medium and pumped into the thylakoids (where they reduce the pH to about 4.0 or so). The interior of thylakoids can be
deliberately made acid (low pH) by suspending isolated chloroplasts in an acid medium (pH 4.0) for a period of time. When these
chloroplasts are then transferred to a slightly alkaline medium (pH 8.5), that is, one with a lower concentration of protons and given
a supply of ADP and inorganic phosphate (Pi), they spontaneously synthesize ATP. No light is needed.

Figure 4.10.1 : Chemiosmosis demo

This is a direct evidence that a gradient of protons can be harnessed to the synthesis of ATP.

This page titled 4.10: Chemiosmosis is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

4.10.1 https://bio.libretexts.org/@go/page/4636
4.11: Metabolism
All living things must have an unceasing supply of energy and matter. The transformation of this energy and matter within the body
is called metabolism.

Catabolism and Anabolism

Catabolism is destructive metabolism. Typically, in catabolism, larger organic molecules are broken down into smaller
constituents. This usually occurs with the release of energy (usually as ATP). Anabolism is constructive metabolism. Typically, in
anabolism, small precursor molecules are assembled into larger organic molecules. This always requires the input of energy (often
as ATP).

Autotrophic vs. Heterotrophic Nutrition

Green plants, algae, and some bacteria are autotrophs ("self-feeders"). Most of them use the energy of sunlight to assemble
inorganic precursors, chiefly carbon dioxide and water, into the array of organic macromolecules of which they are made. The
process is photosynthesis. Photosynthesis makes the ATP needed for the anabolic reactions in the cell. All other organisms,
including ourselves, are heterotrophs. We secure all our energy from organic molecules taken in from our surroundings ("food").
Although heterotrophs may feed partially (as most of us do) or exclusively on other heterotrophs, all the food molecules come
ultimately from autotrophs. We may eat beef but the steer ate grass. Heterotrophs degrade some of the organic molecules they take
in (catabolism) to make the ATP that they need to synthesize the others into the macromolecules of which they are made
(anabolism).

How humans (and other animals) do it

Humans are heterotrophs. We are totally dependent on ingested preformed organic molecules to meet all our energy needs. We are
also dependent on preformed organic molecules as the building blocks to meet our anabolic needs.

Figure 4.11.1 : Human Topology

The steps for converting food to energy in animals:
1. Ingestion: taking food within the body (although as the figure shows, it is still topologically in the external world, not the
internal).
2. Digestion: The enzyme-catalyzed hydrolysis of polysaccharides (e.g., starch) to sugars, proteins to amino acids, fats to fatty
acids and glycerol, and nucleic acids to nucleotides.
3. Absorption into the body and transport to the cells.
4. Absorption into cells.

4.11.1 https://bio.libretexts.org/@go/page/4648
 Figure 4.11.2 : Metabolic Pathways
Within cells, these molecules are further degraded into still simpler molecules containing two to four carbon atoms. These
fragments (acetyl-CoA for example) face one of two alternatives. They may proceed up various metabolic pathways and serve as
the building blocks of, for example, sugars and fatty acids. From these will be assembled the macromolecules of the cell (e.g.,
polysaccharides, fats, proteins, and nucleic acids). Alternatively, the molecules in this pool of two- to four-carbon fragments may
be still further degraded — ultimately to simple inorganic molecules such as carbon dioxide (CO2), H2O, and ammonia (NH3).
This phase of catabolism releases large amounts of energy (in the form of ATP). One use to which this energy is put is to run the
anabolic activities of the cell.

This page titled 4.11: Metabolism is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

4.11.2 https://bio.libretexts.org/@go/page/4648
4.12: Intermediary Metabolism
The immediate source of energy for most cells is glucose. But glucose is not the only fuel on which cells depend. Other
carbohydrates, fats and proteins may in certain cells or at certain times be used as a source of ATP. The complexity of the
mechanism by which cells use glucose may make you fervently hope that a similarly-constructed system is not needed for each
kind of fuel. And indeed it is not.
One of the great advantages of the step-by-step oxidation of glucose into CO2 and H2O is that several of the intermediate
compounds formed in the process link glucose metabolism to the metabolism of other food molecules.

Figure 4.12.1 : Intermediary Metabolism

For example, when fats are used as fuel, the glycerol portion of the molecule is converted into PGAL and enters the glycolytic
pathway at that point. Fatty acids are converted into molecules of acetyl-CoA and enter the respiratory pathway to be oxidized in
the mitochondria. The amino acids liberated by the hydrolysis of proteins can also serve as fuel.
First, the nitrogen is removed, a process called deamination.
The remaining fragments then enter the respiratory pathway at several points.
For examples,
the amino acids Gly, Ser, Ala, and Cys are converted into pyruvic acid and enter the mitochondria to be respired.
acetyl-CoA and several intermediates in the citric acid cycle serve as entry points for other amino acid fragments (shown in
blue).
These links thus permit the respiration of excess fats and proteins in the diet. No special mechanism of cellular respiration is
needed by those animals that depend largely on ingested fats (e.g., many birds) or proteins (e.g., carnivores) for their energy supply.
Much of the protein we consume is ultimately converted into glucose (a process called gluconeogenesis) to provide fuel for the
brain and other tissues. Although all our foods are interconvertible to some extent, they are not completely so. In other words, no
single food can supply all our anabolic needs. We can indeed synthesize many fats from glucose, but certain unsaturated fats cannot
be synthesized and must be taken in directly in our diet. These are linoleic acid, linolenic acid, and arachidonic acid. All are
unsaturated; that is, have double bonds. Although we can synthesize 11 of the amino acids from carbohydrate precursors, we must
obtain 9 others (the "essential amino acids") directly.
Many of the points that connect carbohydrate metabolism to the catabolism of fats and proteins serve as two-way valves (indicated
in the figure by double-headed arrows). They provide points of entry not only for the catabolism (cellular respiration) of fatty acids,
glycerol, and amino acids, but for their synthesis (anabolism) as well. Thus the catabolic breakdown of starches can lead (through
acetyl-CoA and PGAL) to the synthesis of fat.

Fructose presents a special problem

Fructose is produced by the digestion of the disaccharide sucrose (common table sugar) into the monosaccharides glucose and
fructose. Both glucose and fructose share the same empirical formula (C6H12O6) and the same caloric content (686 kcal/mole).

4.12.1 https://bio.libretexts.org/@go/page/4650
But the body treats them very differently.
Glucose is taken up and metabolized by all cells to generate ATP by glycolysis and cellular respiration, and excess glucose is
preferentially converted into glycogen rather than fats. Fructose is taken up only by liver cells, and excess fructose is converted in
fats (fatty acids and glycerol). In the U.S., most soft drinks and prepared foods are now sweetened with high-fructose (60%
fructose, 40% glucose) corn syrup. Excessive consumption of these products may well be linked to the growing prevalence in the
U.S. of obesity and type 2 diabetes.

This page titled 4.12: Intermediary Metabolism is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

4.12.2 https://bio.libretexts.org/@go/page/4650
4.13: G Proteins

Figure 4.13.1 : G Proteins

G proteins are so-called because they bind the guanine nucleotides GDP and GTP. They are heterotrimers (i.e., made of three
different subunits) associated with the inner surface of the plasma membrane and transmembrane receptors of hormones, etc.
These are called G protein-coupled receptors (GPCRs).
The three subunits are:
Gα, which carries the binding site for the nucleotide. At least 20 different kinds of Gα molecules are found in mammalian cells.
Gβ
Gγ

How G Proteins Work

In the inactive state, Gα has GDP in its binding site.
When a hormone or other ligand binds to the associated GPCR, an allosteric change takes place in the receptor (that is, its
tertiary structure changes).
This triggers an allosteric change in Gα causing
GDP to leave and be replaced by GTP.
GTP activates Gα causing it to dissociate from GβGγ (which remain linked as a dimer).
Activated Gα in turn activates an effector molecule.
In a common example (shown here), the effector molecule is adenylyl cyclase - an enzyme in the inner face of the plasma
membrane which catalyzes the conversion of ATP into the "second messenger" cyclic AMP (cAMP).
Activated Gα is a GTPase so it quickly converts its GTP to GDP. This conversion, coupled with the return of the Gβ and Gγ
subunits, restores the G protein to its inactive state.

Some Types of Gα Subunits

Gαs
This type stimulates (s = "stimulatory") adenylyl cyclase. It is the one depicted here. It is associated with the receptors for many
hormones such as:
adrenaline
glucagon
luteinizing hormone (LH)
parathyroid hormone (PTH)
adrenocorticotropic hormone (ACTH)

4.13.1 https://bio.libretexts.org/@go/page/4652
Gαs is the target of the toxin liberated by Vibrio cholerae, the bacterium that causes cholera. Binding of cholera toxin to Gαs keeps
it turned "on". The resulting continuous high levels of cAMP causes a massive loss of salts from the cells of the intestinal
epithelium. Massive amounts of water follow by osmosis causing a diarrhea that can be fatal if the salts and water are not quickly
replaced.

Gαq
This activates phospholipase C (PLC) which generates the second messengers:
inositol trisphosphate (IP3)
diacylglycerol (DAG)
Gαq is found in G proteins coupled to receptors for vasopressin, thyroid-stimulating hormone (TSH), and angiotensin.

Gαi
This inhibits (i = "inhibitory") adenylyl cyclase lowering the level of cAMP in the cell. Gai is activated by the receptor for
somatostatin.

Gαt
The "t" is for transducin, the molecule responsible for generating a signal in the rods of the retina in response to light. Gαt triggers
the breakdown of cyclic GMP (cGMP).

This page titled 4.13: G Proteins is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

4.13.2 https://bio.libretexts.org/@go/page/4652
4.14: Secondary Messengers
Second messengers are molecules that relay signals received at receptors on the cell surface — such as the arrival of protein
hormones, growth factors, etc. — to target molecules in the cytosol and/or nucleus. But in addition to their job as relay molecules,
second messengers serve to greatly amplify the strength of the signal. Binding of a ligand to a single receptor at the cell surface
may end up causing massive changes in the biochemical activities within the cell.
There are 3 major classes of second messengers:
1. cyclic nucleotides (e.g., cAMP and cGMP)
2. inositol trisphosphate (IP3) and diacylglycerol (DAG)
3. calcium ions (Ca2+)

Cyclic Nucleotides

Figure 4.14.1 : Cyclic Nucleotides

Cyclic AMP (cAMP)

Some of the hormones that achieve their effects through cAMP as a second messenger:
adrenaline
glucagon
luteinizing hormone (LH)
Cyclic AMP is synthesized from ATP by the action of the enzyme adenylyl cyclase.
Binding of the hormone to its receptor activates
a G protein which, in turn, activates
adenylyl cyclase.
The resulting rise in cAMP turns on the appropriate response in the cell by either (or both):
changing the molecular activities in the cytosol, often using Protein Kinase A (PKA) — a cAMP-dependent protein kinase
that phosphorylates target proteins
turning on a new pattern of gene transcription

Cyclic GMP (cGMP)

Cyclic GMP is synthesized from the nucleotide GTP using the enzyme guanylyl cyclase. Cyclic GMP serves as the second
messenger for
atrial natriuretic peptide (ANP)
nitric oxide (NO)
the response of the rods of the retina to light
Some of the effects of cGMP are mediated through Protein Kinase G (PKG) — a cGMP-dependent protein kinase that
phosphorylates target proteins in the cell.

3
Inositol trisphosphate (IP ) and diacylglycerol (DAG)
Peptide and protein hormones like vasopressin, thyroid-stimulating hormone (TSH), and angiotensin and neurotransmitters like
GABA bind to G protein-coupled receptors (GPCRs) that activate the intracellular enzyme phospholipase C (PLC).

4.14.1 https://bio.libretexts.org/@go/page/4657
 Figure 4.14.3 IP3 and DAG
As its name suggests, it hydrolyzes phospholipids — specifically phosphatidylinositol-4,5-bisphosphate (PIP2) which is found in
the inner layer of the plasma membrane. Hydrolysis of PIP2 yields two products:
diacylglycerol (DAG): DAG remains in the inner layer of the plasma membrane. It recruits Protein Kinase C (PKC) — a
calcium-dependent kinase that phosphorylates many other proteins that bring about the changes in the cell. As its name
suggests, activation of PKC requires calcium ions. These are made available by the action of the other second messenger —
IP3.
inositol-1,4,5-trisphosphate (IP3): This soluble molecule diffuses through the cytosol and binds to receptors on the
endoplasmic reticulum causing the release of calcium ions (Ca2+) into the cytosol. The rise in intracellular calcium triggers the
response.
Example:
The calcium rise is needed for NF-AT (the "nuclear factor of activated T cells") to turn on the appropriate genes in the nucleus.
The remarkable ability of tacrolimus and cyclosporine to prevent graft rejection is due to their blocking this pathway.
The binding of an antigen to its receptor on a B cell (the BCR) also generates the second messengers DAG and IP3.

Calcium ions (Ca2+)

As the functions of IP3 and DAG indicate, calcium ions are also important intracellular messengers. In fact, calcium ions are
probably the most widely used intracellular messengers.
In response to many different signals, a rise in the concentration of Ca2+ in the cytosol triggers many types of events such as
muscle contraction
exocytosis, e.g.
release of neurotransmitters at synapses (and essential for the long-term synaptic changes that produce Long-Term
Potentiation (LTP) and Long-Term Depression (LTD);
secretion of hormones like insulin
activation of T cells and B cells when they bind antigen with their antigen receptors (TCRs and BCRs respectively)
adhesion of cells to the extracellular matrix (ECM)
apoptosis
a variety of biochemical changes mediated by Protein Kinase C (PKC).
Normally, the level of calcium in the cell is very low (~100 nM). There are two main depots of Ca2+ for the cell:
The extracellular fluid (ECF — made from blood), where the concentration is ~ 2 mM or 20,000 times higher than in the
cytosol;
the endoplasmic reticulum ("sarcoplasmic" reticulum in skeletal muscle).
However, its level in the cell can rise dramatically when channels in the plasma membrane open to allow it in from the extracellular
fluid or from depots within the cell such as the endoplasmic reticulum and mitochondria.

Getting Ca2+ into (and out of) the cytosol

Voltage-gated channels
open in response to a change in membrane potential, e.g. the depolarization of an action potential
are found in excitable cells:
skeletal muscle

4.14.2 https://bio.libretexts.org/@go/page/4657
 smooth muscle (These are the channels blocked by drugs, such as felodipine [Plendil®], used to treat high blood
pressure. The influx of Ca2+ contracts the smooth muscle walls of the arterioles, raising blood pressure. The drugs block
this.)
neurons. When the action potential reaches the presynaptic terminal, the influx of Ca2+ triggers the release of the
neurotransmitter.
the taste cells that respond to salt.
allow some 106 ions to flow in each second following the steep concentration gradient.
Receptor-operated channels
These are found in the post-synaptic membrane and open when they bind the neurotransmitter. Example: NMDA receptors.
G-protein-coupled receptors (GPCRs). These are not channels but they trigger a release of Ca2+ from the endoplasmic reticulum
as described above. They are activated by various hormones and neurotransmitters (as well as bitter substances on taste cells in
the tongue).
Ca2+ ions are returned
to the ECF by active transport using
an ATP-driven pump called a Ca2+ ATPase;
two Na+/Ca2+ exchangers. These antiport pumps harness the energy of
3 Na+ ions flowing DOWN their concentration gradient to pump one Ca2+ against its gradient and
4 Na+ ions flowing down to pump 1 Ca2+ and 1 K+ ion up their concentration gradients.
to the endoplasmic (and sarcoplasmic) reticulum using another Ca2+ ATPase.
How can such a simple ion like Ca2+ regulate so many different processes? Some factors at work:
localization within the cell (e.g., released at one spot — the T-system is an example — or spread throughout the cell)
by the amount released (amplitude modulation, "AM")
by releasing it in pulses of different frequencies (frequency modulation, "FM")

This page titled 4.14: Secondary Messengers is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

4.14.3 https://bio.libretexts.org/@go/page/4657
4.15: Bioluminescence
Bioluminescence is the ability of living things to emit light. It is found in many marine animals, both invertebrate (e.g., some
cnidarians, crustaceans, squid) and vertebrate (some fishes); some terrestrial animals (e.g., fireflies, some centipedes); and some
fungi and bacteria. The molecular details vary from organism to organism, but each involves a luciferin (a light-emitting substrate),
a luciferase (an enzyme that catalyzes the reaction), ATP (the source of energy) and molecular oxygen, O2.
The more ATP available, the brighter the light. In fact, firefly luciferin and luciferase are commercially available for measuring the
amount of ATP in biological materials. Fireflies use their flashes to attract mates. The pattern differs from species to species. In one
species, the females sometimes mimic the pattern used by females of another species. When the males of the second species
respond to these "femmes fatales", they are eaten!

How Fireflies Control their Flashing

Barry Trimmer and his colleagues at Tufts University have recently discovered how fireflies turn their luminescent organs (called
lanterns) ON.

Figure 4.15.1 : Firefly (species unknown) captured in eastern Canada – the top picture is taken with a flash, the bottom only with
the self-emitted light. (CC SABy 3.0; Emmanuelm).
The luminescent cells of the lanterns are close to cells at the end of the tracheoles (that bring oxygen to — and take carbon
dioxide away from — the insect's tissues).
These cells contain nitric oxide synthase (NOS), the enzyme that liberates the gas nitric oxide (NO) from arginine.
Nerve impulses activate the release of NO from these cells.
The NO diffuses into the lantern cells and inhibits cellular respiration in the mitochondria (probably by blocking the action of
cytochrome c oxidase)
With cellular respiration inhibited, the oxygen content of the cells increases.
This turns on light production in the peroxisomes that contain luciferase and luciferin-ATP (the ATP is generated when the
lanterns are dark).
The quick decay of NO probably contributes to the short duration of the flash.

Bioluminescence in Marine Animals

The widespread occurrence of luminescence among deep-sea animals reflects the perpetual darkness in which they live. At least
one fish has its luminescent organ located at the tip of a protruding stalk and uses it as bait to lure prey within reach of its jaws.
When disturbed, one species of squid emits a cloud of luminescent water instead of the ink that its shallow-water relatives use.
Some marine animals that live near the surface have luminescent organs on their underside. These probably make it more difficult
for predators beneath them to see them against the light background of the surface.

Fig 4.15.2: Bioluminescence in fish courtesy of Prof. J. W. Hastings

In the case of fishes, the light is emitted by luminescent bacteria that grow in luminescent organs. The photos show the flashlight
fish, Photoblepharon palpebratus, with the lid of its luminescent organ open (left) and closed (right). The light is produced by

4.15.1 https://bio.libretexts.org/@go/page/4659
continuously-emitting luminescent bacteria within the organs, but its display is controlled by the fish. These animals, which were
photographed along reefs in the Gulf of Elat, Israel, appear to use their luminescent organs for such varied functions as: (1)
attracting prey, (2) signaling other members of their species, and (3) confusing potential predators.

This page titled 4.15: Bioluminescence is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

4.15.2 https://bio.libretexts.org/@go/page/4659
 CHAPTER OVERVIEW
Unit 5: DNA
5.1: Transformation in Bacteria
5.2: The Hershey - Chase Experiments
5.3: The Double Helix of DNA
5.4: Base Pairing in DNA and RNA
5.5: DNA Replication
5.6: The Meselson - Stahl Experiment
5.7: Restriction Enzymes
5.8: DNA Sequencing by the Dideoxy Method
5.9: Genome Sizes
5.10: The Human Genome Projects
5.11: The Human and Chimpanzee Genomes
5.12: Pyrosequencing
5.13: DNA Repair
5.14: Harlequin Chromosomes
5.15: Metagenomics - Exploring the Microbial World

This page titled Unit 5: DNA is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1
5.1: Transformation in Bacteria
Bacteria have no sexual reproduction in the sense that eukaryotes do. The have no alternation of diploid and haploid generations,
no gametes, and no meiosis. However, the essence of sex is genetic recombination, and bacteria do have three mechanisms to
accomplish that: transformation, conjugation and transduction.

Transformation
Many bacteria can acquire new genes by taking up DNA molecules (e.g., a plasmid) from their surroundings. The ability to
deliberately transform the bacterium E. coli has made possible the cloning of many genes, including human genes, and the
development of the biotechnology industry. The first demonstration of bacterial transformation was done with Streptococcus
pneumoniae and led to the discovery that DNA is the substance of the genes. The path leading to this epoch-making discovery
began in 1928 with the work of an English bacteriologist, Fred Griffith.

Figure 5.1.1: Streptococcus pneumoniae colonies. (left) Smooth (S) colonies and (right) Rough (R) colonies. Courtesy of Robert
Austrian, J. Exp. Med. 98:21, 1953.
The cells of S. pneumoniae (also known as the pneumococcus) are usually surrounded by a gummy capsule made of a
polysaccharide. When grown on the surface of a solid culture medium, the capsule causes the colonies to have a glistening, smooth
appearance. These cells are called "S" cells. However, after prolonged cultivation on artificial medium, some cells lose the ability
to form the capsule, and the surface of their colonies is wrinkled and rough ("R"). With the loss of their capsule, the bacteria also
lose their virulence. Injection of a single S pneumococcus into a mouse will kill the mouse in 24 hours or so. But an injection of
over 100 million (100 x 106) R cells is entirely harmless.

Figure 5.1.2: Encapsulated (left) and nonencapsulated (right) pneumococci Courtesy of Robert Austrian, J. Exp. Med. 98:21, 1953
The reason? The capsule prevents the pneumococci from being engulfed and destroyed by scavenging cells, neutrophils and
macrophages, in the body. The R forms are completely at the mercy of phagocytes. Pneumococci also occur in over 90 different
types: I, II, III and so on. The types differ in the chemistry of their polysaccharide capsule. Unlike the occasional shift of S -> R,

5.1.1 https://bio.libretexts.org/@go/page/4739
the type of the organism is constant. Mice injected with a few S cells of, say, Type II pneumococci, will soon have their bodies
teeming with descendant cells of the same type.

Figure 5.1.3: Griffith's experiment - injecting mice with Type II pneumococci

However, Griffith found that when living R cells (which should have been harmless) and dead S cells (which also should have
been harmless) were injected together, the mouse became ill and living S cells could be recovered from its body. Furthermore, the
type of the cells recovered from the mouse's body was determined by the type of the dead S cells. In the experiment shown above,
injection of living R-I cells and dead S-II cells produced a dying mouse with its body filled with living S-II pneumococci. The S-II
cells remained true to their new type. Something in the dead S-II cells had made a permanent change in the phenotype of the R-I
cells. The process was named transformation.
Oswald Avery and his colleagues at The Rockefeller Institute in New York City eventually showed that the "something" was
DNA. In pursuing Griffith's discovery, they found that they could bring about the same kind of transformation in vitro using an
extract of the bacterial cells. They treated this extract with:
an enzyme to destroy the polysaccharide of the capsule (S-III in their experiments)
solvents to remove all lipids
trypsin and chymotrypsin to destroy any residual proteins
RNase to destroy RNA
They discovered that it did not destroy the ability of their extracts to transform the bacteria. However, treating the extracts with
DNase to destroy the DNA in them did abolish their transforming activity. So DNA was the only material in the dead cells capable
of transforming cells from one type to another. DNA was the substance of genes.
Although the chemical composition of the capsule is determined by genes, the relationship is indirect. DNA is transcribed into
RNA and RNA is translated into proteins. The phenotype of the pneumococci — the chemical composition of the polysaccharide
capsule — is determined by the particular enzymes (proteins) used in polysaccharide synthesis. Avery and his colleagues Colin
MacLeod and Maclyn McCarty published their epoch-making findings on February 1, 1944. Unfortunately, the importance of their
discovery was not sufficiently appreciated by scientists in general and the Nobel Committee in particular, and Avery died before
their work could be honored with a Nobel Prize. (Nobel prizes are never given posthumously.)

Conjugation
Some bacteria, E. coli is an example, can transfer a portion of their chromosome to a recipient with which they are in direct contact.
As the donor replicates its chromosome, the copy is injected into the recipient. At any time that the donor and recipient become
separated, the transfer of genes stops. Those genes that successfully made the trip replace their equivalents in the recipient's
chromosome.
Conjugation can only occur between cells of opposite mating types: the donor (or "male") carries a fertility factor (F+) and the
recipient ("female") does not (F−). The fertility factor is a set of genes originally acquired from a plasmid and now integrated into
the bacterial chromosome. It establishes the origin of replication for the chromosome. A portion of F is the "locomotive" that pulls
the chromosome into the recipient cell and the rest of it is the "caboose".
In E. coli, about one gene gets across each second that the cells remain together. (So, it takes about 100 min for the entire genome
(4377 genes) to make it. However, the process is easily interrupted so it is more likely that host genes close behind the leading F
genes ("locomotive") will make it than those farther back. The "caboose" seldom makes it so failing to receive a complete F factor,
the recipient cell continues to be "female".

5.1.2 https://bio.libretexts.org/@go/page/4739
The DNA that makes it across finds the homologous region on the female chromosome and replaces it (by a double crossover). By
deliberately separating the cells (in a kitchen blender) at different times, the order and relative spacing of the genes can be
determined. In this way, a genetic map — equivalent to the genetic maps of eukaryotes — can be made. However, here the map
intervals are seconds, not centimorgans (cM).
Figure 5.1.4 shows the mechanism of conjugation in E. coli cells where the "male" lacks functional genes needed to synthesize the
vitamin biotin and the amino acid methionine (Bio−, Met−) so these must be added to its culture medium. The "female" has those
genes (Bio+, Met+) but has nonfunctional (mutant) genes that prevent it from being able to synthesize the amino acids threonine
and leucine (Thr−, Leu−), so these must be added to its culture medium.

Figure 5.1.4: Conjugation in E. Coli cells

When cultured together, some female cells receive the functional Thr and Leu genes from the male donor. A double crossover
enables them to replace the nonfunctional alleles. Now the cells now can grow on a "minimal" medium containing only glucose
and salts.

Transduction
Bacteriophages are viruses that infect bacteria. In the process of assembling new virus particles, some host DNA may be
incorporated in them. The virion head can hold only so much DNA so these viruses while still able to infect new host cells and may
be unable to lyze them. Instead the hitchhiker bacterial gene (or genes) may be inserted into the DNA of the new host, replacing
those already there and giving the host an altered phenotype. This phenomenon is called transduction.

 Reductionist vs. holistic Approach

The understanding of complex systems almost always has to await unraveling the details of some simpler system. You may
feel that trying to find out how one type of pneumococcus could be converted into another was an exceedingly specialized and
esoteric pursuit. But Avery and his coworkers realized the broader significance of what they were observing and, in due course,
the rest of the scientific world did as well. By electing to work with a well-defined system: the conversion of R forms of one
type into S forms of a different type, these researchers made a discovery that has revolutionized biology and medicine.
Attempting to understand the workings of complex systems by first understanding the workings of their parts is called
reductionism. Some scientists (and many nonscientists) question the value of reductionism. They favor a holistic approach
emphasizing the workings of the complete system.
However, the record speaks for itself. From skyscrapers to moon walks, to computer chips to the advances of modern
medicine, progress comes from first understanding the properties of the parts that make up the whole. The late George Wald,
who won the 1967 Nobel Prize in Physiology for his discoveries of the molecular basis of detecting light, once worried that his
work was overly specialized — studying not vision, not the eye, not the whole retina, not even their rods and cones, but just the
chemical reactions of their rhodopsins. But he came to realize "it is as though this were a very narrow window through which
at a distance one can see only a crack of light. As one comes closer, the view grows wider and wider, until finally through this
same window one is looking at the universe. I think this is the way it always goes in science, because science is all one. It
hardly matters where one enters, provided one can come closer....".

Significance of Genetic Recombination in Bacteria

Transformation, conjugation, and transduction were discovered in the laboratory. How important are these mechanisms of genetic
recombination in nature? The completion of the sequence of the entire genome of a variety of different bacteria (and archaea)
suggest that genes have in the past moved from one species to another. This phenomenon is called lateral gene transfer (LGT).
The remarkable spread of resistance to multiple antibiotics may have been aided by the transfer of resistance genes within
populations and even between species. Many bacteria have enzymes that enable them to destroy foreign DNA that gets into their

5.1.3 https://bio.libretexts.org/@go/page/4739
cells. It seem unlikely that these would be needed if that did not occur in nature. In any case, these restriction enzymes have
provided the tools upon which the advances of molecular biology and the biotechnology industry depend.

This page titled 5.1: Transformation in Bacteria is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

5.1.4 https://bio.libretexts.org/@go/page/4739
5.2: The Hershey - Chase Experiments
In 1952 (seven years after Avery's demonstration that genes were DNA), two geneticists: A. D. Hershey and Martha Chase,
provided further proof. They worked with a DNA virus, called T2, which infects E. coli (and so is a bacteriophage). Figure 5.2.1
shows the essential elements of the infective cycle of DNA bacteriophages like T2. The virions attach to the surface of their host
cell (a). The proteins of the capsid inject the DNA core into the cell (b). Once within the cell, some of the bacteriophage genes (the
"early" genes) are transcribed (by the host's RNA polymerase) and translated (by the host's ribosomes, tRNA, etc.) to produce
enzymes that will make many copies of the phage DNA and will turn off (even destroy) the host's DNA.

Figure 5.2.1: The Hershey - Chase Experiment

As fresh copies of phage DNA accumulate, other genes (the "late" genes) are transcribed and translated to form the proteins of the
capsid (c). The stockpile of DNA cores and capsid proteins are assembled into complete virions (d). Another "late" gene is
transcribed and translated into molecules of lysozyme. The lysozyme attacks the peptidoglycan wall (from the inside, of course).
Eventually the cell ruptures and releases its content of virions ready to spread the infection to new host cells (e).
Bacteriophages produced within bacteria growing in radioactive culture medium will themselves be radioactive. If radioactive
sulfur atoms (35S) are present, they will be incorporated into the protein coats of the bacteriophages since two of the amino acids —
cysteine and methionine — contain sulfur (Figure 5.2.2). However, the DNA will be nonradioactive because there are no sulfur
atoms in DNA. If radioactive phosphorus (32P) is used instead, the DNA become radioactive — because of its many phosphorus
atoms — but not the proteins.

Figure 5.2.2: Diagram of the Hershey Chase experiment. (GFDL; Thomasione )

Hershey and Chase found that when bacteriophages containing 32P (radioactive), were allowed to infect nonradioactive bacteria, all
the infected cells became radioactive and, in fact, much of the radioactivity was passed on to the next generation of bacteriophages.
However, when the bacteria were infected with bacteriophages labeled with 35S, and then the virus coats removed (by whirling
them in an electric blender), practically no radioactivity could be detected in the infected cells. From these experiments, it was clear
that the DNA component of the bacteriophages is injected into the bacterial cell while the protein component remains outside.

5.2.1 https://bio.libretexts.org/@go/page/4740
However, it is the injected component — DNA — that is able to direct the formation of new virus particles complete with protein
coats. So here is further proof that genes are DNA.

This page titled 5.2: The Hershey - Chase Experiments is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

5.2.2 https://bio.libretexts.org/@go/page/4740
5.3: The Double Helix of DNA

Figure 5.3.1: Double Helix of DNA

This structure of DNA was worked out by Francis Crick and James D. Watson in 1953. It revealed how DNA - the molecule that
Avery had shown was the physical substance of the genes. It could be replicated and so passed on from generation to generation.
For this epochal work, they shared a Nobel Prize in 1962.

This page titled 5.3: The Double Helix of DNA is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

5.3.1 https://bio.libretexts.org/@go/page/4741
5.4: Base Pairing in DNA and RNA
Rules of Base Pairing

Figure 5.4.1: Base Pairing

The rules of base pairing (or nucleotide pairing) are:
A with T: the purine adenine (A) always pairs with the pyrimidine thymine (T)
C with G: the pyrimidine cytosine (C) always pairs with the purine guanine (G)
This is consistent with there not being enough space (20 Å) for two purines to fit within the helix and too much space for two
pyrimidines to get close enough to each other to form hydrogen bonds between them. But why not A with C and G with T? The
answer: only with A & T and with C & G are there opportunities to establish hydrogen bonds (shown here as dotted lines)
between them (two between A & T; three between C & G). These relationships are often called the rules of Watson-Crick base
pairing, named after the two scientists who discovered their structural basis.
Table 5.4.1: Relative Proportions (%) of Bases in DNA
Organism A T G C

Human 30.9 29.4 19.9 19.8

Chicken 28.8 29.2 20.5 21.5

Grasshopper 29.3 29.3 20.5 20.7

Sea Urchin 32.8 32.1 17.7 17.3

Wheat 27.3 27.1 22.7 22.8

Yeast 31.3 32.9 18.7 17.1

E. coli 24.7 23.6 26.0 25.7

The rules of base pairing tell us that if we can "read" the sequence of nucleotides on one strand of DNA, we can immediately
deduce the complementary sequence on the other strand. The rules of base pairing explain the phenomenon that whatever the
amount of adenine (A) in the DNA of an organism, the amount of thymine (T) is the same (called Chargaff's rule). Similarly,
whatever the amount of guanine (G), the amount of cytosine (C) is the same. The C+G:A+T ratio varies from organism to
organism, particularly among the bacteria, but within the limits of the experimental error, A=T and C=G.

This page titled 5.4: Base Pairing in DNA and RNA is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

5.4.1 https://bio.libretexts.org/@go/page/4742
5.5: DNA Replication

Figure 5.5.3: Control of Replication

With their multiple origins, how does the eukaryotic cell know which origins have been already replicated and which still await
replication?
An observation: When a cell in G2 of the cell cycle is fused with a cell in S phase, the DNA of the G2 nucleus does not begin
replicating again even though replication is proceeding normally in the S-phase nucleus. Not until mitosis is completed, can
freshly-synthesized DNA be replicated again.
Two control mechanisms have been identified — one positive and one negative. This redundancy probably reflects the crucial
importance of precise replication to the integrity of the genome.

Licensing: positive control of replication

In order to be replicated, each origin of replication must be bound by:
an Origin Recognition Complex of proteins (ORC). These remain on the DNA throughout the process.
Accessory proteins called licensing factors. These accumulate in the nucleus during G1 of the cell cycle. They include:
Cdc-6 and Cdt-1, which bind to the ORC and are essential for coating the DNA with
MCM proteins. Only DNA coated with MCM proteins (there are 6 of them) can be replicated.
Once replication begins in S phase,
Cdc-6 and Cdt-1 leave the ORCs (the latter by ubiquination and destruction in proteasomes).
The MCM proteins leave in front of the advancing replication fork.

This page titled 5.5: DNA Replication is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

5.5.1 https://bio.libretexts.org/@go/page/4743
5.6: The Meselson - Stahl Experiment
DNA Replication is Semiconservative
The structure of DNA suggested to Watson and Crick the mechanism by which DNA — hence genes — could be copied faithfully.
They proposed that when the time came for DNA to be replicated, the two strands of the molecule
separated from each other but
remained intact as each served as the template for the synthesis of
a complementary strand.

Figure 5.6.1 Meselson - Stahl experiment interpretation

As this interpretative figure indicates, their results show that DNA molecules are not degraded and reformed from free nucleotides
between cell divisions, but instead, each original strand remains intact as it builds a complementary strand from the nucleotides
available to it. This is called semiconservative replication because each daughter DNA molecule is one-half "old" and one-half
"new".

Immortal strands. Note that the "old" strand (the red one in the top half of the figure) is
immortal because — barring mutations or genetic recombination — it will continue to
serve as an unchanging template down through the generations.
E. coli is a bacterium, but semiconservative replication of DNA also occurs in eukaryotes. And because each DNA molecule in a
eukaryote is incorporated in one chromosome, the replication of entire chromosomes is semiconservative as well. This also means
that the eukaryotic chromosome contains one "immortal strand" of DNA.

This page titled 5.6: The Meselson - Stahl Experiment is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

5.6.1 https://bio.libretexts.org/@go/page/4745
5.7: Restriction Enzymes
Restriction enzymes are DNA-cutting enzymes found in bacteria (and harvested from them for use). Because they cut within the
molecule, they are often called restriction endonucleases. To be able to sequence DNA, it is first necessary to cut it into smaller
fragments. Many DNA-digesting enzymes (like those in your pancreatic fluid) can do this, but most of them are no use for
sequence work because they cut each molecule randomly. This produces a heterogeneous collection of fragments of varying sizes.
What is needed is a way to cleave the DNA molecule at a few precisely-located sites so that a small set of homogeneous fragments
are produced. The tools for this are the restriction endonucleases. The rarer the site it recognizes, the smaller the number of pieces
produced by a given restriction endonuclease.

Figure 5.7.1: Restriction Digest

A restriction enzyme recognizes and cuts DNA only at a particular sequence of nucleotides. For example, the bacterium
Hemophilus aegypticus produces an enzyme named HaeIII that cuts DNA wherever it encounters the sequence
5'GGCC3'
3'CCGG5'

Figure 5.7.2: Restriction Enzymes

The cut is made between the adjacent G and C. This particular sequence occurs at 11 places in the circular DNA molecule of the
virus φX174. Thus treatment of this DNA with the enzyme produces 11 fragments, each with a precise length and nucleotide
sequence. These fragments can be separated from one another and the sequence of each determined. HaeIII and AluI cut straight
across the double helix producing "blunt" ends. However, many restriction enzymes cut in an offset fashion. The ends of the cut
have an overhanging piece of single-stranded DNA. These are called "sticky ends" because they are able to form base pairs with
any DNA molecule that contains the complementary sticky end. Any other source of DNA treated with the same enzyme will
produce such molecules. Mixed together, these molecules can join with each other by the base pairing between their sticky ends.
The union can be made permanent by another enzyme, a DNA ligase, that forms covalent bonds along the backbone of each strand.
The result is a molecule of recombinant DNA (rDNA).
The ability to produce recombinant DNA molecules has not only revolutionized the study of genetics, but has laid the foundation
for much of the biotechnology industry. The availability of human insulin (for diabetics), human factor VIII (for males with
hemophilia A), and other proteins used in human therapy all were made possible by recombinant DNA.

5.7.1 https://bio.libretexts.org/@go/page/4746
Artificial Restriction Enzymes
In addition to the many natural restriction enzymes isolated from bacteria and archaea, it is now possible to synthesize artificial
restriction enzymes that cut DNA at any desired sequence. Examples:
zinc-finger nucleases
TALENs
CRISPR RNA molecules

This page titled 5.7: Restriction Enzymes is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

5.7.2 https://bio.libretexts.org/@go/page/4746
5.8: DNA Sequencing by the Dideoxy Method

Figure 5.8.2: Sample DNA Sequencing

The DNA to be sequenced is prepared as a single strand. This template DNA is supplied with
a mixture of all four normal (deoxy) nucleotides in ample quantities
dATP
dGTP
dCTP
dTTP
a mixture of all four dideoxynucleotides, each present in limiting quantities and each labeled with a "tag" that fluoresces a
different color:
ddATP
ddGTP
ddCTP
ddTTP
DNA polymerase I

Figure 5.8.3 example of a DNA sequence (455 nucleotides of the lysU gene of E. coli) courtesy of Pharmacia Biotech Inc.,
Piscataway, NJ

5.8.1 https://bio.libretexts.org/@go/page/4747
This page titled 5.8: DNA Sequencing by the Dideoxy Method is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by
John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

5.8.2 https://bio.libretexts.org/@go/page/4747
5.9: Genome Sizes
The genome of an organism is the complete set of genes specifying how its phenotype will develop (under a certain set of
environmental conditions). In this sense, then, diploid organisms (like ourselves) contain two genomes, one inherited from our
mother, the other from our father. The table below presents a selection of representative genome sizes from the rapidly-growing list
of organisms whose genomes have been sequenced.
Table of Genome Sizes (haploid)
Base pairs Genes Notes

φX174 5,386 11 virus of E. coli

Human mitochondrion 16,569 37

smallest genome yet found in a

bacterium. This β-proteobacterium
lives in a mutualistic relationship
Nasuia deltocephalinicola 112,091 137
within a special organ of an insect
(a leaf hopper) which it supplies
with essential amino acids.

Epstein-Barr virus (EBV) 172,282 80 causes mononucleosis

all that remains of the nuclear

genome of a red alga (a eukaryote)
nucleomorph of Guillardia theta 551,264 511
engulfed long ago by another
eukaryote

Mycoplasma genitalium 580,073 525

two of the smallest true organisms
Mycoplasma pneumoniae 816,394 679

bacterium that causes epidemic

Rickettsia prowazekii 1,111,523 834
typhus

Treponema pallidum 1,138,011 1,039 bacterium that causes syphilis

smallest genome yet found in a

Pelagibacter ubique 1,308,759 1,354 free-living organism (marine α-
proteobacterium)
chief cause of stomach ulcers (not
Helicobacter pylori 1,667,867 1,589
stress and diet)

Methanocaldococcus jannaschii 1,664,970 1,783 These unicellular microbes look

like typical bacteria but their genes
Aeropyrum pernix 1,669,695 1,885 are so different from those of
either bacteria or eukaryotes that
Methanothermobacter they are classified in a third
1,751,377 2,008
thermoautotrophicus kingdom: Archaea.

Streptococcus pneumoniae 2,160,837 2,236 the pneumococcus

A virus (of an amoeba) with a

genome larger than that of the
Pandoravirus 2,473,870 2556 bacteria and archaea above and
about the same as that of some
parasitic eukaryotes.
2,853 of these encode proteins; the
Listeria monocytogenes 2,944,528 2,926
rest RNAs
a marine cyanobacterium ("blue-
Synechocystis 3,573,470 4,003
green alga")
4,290 of these genes encode
E. coli K-12 4,639,221 4,377
proteins; the rest RNAs

5.9.1 https://bio.libretexts.org/@go/page/4748
 Base pairs Genes Notes

strain that is pathogenic for

E. coli O157:H7 5.44 x 106 5,416 humans; has 1,346 genes not
found in E. coli K-12
Fission yeast. A eukaryote with
Schizosaccharomyces pombe 12,462,637 4,929 fewer genes than the three bacteria
below.
Useful vector for making
Agrobacterium tumefaciens 4,674,062 5,419 transgenic plants; shares many
genes with Sinorhizobium meliloti
Increasingly common cause of
Pseudomonas aeruginosa 6.3 x 106 5,570 opportunistic infections in
humans.
The rhizobial symbiont of alfalfa.
Sinorhizobium meliloti 6,691,694 6,204 Genome consists of one
chromosome and 2 large plasmids.

Saccharomyces cerevisiae 12,495,682 5,770 Budding yeast. A eukaryote.

Neurospora crassa 38,639,769 10,082 Plus 498 RNA genes.

A diatom. Plus 144 chloroplast

Thalassiosira pseudonana 34.5 x 106 11,242 and 40 mitochondrial genes
encoding proteins
This free-living unicellular
organism lives as both an
amoeboid and a flagellated form.
4,133 of its genes are also found in
other eukaryotes suggesting that
they were present in the common
Naegleria gruberi 41 x 106 15,727 ancestor of all eukaryotes. The
great variety of functions encoded
by these genes also suggests that
the common ancestor of all
eukaryotes was itself as complex
as many of the present-day
unicellular members.

Drosophila melanogaster 122,653,977 ~17,000 the "fruit fly"

Caenorhabditis elegans 100,258,171 21,733

Humans 3.3 x 109 ~21,000

Although Tetraodon seems to have

more protein-encoding genes than
Tetraodon nigroviridis (a
3.42 x 108 27,918 we do, it has much less non-coding
pufferfish)
DNA so its total genome is about a
tenth the size of ours.

Mouse 2.8 x 109 ~23,000

Amphibians 109–1011 ?

a flowering plant (angiosperm)

Arabidopsis thaliana 0.135 x 109 27,407 with one of the smallest genomes
known in the plant kingdom.

5.9.2 https://bio.libretexts.org/@go/page/4748
 Base pairs Genes Notes

the Norway spruce, a conifer

(gymnosperm). Even though it has
only ~900 more genes than
Picea abies 19.6 x 109 28,354
Arabidopsis, it has 145 times as
much DNA. Most of this appears
to be derived from transposons.

Psilotum nudum 2.5 x 1011 ?

Even though Psilotum nudum (sometimes called the "whisk fern") is a far simpler plant than Arabidopsis (it has no true leaves,
flowers, or fruit), it has 3000 times as much DNA. No one knows why, but 80% or more of it is repetitive DNA containing no
genetic information. This is also the case for some amphibians, which contain 30 times as much DNA as we do, but certainly are
not 30 times as complex. The total amount of DNA in the haploid genome is called its C value. The lack of a consistent relationship
between the C value and the complexity of an organism (e.g., amphibians vs. mammals) is called the C value paradox.

Not all genes are Indispensable

The scientists at The Institute for Genomic Research (now known as the J. Craig Venter Institute) who determined the Mycoplasma
genitalium sequence have followed this work by systematically destroying its genes (by mutating them with insertions) to see
which ones are essential to life and which are dispensable. Of the 485 protein-encoding genes, they have concluded that only 381
of them are essential to life. In other words, the loss of any one of the 381 is lethal; the loss of any one of the others is not. (This is
not to say that all the organism needs are those 381 — see "A Minimal Genome?" below.)
Using similar techniques, three groups have recently found that only about 10% of the genes in the human genome (~2000 of them)
must be present for human cells to grow successfully in culture. These genes encode proteins for such essential functions as
controlling the cell cycle, DNA replication, DNA transcription and RNA translation. The cells can tolerate the loss of any one of
the other ~18,000 genes. Thus the human genome appears to have redundant pathways that can often compensate for the loss of a
single gene at least for cells growing in culture. Probably others will turn out to be essential for the development and functioning of
the various types of differentiated cells in the intact body.

 A Minimal Genome?

In March of 2016, workers at the J. Craig Venter Institute reported that they had created a strain of mycoplasma containing
only 473 genes. This synthetic organism, which grows vigorously in culture, now holds the record for the smallest genome of a
free-living organism.

This page titled 5.9: Genome Sizes is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

5.9.3 https://bio.libretexts.org/@go/page/4748
5.10: The Human Genome Projects
Shortly after their press conferences, the two groups that had been striving for several years to map the human genome published
their findings:
The International Human Genome Sequencing Consortium (IHGSC) in the 15 February 2001 issue of Nature
Celera Genomics, a company in Rockville, Maryland, in the 16 February issue of Science
These achievements were monumental, but before we examine them, let us be clear as to what they were not.

What was not found

Neither group had determined the complete sequence of the human genome. Each of our chromosomes is a single molecule of
DNA. Some day the sequence of base pairs in each will be known from one end to the other. But in 2001, thousands of gaps
remained to be filled. What they had done was present a series of draft sequences that represented about 90% (probably the
most interesting 90%) of the genome.
Even taken together, the results did not provide an accurate count of the number of protein-encoding genes in our genome (in
contrast to such genomes as those of mitochondrial DNA, the Epstein-Barr virus and many of the bacterial genomes.
One reason: the large number and large size of the introns that split these genes make it difficult to recognize the open reading
frames (ORFs) that encode proteins.

The number of genes were much smaller than predicted

The two groups came up with slightly different estimates of the number of protein-encoding genes, but both in the range of 30 to 38
thousand:
barely two times larger than the genomes of
Drosophila (~17,000 genes)
C. elegans (<22,000 genes)
and representing only 1– 2% of the total DNA in the cell;
and a third of the 100,000 genes that many had predicted would be found.
(By 2011, the number had been reduced to some 21,000.)
Are the tiny roundworm and fruit fly almost as complex as we are?
Probably not, although we share many homologous genes (called "orthologs") with both these animals. But many of our protein-
encoding genes produce more than one protein product (e.g., by alternative splicing of the primary transcript of the gene). On
average, each of our ORFs produces 2 to 3 different proteins. So the human "proteome" (our total number of proteins) may be 10
or more times larger than that of the fruit fly and roundworm.
A larger proportion of our genome encodes transcription factors and is dedicated to control elements (e.g., enhancers) to which
these transcription factors bind. The combinatorial use of these elements probably provides much greater flexibility of gene
expression than is found in Drosophila and C. elegans.

Gene diversity and density

There are some giants such as dystrophin with its 79 exons spread over 2.4 million base pairs of DNA and titin whose 363 exons
can encode a single protein with as many as ~38,000 amino acids. The average human gene contains 4 exons totaling 1,350 base
pairs and thus encodes an average protein of 450 amino acids. The density of genes on the different chromosomes varies from 23
genes per million base pairs on chromosome 19 (for a total of 1,400 genes) to only 5 genes per million base pairs on chromosome
13.

Humans have many genes not found in invertebrates

Humans, and presumably most vertebrates, have genes not found in invertebrate animals like Drosophila and C. elegans. These
include genes encoding:
antibodies and T cell receptors for antigen (TCRs)
the transplantation antigens of the major histocompatibility complex (MHC) (HLA, the MHC of humans)
cell-signaling molecules including the many types of cytokines

5.10.1 https://bio.libretexts.org/@go/page/4749
 the molecules that participate in blood clotting
mediators of apoptosis. Although these proteins occur in Drosophila and C. elegans, we have a much richer assortment of them.

Gene Duplication
Both groups added to the list of human genes that have arisen by repeated duplication (e.g., by unequal crossing over) from a
single precursor gene; for examples, the genes (several hundred) for olfactory receptors and the various globin genes.

Repetitive DNA
Both groups verified the presence of large amounts of repetitive DNA. In fact, this DNA — with similar sequences occurring over
and over — is one of the main obstacles to assembling the DNA sequences in proper order.
LINES (long interspersed elements)
SINES (short interspersed elements) including Alu elements
Retrotransposons
DNA transposons
All told, repetitive DNA probably accounts for over 50% of our total genome.

What remains to be done?

Keep looking for genes.
As of March 2010, 19,956 protein-encoding genes had been positively identified, but there probably are a thousand or more still
to be found.
Determine the human proteome; that is, the total complement of proteins we synthesize.
Analyze how clusters of genes are coordinately expressed
in various types of cells
at different times in the life of a cell.
Such analysis will benefit greatly from the availability to gene chip technology and will also help us to understand how such a
modest increase in gene number from Drosophila to humans could produce such a different outcome!
Determine the genomes of other vertebrates.
This will not only help us recognize more human genes but will give us insight into what makes us unique.
Already we know that large sections of our genome have closely-related homologs in the mouse.
Examples:
The collection of genes — and even their order — on human chromosome 17 matches closely those of mouse chromosome
11. The same is true of human chromosome 20 and mouse chromosome 2.
Humans and mice (also rats) share several hundred absolutely identical stretches of DNA extending for 200–800 base
pairs.
Some are present in the exons of genes, especially genes involved in RNA processing.
Some are found in or near the introns of genes, especially genes encoding proteins involved in DNA transcription.
Some are found between genes — especially those, like Pax6, essential to embryonic development — and may serve as
enhancers.
To have avoided any mutations for 60 million years since humans and rodents went their separate evolutionary ways suggest
that these regions perform functions absolutely essential to mammalian life.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 5.10: The Human Genome Projects is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

5.10.2 https://bio.libretexts.org/@go/page/4749
5.11: The Human and Chimpanzee Genomes
Now that the genomes of both the human and the chimpanzee have been determined, it is possible to make more direct
comparisons between the two species.

Comparison results
Their genomes are 98.8% identical (between any two humans — picked at random — the figure is closer to 99.5%).
Another gene product that differs between the two species is the protein FoxP2. FoxP2 is a transcription factor. Rare humans
with only one copy of the gene (FOXP2) have severe language defects.
The human FOXP2 gene differs from that of the chimp by 5 nucleotides, 2 of which result in non-synonymous codons encoding
2 different amino acids in the protein. The human protein differs from that in the mouse by only 3 amino acids. When you
consider that we shared a common ancestor with mice over 60 million years ago but with the champanzee only about 6 million
years ago, it is tempting to think that these recent changes in the human gene are related to the acquisition of language.
While there are only small (~1%) coding differences in their genes, their genomes differ in other ways.
Many insertions and deletions ("indels") and
many gene duplications
are found in one species but not the other. Later work has revealed that of 510 chimpanzee sequences that are deleted in the
human genome, only one occurs in the coding region of a gene. The others are found in introns or between genes, and at least
some of these occur in gene-regulatory regions like enhancers.
Many single-nucleotide differences create different splicing sites so alternative splicing can produce substantial differences in
the proteins of two species.

This page titled 5.11: The Human and Chimpanzee Genomes is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by
John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

5.11.1 https://bio.libretexts.org/@go/page/4759
5.12: Pyrosequencing
In laboratories around the world there is an intense desire to sequence more genomes.
those of a wide variety of organisms to aid in establishing evolutionary relationships;
those of pooled populations of microorganisms in, for examples, sea water, soil, the large intestine;
other humans to look for genes that predispose to disease and genetic patterns in various ethnic groups.
All of the sequenced genomes listed in Genome Sizes were determined using the dideoxy method invented by Frederick Sanger
and described elsehwere. However, now a great effort is being expended to find ways to sequence DNA more rapidly (and more
cheaply).

The Genome Sequencer

Several new methods are being developed and one is already commercially available (the Genome Sequencer 20 System). Its
method is called pyrosequencing or sequencing by synthesis. It works like this.
The DNA to be sequenced is broken up into fragments of ~100 base pairs and denatured to form single-stranded DNA
(ssDNA).
Single ssDNA fragments are attached to microscopic beads, which are separated from each other.
The polymerase chain reaction (PCR) is run on each bead so that each becomes coated with ~ 10 million identical copies of that
fragment.
The beads are placed singly into separate, microscopic wells (~200,000 of them).
Each well receives a cocktail of reagents:
DNA polymerase — for adding deoxyribonucleotides to the ssDNA
adenosine phosphosulfate (APS)
ATP sulfurylase — an enzyme that forms ATP from adenosine phosphosulfate (APS) and pyrophosphate (PPi)
luciferin
luciferase - an ATPase that catalyzes the conversion of luciferin to oxyluciferin with the liberation of light

Figure 5.12.1 Pyrosequencing run and the data produced by a single well
The sequencing run:
Each of the thousands of wells is flooded with one four deoxyribonucleotides, dTTP, dCTP, and dGTP, but instead of dATP
(which would trigger the luciferin reaction), deoxyadenosine alpha-thiotriphosphate (dATPαS) is used instead. DNA
polymerase ignores the difference and uses it whenever a T is encountered on the ssDNA template, but luciferase doesn't
recognize to it.
In any well where the complementary nucleotide is present at the 3' end of the template, the nucleotide is added and
pyrophosphate is liberated.

5.12.1 https://bio.libretexts.org/@go/page/4760
 The amount of light is proportional to the number of that nucleotide added. So if, for example, the incoming nucleotide is dGTP,
and there is a string of 3 Cs on the template, the light emitted will be 3 times brighter than if only one C is present.
A detector picks up the light (if any) from each well and the data are recorded.
Then each of the remaining 3 nucleotides are added in sequence.
Then the sequence of 4 additions is repeated until synthesis is complete.
The above diagram also shows the type of data produced in a single well. The height of the peak of light production gives the
number of additions that occurred when a particular nucleotide was added (bottom). Computer software then displays the template
sequence (top) for each of the thousands of different fragments sequenced. With this technology, as many as 20 million base pairs
of genome sequence can be learned in an instrument run of less than 6 hours.

This page titled 5.12: Pyrosequencing is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

5.12.2 https://bio.libretexts.org/@go/page/4760
5.13: DNA Repair
DNA in the living cell is subject to many chemical alterations (a fact often forgotten in the excitement of being able to do DNA
sequencing on dried and/or frozen specimens). If the genetic information encoded in the DNA is to remain uncorrupted, any
chemical changes must be corrected.
A failure to repair DNA produces a mutation.
The recent publication of the human genome has already revealed 130 genes whose products participate in DNA repair. More will
probably be identified soon.

Agents that Damage DNA

Certain wavelengths of radiation including ionizing radiation such as gamma rays and X-rays and ultraviolet rays, especially
the UV-C rays (~260 nm) that are absorbed strongly by DNA but also the longer-wavelength UV-B that penetrates the ozone
shield.
Highly-reactive oxygen radicals produced during normal cellular respiration as well as by other biochemical pathways.
Chemicals in the environment
many hydrocarbons, including some found in cigarette smoke
some plant and microbial products, e.g. the aflatoxins produced in moldy peanuts
Chemicals used in chemotherapy, especially chemotherapy of cancers

Types of DNA Damage

1. All four of the bases in DNA (A, T, C, G) can be covalently modified at various positions.
One of the most frequent is the loss of an amino group ("deamination") - resulting, for example, in a C being converted to a
U.
2. Mismatches of the normal bases because of a failure of proofreading during DNA replication.
Common example: incorporation of the pyrimidine U (normally found only in RNA) instead of T.
3. Breaks in the backbone.
Can be limited to one of the two strands (a single-stranded break, SSB) or on both strands (a double-stranded break (DSB).
Ionizing radiation is a frequent cause, but some chemicals produce breaks as well.
4. Crosslinks Covalent linkages can be formed between bases
on the same DNA strand ("intrastrand") or
on the opposite strand ("interstrand").
Several chemotherapeutic drugs used against cancers crosslink DNA

Repairing Damaged Bases

Damaged or inappropriate bases can be repaired by several mechanisms:
Direct chemical reversal of the damage
Excision Repair, in which the damaged base or bases are removed and then replaced with the correct ones in a localized burst
of DNA synthesis. There are three modes of excision repair, each of which employs specialized sets of enzymes.
1. Base Excision Repair (BER)
2. Nucleotide Excision Repair (NER)
3. Mismatch Repair (MMR)
The 2015 Nobel Prize in chemistry was shared by three researchers for their pioneering work in DNA repair: Tomas Lindahl
(BER), Aziz Sancar (NER), and Paul Modrich (MMR).

Direct Reversal of Base Damage

Perhaps the most frequent cause of point mutations in humans is the spontaneous addition of a methyl group (CH3-) (an example of
alkylation) to Cs followed by deamination to a T. Fortunately, most of these changes are repaired by enzymes, called glycosylases,

5.13.1 https://bio.libretexts.org/@go/page/4761
that remove the mismatched T restoring the correct C. This is done without the need to break the DNA backbone (in contrast to the
mechanisms of excision repair described below).
Some of the drugs used in cancer chemotherapy ("chemo") also damage DNA by alkylation. Some of the methyl groups can be
removed by a protein encoded by our MGMT gene. However, the protein can only do it once, so the removal of each methyl group
requires another molecule of protein.
This illustrates a problem with direct reversal mechanisms of DNA repair: they are quite wasteful. Each of the myriad types of
chemical alterations to bases requires its own mechanism to correct. What the cell needs are more general mechanisms capable of
correcting all sorts of chemical damage with a limited toolbox. This requirement is met by the mechanisms of excision repair.

Base Excision Repair (BER)

The steps and some key players:
1. removal of the damaged base (estimated to occur some 20,000 times a day in each cell in our body!) by a DNA glycosylase. We
have at least 8 genes encoding different DNA glycosylases each enzyme responsible for identifying and removing a specific
kind of base damage.
2. removal of its deoxyribose phosphate in the backbone, producing a gap. We have two genes encoding enzymes with this
function.
3. replacement with the correct nucleotide. This relies on DNA polymerase beta, one of at least 11 DNA polymerases encoded by
our genes.
4. ligation of the break in the strand. Two enzymes are known that can do this; both require ATP to provide the needed energy.

Nucleotide Excision Repair (NER)

NER differs from BER in several ways.
It uses different enzymes.
Even though there may be only a single "bad" base to correct, its nucleotide is removed along with many other adjacent
nucleotides; that is, NER removes a large "patch" around the damage.
The steps and some key players:
1. The damage is recognized by one or more protein factors that assemble at the location.
2. The DNA is unwound producing a "bubble". The enzyme system that does this is Transcription Factor IIH, TFIIH, (which
also functions in normal transcription).
3. Cuts are made on both the 3' side and the 5' side of the damaged area so the tract containing the damage can be removed.
4. A fresh burst of DNA synthesis — using the intact (opposite) strand as a template — fills in the correct nucleotides. The DNA
polymerases responsible are designated polymerase delta and epsilon.
5. A DNA ligase covalently inserts the fresh piece into the backbone.

 Xeroderma Pigmentosum (XP)

XP is a rare inherited disease of humans which, among other things, predisposes the patient to
pigmented lesions on areas of the skin exposed to the sun and
an elevated incidence of skin cancer.
It turns out that XP can be caused by mutations in any one of several genes — all of which have roles to play in NER. Some of
them:
XPA, which encodes a protein that binds the damaged site and helps assemble the other proteins needed for NER.
XPB and XPD, which are part of TFIIH. Some mutations in XPB and XPD also produce signs of premature aging. [Link]
XPF, which cuts the backbone on the 5' side of the damage
XPG, which cuts the backbone on the 3' side.

Transcription-Coupled NER
Nucleotide-excision repair proceeds most rapidly in cells whose genes are being actively transcribed on the DNA strand that is
serving as the template for transcription. This enhancement of NER involves XPB, XPD, and several other gene products. The

5.13.2 https://bio.libretexts.org/@go/page/4761
genes for two of them are designated CSA and CSB (mutations in them cause an inherited disorder called Cockayne's syndrome).
The CSB product associates in the nucleus with RNA polymerase II, the enzyme responsible for synthesizing messenger RNA
(mRNA), providing a molecular link between transcription and repair. One plausible scenario: If RNA polymerase II, tracking
along the template (antisense) strand), encounters a damaged base, it can recruit other proteins, e.g., the CSA and CSB proteins, to
make a quick fix before it moves on to complete transcription of the gene.

Mismatch Repair (MMR)

Mismatch repair deals with correcting mismatches of the normal bases; that is, failures to maintain normal Watson-Crick base
pairing (A•T, C•G). It can enlist the aid of enzymes involved in both base-excision repair (BER) and nucleotide-excision repair
(NER) as well as using enzymes specialized for this function.
Recognition of a mismatch requires several different proteins including one encoded by MSH2.
Cutting the mismatch out also requires several proteins, including one encoded by MLH1.
Mutations in either of these genes predisposes the person to an inherited form of colon cancer. So these genes qualify as tumor
suppressor genes.

 How does the MMR system know which is the incorrect nucleotide?

In E. coli, certain adenines become methylated shortly after the new strand of DNA has been synthesized. The MMR system
works more rapidly, and if it detects a mismatch, it assumes that the nucleotide on the already-methylated (parental) strand is
the correct one and removes the nucleotide on the freshly-synthesized daughter strand. How such recognition occurs in
mammals is not yet known.

Synthesis of the repair patch is done by DNA polymerase delta. Cells also use the MMR system to enhance the fidelity of
recombination; i.e., assure that only homologous regions of two DNA molecules pair up to cross over and recombine segments
(e.g., in meiosis).

Repairing Strand Breaks

Ionizing radiation and certain chemicals can produce both single-strand breaks (SSBs) and double-strand breaks (DSBs) in the
DNA backbone.

Single-Strand Breaks (SSBs)

Breaks in a single strand of the DNA molecule are repaired using the same enzyme systems that are used in Base-Excision Repair
(BER).

Double-Strand Breaks (DSBs)

There are two mechanisms by which the cell attempts to repair a complete break in a DNA molecule:
Direct joining of the broken ends. This requires proteins that recognize and bind to the exposed ends and bring them together
for ligating. They would prefer to see some complementary nucleotides but can proceed without them so this type of joining is
also called Nonhomologous End-Joining (NHEJ). A protein called Ku is essential for NHEJ. Ku is a heterodimer of the
subunits Ku70 and Ku80. Errors in direct joining may be a cause of the various translocations that are associated with cancers.
Some examples include Burkitt's lymphoma, the Philadelphia chromosome in chronic myelogenous leukemia (CML) and B-cell
leukemia.
Homologous Recombination (also known as Homology-Directed Repair — HDR). Here the broken ends are repaired using
the information on the intact sister chromatid (available in G2 after chromosome duplication), or on the homologous
chromosome (in G1; that is, before each chromosome has been duplicated). This requires searching around in the nucleus for
the homolog — a task sufficiently uncertain that G1 cells usually prefer to mend their DSBs by NHEJ. or on the
same chromosome if there are duplicate copies of the gene on the chromosome oriented in opposite directions (head-to-head or
back-to-back).
Two of the proteins used in homologous recombination are encoded by the genes BRCA1 and BRCA2. Inherited mutations in
these genes predispose women to breast and ovarian cancers.

5.13.3 https://bio.libretexts.org/@go/page/4761
The Generation of Antibody Diversity
Some of the same enzymes used to repair DSBs by direct joining are also used to break and reassemble the gene segments used to
make
antibody variable regions; that is, to accomplish V(D)J joining — (mice whose Ku80 genes have been knocked out cannot do
this);
different antibody classes; that is, to accomplish class switching

Meiosis also involves DSBs

Recombination between homologous chromosomes in meiosis I also involves the formation of DSBs and their repair. So it is not
surprising that this process uses the same enzymes.
Meiosis I with the alignment of homologous sequences provides a mechanism for repairing damaged DNA; that is, mutations. in
fact, many biologists feel that the main function of sex is to provide this mechanism for maintaining the integrity of the genome.
However, most of the genes on the human Y chromosome have no counterpart on the X chromosome, and thus cannot benefit from
this repair mechanism. They seem to solve this problem by having multiple copies of the same gene — oriented in opposite
directions. Looping the intervening DNA brings the duplicates together and allowing repair by homologous recombination.

Gene Conversion
If the sequence used as a template for repairing a gene by homologous recombination differs slightly from the gene needing repair;
that is, is an allele, the repaired gene will acquire the donor sequence. This nonreciprocal transfer of genetic information is called
gene conversion.
The donor of the new gene sequence may be:
the homologous chromosome (during meiosis)
the sister chromatid (also during meiosis)
a duplicate of the gene on the same chromosome (during mitosis)
Gene conversion during meiosis alters the normal mendelian ratios. Normally, meiosis in a heterozygous (A,a) parent will produce
gametes or spores in a 1:1 ratio; e.g., 50% A; 50% a. However, if gene conversion has occurred, other ratios will appear. If, for
example, an A allele donates its sequence as it repairs a damaged a allele, the repaired gene will become A, and the ratio will be
75% A; 25% a.

Cancer Chemotherapy
The hallmark of all cancers is continuous cell division.
Each division requires both
the replication of the cell's DNA (in S phase) and
transcription and translation of many genes needed for continued growth.
So, any chemical that damages DNA has the potential to inhibit the spread of a cancer.
Many (but not all) drugs used for cancer therapy do their work by damaging DNA.
The table lists (by trade name as well as generic name) some of the anticancer drugs that specifically target DNA.

purine analog. One effect: substitutes for G,

6-mercaptopurine Purinethol®
inducing abortive MMR and strand breaks
pyrimidine analog substitutes for C blocking
Gemcitabine Gemzar®
strand elongation

Cyclophosphamide Cytoxan®

Melphalan Alkeran®
alkylating agents; form interstrand and/or
Busulfan Myleran®
intrastrand crosslinks
Chlorambucil Leukeran®

Mitomycin Mutamycin®

5.13.4 https://bio.libretexts.org/@go/page/4761
 Cisplatin Platinol® forms crosslinks

Bleomycin Blenoxane® cuts DNA strands between GT or GC

Irinotecan Camptosar®
inhibit the proper functioning of enzymes
Mitoxantrone Novantrone® (topoisomerases) needed to unwind DNA for
replication and transcription
Doxorubicin Adriamycin®

inserts into the double helix preventing its

Dactinomycin Cosmegen®
unwinding

The cancer patient has many other cell types that are also proliferating rapidly, e.g., cells of the intestinal endothelium, bone
marrow and hair follicles. Anticancer drugs also damage these — producing many of the unpleasant side effects of "chemo".
Agents that damage DNA are themselves carcinogenic, and chemotherapy poses a significant risk of creating a new cancer, often a
leukemia.

This page titled 5.13: DNA Repair is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

5.13.5 https://bio.libretexts.org/@go/page/4761
5.14: Harlequin Chromosomes

Figure 5.14.2 Immortal Strands

Most eukaryotes have several to many pairs of chromosomes, and we might expect that at metaphase of mitosis the chromosomes
would align at the metaphase plate at random so that some containing the immortal DNA strand would go to one pole; the
remainder to the other. And this is generally the case. However, there may be some exceptions.
Stem cells divide to produce two daughter cells:
one that will continue as a stem cell and
one that will go on to differentiate.
There is evidence that when some types of stem cells divide, for example a subset found in skeletal muscle, the chromatids
containing the immortal strand all line up on one side of the metaphase plate and the daughter cell receiving this set is the one that
remains a stem cell. Although the mechanism by which this occurs is unknown, one can appreciate a potential value to the
organism. Errors (mutations) in DNA occur most often during its replication. By keeping the original template in the stem cell
population, introduced errors (mutations) disappear when the differentiated cell dies at the end of its useful life. Another possible
advantage of nonrandom segregation of parental vs. newly-synthesized DNA: it may assure that epigenetic alterations of their
respective DNA strands are transmitted to the appropriate daughter cells.
(The figure represents a haploid cell with n = 2. Each bar represents one strand of the DNA double helix.)
However, other experiments, with other types of stem cells, find that
only certain chromosomes (e.g., the X and Y in Drosophila male germline stem cells) preferentially segregate the parental
chromatids to the cell that will remain a stem cell;
and for others, the distribution of immortal strands at metaphase is random, and thus the drawing on the right does not reflect
what happens in those cases.

This page titled 5.14: Harlequin Chromosomes is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

5.14.1 https://bio.libretexts.org/@go/page/4762
5.15: Metagenomics - Exploring the Microbial World
All the genomes listed on my page Genome Sizes describe the complete genome of a single species. For bacteria and archaeons,
this means that the organism was grown in pure culture to provide the DNA for sequencing. But it is now clear that the microbial
world contains vast numbers of both groups that have never been grown in the laboratory and thus have escaped study. Soil, water,
and the contents of our large intestine are examples of habitats that teem with unknown microorganisms.
Thanks to the recent development of sequencing machines capable of rapidly (and inexpensively) sequencing huge amounts of
DNA, it is now practical to sequence the DNA extracted from complex microbial ecosystems like that found in a soil sample.
Several different approaches are used, but all depend on a first step of extracting the microbial DNA from the sample (and
separating it from the far more complex DNA of any eukaryotes that may be present).

Assessing Microbial Diversity

The DNA encoding the small subunit (16S) of the ribosomes of both bacteria and archaeons contain some highly conserved
regions; that is, regions of identical or almost identical sequence. Using primers that target these regions, one can then produce
enough material by the polymerase chain reaction PCR to sequence the entire 16S rRNA gene.
Comparing the various sequences to a database of sequences from known organisms, one can estimate how many different types of
microbes are present. Because of the substantial genetic diversity found between "strains" of a single species (e.g., E. coli K-12 and
E.coli O157:H7), closely-related (> 97% identity) 16S rDNA sequences are assigned to a single "phylotype" because we cannot be
sure whether they belong to separate species or to two strains of the same species. In either case, the collection of 16S rDNA
sequences can be arranged to form a phylogenetic tree to show the patterns of relatedness.

Cataloging the Genes in a Microbial Ecosystem

Analyzing the 16S rDNA genes in a sample tells us who is there, but, of course, is not a complete genome and tells us nothing
about the other genes present in the various members of the population. This information can be gained by "shotgun" sequencing of
the environmental DNA sample.
The Steps:
Break the DNA in short fragments.
Insert these into a vector, e.g. a plasmid capable of growing in E. coli K-12.
Expose E. coli cells to this random mix and grow the individual bacterial cells into colonies.
The result: a library containing millions of random DNA fragments from the original sample.
Isolate the plasmids and sequence them. Sequence "reads" average around 100 nucleotides — far shorter than a gene but often
enough to move on to the next step.
Use a powerful computer to attempt to assemble the fragments into a linear sequence of DNA. The computer looks for identical
stretches of nucleotides in different fragments and uses the overlap to assemble them into a "contig".

Look (have the computer look) for open reading frames (ORFs) of protein-encoding genes.
Compare the ORFs with those of known microbes already in databases to see if a function can be deduced.
The sheer diversity of organisms in most microbial ecosystems makes it virtually impossible to find enough contigs to assemble a
complete genome for any one organism like those listed in Genome Sizes. What you get instead is a window into the many kinds of
genes present in one inhabitant or another of that ecosystem. For example, you may discover genes that encode proteins able to
degrade environmental pollutants or genes able to synthesize a new antibiotic.

Finding New Functions in Microbial Populations

Another way of exploiting metagenomics is to look for new functions in the host (e.g. E. coli) if it can express the new gene with
which it was transformed. For example, screening the library of E. coli clones for the ability to resist an antibiotic can reveal genes
involved in antibiotic resistance — a worrisome development in recent years.

5.15.1 https://bio.libretexts.org/@go/page/4763
Some Applications of Metagenomics
The Sargasso Sea: Metagenomic analysis of the DNA extracted from sea water in the Sargasso Sea revealed the presence of
over a thousand different 16S rDNA genes (and thus approximately that number of different species) and over a million protein-
encoding genes.
The Human Colon: 0.3 g fecal samples from two healthy humans produced 78 million base pairs of sequence. Each subject
produced some 25 thousand open reading frames (ORFs) of which about half could be recognized as already-known bacterial or
archaeal genes. Included were genes encoding enzymes for the synthesis of vitamins (e.g., vitamin B1), amino acids, and
enzymes for the digestion of complex polysaccharides in our diet which would otherwise be indigestible. Perhaps as much as
10% of the energy we extract from our food is made available to us by the activity of these microorganisms.
Acid Mine Drainage: Metagenomic analysis of the acidic water (pH ~0.5) flowing from an abandoned metal mine in
California revealed a much simpler ecosystem than those described above: only 3 species of bacteria and 2 of archaea. With
such limited diversity, it was possible to assemble almost-complete genomes for two of these organisms.
A South African Gold Mine: Simpler still was the ecosystem found in water 2.8 km (1.7 miles) down in a gold mine. Only
one organism turned up: an autotrophic bacterium capable of extracting energy from inorganic substances in its environment
and synthesizing all the molecules needed for its life from them.

This page titled 5.15: Metagenomics - Exploring the Microbial World is shared under a CC BY 3.0 license and was authored, remixed, and/or
curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is
available upon request.

5.15.2 https://bio.libretexts.org/@go/page/4763
 CHAPTER OVERVIEW
Unit 6: Gene Expression
6.1: One Gene - One Enzyme Theory
6.2: The Transcription of DNA into RNA
6.3: Genetic Code
6.4: The Translation of RNA into Proteins
6.5: RNA Editing
6.6: Expressed Sequence Tags
6.7: Ribosomal RNA (rRNA) Gene Cluster

This page titled Unit 6: Gene Expression is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1
6.1: One Gene - One Enzyme Theory
Neurospora crassa
Neurospora crassa is an ascomycete, the red bread mold. Like all fungi, it reproduces by spores. It produces two kinds of spores:
Conidia are spores produced by asexual reproduction. Mitosis of the haploid nuclei of the active, growing fungus generates the
conidia.
Ascospores, on the other hand, are formed following sexual reproduction. If two different mating types ("sexes") are allowed to
grow together, they will fuse to form a diploid zygote. Meiosis of this zygote then gives rise to the haploid ascospores.
Neurospora is particularly well suited for genetic studies because
It can be grown quickly on simple culture medium.
It spends most of its life cycle in the haploid condition so any recessive mutations will show up in its phenotype.
When the diploid zygote undergoes meiosis, the nuclei produced by
Meiosis I, followed by
Meiosis II, followed by
one mitotic division
are confined to a narrow tube, the ascus.
Because the nuclei cannot slip past one another, if
the zygote nucleus is heterozygous for a gene (shown here as a and A) and
no crossing over near that locus occurs during meiosis I,
the ascus will finally have four spores at one end containing one allele and four spores at the other end containing the other
allele.

The One Gene - One Enzyme Theory

Sucrose, a few salts, and one vitamin — biotin — provide the nutrients that Neurospora needs to synthesize all the macromolecules
of its cells.

Figure 6.1.1 Beadle - Tatum Experiment on Neurospora

Geneticists George W. Beadle and E. L. Tatum exposed some of the conidia of one mating type of Neurospora to ultraviolet rays in
order to induce mutations.
Then individual irradiated spores were allowed to germinate on a "complete" medium; that is, one enriched with various
vitamins and amino acids.
Once each had developed a mycelium, it was allowed to mate with the other mating type.
The ascospores produced were dissected out individually and each one placed on complete medium.
After growth had occurred, portions of each culture were subcultured on minimal medium.
Sometimes growth continued; sometimes it didn't.
When it did not ("1st" in the figure) , the particular strain was then supplied with a mixture of vitamins, amino acids, etc. until
growth did occur ("2nd ").
Eventually each mutated strain was found to have acquired a need for one nutrient; in the example illustrated here, the vitamin
thiamine ("3rd").

6.1.1 https://bio.libretexts.org/@go/page/4833
Beadle and Tatum reasoned that radiation had caused a gene that permits the synthesis of thiamine from the simple ingredients in
minimal medium to mutate to an allele that does not. The synthesis of thiamine from sucrose requires a number of chemical
reactions, each one catalyzed by a specific enzyme.
By adding, one at a time, the different precursors of thiamine to the medium in which their mutant mold was placed, they were able
to narrow down the defect to the absence of a single enzyme.
If they added to the minimal medium any precursor further along in the process, growth occurred.
Any precursor before the blocked step could not support growth.
Thus, in this example, the conversion of precursor C to precursor D was blocked because of the absence of the needed enzyme (c).
This led them to postulate the one gene - one enzyme theory: each gene in an organism controls the production of a specific
enzyme. It is these enzymes that catalyze the reactions that lead to the phenotype of the organism.
Today, we know that, in fact, not only enzymes, but all the other proteins from which the organism is built are encoded by genes.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 6.1: One Gene - One Enzyme Theory is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

6.1.2 https://bio.libretexts.org/@go/page/4833
6.2: The Transcription of DNA into RNA
The majority of genes are expressed as the proteins they encode. The process occurs in two steps:

Transcription = DNA → RNA

Translation = RNA → protein

Figure 6.2.1: Here is an overview of the central dogma.

Gene Transcription: DNA → RNA

DNA serves as the template for the synthesis of RNA much as it does for its own replication.

The Steps of Transcription

Some 50 different protein transcription factors bind to promoter sites, usually on the 5′ side of the gene to be transcribed.
An enzyme, an RNA polymerase, binds to the complex of transcription factors.
Working together, they open the DNA double helix.
The RNA polymerase proceeds to read one strand moving in it's 3'→ 5' direction.
In eukaryotes, this requires — at least for protein-encoding genes — that the nucleosomes in front of the advancing RNA
polymerase (Pol II) be removed. A complex of proteins is responsible for this. The same complex replaces the nucleosomes
after the DNA has been transcribed and Pol II has moved on.
As the RNA polymerase travels along the DNA strand, it assembles ribonucleotides (supplied as triphosphates, e.g., ATP) into
a strand of RNA.
Each ribonucleotide is inserted into the growing RNA strand following the rules of base pairing. Thus for each C encountered
on the DNA strand, a G is inserted in the RNA; for each G, a C; and for each T, an A. However, each A on the DNA guides the
insertion of the pyrimidine uracil (U, from uridine triphosphate, UTP). There is no T in RNA.

 .)

Synthesis of the RNA proceeds in the 5′ → 3′ direction.

As each nucleoside triphosphate is brought in to add to the 3′ end of the growing strand, the two terminal phosphates are
removed.
When transcription is complete, the transcript is released from the polymerase and, shortly thereafter, the polymerase is released
from the DNA.
Note that at any place in a DNA molecule, either strand may be serving as the template; that is, some genes "run" one way, some
the other (and in a few remarkable cases, the same segment of double helix contains genetic information on both strands!). In all
cases, however, RNA polymerase transcribes the DNA strand in its 3'→ 5' direction.

 A report in the 4 January 2001 issue of Nature shows that RNA polymerase actually tracks around the
double helix of DNA. In vitro, at least, when RNA polymerase is immobilized, it spins the DNA molecule around
and around as it moves along the molecule. Whether it is the polymerase or the DNA that does the spinning in
vivo remains to be determined.

Types of RNA

Figure 6.2.1 Sedimentation pattern of RNA

6.2.1 https://bio.libretexts.org/@go/page/4834
Sedimentation pattern produced by high-speed centrifugation of RNA extracted from the precursors of rabbit red blood cells. The
discrete bands represent particular classes of RNA. The transfer RNAs band at about 4S. The ribosomal RNAs of eukaryotes
sediment at 5S, 5.8S, 18S, and 28S. (The larger the sedimentation unit, S, the larger the molecule — but not proportionally.) The
RNA forming the band at 9S is the messenger RNA for the synthesis of hemoglobin, the major protein synthesized in these cells. In
most types of cells, the messenger RNAs are extremely heterogenous, with small amounts distributed from 6S to 25S.
Several types of RNA are synthesized in the nucleus of eukaryotic cells.
messenger RNA (mRNA)
ribosomal RNA (rRNA)
transfer RNA (tRNA)
small nuclear RNA (snRNA)
small nucleolar RNA (snoRNA)
microRNA (miRNA). These are tiny (~22 nucleotides) RNA molecules that regulate the expression of messenger RNA
(mRNA) molecules.
long non-coding RNA (lncRNA)

Messenger RNA (mRNA)

Messenger RNA will be translated into a polypeptide. Messenger RNA comes in a wide range of sizes reflecting the size of the
polypeptide it encodes. Most cells produce small amounts of thousands of different mRNA molecules, each to be translated into a
peptide needed by the cell. Many mRNAs are common to most cells, encoding "housekeeping" proteins needed by all cells (e.g.,
the enzymes of glycolysis). Other mRNAs are specific for only certain types of cells. These encode proteins needed for the function
of that particular cell (e.g., the mRNA for hemoglobin in the precursors of red blood cells).

Ribosomal RNA (rRNA)

This will be used in the building of ribosomes: machinery for synthesizing proteins by translating mRNA. There are 4 kinds. In
eukaryotes, these are
18S rRNA. One of these molecules, along with some 30 different protein molecules, is used to make the small subunit of the
ribosome.
28S, 5.8S, and 5S rRNA. One each of these molecules, along with some 45 different proteins, are used to make the large
subunit of the ribosome.
The S number given each type of rRNA reflects the rate at which the molecules sediment in the ultracentrifuge. The larger the
number, the larger the molecule (but not proportionally). The 28S, 18S, and 5.8S molecules are produced by the processing of a
single primary transcript from a cluster of identical copies of a single gene. The 5S molecules are produced from a different cluster
of identical genes.

Transfer RNA (tRNA)

These are the RNA molecules that carry amino acids to the growing polypeptide. There are some 32 different kinds of tRNA in a
typical eukaryotic cell.
Each is the product of a separate gene.
They are small (~4S), containing 73-93 nucleotides.
Many of the bases in the chain pair with each other forming sections of double helix.
The unpaired regions form 3 loops.
Each kind of tRNA carries (at its 3′ end) one of the 20 amino acids (thus most amino acids have more than one tRNA
responsible for them).
At one loop, 3 unpaired bases form an anticodon.
Base pairing between the anticodon and the complementary codon on a mRNA molecule brings the correct amino acid into the
growing polypeptide chain.

Small Nuclear RNA (snRNA)

DNA transcription of the genes for mRNA, rRNA, and tRNA produces large precursor molecules ("primary transcripts") that
must be processed within the nucleus to produce the functional molecules for export to the cytosol. Some of these processing steps
are mediated by snRNAs.

6.2.2 https://bio.libretexts.org/@go/page/4834
Approximately a dozen different genes for snRNAs, each present in multiple copies, have been identified. The snRNAs have
various roles in the processing of the other classes of RNA. For example, several snRNAs are part of the spliceosomes that
participate in converting pre-mRNA into mRNA by excising the introns and splicing the exons.

Small Nucleolar RNA (snoRNA)

As the name suggests, these small (60–300 nucleotides) RNAs are found in the nucleolus where they are responsible for several
functions:
Some participate in making ribosomes by helping to cut up the large RNA precursor of the 28S, 18S, and 5.8S molecules.
Others chemically modify many of the nucleotides in rRNA, tRNA, and snRNA molecules, e.g., by adding methyl groups to
ribose.
Some have been implicated in the alternative splicing of pre-mRNA to different forms of mature mRNA.
One snoRNA serves as the template for the synthesis of telomeres.
In vertebrates, the snoRNAs are made from introns removed during RNA processing.

MicroRNAs (miRNAs)
MicroRNAs" ("miRNAs") are single-stranded RNA molecules containing about 22 nucleotides and are about the same size as
siRNAs. MicroRNAs are found in all animals (humans generate some 1000 miRNAs) and plants but not in fungi. They contain 19–
25 nucleotide. They are
encoded in the genome
some by stand-alone genes (that may encode several miRNAs)
some by portions of an intron of the gene whose mRNA they will regulate.
may be expressed in
only certain cell types and
at only certain times in the differentiation of a particular cell type.
While direct evidence of the function of many of these newly-discovered gene products remains to be discovered, they regulate
gene expression by regulating messenger RNA (mRNA), either
destroying the mRNA when the sequences match exactly (the usual situation in plants) or
repressing its translation when the sequences are only a partial match.
MicroRNAs have two traits ideally suited for this:
Being so small, they can be rapidly transcribed from their genes.
They do not need to be translated into a protein product to act.
MicroRNAs regulate (repress) expression of genes in mammals as well. Genome analysis has revealed thousands of human genes
whose transcripts (mRNAs) contain sequences to which one or more of our miRNAs might bind. Probably each miRNA can bind
to as many as 200 different mRNA targets while each mRNA has binding sites for multiple miRNAs. Such a system provides many
opportunities for coordinated mRNA translation

Long Non-coding RNA (lncRNA)

Only messenger RNA encodes polypeptides. All the other classes of RNA are thus called non-coding RNA. In addition to the
rRNAs, snRNAs, and snoRNAs, there is a large (more than 10,000 in humans), heterogenous collection of transcripts longer than
200 nucleotides that are classified as lncRNAs. The function, if any, of most of these remains to be discovered.
However, some lncRNAs have been found to participate in the regulation of such diverse activities as splicing, translation,
imprinting, and transcription. Two examples:
XIST RNA, which contains thousands of nucleotides, inactivates one of the two X chromosomes in female vertebrates.
Some lncRNAs participate in bringing the enhancer and promoter regions of genes close together ("looping") to regulate gene
transcription.
While much remains to be learned about their functions, taken together non-coding RNAs probably account for three-quarters of
the transcription going on in the nucleus.

6.2.3 https://bio.libretexts.org/@go/page/4834
The RNA polymerases
The RNA polymerases are huge multi-subunit protein complexes. Three kinds are found in eukaryotes.
RNA polymerase I (Pol I). It transcribes the rRNA genes for the precursor of the 28S, 18S, and 5.8S molecules (and is the
busiest of the RNA polymerases).
RNA polymerase II (Pol II; also known as RNAP II). It transcribes protein-encoding genes into mRNA (and also the snRNA
genes).
RNA polymerase III (Pol III). It transcribes the 5S rRNA genes and all the tRNA genes.

RNA Processing: pre-mRNA → mRNA

All the primary transcripts produced in the nucleus must undergo processing steps to produce functional RNA molecules for export
to the cytosol. We shall confine ourselves to a view of the steps as they occur in the processing of pre-mRNA to mRNA.
Most eukaryotic genes are split into segments. In decoding the open reading frame of a gene for a known protein, one usually
encounters periodic stretches of DNA calling for amino acids that do not occur in the actual protein product of that gene. Such
stretches of DNA, which get transcribed into RNA but not translated into protein, are called introns. Those stretches of DNA that
do code for amino acids in the protein are called exons. Examples:
The gene for one type of collagen found in chickens is split into 52 separate exons.
The gene for dystrophin, which is mutated in boys with muscular dystrophy, has 79 exons.
Even the genes for rRNA and tRNA are split by introns.
The human genome is estimated to contain some 180,000 exons. With a current estimate of 21,000 genes, the average exon
content of our genes is about 9.

Figure 6.2.2 RNA Processing

Synthesis of the cap. This is a modified guanine (G) which is attached to the 5′ end of the pre-mRNA as it emerges from RNA
polymerase II (Pol II). The cap
protects the RNA from being degraded by enzymes that degrade RNA from the 5′ end;
serves as an assembly point for the proteins needed to recruit the small subunit of the ribosome to begin translation.
Step-by-step removal of introns present in the pre-mRNA and splicing of the remaining exons. This step takes place as the pre-
mRNA continues to emerge from Pol II.
Synthesis of the poly(A) tail. This is a stretch of adenine (A) nucleotides. When a special poly(A) attachment site in the pre-
mRNA emerges from Pol II, the transcript is cut there, and the poly(A) tail is attached to the exposed 3′ end. This completes the
mRNA molecule, which is now ready for export to the cytosol. (The remainder of the transcript is degraded, and the RNA
polymerase leaves the DNA.)

6.2.4 https://bio.libretexts.org/@go/page/4834
 Figure 6.2.3 mRNA-DNA hybrid molecule
The above image is an electron micrograph of a mRNA-DNA hybrid molecule formed by mixing the messenger RNA (mRNA)
from a clone of antibody-secreting cells with single-stranded DNA from the same kind of cells. The bar represents the length of
1000 bases. The lower diagram is an interpretation of the micrograph. The solid line represents the DNA; the dotted line the
mRNA. The loops (IA, IB, etc.) represent the introns that separate the exons encoding the domains of an antibody heavy chain:
V = variable region
E1 = first constant region (CH1) domain
EH = hinge region
E2 and E3 = the nucleotides encoding the two C-terminal domains (CH2 and CH3)
The unhybridized portion of the mRNA is its poly(A) tail.

Alternative Splicing
The processing of pre-mRNA for many proteins proceeds along various paths in different cells or under different conditions. For
example, early in the differentiation of a B cell (a lymphocyte that synthesizes an antibody) the cell first uses an exon that encodes
a transmembrane domain that causes the molecule to be retained at the cell surface. Later, the B cell switches to using a different
exon whose domain enables the protein to be secreted from the cell as a circulating antibody molecule.
Alternative splicing provides a mechanism for producing a wide variety of proteins from a small number of genes. While we
humans may turn out to have only some 20 thousand genes, we probably make at least 10 times that number of different proteins. It
is now estimated that 92–94% of our genes produce pre-mRNAs that are alternatively-spliced. There is evidence that the pattern of
alternative splicing differs consistently in different tissues and so must be regulated. But whether all the products are functional or
that many are simply the outcome of an error-prone process remains to be seen.
Alternative splicing not only provides different proteins from a single gene but also different 3' UTRs and 5' UTRs. Although not
translated into protein, these untranslated regions contain signals that, for example, dictate where in the cell that protein will
accumulate. Two examples:
The 3' UTR of the bicoid gene in Drosophila directs the mRNA to the anterior of the embryo
the same region in the VegT gene of Xenopus directs its mRNA to the vegetal pole of the embryo
One of the most dramatic examples of alternative splicing is the Dscam gene in Drosophila. This single gene contains some 116
exons of which 17 are retained in the final mRNA. Some exons are always included; others are selected from an array.
Theoretically this system is able to produce 38,016 different proteins. And, in fact, over 18,000 different ones have been found in
Drosophila hemolymph.
These Dscam proteins are used to establish a unique identity for each neuron. It works like this. Each developing neuron
synthesizes a dozen or so Dscam mRNAs out of the thousands of possibilities. Which ones are selected appears to be simply a
matter of chance, but because of the great number of possibilities, each neuron will most likely end up with a unique set of a dozen
or so Dscam proteins. As each developing neuron in the central nervous system sprouts dendrites and an axon, these express its
unique collection of Dscam proteins. If the various extensions of a single neuron should meet each other in the tangled web that is
the hallmark of nervous tissue, they are repelled. In this way, thousands of different neurons can coexist in intimate contact without
the danger of nonfunctional contacts between the various extensions of the same neuron.

6.2.5 https://bio.libretexts.org/@go/page/4834
  neuron should encounter each other, they avoid establishing a synapse by the repulsion mediated by their
identical collection of protocadherins. In this way, thousands of different neurons can coexist in intimate contact
without the danger of nonfunctional contacts between the various extensions of the same neuron.

Whether a particular segment of RNA will be retained as an exon or excised as an intron can vary under different circumstances,
such as
what type of cell the gene is in
what stage of differentiation that cell is passing through
what extracellular signals that cell is receiving.
Clearly the switching to an alternate splicing pathway must be closely regulated.

Trans-splicing
Most genes are transcribed and their transcripts processed as described above. RNA polymerase travels down a single strand of a
single gene locus to form pre-mRNA that is processed (including removal of introns) to form the mature mRNA. But there are
exceptions. A number of cases have been found where two different precursor transcripts have been spliced together to form the
final RNA molecule. The phenomenon is called trans-splicing.
Examples: synthesis of a single RNA molecule by splicing together transcripts from loci
located far apart on the same chromosome or
on opposite strands of the same gene locus or
that are the two alleles of the gene on their separate (homologous) chromosomes.
The biological importance of these trans-spliced transcripts is still unknown for most of them.

This page titled 6.2: The Transcription of DNA into RNA is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

6.2.6 https://bio.libretexts.org/@go/page/4834
6.3: Genetic Code
The genetic code consists of 64 triplets of nucleotides. These triplets are called codons.With three exceptions, each codon encodes
for one of the 20 amino acids used in the synthesis of proteins. That produces some redundancy in the code: most of the amino
acids being encoded by more than one codon.
One codon, AUG serves two related functions:
It signals the start of translation
It codes for the incorporation of the amino acid methionine (Met) into the growing polypeptide chain
The genetic code can be expressed as either RNA codons or DNA codons. RNA codons occur in messenger RNA (mRNA) and are
the codons that are actually "read" during the synthesis of polypeptides (the process called translation). But each mRNA molecule
acquires its sequence of nucleotides by transcription from the corresponding gene. Because DNA sequencing has become so rapid
and because most genes are now being discovered at the level of DNA before they are discovered as mRNA or as a protein product,
it is extremely useful to have a table of codons expressed as DNA. So here are both.
Note that for each table, the left-hand column gives the first nucleotide of the codon, the 4 middle columns give the second
nucleotide, and the last column gives the third nucleotide.

The RNA Codons

Second nucleotide
U C A G

UUU Phenylalanine
UCU Serine (Ser) UAU Tyrosine (Tyr) UGU Cysteine (Cys) U
(Phe)

UUC Phe UCC Ser UAC Tyr UGC Cys C

U
UUA Leucine (Leu) UCA Ser UAA STOP UGA STOP A

UGG Tryptophan
UUG Leu UCG Ser UAG STOP G
(Trp)

CUU Leucine (Leu) CCU Proline (Pro) CAU Histidine (His) CGU Arginine (Arg) U

CUC Leu CCC Pro CAC His CGC Arg C

C CAA Glutamine
CUA Leu CCA Pro CGA Arg A
(Gln)

CUG Leu CCG Pro CAG Gln CGG Arg G

ACU Threonine AAU Asparagine

AUU Isoleucine (Ile) AGU Serine (Ser) U
(Thr) (Asn)

AUC Ile ACC Thr AAC Asn AGC Ser C

A
AUA Ile ACA Thr AAA Lysine (Lys) AGA Arginine (Arg) A

AUG Methionine
ACG Thr AAG Lys AGG Arg G
(Met) or START

GAU Aspartic acid

GUU Valine Val GCU Alanine (Ala) GGU Glycine (Gly) U
(Asp)

GUC (Val) GCC Ala GAC Asp GGC Gly C

G
GAA Glutamic acid
GUA Val GCA Ala GGA Gly A
(Glu)

GUG Val GCG Ala GAG Glu GGG Gly G

6.3.1 https://bio.libretexts.org/@go/page/4835
The DNA Codons
These are the codons as they are read on the sense (5' to 3') strand of DNA. Except that the nucleotide thymidine (T) is found in
place of uridine (U), they read the same as RNA codons. However, mRNA is actually synthesized using the antisense strand of
DNA (3' to 5') as the template.
This table could well be called the Rosetta Stone of life.

The Genetic Code (DNA)

TTT Phe TCT Ser TAT Tyr TGT Cys

TTC Phe TCC Ser TAC Tyr TGC Cys

TTA Leu TCA Ser TAA STOP TGA STOP

TTG Leu TCG Ser TAG STOP TGG Trp

CTT Leu CCT Pro CAT His CGT Arg

CTC Leu CCC Pro CAC His CGC Arg

CTA Leu CCA Pro CAA Gln CGA Arg

CTG Leu CCG Pro CAG Gln CGG Arg

ATT Ile ACT Thr AAT Asn AGT Ser

ATC Ile ACC Thr AAC Asn AGC Ser

ATA Ile ACA Thr AAA Lys AGA Arg

ATG Met* ACG Thr AAG Lys AGG Arg

GTT Val GCT Ala GAT Asp GGT Gly

GTC Val GCC Ala GAC Asp GGC Gly

GTA Val GCA Ala GAA Glu GGA Gly

GTG Val GCG Ala GAG Glu GGG Gly

*When within gene; at beginning of gene, ATG signals where translation of the RNA will begin.

Codon Bias
All but two of the amino acids (Met and Trp) can be encoded by from 2 to 6 different codons. However, the genome of most
organisms reveals that certain codons are preferred over others. In humans, for example, alanine is encoded by GCC four times as
often as by GCG. This probably reflects a greater translation efficiency by the translation apparatus (e.g., ribosomes) for certain
codons over their synonyms.

Exceptions to the Code

The genetic code is almost universal. The same codons are assigned to the same amino acids and to the same START and STOP
signals in the vast majority of genes in animals, plants, and microorganisms. However, some exceptions have been found. Most of
these involve assigning one or two of the three STOP codons to an amino acid instead.

Mitochondrial genes
When mitochondrial mRNA from animals or microorganisms (but not from plants) is placed in a test tube with the cytosolic
protein-synthesizing machinery (amino acids, enzymes, tRNAs, ribosomes) it fails to be translated into a protein.One of the reasons
is because these mitochondria use UGA to encode tryptophan (Trp) rather than as a chain terminator. When translated by cytosolic
machinery, synthesis stops where Trp should have been inserted. In addition, most animal mitochondria use AUA for methionine
not isoleucine and all vertebrate mitochondria use AGA and AGG as chain terminators. Yeast mitochondria assign all codons
beginning with CU to threonine instead of leucine (which is still encoded by UUA and UUG as it is in cytosolic mRNA).
Plant mitochondria use the universal code, and this has permitted angiosperms to transfer mitochondrial genes to their nucleus with
great ease.

6.3.2 https://bio.libretexts.org/@go/page/4835
Nuclear genes
Violations of the universal code are far rarer for nuclear genes.
A few unicellular eukaryotes have been found that use one or two (of their three) STOP codons for amino acids instead.

Nonstandard Amino Acids

The vast majority of proteins are assembled from the 20 amino acids listed above even though some of these may be chemically
altered, e.g. by phosphorylation, at a later time.
However, two cases have been found where an amino acid that is not one of the standard 20 is inserted by a tRNA into the growing
polypeptide.
selenocysteine. This amino acid is encoded by UGA. UGA is still used as a chain terminator, but the translation machinery is
able to discriminate when a UGA codon should be used for selenocysteine rather than STOP. This codon usage has been found
in certain Archaea, eubacteria, and animals (humans synthesize 25 different proteins containing selenium).
pyrrolysine. In several species of Archaea and bacteria, this amino acid is encoded by UAG. How the translation machinery
knows when it encounters UAG whether to insert a tRNA with pyrrolysine or to stop translation is not yet known.

This page titled 6.3: Genetic Code is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

6.3.3 https://bio.libretexts.org/@go/page/4835
6.4: The Translation of RNA into Proteins

Figure 6.4.1 Alanine transfer RNA

This image shows the structure of alanine transfer RNA (tRNAala) from yeast. It consists of a single strand of 77
ribonucleotides. The chain is folded on itself, and many of the bases pair with each other forming four helical regions. Loops are
formed in the unpaired regions of the chain. (The bases circled in blue have been chemically-modified following synthesis of the
molecule.)
At least one kind of tRNA is present for each of the 20 amino acids used in protein synthesis. (Some amino acids employ the
services of two or three different tRNAs, so most cells contain as many as 32 different kinds of tRNA.) The amino acid is attached
to the appropriate tRNA by an activating enzyme (one of 20 aminoacyl-tRNA synthetases) specific for that amino acid as well as
for the tRNA assigned to it.
Each kind of tRNA has a sequence of 3 unpaired nucleotides — the anticodon — which can bind, following the rules of base
pairing, to the complementary triplet of nucleotides — the codon — in a messenger RNA (mRNA) molecule. Just as DNA
replication and transcription involve base pairing of nucleotides running in opposite direction, so the reading of codons in mRNA
(5' -> 3') requires that the anticodons bind in the opposite direction.
Anticodon: 3' CGA 5'
Codon: 5' GCU 3'

The RNA Codons

Second nucleotide
U C A G

UUU Phenylalanine
UCU Serine (Ser) UAU Tyrosine (Tyr) UGU Cysteine (Cys) U
(Phe)

UUC Phe UCC Ser UAC Tyr UGC Cys C

U
UUA Leucine (Leu) UCA Ser UAA STOP UGA STOP A

UGG Tryptophan
UUG Leu UCG Ser UAG STOP G
(Trp)

CUU Leucine (Leu) CCU Proline (Pro) CAU Histidine (His) CGU Arginine (Arg) U

CUC Leu CCC Pro CAC His CGC Arg C

C CAA Glutamine
CUA Leu CCA Pro CGA Arg A
(Gln)

CUG Leu CCG Pro CAG Gln CGG Arg G

ACU Threonine AAU Asparagine

AUU Isoleucine (Ile) AGU Serine (Ser) U
(Thr) (Asn)

AUC Ile ACC Thr AAC Asn AGC Ser C

A
AUA Ile ACA Thr AAA Lysine (Lys) AGA Arginine (Arg) A

AUG Methionine
ACG Thr AAG Lys AGG Arg G
(Met) or START

6.4.1 https://bio.libretexts.org/@go/page/4836
 GAU Aspartic acid
GUU Valine Val GCU Alanine (Ala) GGU Glycine (Gly) U
(Asp)

GUC (Val) GCC Ala GAC Asp GGC Gly C

G
GAA Glutamic acid
GUA Val GCA Ala GGA Gly A
(Glu)

GUG Val GCG Ala GAG Glu GGG Gly G

Note:
Most of the amino acids are encoded by synonymous codons that differ in the third position of the codon.
In some cases, a single tRNA can recognize two or more of these synonymous codons.
Example: phenylalanine tRNA with the anticodon 3' AAG 5' recognizes not only UUC but also UUU.
The violation of the usual rules of base pairing at the third nucleotide of a codon is called "wobble"
The codon AUG serves two related functions
It begins every message; that is, it signals the start of translation placing the amino acid methionine at the amino terminal
of the polypeptide to be synthesized.
When it occurs within a message, it guides the incorporation of methionine.
Three codons, UAA, UAG, and UGA, act as signals to terminate translation. They are called STOP codons.

The Steps of Translation

Figure 6.4.2 Translation

Initiation
The small subunit of the ribosome binds to a site "upstream" (on the 5' side) of the start of the message.
It proceeds downstream (5' -> 3') until it encounters the start codon AUG. (The region between the mRNA cap and the AUG is
known as the 5'-untranslated region [5'-UTR].)
Here it is joined by the large subunit and a special initiator tRNA.
The initiator tRNA binds to the P site (shown in pink) on the ribosome.
In eukaryotes, initiator tRNA carries methionine (Met). (Bacteria use a modified methionine designated fMet.)

Elongation
An aminoacyl-tRNA (a tRNA covalently bound to its amino acid) able to base pair with the next codon on the mRNA arrives
at the A site (green) associated with:
an elongation factor (called EF-Tu in bacteria; EF-1 in eukaryotes)
GTP (the source of the needed energy)

6.4.2 https://bio.libretexts.org/@go/page/4836
 The preceding amino acid (Met at the start of translation) is covalently linked to the incoming amino acid with a peptide bond
(shown in red).
The initiator tRNA is released from the P site.
The ribosome moves one codon downstream.
This shifts the more recently-arrived tRNA, with its attached peptide, to the P site and opens the A site for the arrival of a new
aminoacyl-tRNA.
This last step is promoted by another protein elongation factor (called EF-G in bacteria; EF-2 in eukaryotes) and the energy of
another molecule of GTP.
Note: the initiator tRNA is the only member of the tRNA family that can bind directly to the P site. The P site is so-named because,
with the exception of initiator tRNA, it binds only to a peptidyl-tRNA molecule; that is, a tRNA with the growing peptide attached.
The A site is so-named because it binds only to the incoming aminoacyl-tRNA; that is the tRNA bringing the next amino acid. So,
for example, the tRNA that brings Met into the interior of the polypeptide can bind only to the A site.

Termination
The end of translation occurs when the ribosome reaches one or more STOP codons (UAA, UAG, UGA). (The nucleotides
from this point to the poly(A) tail make up the 3'-untranslated region [3'-UTR] of the mRNA.)
There are no tRNA molecules with anticodons for STOP codons.
However, protein release factors recognize these codons when they arrive at the A site.
Binding of these proteins —along with a molecule of GTP — releases the polypeptide from the ribosome.
The ribosome splits into its subunits, which can later be reassembled for another round of protein synthesis.

Polysomes
A single mRNA molecule usually has many ribosomes traveling along it, in various stages of synthesizing the protein. This
complex is called a polysome.

Codon Bias
All but two of the amino acids (Met and Trp) can be encoded by from 2 to 6 different codons. However, the genome of most
organisms reveals that certain codons are preferred over others. In humans, for example, alanine is encoded by GCC four times as
often as by GCG. This probably reflects a greater translation efficiency by the translation apparatus for certain codons over their
synonyms.
At the start of translation, two or more of a set of synonymous codons (e.g., the 6 codons that incorporate leucine in the growing
protein) are used alternately. The need to locate first one and then another tRNA for that amino acid slows down the rate of
translation.
This may aid in keeping ribosomes from bumping into each other on the polysome.
It may also provide more time for the nascent protein to begin to fold correctly as it emerges from the ribosome.
Once translation is well underway (after 30–50 amino acids have been added), one particular codon tends to be chosen each
time its amino acid is called for. Presumably this now increases the efficiency (speed) of translation.
Most organisms have more than the 61 genes needed to encode a tRNA for each of the 61 codons (we have 270 tRNA genes).
The presence of multiple genes for tRNAs with an identical anticodon increases the concentration of tRNAs able to bind a
particular codon. Messenger RNAs — especially those of active genes — tend to favor codons that correspond to abundant
tRNAs carrying the anticodon.
Codon bias even extends to pairs of codons: wherever a human protein contains the amino acids Ala-Glu, the gene encoding those
amino acids is seven times as likely to use the codons GCAGAG rather than the synonymous GCCGAA. Codon bias is exploited
by the biotechnology industry to improve the yield of the desired product. The ability to manipulate codon bias may also usher in a
era of safer vaccines.

Quality Control
Defective mRNA molecules can be produced by mutations in the gene as well as errors introduced during transcription (albeit at a
remarkably low rate). In addition to producing mRNAs with incorrect codons for amino acids, these errors can produce mRNA
molecules that have

6.4.3 https://bio.libretexts.org/@go/page/4836
 Premature Termination Codons (PTCs); that is, the introduction of a STOP codon before the normal end of the message.
Translation of these mRNAs produces a truncated protein that is probably ineffective and may be harmful. The problem can
sometimes be solved by Nonsense-Mediated mRNA Decay (NMD).
no STOP codon. These produce "nonstop" transcripts. The problem can be solved by Nonstop mRNA Decay.

Nonsense-Mediated mRNA Decay (NMD)

Premature termination codons (PTCs) may be generated by "nonsense" mutations, frameshifts, and RNA processing (intron
removal) errors. They are also an inevitable consequence of creating antigen receptors on B cells and T cells.
Mechanisms
During RNA processing within the nucleus, protein complexes are added at each spot where adjacent exons are spliced
together. (These are important signals for exporting the mRNA to the cytoplasm.)
In the cytoplasm, as the ribosome moves down the mRNA, these complexes are removed (and sent back to the nucleus for
reuse).
If the ribosome encounters a premature termination codon, the final exon-exon tag(s) are not removed, and this marks the
defective mRNA for destruction (in P bodies).
Mutations that introduce premature termination codons are responsible for some cases of such inherited human diseases as cystic
fibrosis and Duchenne muscular dystrophy (DMD).
A drug, designated PTC124 or ataluren, causes the ribosome to skip over PTCs while still enabling normal termination of
translation. PTC124 has shown promise in animal models of cystic fibrosis and DMD and phase II clinical trials are now being
conducted on humans.

Nonstop mRNA Decay

Nonstop transcripts occur when there is no STOP codon in the message. As a result the ribosome is unable to recruit the release
factors needed to leave the mRNA. Nonstop transcripts are formed during RNA processing, e.g., by having the poly(A) tail put on
before the STOP codon is reached.
Mechanisms
Eukaryotes and bacteria handle the problem of no STOP codon differently.
In eukaryotes, when the ribosome stalls at the end of the poly(A) tail, proteins are recruited to release the ribosome for reuse
and to degrade the faulty message.
In bacteria, a special RNA molecule — called tmRNA saves the day. It is called tmRNA because it has the properties of both a
transfer RNA and a messenger RNA. The transfer part adds alanine to the A site on the ribosome. The ribosome then moves on
to the messenger part which encodes 10 amino acids that target the molecule for destruction (and releases the ribosome for
reuse).

Regulation of Translation
The expression of most genes is controlled at the level of their transcription. Transcription factors (proteins) bind to promoters and
enhancers turning on (or off) the genes they control. However, gene expression can also be controlled at the level of translation.

By General RNA-Degradation Machinery

P bodies
The cytosol of eukaryotes contains protein complexes that compete with ribosomes for access to mRNAs. As these increase their
activity, they sequester mRNAs in larger aggregates called P bodies (for "processing bodies", but this processing should not be
confused with the processing of pre-mRNA to mature mRNA that occurs in the nucleus).
These protein complexes break down the mRNA by
removing its "cap"
removing its poly(A) tail
degrading the remaining message (nibbling away in the 5' -> 3' direction)
What controls the dynamic balance between ribosomes and P bodies for access to mRNAs remains to be learned. But this
mechanism provides for

6.4.4 https://bio.libretexts.org/@go/page/4836
 destruction of "bad" mRNAs (e.g., those with premature STOP codons
turnover of mRNAs thus increasing the flexibility of gene expression in the cell
Exosomes
These are hollow macromolecular complexes with two openings. They take in unfolded RNA molecules and degrade them in the 3'
-> 5' direction. (In neither structure nor function do these exosomes resemble the exosomes involved in antigen presentation that
unfortunately share the same name.)

By MicroRNAs (miRNAs)
Here small RNA molecules bind to a complementary portion in the 3'-UTR of the mRNA and prevent it from being translated by
ribosomes and/or trigger its destruction. Both these activities take place in P bodies.

By Riboswitches
It turns out that the regulation of the level of certain metabolites is controlled by riboswitches. A riboswitch is a part of a molecule
of messenger RNA (mRNA) with a specific binding site for the metabolite (or a close relative).
Examples:
If thiamine pyrophosphate (the active form of thiamine [vitamin B1]) is available in the culture medium of E. coli,
It binds to a messenger RNA whose protein product is an enzyme needed to synthesize thiamine from the ingredients in
minimal medium.
Binding induces an allosteric shift in the structure of the mRNA so that it can no longer bind to a ribosome and thus cannot
be translated into the enzyme.
E. coli no longer wastes resources on synthesizing a vitamin that is available preformed.
A thiamine pyrophosphate riboswitch has also been found in plants, archaea, and Neurospora. The one in Neurospora regulates
genes involved in vitamin B1 metabolism by alternative splicing of their transcripts. (Other riboswitches act on transcription
rather than translation
If vitamin B12 is present in the cell, it binds to the mRNA which encodes a protein needed to import the vitamin from the
culture medium. This, too, induces an allosteric shift in the mRNA that prevents it from binding a ribosome. E. coli no longer
wastes resources on synthesizing a transporter for a vitamin that it already has enough of.
Some Gram-positive bacteria (E. coli is Gram-negative) control the level of a sugar needed to synthesize their cell wall with a
riboswitch. In this case, as the concentration of the sugar builds up, it binds to the messenger RNA (mRNA) whose product is
the enzyme that makes the sugar. This causes the mRNA to self-destruct so production of the enzyme — and thus the sugar —
ceases.
It has been suggested that these regulatory mechanisms, which do not involve any protein, are a relict from an "RNA world".

This page titled 6.4: The Translation of RNA into Proteins is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by
John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

6.4.5 https://bio.libretexts.org/@go/page/4836
6.5: RNA Editing
Occasionally researches encounter a gene with a sequence of nucleotides that does not match exactly that in its RNA product:
messenger RNA (mRNA)
ribosomal RNA (rRNA)
transfer RNA (tRNA)
microRNA (miRNA)
If the product is mRNA, some of the codons in the open reading frame (ORF) of the gene specify different amino acids from those
in the protein translated from the mRNA of the gene.
The reason is RNA editing: the alteration of the sequence of nucleotides in the RNA
after it has been transcribed from DNA but
before it is translated into protein
RNA editing occurs by two distinct mechanisms:
Substitution Editing: chemical alteration of individual nucleotides (the equivalent of point mutations).
These alterations are catalyzed by enzymes that recognize a specific target sequence of nucleotides (much like restriction
enzymes):
cytidine deaminases that convert a C in the RNA to uracil (U);
adenosine deaminases that convert an A to inosine (I), which the ribosome translates as a G. Thus a CAG codon (for Gln)
can be converted to a CGG codon (for Arg).

Insertion/Deletion Editing: insertion or deletion of nucleotides in the RNA.

These alterations are mediated by guide RNA molecules that
base-pair as best they can with the RNA to be edited and
serve as a template for the addition (or removal) of nucleotides in the target

Substitution Editing
The human APOB gene

Figure 6.5.1 The Human APOB Gene

Humans have a single locus encoding the APOB gene.
It contains 29 exons (separated by 28 introns).
The exons contain a total of 4564 codons.
Codon 2153 is CAA, which is a codon for the amino acid glutamine (Gln).
The gene is expressed in cells of both the liver and the intestine.
In both locations, transcription produces a pre-messenger RNA that must be spliced to produce the mRNA to be translated into
protein.

6.5.1 https://bio.libretexts.org/@go/page/4837
 In the Liver. Here the process occurs normally producing apolipoprotein B-100 — a protein containing 4,563 amino acids —
that is essential for the transport of cholesterol and other lipids in the blood.
In the Intestine
In the cells of the intestine, an additional step of pre-mRNA processing occurs: the chemical modification of the C
nucleotide in Codon 2153 (CAA) into a U.
This RNA editing changes the codon from one encoding the amino acid glutamine (Gln) to a STOP codon (UAA)
The modification is catalyzed by the enzyme cytidine deaminase that
recognizes the sequence of the RNA at that one place in the molecule and
catalyzes the deamination of C thus forming U.
Translation of the mRNA stops at codon #2153 forming apolipoprotein B-48 — a protein containing 2152 amino acids —
that aids in the absorption of dietary lipids from the contents of the intestine.
DNA can also be edited. B cells express another cytidine deaminase (called activation-induced deaminase or AID) that is
essential for both class switch recombination (CSR) and somatic hypermutation (SHM) of antibody genes. Humans with disabling
mutations in the gene for this enzyme produce only IgM antibodies. However, here the enzyme is acting on DNA, not RNA. In
attempting to repair the mismatch formed (dC•dG converted to dU•dG), the normal DNA repair machinery of the cell produces
CSR or SHM as the situation warrants. (This process is also responsible for the occasional aberrant translocation of the heavy-chain
gene segments to a proto-oncogene. The result is a B-cell cancer — a lymphoma or leukemia.)

Other examples of substitution editing

Some mRNAs, tRNAs, and rRNAs in both the mitochondria and chloroplasts of plants;
mRNAs encoding subunits of some receptors of neurotransmitters in the mammalian brain, e.g.,
the AMPA receptor for Glu
a serotonin receptor
a tRNA in the mitochondria of the duckbill platypus

Insertion/Deletion Editing
The gene in mitochondria of Trypanosoma brucei

Figure 6.5.2 Insertion/ Deleting Editing

Several genes encoded in the mitochondrial DNA of this species (the cause of sleeping sickness in humans) encode transcripts that
must be edited to make the mRNA molecules that will be translated into protein.
Editing requires a special class of RNA molecules called guide RNA (gRNA).
These small molecules have sequences that are complementary to the region around the site to be edited. The guide RNA base-
pairs — as best it can — with this region. Note that in addition to the usual purine-pyrimidine pairing of C-G and A-U, G-U base-
pairing can also occur.
Because of the lack of precise sequence complementarity, bulges occur either
in the guide RNA where, usually, there are As not found in the transcript to be edited (as shown here) or
in the transcript to be edited.
The bulges are eliminated by cutting the backbone of the shorter molecule and inserting complementary bases.

6.5.2 https://bio.libretexts.org/@go/page/4837
 In the first case (shown here) this produces insertions (here of Us)
In the second case (not shown) this produces deletions.
Note that in the example shown here, the insertion of 4 nucleotides has created a frameshift so that the amino acids encoded
downstream (after Val) in the edited RNA are entirely different from those specified by the gene itself.

Other examples of insertion/deletion editing

Insertion/deletion editing has also been found occur with
mRNA, rRNA, and tRNA transcripts in the mitochondria of the slime mold Physarum polycephalum
in measles virus transcripts

Why RNA Editing?

Good question. Some possibilities:
So RNA editing appears to be here to stay. In fact, defects in RNA editing are associated with some human cancers as well as
with amyotrophic lateral sclerosis (ALS — "Lou Gehrig's disease").

This page titled 6.5: RNA Editing is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

6.5.3 https://bio.libretexts.org/@go/page/4837
6.6: Expressed Sequence Tags
Only a very small percentage (1.2% in humans) of the DNA in vertebrate genomes encodes proteins (the "proteome") because the
exons of most genes are separated by much-longer introns between our genes lie vast amounts of DNA much of which appears to
regulate the expression of our genes but is not transcribed and translated into a protein product. So even when the complete
sequence of a genome is known, it is often difficult to spot particular genes (open reading frames or ORFs).
One approach to solving the problem is to examine a transcriptome of the organism. Most commonly this is defined as: All the
messenger RNA (mRNA) molecules transcribed from the genome. It is "a" transcriptome, not "the" transcriptome, because what
genes are transcribed in a cell depends on the kind of cell (e.g., liver cell vs. lymphocyte) and what the cell is doing at that time,
e.g.,
getting ready to divide by mitosis;
responding to the arrival of a hormone or cytokine;
getting ready to secrete a protein product.

Expressed Sequence Tags (ESTs)

ESTs are short (200–500 nucleotides) DNA sequences that can be used to identify a gene that is being expressed in a cell at a
particular time.
The Procedure:
Isolate the messenger RNA (mRNA) from a particular tissue (e.g., liver)
Treat it with reverse transcriptase. Reverse transcriptase is a DNA polymerase that uses RNA as its template. Thus it is able to
make genetic information flow in the reverse (RNA ->DNA) of its normal direction (DNA -> RNA).
This produces complementary DNA (cDNA). Note that cDNA differs from the normal gene in lacking the intron sequences.
Sequence 200–500 nucleotides at both the 5′ and 3′ ends of each cDNA.
Examine the database of the organism's genome to find a matching sequence.

This page titled 6.6: Expressed Sequence Tags is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

6.6.1 https://bio.libretexts.org/@go/page/4838
6.7: Ribosomal RNA (rRNA) Gene Cluster

Figure 6.7.1 Transcription of DNA encoding

The above picture shows an electron micrograph (26,500x) showing transcription of the DNA encoding ribosomal RNA (rRNA)
molecules in the nucleolus of a developing egg cell of the spotted newt.
Eukaryotes have several hundred identical genes encoding ribosomal RNA.
The long filaments (green arrow) are DNA molecules coated with proteins. The fibers extending in clusters from the main axes are
molecules of ribosomal RNA which will be used in the construction of the cell's ribosomes.
Note how transcription begins at one end of each gene, with the RNA molecules getting longer (red arrow) as they proceed toward
completion.
Note also the large number (up to 100) of RNA molecules that are transcribed simultaneously from each gene.
The portions of DNA bare of RNA appear to be genetically inactive. (Courtesy of O. L. Miller, Jr., and Barbara R. Beatty, Biology
Division, Oak Ridge National Laboratory.)

This page titled 6.7: Ribosomal RNA (rRNA) Gene Cluster is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by
John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

6.7.1 https://bio.libretexts.org/@go/page/4839
 CHAPTER OVERVIEW
Unit 7: Cell Division
7.1: Chromosomes
7.2: The Cell Cycle
7.3: Mitosis
7.4: Polyploidy
7.5: Endoreplication
7.6: Sex Chromosomes
7.7: Meiosis

Thumbnail: Life cycle of the cell. (CC BY-SA 4.0; BruceBlaus).

This page titled Unit 7: Cell Division is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1
7.1: Chromosomes
In eukaryotes, chromosomes consist of a single molecule of DNA associated with many copies of 5 kinds of histones. Histones
are proteins rich in lysine and arginine residues and thus positively-charged. For this reason they bind tightly to the negatively-
charged phosphates in DNA. Cchromosomes have a small number of copies of many different kinds of non-histone proteins. Most
of these are transcription factors that regulate which parts of the DNA will be transcribed into RNA.

Structure
For most of the life of the cell, chromosomes are too elongated and tenuous to be seen under a microscope. However, before a cell
is ready to divide by mitosis, each chromosome is duplicated (during S phase of the cell cycle). As mitosis begins, the duplicated
chromosomes condense into short (~ 5 µm) structures which can be stained and easily observed under the light microscope. These
duplicated chromosomes are called dyads.

Figure 7.1.1 Dyads

When first seen, the duplicates are held together at their centromeres. In humans, the centromere contains 1–10 million base pairs
of DNA. Most of this is repetitive DNA: short sequences (e.g., 171 bp) repeated over and over in tandem arrays. While they are
still attached, it is common to call the duplicated chromosomes sister chromatids, but this should not obscure the fact that each is a
bona fide chromosome with a full complement of genes.
The kinetochore is a complex of >80 different proteins that forms at each centromere and serves as the attachment point for the
spindle fibers that will separate the sister chromatids as mitosis proceeds into anaphase. The shorter of the two arms extending from
the centromere is called the p arm; the longer is the q arm. Staining with the trypsin-giemsa method reveals a series of alternating
light and dark bands called G bands. G bands are numbered and provide "addresses" for the assignment of gene loci.

Chromosome Numbers
All animals have a characteristic number of chromosomes in their body cells called the diploid (or 2n) number. These occur as
homologous pairs, one member of each pair having been acquired from the gamete of one of the two parents of the individual
whose cells are being examined. The gametes contain the haploid number (n) of chromosomes. In plants, the haploid stage takes
up a larger part of its life cycle.
Table 7.1.1: Diploid numbers of some commonly studied organisms
Homo sapiens (human) 46

Mus musculus (house mouse) 40

Drosophila melanogaster (fruit fly) 8

Caenorhabditis elegans (microscopic roundworm) 12

Saccharomyces cerevisiae (budding yeast) 32

Arabidopsis thaliana (plant in the mustard family) 10

Xenopus laevis (South African clawed frog) 36

Canis familiaris (domestic dog) 78

Gallus gallus (chicken) 78

Zea mays (corn or maize) 20

Muntiacus reevesi (the Chinese muntjac, a deer) 23

7.1.1 https://bio.libretexts.org/@go/page/4845
 Muntiacus muntjac (its Indian cousin) 6

Myrmecia pilosula (an ant) 2

Parascaris equorum var. univalens (parasitic roundworm) 2

Cambarus clarkii (a crayfish) 200

Equisetum arvense (field horsetail, a plant) 216

Karyotypes
The complete set of chromosomes in the cells of an organism is its karyotype. It is most often studied when the cell is at metaphase
of mitosis when all the chromosomes are present as dyads. The karyotype of the human female contains 23 pairs of homologous
chromosomes: 22 pairs of autosomes and an additional 1 pair of X chromosomes. In contrast, the karyotype of the human male
contains the same 22 pairs of autosomes with one X chromosome and one Y chromosome. A gene on the Y chromosome
designated SRY is the master switch for making a male. Both X and Y chromosomes are called the sex chromosomes.

Figure 7.1.2: Human Karyotype

Above is a human karyotype (of which sex?). It differs from a normal human karyotype in having an extra #21 dyad. As a result,
this individual suffered from a developmental disorder called Down Syndrome. The inheritance of an extra chromosome, is called
trisomy, in this case trisomy 21. It is an example of aneuploidy

Translocations
Karyotype analysis can also reveal translocations between chromosomes. A number of these are associated with cancers, for
example
the Philadelphia chromosome (Ph1) formed by a translocation between chromosomes 9 and 22 and a cause of Chronic
Myelogenous Leukemia (CML)
a translocation between chromosomes 8 and 14 that causes Burkitt's lymphoma
a translocation between chromosomes 18 and 14 that causes B-cell leukemia

Fluorescence in situ Hybridization (FISH)

Figure 7.1.3 provides dramatic evidence of the truth of the story of chromosomes. A piece of single-stranded DNA was prepared
that was complementary to the DNA of the human gene encoding the enzyme muscle glycogen phosphorylase. A fluorescent
molecule was attached to this DNA. The dyads in a human cell were treated to denature their DNA; that is, to make the DNA
single-stranded. When this preparation was treated with the fluorescent DNA, the complementary sequences found and bound each
other. This produced a fluorescent spot close to the centromere of each sister chromatid of two homologous dyads (of chromosome
11, upper right). This analytical procedure, which here revealed the gene locus for the muscle glycogen phosphorylase gene, is
called fluorescence in situ hybridization or FISH.

7.1.2 https://bio.libretexts.org/@go/page/4845
 Figure 7.1.3: Location of the gene for muscle glycogen phosphorylase on human chromosome 11 courtesy of David C. Ward

DNA Content
The molecule of DNA in a single human chromosome ranges in size from 50 x 106 nucleotide pairs in the smallest chromosome
(stretched full-length this molecule would extend 1.7 cm) up to 250 x 106nucleotide pairs in the largest (which would extend 8.5
cm). Stretched end-to-end, the DNA in a single human diploid cell would extend over 2 meters. In the intact chromosome,
however, this molecule is packed into a much more compact structure. The packing reaches its extreme during mitosis when a
typical chromosome is condensed into a structure about 5 µm long (a 10,000-fold reduction in length).

7.1: Chromosomes is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

7.1.3 https://bio.libretexts.org/@go/page/4845
7.2: The Cell Cycle
A eukaryotic cell cannot divide into two, the two into four, etc. unless two processes alternate:
doubling of its genome (DNA) in S phase (synthesis phase) of the cell cycle;
halving of that genome during mitosis (M phase).

Figure 7.2.1 Cell Cycle: The cell cycle consists of: G1 = growth and preparation of the chromosomes for replication, S = synthesis
of DNA and duplication of the centrosome, G2 = preparation for M = mitosis. When a cell is in any phase of the cell cycle other
than mitosis, it is often said to be in interphase.

Control of the Cell Cycle

The passage of a cell through the cell cycle is controlled by proteins in the cytoplasm. Among the main players in animal cells are:
Their levels in the cell rise and fall with the stages of the cell cycle.
Their levels in the cell remain fairly stable, but each must bind the appropriate cyclin (whose levels fluctuate) in order to be
activated. They add phosphate groups to a variety of protein substrates that control processes in the cell cycle.
The anaphase-promoting complex (APC). (The APC is also called the cyclosome, and the complex is often designated as the
APC/C.) The APC/C
triggers the events leading to destruction of cohesin (as described below) thus allowing the sister chromatids to separate
degrades the mitotic (B) cyclins

Steps in the cycle

A rising level of G1-cyclins bind to their Cdks and signal the cell to prepare the chromosomes for replication.
A rising level of S-phase promoting factor (SPF) — which includes A cyclins bound to Cdk2 — enters the nucleus and
prepares the cell to duplicate its DNA (and its centrosomes).
As DNA replication continues, cyclin E is destroyed, and the level of mitotic cyclins begins to rise (in G2).
Translocation of M-phase promoting factor (the complex of mitotic [B] cyclins with the M-phase Cdk [Cdk1]) into the
nucleus initiates
assembly of the mitotic spindle
breakdown of the nuclear envelope
cessation of all gene transcription
condensation of the chromosomes
These events take the cell to metaphase of mitosis.
At this point, the M-phase promoting factor activates the anaphase-promoting complex (APC/C) which
allows the sister chromatids at the metaphase plate to separate and move to the poles (= anaphase), completing mitosis.

Separation of the sister chromatids depends on the breakdown of the cohesin that has been holding them together. It works like
this.
Cohesin breakdown is caused by a protease called separase (also known as separin).
Separase is kept inactive until late metaphase by an inhibitory chaperone called securin.

7.2.1 https://bio.libretexts.org/@go/page/4846
 Anaphase begins when the anaphase promoting complex (APC/C) destroys securin (by tagging it with ubiquitin for deposit
in a proteasome) thus ending its inhibition of separase and allowing
separase to break down cohesin

destroys B cyclins. This is also done by attaching them to ubiquitin which targets them for destruction by
proteasomes.
turns on synthesis of G1 cyclins (D) for the next turn of the cycle.
degrades geminin, a protein that has kept the freshly-synthesized DNA in S phase from being re-replicated before
mitosis.

This is only one of the mechanisms by which the cell ensures that every portion of its genome is copied once — and only once
— during S phase

Some cells deliberately cut the cell cycle short allowing repeated S phases without completing mitosis and/or cytokinesis. This is
called endoreplication.

Meiosis and the Cell Cycle

The special behavior of the chromosomes in meiosis I requires some special controls. Nonetheless, passage through the cell cycle
in meiosis I (as well as meiosis II, which is essentially a mitotic division) uses many of the same players, e.g., MPF and APC. (In
fact, MPF is also called maturation-promoting factor for its role in meiosis I and II of developing oocytes.

Quality Control of the Cell Cycle

The cell has several systems for interrupting the cell cycle if something goes wrong.
DNA damage checkpoints. These sense DNA damage both before the cell enters S phase (a G1 checkpoint) as well as after S phase
(a G2 checkpoint). Damage to DNA before the cell enters S phase inhibits the action of Cdk2 thus stopping the progression of the
cell cycle until the damage can be repaired. If the damage is so severe that it cannot be repaired, the cell self-destructs by apoptosis.
Damage to DNA after S phase (the G2 checkpoint), inhibits the action of Cdk1 thus preventing the cell from proceeding from G2
to mitosis. A check on the successful replication of DNA during S phase. If replication stops at any point on the DNA, progress
through the cell cycle is halted until the problem is solved.
Spindle checkpoints. Some of these that have been discovered to detect any failure of spindle fibers to attach to kinetochores and
arrest the cell in metaphase until all the kinetochores are attached correctly. They detect improper alignment of the spindle itself
and block cytokinesis. Furthermore, they trigger apoptosis if the damage is irreparable. All the checkpoints examined require the
services of a complex of proteins. Mutations in the genes encoding some of these have been associated with cancer; that is, they are
oncogenes. This should not be surprising since checkpoint failures allow the cell to continue dividing despite damage to its
integrity.

Examples of checkpoints
p53
The p53 protein senses DNA damage and can halt progression of the cell cycle in G1 (by blocking the activity of Cdk2). Both
copies of the p53 gene must be mutated for this to fail so mutations in p53 are recessive, and p53 qualifies as a tumor suppressor
gene.
The p53 protein is also a key player in apoptosis, forcing "bad" cells to commit suicide. So if the cell has only mutant versions of
the protein, it can live on — perhaps developing into a cancer. More than half of all human cancers do, in fact, harbor p53
mutations and have no functioning p53 protein.

This page titled 7.2: The Cell Cycle is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

7.2.2 https://bio.libretexts.org/@go/page/4846
7.3: Mitosis

Figure 7.3.1: DNA released from human chromosome courtesy J. R. Paulson and U. C. Laemmli
This image provides a graphic illustration of the problem. It shows a bit (no more than 3%) of the single molecule of DNA released
from a single human chromosome. (The chromosome was treated to remove its histones). Remembering that this is 3% of the DNA
of only one of the 46 chromosomes in the human diploid cell, you can appreciate the problem faced by the cell of how to separate
without error these great lengths of DNA without creating horrible tangles.
The solution to this problem is:
1. Duplicate each chromosome during the S phase of the cell cycle.
2. This produces dyads, each made up of 2 identical sister chromatids. These are held together by a ring of proteins called cohesin.
3. Condense the chromosomes into a compact form. This requires ATP and protein complexes called condensins.
4. Separate the sister chromatids and
5. Distribute these equally between the two daughter cells.

Figure 7.3.2: Kinetochore

This page titled 7.3: Mitosis is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

7.3.1 https://bio.libretexts.org/@go/page/4847
7.4: Polyploidy
Cells (and their owners) are polyploid if they contain more than two haploid (n) sets of chromosomes; that is, their chromosome
number is some multiple of n greater than the 2n content of diploid cells. For example, triploid (3n) and tetraploid cell (4n) cells
are polyploid.

Polyploidy in plants
Polyploidy is very common in plants, especially in angiosperms. From 30% to 70% of today's angiosperms are thought to be
polyploid. Species of coffee plant with 22, 44, 66, and 88 chromosomes are known. This suggests that the ancestral condition was a
plant with a haploid (n) number of 11 and a diploid (2n) number of 22, from which evolved the different polyploid descendants. In
fact, the chromosome content of most plant groups suggests that the basic angiosperm genome consists of the genes on 7–11
chromosomes. Domestic wheat, with its 42 chromosomes, is probably hexaploid (6n), where n (the ancestral haploid number) was
7.
Some other examples:

Probable ancestral haploid Chromosome

Plant Ploidy level
number number

domestic oat 7 42 6n

peanut 10 40 4n

sugar cane 10 80 8n

banana 11 22, 33 2n, 3n

white potato 12 48 4n

tobacco 12 48 4n

cotton 13 52 4n

apple 17 34, 51 2n, 3n

Polyploid plants not only have larger cells but the plants themselves are often larger. This has led to the deliberate creation of
polyploid varieties of such plants as watermelons, marigolds, and snapdragons.

Origin of Polyploidy
Polyploidy has occurred often in the evolution of plants. The process can begin if diploid (2n) gametes are formed. These can arise
in at least two ways.
The gametes may be formed by mitosis instead of meiosis.
Plants, in contrast to animals, form germ cells (sperm and eggs) from somatic tissues. If the chromosome content of a precursor
somatic cell has accidentally doubled (e.g., as a result of passing through S phase of the cell cycle without following up with
mitosis and cytokinesis), then gametes containing 2n chromosomes are formed.
Polyploidy also occurs naturally in certain plant tissues.
As the endosperm (3n) develops in corn (maize) kernels (Zea mays), its cells undergo successive rounds (as many as 5) of
endoreplication producing nuclei that range as high as 96n.
When rhizobia infect the roots of their legume host, they induce the infected cells to undergo endoreplication producing cells
that can become 128n (from 6 rounds of endoreplication).
Polyploidy can also be induced in the plant-breeding laboratory by treating dividing cells with colchicine. This drug disrupts
microtubules and thus prevents the formation of a spindle. Consequently, the duplicated chromosomes fail to separate in mitosis.
Onion cells exposed to colchicine for several days may have over 1000 chromosomes inside.

Polyploidy and Speciation

When a newly-arisen tetraploid (4n) plant tries to breed with its ancestral species (a backcross), triploid offspring are formed.
These are sterile because they cannot form gametes with a balanced assortment of chromosomes. However, the tetraploid plants

7.4.1 https://bio.libretexts.org/@go/page/4848
can breed with each other. So in one generation, a new species has been formed. Polyploidy even allows the formation of new
species derived from different ancestors.
In 1928, the Russian plant geneticist Karpechenko produced a new species by crossing a cabbage with a radish. Although
belonging to different genera (Brassica and Raphanus respectively), both parents have a diploid number of 18. Fusion of their
respective gametes (n=9) produced mostly infertile hybrids. However, a few fertile plants were formed, probably by the
spontaneous doubling of the chromosome number in somatic cells that went on to form gametes (by meiosis). Thus these contained
18 chromosomes — a complete set of both cabbage (n=9) and radish (n=9) chromosomes. Fusion of these gametes produced
vigorous, fully-fertile, polyploid plants with 36 chromosomes. (They had the roots of the cabbage and the leaves of the radish.)
These plants could breed with each other, but not with either the cabbage or radish ancestors, so Karpechenko had produced a new
species. The process also occurs in nature. Three species in the mustard family (Brassicaceae) appear to have arisen by
hybridization and polyploidy from three other ancestral species:

B. oleracea (cabbage, broccoli, etc.) hybridized with B. nigra (black mustard) → B. carinata (Abyssinian mustard).
B. oleracea x B. rapa (turnips) → B. napus (rutabaga)
B. nigra x B. rapa → B. juncea (leaf mustard)
Modern wheat and perhaps some of the other plants listed in the table above have probably evolved in a similar way.

Polyploidy in Animals
Polyploidy is much rarer in animals. It is found in some insects, fishes, amphibians, and reptiles. Until recently, no polyploid
mammal was known. However, the 23 September 1999 issue of Nature reported that a polyploid (tetraploid; 4n = 102) rat has
been found in Argentina. Polyploid cells are larger than diploid ones; not surprising in view of the increased amount of DNA in
their nucleus. The liver cells of the Argentinian rat are larger than those of its diploid relatives, and its sperm are huge in
comparison. Normal mammalian sperm heads contain some 3.3 picograms (10-12 g) of DNA; the sperm of the rat contains 9.2 pg.
Although only one mammal is known to have all its cells polyploid, many mammals have polyploid cells in certain of their organs,
e.g, the liver.

This page titled 7.4: Polyploidy is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

7.4.2 https://bio.libretexts.org/@go/page/4848
7.5: Endoreplication
Endoreplication is the replication of DNA during the S phase of the cell cycle without the subsequent completion of mitosis and/or
cytokinesis. Endoreplication is also known as endoreduplication. Endoreplication occurs in certain types of cells in both animals
and plants. There are several variations:
replication of DNA with completion of mitosis, but no cytokinesis.
repeated replication of DNA without forming new nuclei in telophase. This can result in:
1. Polyploidy: the replicated chromosomes retain their individual identity.
2. Polyteny: the replicated chromosomes remain in precise alignment forming "giant" chromosomes.
3. various intermediate conditions between 1 and 2

Figure 7.5.1 Polytene Chromosomes courtesy of B. P. Kaufmann

The photomicrograph shows the polytene chromosomes in a salivary gland cell of a Drosophila melanogaster larva. Such
chromosomes are found in other large, active cells as well.
Each of Drosophila's 4 pairs of chromosomes has undergone 10 rounds of DNA replication.
The maternal and paternal homologs — as well as all their duplicates — are aligned in exact register with each other.
So each chromosome consists of a cable containing 2048 identical strands of DNA.
These are so large that they can be seen during interphase; even with a low-power light microscope.

Function of polyteny
The probable answer: gene amplification. Having multiple copies of genes permits a high level of gene expression; that is,
abundant transcription and translation to produce the gene products. This would account for polyteny being associated with large,
metabolically active cells (like salivary glands). Polytene chromosomes are subdivided into some 5,000 dense bands separated by
light interbands. The bands are further subdivided into:
dark bands of heterochromatin where the DNA is tightly compacted and there is little gene transcription;
gray bands of euchromatin where the DNA is more loosely compacted and there is active gene transcription.

7.5.1 https://bio.libretexts.org/@go/page/4849
 Figure 7.5.3 Changes in puffing patterns of Chromosomes courtesy of Dr. Michael Ashburner, University of Cambridge
These eight photomicrographs () show the changes in the puffing pattern of equivalent segments of chromosome 3 in Drosophila
melanogaster over the course of some 20 hours of normal development.
Note that during this period, when the larvae were preparing to pupate, certain puffs formed, regressed, and formed again.
However, the order in which they did often differed. For example, in the larva, band 62E becomes active before 63E (c, d, and e),
but when pupation begins, the reverse is true (g, h).
In general, early puffs reflect the activation of genes encoding transcription factors. These proteins then bind to the promoters of
other genes, turning them on and causing a puff to appear at their loci.

This page titled 7.5: Endoreplication is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

7.5.2 https://bio.libretexts.org/@go/page/4849
7.6: Sex Chromosomes
The nuclei of human cells contain 22 autosomes and 2 sex chromosomes. In females, the sex chromosomes are the 2 X
chromosomes. Males have one X chromosome and one Y chromosome. The presence of the Y chromosome is decisive for
unleashing the developmental program that leads to a baby boy.

The Y Chromosome
In making sperm by meiosis, the X and Y chromosomes must separate in anaphase just as homologous autosomes do. This occurs
without a problem because, like homologous autosomes, the X and Y chromosome synapse during prophase of meiosis I. There is a
small region of homology shared by the X and Y chromosome and synapsis occurs at that region.

Figure 7.6.1 Synapsis of the X and Y chromosomes courtesy of C. Tease

This image, shows synapsis of the X and Y chromosomes of a mouse during prophase of meiosis I. Crossing over occurs in two
regions of pairing, called the pseudoautosomal regions. These are located at opposite ends of the chromosome.

The Pseudoautosomal Regions

The pseudoautosomal regions get their name because any genes located within them (so far only 9 have been found) are inherited
just like any autosomal genes. Males have two copies of these genes: one in the pseudoautosomal region of their Y, the other in the
corresponding portion of their X chromosome. So males can inherit an allele originally present on the X chromosome of their
father and females can inherit an allele originally present on the Y chromosome of their father.

Figure 7.6.2 Human Y Chromosome

Genes outside the pseudoautosomal regions
Although 95% of the Y chromosome lies between the pseudoautosomal regions, only 27 different functional genes have been
found here. Over half of this region is genetically-barren heterochromatin. Of the 27 genes found in the euchromatin, some encode
proteins used by all cells. The others encode proteins that appear to function only in the testes. A key player in this latter group is
SRY.

SRY
SRY (for sex-determining region Y) is a gene located on the short (p) arm just outside the pseudoautosomal region. It is the master
switch that triggers the events that converts the embryo into a male. Without this gene, you get a female instead.
What is the evidence?
1. On very rare occasions aneuploid humans are born with such karyotypes as XXY, XXXY, and even XXXXY. Despite their
extra X chromosomes, all these cases are male.
2. This image shows two mice with an XX karyotype (and thus they should be female). However, as you may be able to see, they
have a male phenotype. This is because they are transgenic for SRY. Fertilized XX eggs were injected with DNA carrying the
SRY gene.

7.6.1 https://bio.libretexts.org/@go/page/4850
 Figure 7.6.3 Transgenic mice courtesy of Robin Lovell-Badge from Nature 351:117, 1991
Although these mice have testes, male sex hormones, and normal mating behavior, they are sterile.
3. Another rarity: XX humans with testicular tissue because a translocation has placed the SRY gene on one of the X chromosomes
4. Still another rarity that demonstrates the case: women with an XY karyotype who, despite their Y chromosome, are female
because of a destructive mutation in SRY.
In 1996, a test based on a molecular probe for SRY was used to ensure that potential competitors for the women's Olympic events in
Atlanta had no SRY gene. But because of possibilities like that in case 4, this testing is no longer used to screen female Olympic
athletes.

The X Chromosome
The X chromosome carries nearly 1,000 genes but few, if any, of these have anything to do directly with sex. However, the
inheritance of these genes follows special rules. These arise because:
males have only a single X chromosome
almost all the genes on the X have no counterpart on the Y; thus
any gene on the X, even if recessive in females, will be expressed in males.
Genes inherited in this fashion are described as sex-linked or, more precisely, X-linked.

X-Linkage example
Hemophilia is a blood clotting disorder caused by a mutant gene encoding either
clotting factor VIII, causing hemophilia A or
clotting factor IX, causing hemophilia B.
Both genes are located on the X chromosome (shown here in red). With only a single X chromosome, males who inherit the
defective gene (always from their mother) will be unable to produce the clotting factor and suffer from difficult-to-control episodes
of bleeding. In heterozygous females, the unmutated copy of the gene will provide all the clotting factor they need. Heterozygous
females are called "carriers" because although they show no symptoms, they pass the gene on to approximately half their sons,
who develop the disease, and half their daughters, who also become carriers.

X Y

X XX XY

Xh XhX XhY

Women rarely suffer from hemophilia because to do so they would have to inherit a defective gene from their father as well as their
mother. Until recently, few hemophiliacs ever became fathers.

X-chromosome Inactivation (XCI)

Human females inherit two copies of every gene on the X chromosome, whereas males inherit only one (with some exceptions: the
9 pseudoautosomal genes and the small number of "housekeeping" genes found on the Y). But for the hundreds of other genes on
the X, are males at a disadvantage in the amount of gene product their cells produce? The answer is no, because females have only
a single active X chromosome in each cell.
During interphase, chromosomes are too tenuous to be stained and seen by light microscopy. However, a dense, stainable structure,
called a Barr body (after its discoverer) is seen in the interphase nuclei of female mammals. The Barr body is one of the X

7.6.2 https://bio.libretexts.org/@go/page/4850
chromosomes. Its compact appearance reflects its inactivity. So, the cells of females have only one functioning copy of each X-
linked gene — the same as males.

Figure 7.6.4 Genetic Mosaic due to XChromosome Inactivation

X-chromosome inactivation occurs early in embryonic development. In a given cell, which of a female's X chromosomes becomes
inactivated and converted into a Barr body is a matter of chance (except in marsupials like the kangaroo, where it is always the
father's X chromosome that is inactivated). After inactivation has occurred, all the descendants of that cell will have the same
chromosome inactivated. Thus X-chromosome inactivation creates clones with differing effective gene content. An organism
whose cells vary in effective gene content and hence in the expression of a trait, is called a genetic mosaic.

Mechanism of X-chromosome inactivation

Inactivation of an X chromosome requires a gene on that chromosome called XIST.
XIST is transcribed into a long noncoding RNA.
XIST RNA accumulates along the X chromosome containing the active XIST gene and proceeds to inactivate all (or almost all)
of the hundreds of other genes on that chromosome.
Barr bodies are inactive X chromosomes "painted" with XIST RNA.

The Sequence of Events in Mice

During the first cell divisions of the female mouse zygote, the XIST locus on the father's X chromosome is expressed so most of
his X-linked genes are silent.
By the time the blastocyst has formed, the silencing of the paternal X chromosome still continues in the trophoblast (which will
go on to form the placenta) but
in the inner cell mass (the ICM, which will go on to form the embryo) transcription of XIST ceases on the paternal X
chromosome allowing its hundreds of other genes to be expressed. The shut-down of the XIST locus is done by methylating
XIST regulatory sequences. So the pluripotent stem cells of the ICM express both X chromosomes.
However, as embryonic development proceeds, X-chromosome inactivation begins again. But this time it is entirely random.
There is no predicting whether it will be the maternal X or the paternal X that is inactivated in a given cell.

Some genes on the X chromosome escape inactivation

What about those 18 genes that are found on the Y as well as the X? There should be no need for females to inactivate one copy of
these to keep in balance with the situation in males. And, as it turns out, these genes escape inactivation in females. Just how they
manage this is still under investigation.

X-chromosome Abnormalities
As we saw above, people are sometimes found with abnormal numbers of X chromosomes. Unlike most cases of aneuploidy, which
are lethal, the phenotypic effects of aneuploidy of the X chromosome are usually not severe.
Examples:
Females with but a single intact X chromosome (usually the one she got from her mother) in some (thus a genetic mosaic) or all
of her cells show a variable constellation of phenotypic traits called Turner syndrome. For those girls that survive to birth, the
phenotypic effects are generally mild because each cell has a single functioning X chromosome like those of XX females.
Number of Barr bodies = zero.
XXX, XXXX, XXXXX karyotypes: all females with mild phenotypic effects because in each cell all the extra X chromosomes
are inactivated. Number of Barr bodies = number of X chromosomes minus one.
Klinefelter's syndrome: people with XXY or XXXY karyotypes are males (because of their Y chromosome). But again, the
phenotypic effects of the extra X chromosomes are mild because, just as in females, the extra Xs are inactivated and converted

7.6.3 https://bio.libretexts.org/@go/page/4850
 into Barr bodies.

Sex Determination in Other Animals

Although the male fruit fly, Drosophila melanogaster, is X-Y, the Y chromosome does not dictate its maleness but rather the
absence of a second X. Furthermore, instead of females shutting down one X to balance the single X of the males — as we do —
male flies double the output of their single X relative to that of females.
In birds, moths, schistosomes, and some lizards, the male has two of the same chromosome (designated ZZ), whereas the female
has "heterogametic" chromosomes (designated Z and W). In chickens, a single gene on the Z chromosome (designated DMRT1),
when present in a double dose (ZZ), produces males while the presence of only one copy of the gene produces females (ZW).

Environmental Sex Determination

In some cold-blooded vertebrates such as
fishes
reptiles (e.g. certain snakes, lizards, turtles, and all crocodiles and alligators)
invertebrates (e.g. certain crustaceans),
sex is determined after fertilization — not by sex chromosomes deposited in the egg.
The choice is usually determined by the temperature at which early embryonic development takes place.
In some cases (e.g. many turtles and lizards), a higher temperature during incubation favors the production of females.
In other cases (e.g., alligators), a higher temperature favors the production of males.
Even in cases (e.g. some lizards) where there are sex chromosomes, a high temperature can convert a genotypic male (ZZ) into a
female.

Hermaphrodites
Hermaphrodites have both male and female sex organs. Many species of fish are hermaphroditic.
Some start out as one sex and then, in response to stimuli in their environment, switch to the other.
Other species have both testes and ovaries at the same time (but seldom fertilize themselves). However, populations of C. elegans
consist mostly of hermaphrodites and these only fertilize themselves.
Hermaphroditic fishes have no sex chromosomes.

This page titled 7.6: Sex Chromosomes is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

7.6.4 https://bio.libretexts.org/@go/page/4850
7.7: Meiosis
Mitosis produces two cells with the same number of chromosomes as the parent cell. Mitosis of a diploid cell (2n) produces two
diploid daughter cells. If two diploid cells went on to participate in sexual reproduction, their fusion would produce a tetraploid
(4n) zygote. The solution for this problem is Meiosis.

Meiosis
Meiosis is a process of cell division in eukaryotes characterized by:
two consecutive divisions: meiosis I and meiosis II
no DNA synthesis (no S phase) between the two divisions
the result: 4 cells with half the number of chromosomes of the starting cell, e.g., 2n → n
Fusion of two such cells produces a 2n zygote.

Meiosis in Animals
Used to produced the gametes: sperm and eggs

Meiosis in Plants
Used to produce spores. Spores are the start of the gametophyte generation which, in time, will produce gametes (by mitosis
because the starting cells are already haploid).

Meiosis I
Prophase of meiosis I (prophase I) is a more elaborate process than prophase of mitosis (and usually takes much longer).
Here is a brief overview of the process. A more detailed view is provided below.
When the chromosomes first become visible they are already doubled, each homologue having been duplicated during the
preceding S phase.
Result: pairs of homologous dyads each dyad consisting of two sister chromatids held together by a protein complex called
cohesin.
Pairing: Each pair of homologous dyads align lengthwise with each other.
Result: a tetrad. (These structures are sometimes referred to as bivalents because at this stage you cannot distinguish the
individual sister chromatids under the microscope.)
The two homologous dyads are held together by
one or more chiasmata (sing. = chiasma) which form between two nonsister chromatids at points where they have crossed
over.
the synaptonemal complex (SC), a complex assembly of proteins (including cohesin)

Figure 7.7.1 Meiosis I

At metaphase I, microtubules of the spindle fibers attach to the

7.7.1 https://bio.libretexts.org/@go/page/4851
 sister kinetochores of one homologue, pulling both sister chromatids toward one pole of the cell;
sister kinetochores of the other homologue pulling those sisters toward the opposite pole.
Result: one homologue is pulled above the metaphase plate, the other below. The chiasmata keep the homologues attached to each
other, and the cohesin keeps the sister chromatids together.
At anaphase I,
the cohesin between the chromosome arms breaks down allowing
the chiasmata to slip apart.
Result: the homologous dyads separate and migrate toward their respective poles.

Meiosis II
Chromosome behavior in meiosis II is like that of mitosis.
At metaphase II, spindle fibers attach one kinetochore of the dyad to one pole, the other to the opposite pole.
At anaphase II, the chromatids separate and (each now an independent chromosome) move to their respective poles.

Genetic Recombination
Meiosis not only preserves the genome size of sexually reproducing eukaryotes but also provides three mechanisms to diversify the
genomes of the offspring.

Crossing Over
Chiasmata represent points where earlier (and unseen) nonsister chromatids had swapped sections. The process is called crossing
over. It is reciprocal; the segments exchanged by each nonsister chromatid are identical (but may carry different alleles).
Each chromatid contains a single molecule of DNA. So the problem of crossing over is really a problem of swapping portions of
adjacent DNA molecules. It must be done with great precision so that neither chromatid gains or loses any genes. In fact, crossing
over has to be sufficiently precise that not a single nucleotide is lost or added at the crossover point if it occurs within a gene.
Otherwise a frameshift would result and the resulting gene would produce a defective product or, more likely, no product at all.

Figure 7.7.2 Single Chiasma courtesy of Prof. Bernard John

In the diagram above, only a single chiasma is shown. However, multiple chiasmata are commonly found (in humans the average
number of chiasmata per tetrad is just over two). In this photomicrograph, a tetrad of the grasshopper Chorthippus parallelus
shows 5 chiasmata.

Random Assortment
In meiosis I, the orientation of paternal and maternal homologues at the metaphase plate is random. Therefore, although each cell
produced by meiosis contains only one of each homologue, the number of possible combinations of maternal and paternal
homologues is 2n, where n = the haploid number of chromosomes. In this diagram, the haploid number is 3, and 8 (23) different
combinations are produced.

7.7.2 https://bio.libretexts.org/@go/page/4851
 Figure 7.7.3 Random Assortment
Random assortment of homologues in humans produces 223 (8,388,608) different combinations of chromosomes.
Furthermore, because of crossing over, none of these chromosomes is "pure" maternal or paternal. The distribution of recombinant
and non-recombinant sister chromatids into the daughter cells at anaphase II is also random.
So I think it is safe to conclude that of all the billions of sperm produced by a man during his lifetime (and the hundreds of eggs
that mature over the life of a woman), no two have exactly the same gene content.

Fertilization
By reducing the number of chromosomes from 2n to n,the stage is set for the union of two genomes. If the parents differ
genetically, new combinations of genes can occur in their offspring.
Taking these three mechanisms together, I think that it is safe to conclude that no two human beings have ever shared an identical
genome unless they had an identical sibling; that is a sibling produced from the same fertilized egg.
The behavior of chromosomes during meiosis (2n → n) and fertilization (n + n → 2n) provide the structural basis for Mendel's
rules of inheritance.

Prophase I — a detailed view

The lengthy and complex events of prophase I can be broken down into 5 stages.

Figure 7.7.4 Prophase I

Leptotene
All the chromosomes condense.
Pairing. Homologous dyads (pairs of sister chromatids) find each other and align themselves from end to end with the aid of an
axial element (that contains cohesin). In budding yeast (and perhaps other eukaryotes) the process follows a period of trial-and-
error. Any two dyads pair at their centromeres. If they are not homologs, they separate and try again.
How the nonsisters recognize their shared regions of DNA homology is uncertain. Double-stranded breaks (DSBs) often occur
in the DNA of the chromatids, and these may be necessary for the homologs to recognize each other.

7.7.3 https://bio.libretexts.org/@go/page/4851
Zygotene
Synapsis. The synaptonemal complex begins to form.
DNA strands of nonsister chromatids begin the process of recombination. How they are able to do so across the synaptonemal
complex, which is over 100 nm thick, is unknown.

Pachytene
Synapsis is now complete.
Recombination nodules appear (at least in some organisms, including humans). They are named for the idea that they
represent points where DNA recombination is occurring.
There must be at least one for each bivalent if meiosis is to succeed. There are often more, each one presumably
representing the point of a crossover.
They contain enzymes known to be needed for DNA recombination and repair.
The steps in recombining DNA continue to the end of pachytene.

Diplotene
DNA recombination is complete.
The synaptonemal complex begins to break down.
The chromatids begin to pull apart revealing
chiasmata. At first the chiasmata are located at the sites of the recombination nodules, but later they migrate towards the ends
of the chromatids.

Diakinesis
In some organisms, the chromosomes decondense and begin to be transcribed for a time. This is followed by the chromosomes
recondensing in preparation for metaphase I.
In creatures where this does not occur, the chromosomes condense further in preparation for metaphase I.

Quality Control of Meiosis

It shouldn't be surprising that things can go wrong in such a complicated process. However, cells going through meiosis have
checkpoints that monitor each pair of homologues for
proper recombination of their DNA
correct formation of the synaptonemal complex
Any failure that is detected stops the process and usually causes the cell to self-destruct by apoptosis.
However, despite these checkpoints, errors occasionally do go uncorrected.

Errors in Meiosis
It is estimated that from 10–25% of all human fertilized eggs contain chromosome abnormalities, and these are the most common
cause of pregnancy failure (35% of the cases).
These chromosome abnormalities
arise from errors in meiosis, usually meiosis I;
occur more often (90%) during egg formation than during sperm formation;
become more frequent as a woman ages.
Aneuploidy — the gain or loss of whole chromosomes — is the most common chromosome abnormality. It is caused by
nondisjunction, the failure of chromosomes to correctly separate:
homologues during meiosis I or
sister chromatids during meiosis II
Zygotes missing one chromosome ("monosomy") cannot develop to birth (except for females with a single X chromosome).
Three of the same chromosome ("trisomy") is also lethal except for chromosomes 13, 18, and 21 (trisomy 21 is the cause of
Down syndrome).
Three or more X chromosomes are viable because all but one of them are inactivated.

7.7.4 https://bio.libretexts.org/@go/page/4851
Contributors and Attributions
John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 7.7: Meiosis is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

7.7.5 https://bio.libretexts.org/@go/page/4851
 CHAPTER OVERVIEW
Unit 8: The Genetic Consequences of Meiosis
8.1: Mendel's Monohybrid Crosses
8.2: Crossing Over and Genetic Recombination in Meiosis
8.3: The Evidence of Creighton and McClintock
8.4: Genetic linkage and Genetic Maps
8.5: Gene Mapping with Three-point Crosses
8.6: Quantitative Trait Loci
8.7: Mapping the Genes of T2
8.8: rII Locus of T4

This page titled Unit 8: The Genetic Consequences of Meiosis is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by
John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

1
8.1: Mendel's Monohybrid Crosses
Gregor Mendel (1822-1884) was an Austrian monk who discovered the basic rules of inheritance. From 1858 to 1866, he bred
garden peas in his monastery garden and analyzed the offspring of these matings. The garden pea was good choice of experimental
organism because many varieties were available that bred true for clear-cut, qualitative traits like
seed texture (round vs wrinkled)
seed color (green vs yellow)
flower color (white vs purple)
tall vs dwarf growth habit
and three others that also varied in a qualitative — rather than quantitative — way.
Furthermore, peas are normally self-pollinated because the stamens and carpels are enclosed within the petals. By removing the
stamens from unripe flowers, Mendel could brush pollen from another variety on the carpels when they ripened.

The First Cross

Mendel crossed a pure-breeding round-seeded variety with a pure-breeding wrinkled-seeded one. The parents (designated the P
generation) were pure-breeding because each was homozygous for the alleles at the gene locus (on chromosome 7) controlling seed
texture (RR for round; rr for wrinkled).
The results
All the peas produced in the second or hybrid generation were round.
Interpretation
All the peas of this F1 generation have an Rr genotype. All the haploid sperm and eggs produced by meiosis received one
chromosome 7. All the zygotes received one R allele (from the round parent) and one r allele (from the wrinkled parent). Because
the round trait is dominant, the phenotype of all the seeds was round.

P gametes (round parent)

R R

P gametes r Rr Rr
(wrinkled parent) r Rr Rr

The Second Cross

Mendel then allowed his hybrid peas to self-pollinate.
The results
The wrinkled trait — which had disappeared in his hybrid generation — reappeared in 25% of the new crop of peas.
Interpretation
Random union of equal numbers of R and r gametes produced an F2 generation with 25% RR and 50% Rr — both with the round
phenotype — and 25% rr with the wrinkled phenotype.

F1 gametes

R r

R RR Rr
F1 gametes
r Rr rr

The Third Cross

Mendel then allowed some of each phenotype in the F2 generation to self-pollinate. His results:
All the wrinkled seeds in the F2 generation produced only wrinkled seeds in the F3.
One-third (193/565) of the round F1 seeds produced only round seeds in the F3 generation, but

8.1.1 https://bio.libretexts.org/@go/page/4852
 two-thirds (372/565) of them produced both types of seeds in the F3 and — once again — in a 3:1 ratio.
Interpretation
One-third of the round seeds and all of the wrinkled seeds in the F2 generation were homozygous and produced only seeds of the
same phenotype. But two thirds of the round seeds in the F2 were heterozygous and their self-pollination produced both
phenotypes in the ratio of a typical F1 cross.

Phenotype ratios are approximate

The union of sperm and eggs is random. So the pod in the color photo () — with its 9 smooth seeds and 3 wrinkled seeds! —
represents something of a statistical fluke. As the size of the sample gets larger, however, chance deviations become minimized and
the ratios approach the theoretical predictions more closely. The table shows the actual seed production by ten of Mendel's F1
plants. While his individual plants deviated widely from the expected 3:1 ratio, the group as a whole approached it quite closely.

Figure 8.1.1 courtesy of Cathie Martin from Cell 12 January 1990

Round Wrinkled

1. 45 12

2. 27 8

3. 24 7

4. 19 16

5. 32 11

6. 26 6

7. 88 24

8. 22 10

9. 28 6

10. 25 7

Total 336 107

Mendel's Hypothesis
To explain his results, Mendel formulated a hypothesis that included the following:
1. In the organism there is a pair of factors that controls the appearance of a given characteristic. (We call them genes.)
2. The organism inherits these factors from its parents, one from each.
3. Each is transmitted from generation to generation as a discrete, unchanging unit. (The wrinkled seeds in the F2 generation were
no less wrinkled than those in the P generation although they had passed through the round-seeded F1 generation.)
4. When the gametes are formed, the factors separate and are distributed as units to each gamete. This statement is often called
Mendel's rule of segregation.
5. If an organism has two unlike factors (we call them alleles) for a characteristic, one may be expressed to the total exclusion of
the other (dominant vs recessive).

8.1.2 https://bio.libretexts.org/@go/page/4852
The Testcross: A Test of Mendel's Hypothesis
A good hypothesis meets several standards.
It should provide an adequate explanation of the observed facts.
If two or more hypotheses meet this standard, the simpler one is preferred.
It should be able to predict new facts.
So if a generalization is valid, then certain specific consequences can be deduced from it. To test his hypothesis, Mendel predicted
the outcome of a breeding experiment that he had not yet carried out. He crossed heterozygous round peas (Rr) with wrinkled
(homozygous, rr) ones. He predicted that in this case one-half of the seeds produced would be round (Rr) and one-half wrinkled
(rr)

F1 gametes

R r

r Rr rr
P gametes
r Rr rr

To a casual observer in the monastery garden, the cross appeared no different from the P cross described above: round-seeded peas
being crossed with wrinkled-seeded ones. But Mendel predicted that this time he would produce both round and wrinkled seeds and
in a 50:50 ratio. He performed the cross and harvested 106 round peas and 101 wrinkled peas.
This kind of mating is called a testcross. It "tests" the genotype in those cases where two different genotypes (like RR and Rr)
produce the same phenotype.
Mendel did not stop here.
He went on to cross pea varieties that differed in six other qualitative traits. In every case, the results supported his hypothesis.
He crossed peas that differed in two traits. He found that the inheritance of one trait was independent of that of the other and so
framed his second rule: the rule of independent assortment.

Mendel's rules today

Little attention was paid when Mendel published his findings in 1866. Not until 1900, 34 years later and 16 years after his death,
was his work brought to light. By then, three men — working independently — discovered the same principles. So the present
remarkable development of genetics dates from only the start of the 20th century.
The discovery of chromosomes — and their behavior during meiosis (2n -> n) and fertilization (n + n -> 2n) — established the
structural basis for Mendel's rules.
What is the status today of Mendel's rules? Although many important exceptions to them have been discovered — three examples:
both members of many allelic pairs affect the phenotype; that is, neither is fully dominant
several different pairs of genes — often on different chromosomes — affect a phenotype additively with none being fully
dominant.
many gene loci are not inherited independently but show linkage (because they are relatively close together on the same
chromosome)
His rules still form the foundation upon which the science of genetics rests.

This page titled 8.1: Mendel's Monohybrid Crosses is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

8.1.3 https://bio.libretexts.org/@go/page/4852
8.2: Crossing Over and Genetic Recombination in Meiosis
Crossing over occurs between equivalent portions of two nonsister chromatids.
Each chromatid contains a single molecule of DNA. So the problem of crossing over is really a problem of swapping portions of
adjacent DNA molecules.
It must be done with great precision so that neither chromatid gains or loses any genes. In fact, crossing over has to be sufficiently
precise that not a single nucleotide is lost or added at the crossover point if it occurs within a gene. Otherwise a frameshift would
result and the resulting gene would produce a defective product or, more likely, no product at all.

This page titled 8.2: Crossing Over and Genetic Recombination in Meiosis is shared under a CC BY 3.0 license and was authored, remixed,
and/or curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history
is available upon request.

8.2.1 https://bio.libretexts.org/@go/page/4853
8.3: The Evidence of Creighton and McClintock

Figure 8.3.1 Unusual Corn Chromosome

Here was an organism with a rare chromosomal aberration that made it possible to distinguish two homologs from each other under
the microscope. Furthermore, this unusual chromosome carried the dominant allele for colored kernels (C) and the recessive allele
for waxy endosperm (wx). Its normal-appearing mate carried the recessive allele for colorless kernels (c) and the dominant allele
for normal (starchy) endosperm (Wx). Thus the plant was a dihybrid for these two linked traits and, in addition, one chromosome of
the pair was visibly marked at each end.
Creighton and McClintock reasoned that this plant would produce 4 kinds of gametes: The parental kinds (Cwx and cWx) and the
recombinant kinds produced by crossing over (cwx and CWx). Fertilization of these gametes by gametes containing a chromosome
of normal appearance and both recessive alleles cwx (a typical testcross) should produce 4 kinds of kernels:
colored waxy (Ccwxwx) kernels
colorless kernels with normal endosperm (ccWxwx)
colorless waxy (ccwxwx) and
colored kernels with normal endosperm (CcWxwx).

Figure 8.3.2 Creighton - McClintock test cross chromosomes

1. In the first case, there should be one normal chromosome and one extra-long chromosome with the knob at the end.

8.3.1 https://bio.libretexts.org/@go/page/4854
 2. In the second case, both chromosomes should be of normal appearance. However,
3. in the third case (colorless, waxy), where crossing over had occurred, one would hope to find evidence that a physical exchange
of parts between the homologous chromosomes of the dihybrid parent had occurred. Either a chromosome of normal length, but
with a knob at one end, or an extra-long chromosome with no knob should be present. Creighton and McClintock found the
latter, thus indicating that the gene locus for wx was associated with (and thus near) the end of the chromosome with the extra
segment. The gene locus for kernel color must then be neared the end with the knob.
4. Examination of the plants in class 4 (colored kernels and normal endosperm) revealed a chromosome of normal length but with
a knob at the end.
Thus, behavior of the genes as revealed by the study of the phenotypes produced was shown to be directly related to the behavior of
chromosomes as seen under the microscope. The recombination of genes occurs when homologous chromosomes exchange parts.

This page titled 8.3: The Evidence of Creighton and McClintock is shared under a CC BY 3.0 license and was authored, remixed, and/or curated
by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available
upon request.

8.3.2 https://bio.libretexts.org/@go/page/4854
8.4: Genetic linkage and Genetic Maps
Background

Figure 8.4.1 Dihybrid Cross

Mendel then crossed these dihybrids. If it is inevitable that round seeds must always be yellow and wrinkled seeds must be green,
then he would have expected that this would produce a typical monohybrid cross: 75% round-yellow; 25% wrinkled-green. But, in
fact, his mating generated seeds that showed all possible combinations of the color and texture traits.
9/16 of the offspring were round-yellow
3/16 were round-green
3/16 were wrinkled-yellow, and
1/16 were wrinkled-green

Rule of Independent Assortment

Finding in every case that each of his seven traits was inherited independently of the others, he formed his "second rule" the Rule
of Independent Assortment:

The inheritance of one pair of factors (genes) is independent of the

inheritance of the other pair.
Today we know that this rule holds only if two conditions are met:
the genes are on separate chromosomes or
the genes are widely separated on the same chromosome.
Mendel was lucky in that every pair of genes he studied met one requirement or the other. The table shows the chromosome
assignments of the seven pairs of alleles that Mendel studied. Although all of these genes showed independent assortment, several
were, in fact, syntenic with three loci occurring on chromosome 4 and two on chromosome 1. However, the distance separating the
syntenic loci was sufficiently great that the genes were inherited as though they were on separate chromosomes.

Trait Phenotype Alleles Chromosome

Seed form round-wrinkled R-r 7

Seed color yellow-green I-i 1

Pod color green-yellow Gp-gp 5

Pod texture smooth-wrinkled V-v 4

Flower color purple-white A-a 1

Flower location axial-terminal Fa-fa 4

Plant height tall-dwarf Le-le 4

8.4.1 https://bio.libretexts.org/@go/page/4855
 Figure 8.4.2. Linkage in corn
Start with two different strains of corn (maize).
one that is homozygous for two traits
yellow kernels (C,C) which are filled with endosperm causing the kernels to be
smooth (Sh,Sh).
a second that is homozygous for
colorless kernels (c,c) that are wrinkled because their endosperm is
shrunken (sh,sh)
When the pollen of the first strain is dusted on the silks of the second (or vice versa), the kernels produced (F1) are all yellow and
smooth. So the alleles for yellow color (C) and smoothness (Sh) are dominant over those for colorlessness (c) and shrunken
endosperm (sh).
To simplify the analysis, mate the dihybrid with a homozygous recessive strain (ccshsh). Such a mating is called a test cross
because it exposes the genotype of all the gametes of the strain being evaluated.
According to Mendel's second rule, the genes determining color of the endosperm should be inherited independently of the genes
determining texture. The F1 should thus produce gametes in approximately equal numbers.
CSh, as inherited from one parent.
csh, as inherited from the other parent
Csh, a recombinant
cSh, the other recombinant.

Figure 8.4.4 Plot Linkage

In fact, the recombination frequency is 2.0%, telling us that the actual order of loci is
c — sh — bz.

8.4.2 https://bio.libretexts.org/@go/page/4855
Mapping by linkage analysis is best done with loci that are relatively close together; that is, within a few centimorgans of each
other. Why? Because as the distance between two loci increases, the probability of a second crossover occurring between them also
increases.
But a second crossover would undo the effect of the first and restore the parental combination of alleles. These would show up
as nonrecombinants. Thus as the distance between two loci increases, the percentage of recombinants that forms understates the
actual distance in centimorgans that separates them. And, in fact, that has happened in this example. Using a three-point cross
reveals the existence of a small number of double recombinants and tells us that the actual distance c—bz is indeed 5 cM as we
would expect by summing
c—sh = 3 cM
sh—bz = 2 cM
and not the 4.6 cM revealed by the dihybrid cross.
A three-point cross also tells us the gene order in a single cross rather than the three we needed here.
There are other problems with preparing genetic maps of chromosomes.
The probability of a crossover is not uniform along the entire length of the chromosome.
Crossing over is inhibited in some regions (e.g., near the centromere).
Some regions are "hot spots" for recombination (for reasons that are not clear). Approximately 80% of genetic
recombination in humans is confined to just one-quarter of our genome.
In humans, the frequency of recombination of loci on most chromosomes is higher in females than in males. Therefore, genetic
maps of female chromosomes are longer than those for males.

Figure 8.4.5 Genetic Map of Chromosome 9

A genetic map of chromosome 9 (the one that carries the C, Sh, and bz loci) of the corn plant (Zea mays) is shown above. If one
maps in small intervals from one end of a chromosome to the other, the total number of centimorgans often exceeds 100 (as you
can see for chromosome 9). However, even for widely-separated loci, the maximum frequency of recombinants that can form is
50%. And this is also the frequency of recombinants that we see for genes independently assorting on separate chromosomes. So
we cannot tell by simply counting recombinants whether a pair of gene loci is located far apart on the same chromosome or are on
different chromosomes. As we saw above, several of Mendel's independently assorting traits are controlled by genes on the same
chromosome but located so far apart that they are inherited as if they were located on different chromosomes.
Genes that are present on the same chromosome are called syntenic.

This page titled 8.4: Genetic linkage and Genetic Maps is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

8.4.3 https://bio.libretexts.org/@go/page/4855
8.5: Gene Mapping with Three-point Crosses
Mechanisms discussed previously show how carrying out three different dihybrid test crosses in the corn plant reveals the order
of the gene loci and the distance between them (in centimorgans, cM). Here we shall see how a single test cross of a trihybrid corn
plant; that is, one parent is heterozygous for three linked alleles (C,Sh, Bz, on one chromosome; c,sh,bz on the other) and the other
parent is homozygous for the recessive version of all three genes (c,c,sh,sh,bz,bz) reveals the gene order and gives a more accurate
measurement of the distance in cM separating the outermost loci (in this case C and Bz) than a dihybrid cross involving those loci
would. Hypothetical breeding data are shown in Table 8.5.1.
Table 8.5.1: Hypothetical breeding data
Expressed Alleles
Group Crossovers Number Totals
(Phenotype)

1 CShBz 479
None; the parentals 952
2 cshbz 473

3 C|shbz Single; between C and 15

28
4 c|ShBz others 13

5 CSh|bz Single, between Bz and 9

18
6 csh|Bz others 9

7 C|sh|Bz 1
Double recombinants 2
8 c|Sh|bz 1

Totals 1000

Eight different phenotypes — representing the 8 possible genotypes (23 = 8) are produced. Scoring them reveals
The percentage of recombinants between C and Sh is 3.0%: 28/1000 of single recombinants plus 2/1000 double recombinants.
That between Sh and Bz is 2.0%: 18/1000 single recombinants plus 2/1000 double recombinants.
That between C and Bz is 4.6%: 28 + 18 = 46/1000.
But adding the distances between C and Sh and Sh and Bz gives a map distance between C and Bz of 5.0 cM not the 4.6 cM
revealed by the data (and the same number that a C,c,Bz,bz dihybrid cross would have produced). Why the discrepancy? Because
the double recombinants restored the parental configuration, they were missed in the scoring. So the two rare classes of double
recombinants need to be added (twice) to the data.

28 + 18 + 2 + 2 = 50/1000 = 5% (8.5.1)

to get the true value. So the map of this region of the chromosome is:

This exercise underscores the rule that the closer the intervals examined, the more accurate the map. A three-point cross also gives
the gene order immediately. The procedure is:
1. Determine the rarest classes (here, C,sh,Bz and c,Sh,bz) because two crossovers between a pair of loci will be rarer than one.
2. In these two groups, the alleles that specify the trait that was not seen in the parents (sh and Sh) occupy the middle locus.

This page titled 8.5: Gene Mapping with Three-point Crosses is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by
John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

8.5.1 https://bio.libretexts.org/@go/page/4856
8.6: Quantitative Trait Loci
The rules of inheritance discovered by Mendel depended on his wisely choosing traits that varied in a clear-cut, easily
distinguishable, qualitative way. But humans are not either tall or short nor are they either heavy or light. Many traits differ in a
continuous, quantitative way throughout a population.

Figure 8.6.1: Distribution of heights among group of male secondary-school seniors

This histogram shows the distribution of heights among a group of male secondary-school seniors. As you can see, the plot
resembles a bell-shaped curve. Such distributions are typical of quantitative traits. Some of the variation can be explained by
differences in diet and perhaps other factors in the environment. Environment alone is not, however, sufficient to explain the full
range of heights or weights.
An understanding of how genes can control quantitative traits emerged in 1908 from the work of the Swedish geneticist Nilsson-
Ehle who studied quantitative traits in wheat. Using Mendel's methods, he mated pure-breeding red-kernel strains with pure-
breeding white-kernel strains. The offspring were all red, but the intensity of color was much less that in the red parent. It seemed
as though the effect of the red allele in the F1 generation was being modified by the presence of the white allele.

Nilsson-Ehle: Genetics of Two Crosses

When Nilsson-Ehle mated two F1 plants, he produced an F2 generation in which red-kerneled plants outnumbered white-kerneled
plants 15:1. But the red kernels were not all alike. They could quite easily be sorted into four categories. One sixteenth of them
were deep red, like the P type. Four sixteenths were medium dark red, six sixteenths were medium red (like the F1 generation), and
four sixteenths were light red. The genetics of the two crosses is shown here. The alleles at one locus are indicated with prime
marks; at the other, without.

Figure 8.6.2: Genetics of the two crosses by Nilsson-Ehle

8.6.1 https://bio.libretexts.org/@go/page/4857
These results could be explained by assuming that kernel color in wheat is controlled by not one, but two pairs of genes, the effects
of which add up without distinct dominance. Each pair is located on a different chromosome or so far apart on the same
chromosome that there is no linkage. Four alleles for red produce a deep red kernel. Four alleles for white produce a white kernel.
Just one red allele out of four produces a light red kernel. Any two out of the four produce a medium red kernel. Any three of the
four produce a medium dark red kernel. If one plots the numbers of the different colored offspring in the F2 generation against
color intensity, one gets a graph like Figure 8.6.3.

Figure 8.6.3: Genetics of the two crosses results interpretation by Nilsson-Ehle,

In other wheat varieties, Nilsson-Ehle found F2 generations with a ratio of red kernels to white of 63:1. These could be explained
by assuming that three pairs of alleles were involved. In these cases, six different shades of red could be detected, but the color
differences were very slight. Environmental influences also caused alterations in intensity so that in practice the collection of
kernels displayed a continuous range of hues all the way from deep red to white.
So the occurrence of continuous variation of a trait in a population can be explained by assuming it is controlled by several pairs of
genes — called quantitative trait loci (QTL) — the effects of which are added together. This is called polygenic inheritance or
the multiple-factor hypothesis. At first the study of quantitative traits was mostly confined to animal husbandry and the breeding
of agricultural crops. It was based on the premise that
When two extreme types ae mated (e.g., AABB and aabb). the offspring are intermediate in type.
When two intermediate types are mated, most of their offspring are also intermediate, but some extreme types will be produced.
The results of random matings in a large population will be a large range of types with the greatest number in the middle range
and the fewest at the extremes.
In more recent times, the search for quantitative trait loci has turned to humans. A number of diseases, cancers for example, are
thought to be caused by the additive effects of genes at different loci. Pedigree analysis has provided some insights, but the use of
microarrays promises to provide more.

This page titled 8.6: Quantitative Trait Loci is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

8.6.2 https://bio.libretexts.org/@go/page/4857
8.7: Mapping the Genes of T2
T2 and its close relative T4 are viruses that infect the bacterium E. coli. The infection ends with destruction (lysis) of the bacterial
cell so these viruses are examples of bacteriophages ("bacteria eaters"). Each virus particle (virion) consists of:
a protein head (~0.1 µm) inside of which is a single, circular molecule of double-stranded DNA containing 166,000 base pairs.
a protein tail from which extend
thin protein fibers

Life Cycle

Figure 8.7.1: T4: bacteriophage lysogenic and lytic cycle. (CC BY-SA 3.0; Suly12)
The virus attaches to the E. coli cell (a). This requires a precise molecular interaction between the fibers and the cell wall of the
host.
The DNA molecule is injected into the cell (b).
Within 1 minute, the viral DNA begins to be transcribed and translated into some of the viral proteins, and synthesis of host
proteins is stopped.
At 5 minutes, viral enzymes needed for synthesis of new viral DNA molecules are produced (c).
At 8 minutes, some 40 different structural proteins for the viral head and tail are synthesized.
At 13 minutes, assembly of new viral particles begins (d).
At 25 minutes, the viral lysozyme destroys the bacterial cell wall and the viruses burst out — ready to infect new hosts (e).
If the bacterial cells are growing in liquid culture, it turns clear.
If the bacterial cells are growing in a "lawn" on the surface of an agar plate, then holes, called plaques, appear in the lawn.
Occasionally, new phenotypes appear such as a change in the appearance of the plaques or even a loss in the ability to infect the
host.
Examples:
h
Some strains of E. coli, e.g. one designated B/2, gain the ability to resist infection by normal ("wild-type") T2. The mutation
has caused a change in the structure of their cell wall so that the tail fibers of T2 can no longer bind to it. However, T2 can
strike back. Occasional T2 mutants appear that overcome this resistance. The mutated gene, designated h (for "host range"),

8.7.1 https://bio.libretexts.org/@go/page/4858
 encodes a change in the tail fibers so they can once again bind to the cell wall of strain B/2. The normal or "wild-type" gene
is designated h+ .
When plated on a lawn containing both E. coli B and E. coli B/2,
the mutant (h) viruses can lyze both strains of E. coli, producing clear plaques, while
the wild-type (h+) viruses can only lyze E. coli B producing mottled or turbid plaques.
r
Occasional T2 mutants appear that break out of their host cell earlier than normal.
The mutation occurs in a gene designated r (for "rapid lysis"). It reveals itself by the extra-large plaques that it forms.
The wild-type gene, producing a normal time of lysis, is designated r+. It forms normal-size plaques.
As with so many organisms, the occurrence of mutations provides the tools to learn about such things as
the function of the gene
its location in the DNA molecule (mapping)

Mapping by Recombination Frequencies

As we have seen, E. coli strain B can be infected by both h+ and h strains of T2. In fact, a single bacterial cell can be infected
simultaneously by both. Let us infect a liquid culture of E. coli B with two different mutant T2 viruses: h r+ and h+ r. When this is
done in liquid culture, and then plated on a mixed lawn of E. coli B and B/2, four different kinds of plaques appear.

Figure 8.7.2 E. Coli B mapping

Genotype Phenotype Number of Plaques

hr+ clear, small 460

h+r turbid, large 460

h+r+ turbid, small 40

hr clear, large 40

Total = 1000

The most abundant (460 each) are those representing the parental types; that is, the phenotypes are those expected from the two
infecting strains. However, small numbers (40 each) of two new phenotypes appear. These can be explained by genetic
recombination having occasionally occurred between the DNA of each parental type within the bacterial cell.

Just as in higher organisms, one assumes that the frequency of recombinants is proportional to the distance between the gene loci.
In this case, 80 out of 1000 plaques were recombinant, so the distance between the h and r loci is assigned a value of 8 map units
or centimorgans (cM). Now coinfect E. coli B with two other strains of T2:

8.7.2 https://bio.libretexts.org/@go/page/4858
 hm+ and
h+m

hm+ 470

h+m 470

h+m+ 30

hm 30

Total = 1000

Again, 4 kinds of plaques are produced: parental (470 each) and recombinant (30 each).
The smaller number of recombinants indicates that these two gene loci (h and m) are closer together (6 cM) than h and r (8 cM).
But the order of the three loci could be either
m–6–h—8—r
or
h–6–m-2-r
To find out which is the correct order, perform a third mating using
mr+ and
m+r

mr+ 440

m+r 440

m+r+ 60

mr 60

Total = 1000

This makes it clear that the order is m—h—r, not h—m—r.

But why only 12 cM between the outside loci (m and r) instead of the 14 cM produced by adding the map distances found in the
first two matings?

A Three-Point Cross
The answer comes from performing a mating between T2 viruses differing at all three loci:
hmr
and
h+m+r+
(Note: this time one parent has all mutant; the other all wild-type alleles — don't be confused!)
The
Group 1 hmr 435
res
ult: Group 2 h+m+r+ 435
8 Group 3 h+mr+ 25
diff
Group 4 hm+r 25
ere

8.7.3 https://bio.libretexts.org/@go/page/4858
nt Group 5 hmr+ 35
typ
Group 6 h+m+r 35
es
of Group 7 hm+r+ 5
pla Group 8 h+mr 5
que
Total = 1000
s
are
formed.
parentals; that is, nonrecombinants in Groups 1 and 2;
recombinants — all the others
Analyzing these data shows how the two-point cross between m and r understated the true distance between them.
Let's first look at single pairs of recombinants as we did before (thus ignoring the third locus).
If we look at all the recombinants between h and r but ignore m (as in the first experiment), we find that they are contained in
Groups 5, 6, 7, and 8 — giving the total of 80 that we found originally.
If we look at recombinants between h and m but ignore r (as in the second experiment), we find that they are contained in
Groups 3, 4,7, and 8 — giving the same total of 60 that we found before.
But if we focus only on m and r (as we did in the third experiment), we find that the recombinants are contained in Groups 3, 4,
5, and 6 — giving the same total of 120 as before while the non-recombinants are not only in Groups 1 and 2 but also in Groups
7 and 8. The reason: a double-crossover occurred in these cases, restoring the parental configuration of the m and r alleles.
Because these double crossovers were hidden in the third experiment, the map
distance (12 cM) was understated. To get the true map distance, we add their number
to each of the other recombinant groups (Groups 3,4,5, and 6) so 25 + 5 +25 +5 +35
+ 5 + 35 + 5 = 140, and the true map distance between m and r is the 14 cM that we
found by adding the map distances between h and r (8 cM) and h and m (6 cM).

The three-point cross is also useful because it gives the gene order simply by inspection:
Find the rarest genotypes (here Groups 7 and 8)
The gene NOT in the parental configuration (here h) is always the middle one.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 8.7: Mapping the Genes of T2 is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

8.7.4 https://bio.libretexts.org/@go/page/4858
8.8: rII Locus of T4
Mapping Within A Gene: the RII Locus
T2 and its close relative T4 are viruses that infect the bacterium E. coli. The infection ends with destruction (lysis) of the bacterial
cell so these viruses are examples of bacteriophages ("bacteria eaters"). They have been enormously useful in genetic studies
because:
Viruses of two (or more) different genotypes can simultaneously infect a single bacterium.
The DNA molecules of one of the infecting viruses can recombine with that of another forming recombinant molecules.
The huge number of viruses released from a huge number of bacterial hosts enables even rare recombination events to be
detected.
Another page — Bacteriophage Genetics — describes how T2 is used to map the order and relative spacing of genes on the single
circular molecule of DNA that is the virus's genome. Here let us see how T4 can be used to detect mutations within a single gene
and speed up the process of mapping these point mutations by the use of deletion mutants.

Detecting Mutation within a Single Gene

In Bacteriophage Genetics, we examined mutation of a gene designated r, for "rapid lysis". It turned out that actually there are three
different gene loci — rI, rII, and rIII — mutations in any one of which produced a rapid-lysis phenotype. But, in addition, there
were many mutations found in each of these. Could wild-type virus be formed by recombination between mutations within the
same gene? Seymour Benzer decided to find out.
As we saw in Bacteriophage Genetics, the recombination frequency between different genes is low (on the order of 10-2). One
would expect that recombination frequencies between mutations in a single gene would be far lower (10-4 or less). Fortunately
Benzer could exploit a phenomenon to enable him to detect such rare events: rII mutants as well as wild-type T4 can infect and
complete their life cycle in a strain of E. coli designated B. However, while rII mutants can infect a strain of E. coli designated K,
they cannot complete their life cycle in strain K. Wild-type T4 can.

The procedure was to infect strain B in liquid culture with two mutants to be tested (designated here as rx and ry). After incubation,
these were plated on a lawn of:
strain B — which supports the growth of all viruses thus giving the total number of viruses liberated.
strain K — on which only wild-type viruses can grow.
The recombination frequency between any pair of mutations is calculated as
2 × number of wild-type plaques (strain K plaques)
Recombination Frequency = (8.8.1)
total number of plaques (on strain B)

You have to double the number found on strain K because you only see one-half the recombinants — the other half consists of
double mutants. Using this technique, Benzer eventually found some 2000 different mutations in the rII gene. The recombination
frequency between some pairs of these was as low as 0.02.
The T4 genome has 160,000 base pairs of DNA extending over ~1,600 centimorgans (cM).
So 1 cM ≅ 100 base pairs
So 0.02 cM represents a pair of adjacent nucleotides.
From these data, Benzer concluded that the
smallest unit of mutation and
the smallest unit of recombination

8.8.1 https://bio.libretexts.org/@go/page/4859
 was a single base pair of DNA.
In other words, these mutations represent a change in a single base pair — we call these point mutations. Recombination between
two molecules of DNA can occur at any pair of nucleotides.

Mapping Point Mutations Within A Gene

The relative order and spacing of any two point mutations in a single gene like rII can be done using the procedure describe in
Bacteriophage Genetics. But with some 2000 different mutations to test, the process would be tremendously time-consuming.
(Even using the procedure to be described now, Benzer spent some 10 years on the project.) Benzer was able to speed up the
mapping process by taking advantage of the discovery that some of his mutants did not have point mutations but deletions instead.
In contrast to the properties of T4 viruses with point mutations, T4 viruses with deletions in rII showed no recombination with
other rII mutants or any other genes for that matter. Moreover, these deletions never back-mutated.

Deletion Mapping
Deletions can be mapped by the same procedure used for point mutations. Simply cross pairs of deletion mutants and see if they
produce progeny that can grow on E. coli strain K. Here is a hypothetical example. Each of 6 strains of deletion mutants are crossed
with each of the others.
Table 8.8.1:
Strains 1 2 3 4 5 6

1 and 3 do not
1 0 0 + 0 0 0
overlap
must shift 4
2 0 + + 0 0
away from 2
6 must extend
3 0 + + 0
under 3
right-hand end
of 4 must be
4 0 + +
removed from
over 6
left-hand end of
6 must not
overlap 5 but
5 0 + must continue to
overlap 2.
∴ shorten right-
hand end of 5

6 0

From the results, one can draw a map showing the order and relative size of the deletions.
With such a deletion map, one can now quickly map the location of point mutations by
coinfecting each of the different deletion strains (here 1–6) with the mutant strain ("x").
There is no longer any need to count plaques; simple see whether there is growth or not.

Coinfect with
1 2 3 4 5 6
strain

and mutant "x"

0 0 + + 0 +
Results →

From these results, we learn that the point mutation "x" is located on the T4 DNA within the region shown above in blue.

8.8.2 https://bio.libretexts.org/@go/page/4859
Complementation
As we saw above, rapid lysis (r) mutants were found that mapped to three different regions of the T4 genome: rI, rII, and rIII. This
meant that those in different regions were not alleles of the same gene and more than one gene product participated in the lysis
function. Even within one "locus", rII, there turned out to be two different stretches of DNA both of which were needed intact for
the lysis function. This was revealed by the complementation test that Benzer used. In this test,
E. coli strain K (which rII mutants can infect but not complete their life cycle) — growing in liquid culture — was
coinfected with two different rII mutants (shown in the figure as "1" and "2").
Note that this procedure differs from the earlier one (recombination) in that the nonpermissive E. coli K is used for the initial
infection (not strain B as before). Neither strain rII"1" nor strain rII"2" is able to grown in E. coli K. But if the lost function in
rII"1" is NOT the same as the lost function in rII"2", then
each should be able to produce the gene product missing in the other — complementation — and
living phages will be produced. (Again, there is no need to count plaques; simply see if they are formed or not.)

Mutant strains 1 2 3 4 5

1 0 0 + 0 +

2 0 + 0 +

3 0 + 0

4 0 +

5 0

From these results, you can deduce that these 5 rII mutants fall into two different complementation groups, which Benzer
designated A (containing strains 1, 2, and 4) and B (containing strains 3 and 5). Later work showed that the function of rII
depended on the polypeptide products encoded by two adjacent regions (A and B) of rII (perhaps acting as a heterodimer). In terms
of function, then, both A and B qualify as independent genes. In coinfections by two mutant strains,
If either A or B is mutated on the same DNA molecule ("cis"), there is no function while
if A is mutated in one DNA molecule and B in the other ("trans"), function is restored.
Complementation, then, is the ability of two different mutations to restore wild-type function when they are in the "trans" (on
different DNA molecules), but not when they are in "cis" (on the same DNA molecule). Benzer coined the term cistron for these
genetic units of function. But today, we simply modify earlier concepts of the "gene" to fit this operational definition.

This page titled 8.8: rII Locus of T4 is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

8.8.3 https://bio.libretexts.org/@go/page/4859
 CHAPTER OVERVIEW
Unit 9: Regulation of Gene Expression
9.1: Regulation of Gene Expression in Bacteria
9.2: The Tryptophan Repressor
9.3: Regulation of Gene Expression in Eukaryotes
9.4: Steroid Response Elements
9.5: Epigenetics
9.6: Visualization of Transcription and Translation in Bacteria
9.7: Footprinting
9.8: Chromatin Immunoprecipitation
9.9: Isolating Transcription Factors
9.10: Palindromes
9.11: Cell-specific gene expression
9.12: Imprinted Genes
9.13: Ribozymes

This page titled Unit 9: Regulation of Gene Expression is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

1
9.1: Regulation of Gene Expression in Bacteria
The Operon
Within its tiny cell, the bacterium E. coli contains all the genetic information it needs to metabolize, grow, and reproduce. It can
synthesize every organic molecule it needs from glucose and a number of inorganic ions. Many of the genes in E. coli are
expressed constitutively; that is, they are always turned "on". Others, however, are active only when their products are needed by
the cell, so their expression must be regulated.
Two examples:
If the amino acid tryptophan (Trp) is added to the culture, the bacteria soon stop producing the five enzymes previously needed
to synthesize Trp from intermediates produced during the respiration of glucose. In this case, the presence of the products of
enzyme action represses enzyme synthesis.
Conversely, adding a new substrate to the culture medium may induce the formation of new enzymes capable of metabolizing
that substrate. If we take a culture of E. coli that is feeding on glucose and transfer some of the cells to a medium contain
lactose instead, a revealing sequence of events takes place.
At first the cells are quiescent: they do not metabolize the lactose, their other metabolic activities decline, and cell division
ceases.
Soon, however, the culture begins growing rapidly again with the lactose being rapidly consumed. What has happened?
During the quiescent interval, the cells began to produce three enzymes.
The three enzymes are
a permease that transports lactose across the plasma membrane from the culture medium into the interior of the cell
beta-galactosidase which converts lactose into the intermediate allolactose and then hydrolyzes this into glucose and galactose.
Once in the presence of lactose, the quantity of beta-galactosidase in the cells rises from a tiny amount to almost 2% of the
weight of the cell.
a transacetylase whose function is still uncertain.

The lac operon

The capacity to respond to the presence of lactose was always there. The genes for the three induced enzymes are part of the
genome of the cell. But until lactose was added to the culture medium, these genes were not expressed (β-galactosidase was
expressed weakly — just enough to convert lactose into allolactose). The most direct way to control the expression of a gene is to
regulate its rate of transcription; that is, the rate at which RNA polymerase transcribes the gene into molecules of messenger
RNA (mRNA).

Figure 9.1.1 The lac DNA transciprtion

Gene transcription begins at a particular nucleotide shown in the figure as "+1". RNA polymerase actually binds to a site
"upstream" (i.e., on the 5' side) of this site and opens the double helix so that transcription of one strand can begin. The binding site
for RNA polymerase is called the promoter. In bacteria, two features of the promoter appear to be important:
a sequence of TATAAT (or something similar) centered 10 nucleotides upstream of the +1 site and
another sequence (TTGACA or something quite close to it) centered 35 nucleotides upstream.
The exact DNA sequence between the two regions does not seem to be important. Each of the three enzymes synthesized in
response to lactose is encoded by a separate gene. The three genes are arranged in tandem on the bacterial chromosome.

9.1.1 https://bio.libretexts.org/@go/page/4874
 Figure 9.1.2 The lac Operon
In the absence of lactose, the repressor protein encoded by the I gene binds to the lac operator and prevents transcription. Binding
of allolactose to the repressor causes it to leave the operator. This enables RNA polymerase to transcribe the three genes of the
operon. The single mRNA molecule that results is then translated into the three proteins.
The lac repressor binds to a specific sequence of two dozen nucleotides called the operator. Most of the operator is downstream
of the promoter. When the repressor is bound to the operator, RNA polymerase is unable to proceed downstream with its task of
gene transcription. The lac repressor represents only a tiny fraction of the proteins in the E. coli cell.
The operon is the combination of the operator and the three protein-encoding genes associated with it.
The gene encoding the lac repressor is called the I gene. It happens to be located just upstream of the lac promoter. However, its
precise location is probably not important because it achieves its effect by means of its protein product, which is free to diffuse
throughout the cell. And, in fact, the genes for some repressors are not located close to the operators they control.
Although repressors are free to diffuse through the cell, how does — for example — the lac repressor find the single stretch of 24
base pairs of the operator out of the 4.6 million base pairs of DNA in the E. coli genome? It turns out the repressor is free to bind
anywhere on the DNA using both
hydrogen bonds and
ionic (electrostatic) interactions between its positively-charged amino acids (Lys, Arg) and the negative charges on the
deoxyribose-phosphate backbone of the DNA.
Once astride the DNA, the repressor can move along it until it encounters the operator sequence. Now an allosteric change in the
tertiary structure of the protein allows the same amino acids to establish bonds — mostly hydrogen bonds and hydrophobic
interactions — with particular bases in the operator sequence.
The lac repressor is made up of four identical polypeptides (thus a "homotetramer"). Part of the molecule has a site (or sites) that
enable it to recognize and bind to the 24 base pairs of the lac operator. Another part of the repressor contains sites that bind to
allolactose. When allolactose unites with the repressor, it causes a change in the shape of the molecule, so that it can no longer
remain attached to the DNA sequence of the operator. Thus, when lactose is added to the culture medium, it causes the repressor to
be released from the operator and RNA polymerase can now begin transcribing the 3 genes of the operon into a single molecule of
messenger RNA.
Hardly does transcription begin, before ribosomes attach to the growing mRNA molecule and move down it to translate the
message into the three proteins. You can see why punctuation codons — UAA, UAG, or UGA — are needed to terminate
translation between the portions of the mRNA coding for each of the three enzymes. This mechanism is characteristic of bacteria,
but differs in several respects from that found in eukaryotes:
Genes in eukaryotes are not linked in operons (except for nematodes like C. elegans and tunicates like Ciona intestinalis).
Primary transcripts in eukaryotes contain the transcript of only a single gene (with the above exceptions).
Transcription and translation are not physically linked in eukaryotes as they are in bacteria; transcription occurs in the nucleus
while translation occurs in the cytosol (with a few exceptions).

9.1.2 https://bio.libretexts.org/@go/page/4874
  C. elegans

C. elegans differs from most eukaryotes in having a substantial fraction (15–20%) of its genes grouped in operons containing
from 2 to 8 genes each. Like bacteria, all the genes in an operon are transcribed from a single promoter producing a single
primary transcript (pre-mRNA). Some of the genes in these operons appear — as in bacteria — to be involved in the same
biochemical function, but this may not be the case for most. C. elegans operons also differ from those in bacteria in that each
pre-mRNA is processed into a separate mRNA for each gene rather than being translated as a unit.

Corepressors
As mentioned above, the synthesis of tryptophan from precursors available in the cell requires 5 enzymes. The genes encoding
these are clustered together in a single operon with its own promoter and operator. In this case, however, the presence of
tryptophan in the cell shuts down the operon. When Trp is present, it binds to a site on the Trp repressor and enables the Trp
repressor to bind to the operator. When Trp is not present, the repressor leaves its operator, and transcription of the 5 enzyme-
encoding genes begins.

Figure 9.1.3: Tryptophan Repressor courtesy of P. B. Sigler

The above picure shows stereo view of the tryptophan repressor (right side of each panel) bound to its operator DNA (left side).
The repressor is a homodimer of two identical polypeptides (on either side of the horizontal red line). Binding to DNA occurs only
when a molecule of tryptophan (red rings) is bound to each monomer of the repressor. The usefulness to the cell of this control
mechanism is clear. The presence in the cell of an essential metabolite, in this case tryptophan, turns off its own manufacture and
thus stops unneeded protein synthesis. As its name suggests, repressors are negative control mechanisms, shutting down operons
in the absence of a substrate (lactose in our example) or
the presence of an essential metabolite (tryptophan is our example).
However, some gene transcription in E. coli is under positive control.

Positive Control of Transcription: CAP

Absence of the lac repressor is essential but not sufficient for effective transcription of the lac operon. The activity of RNA
polymerase also depends on the presence of another DNA-binding protein called catabolite activator protein (CAP). Like the lac
repressor, CAP has two types of binding sites: One binds the nucleotide cyclic AMP and the other binds a sequence of 16 base
pairs upstream of the promoter
However, CAP can bind to DNA only when cAMP is bound to CAP. so when cAMP levels in the cell are low, CAP fails to bind
DNA and thus RNA polymerase cannot begin its work, even in the absence of the repressor. So the lac operon is under both
negative (the repressor) and positive (CAP) control. Why?
It turns out that it is not simply a matter of belt and suspenders. This dual system enables the cell to make choices. What, for
example, should the cell do when fed both glucose and lactose? Presented with such a choice, E. coli (for reasons about which we
can only speculate) chooses glucose. It makes its choice by using the interplay between these two control devices.

9.1.3 https://bio.libretexts.org/@go/page/4874
 Figure 9.1.4 Control of Transciprtion CAP
Although the presence of lactose removes the repressor, the presence of glucose lowers the level of cAMP in the cell and thus
removes CAP.Without CAP, binding of RNA polymerase is inhibited even though there is no repressor to interfere with it if it could
bind. The molecular basis for its choices is shown in the above figure.
CAP consists of two identical polypeptides (hence it is a homodimer). Toward the C-terminal, each has two regions of alpha helix
with a sharp bend between them. The longer of these is called the recognition helix because it is responsible for recognizing and
binding to a particular sequence of bases in DNA.

Figure 9.1.5 Model of CAP

The above figure shows a model of CAP. The two monomers are identical. Each monomer recognizes a sequence of nucleotides in
DNA by means of the region of alpha helix labeled F. Note that the two recognition helices are spaced 34Å apart, which is the
distance that it takes the DNA molecule (on the left) to make precisely one complete turn.

Figure 9.1.6 Recognition Helix

The recognition helices of each polypeptide of CAP are, of course, identical. But their orientation in the dimer is such that the
sequence of bases they recognize must run in the opposite direction for each recognition helix to bind properly. This arrangement
of two identical sequences of base pairs running in opposite directions is called an inverted repeat.
The strategy illustrated by CAP and its binding site has turned out to be used widely. As more and more DNA-regulating proteins
have been discovered, many turn out to share the traits we find in CAP:
They usually contain two subunits. Therefore, they are dimers.
They recognize and bind to DNA sequences with inverted repeats.
In bacteria, recognition and binding to a particular sequence of DNA is accomplished by a segment of alpha helix. Hence these
proteins are often described as helix-turn-helix proteins. The Trp repressor shown above is a member of this group.

9.1.4 https://bio.libretexts.org/@go/page/4874
Riboswitches
Protein repressors and corepressors are not the only way in which bacteria control gene transcription. It turns out that the
regulation of the level of certain metabolites can also be controlled by riboswitches. A riboswitch is section of the 5'-untranslated
region (5'-UTR) in a molecule of messenger RNA (mRNA) which has a specific binding site for the metabolite (or a close relative).
Some of the metabolites that bind to riboswitches include:
the purines adenine and guanine
the amino acids glycine and lysine
flavin mononucleotide (the prosthetic group of NADH dehydrogenase)
S-adenosyl methionine that donates methyl groups to many molecules, including DNA and the cap at the 5' end of messenger
RNA
tRNAs. When these are bound to their amino acid (aminoacyl-tRNA), they bind to the riboswitch in the mRNA that encodes the
enzyme (an aminoacyl-tRNA synthetase) responsible for loading the amino acid onto the tRNA. This causes transcription of the
mRNA to terminate prematurely. tRNAs with no amino acid attached also bind to the riboswitch but in such a way that
transcription of the mRNA continues. Its translation (in bacteria, translation begins while transcription is still going on)
produces the aminoacyl-tRNA synthetase used to load the amino acid onto the tRNA. Thus these riboswitches regulate the level
of aminoacyl-tRNAs producing more when needed, less when not (a kind of feedback inhibition.)
In each case, the riboswitch regulates transcription of genes involved in the metabolism of that molecule. The metabolite binds to
the growing mRNA and induces an allosteric change that for some genes causes further synthesis of the mRNA to terminate before
forming a functional product and for other genes, enhances completion of synthesis of the mRNA. In both cases, one result is to
control the level of that metabolite.
Some riboswitches control mRNA translation rather than its transcription. It has been suggested that these regulatory mechanisms,
which do not involve any protein, are a relict from an "RNA world".

This page titled 9.1: Regulation of Gene Expression in Bacteria is shared under a CC BY 3.0 license and was authored, remixed, and/or curated
by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available
upon request.

9.1.5 https://bio.libretexts.org/@go/page/4874
9.2: The Tryptophan Repressor
In E. coli, the synthesis of the amino acid tryptophan from precursors available to the cell requires 5 enzymes. The genes encoding
these are clustered together in a single operon with its own promoter and operator. When tryptophan is available to the cell, its
presence shuts down the operon.

Mechanism
One molecule of tryptophan binds to a site on each monomer of the Trp repressor.
The Trp repressor, a homodimer of two of these complexes, binds to the operator of the Trp operon.
This shuts down transcription of the 5 genes of the operon so the enzymes used in Trp synthesis are not synthesized.

Figure 9.2.1: The Tryptophan Repressor courtesy of P. B. Sigler

This stereoscopic view () shows the tryptophan repressor (right side of each panel) bound to its operator DNA (left side). The two
identical polypeptides of the repressor are shown on either side of the horizontal red line. The two tryptophan molecules are shown
as red rings. Look also for the stretches of alpha helix in each monomer. You may find it easier to fuse the two images into a 3D
view by holding a sheet of 8.5 x 11" (22 x 28 cm) paper vertically between your nose and the dividing line between the two images
on the screen so that your left eye sees only the left image, your right eye only the right.

This page titled 9.2: The Tryptophan Repressor is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

9.2.1 https://bio.libretexts.org/@go/page/4876
9.3: Regulation of Gene Expression in Eukaryotes
The latest estimates are that a human cell, a eukaryotic cell, contains some 21,000 genes. Some of these are expressed in all cells all
the time. These so-called housekeeping genes are responsible for the routine metabolic functions (e.g. respiration) common to all
cells. Some are expressed as a cell enters a particular pathway of differentiation. Some are expressed all the time in only those cells
that have differentiated in a particular way. For example, a plasma cell expresses continuously the genes for the antibody it
synthesizes. Some are expressed only as conditions around and in the cell change. For example, the arrival of a hormone may turn
on (or off) certain genes in that cell.
How is gene expression regulated? There are several methods used by eukaryotes.
Altering the rate of transcription of the gene. This is the most important and widely-used strategy.
However, eukaryotes supplement transcriptional regulation with several other methods:
Altering the rate at which RNA transcripts are processed while still within the nucleus.
Altering the stability of messenger RNA (mRNA) molecules; that is, the rate at which they are degraded.
Altering the efficiency with which ribosomes translate the mRNA into a polypeptide.
Protein-coding genes have
exons whose sequence encodes the polypeptide
introns that will be removed from the mRNA before it is translated
a transcription start site
promoters
a basal or core promoter located within about 40 base pairs (bp) of the start site
"upstream" promoters, which may extend over as many as 200 bp farther upstream
enhancers
silencers
Adjacent genes are often separated by an insulator which helps them avoid cross-talk between each other's promoters and
enhancers (and/or silencers).

Transcription start site

This is where a molecule of RNA polymerase II (pol II, also known as RNAP II) binds. Pol II is a complex of 12 different
proteins (shown in the figure in yellow with small colored circles superimposed on it). The start site is where transcription of the
gene into RNA begins.

The core promoter

All eukaryotic genes contain a core promoter. One common example is a sequence of bases (e.g., TATAAAAAA) called the TATA
box. It is bound by a large complex of some 50 different proteins, including
Transcription Factor IID (TFIID) which is a complex of
TATA-binding protein (TBP), which recognizes and binds to the TATA box
13 other protein factors which bind to TBP, each other, and (some of them) to the DNA.
Transcription Factor IIB (TFIIB) which binds both the DNA and pol II.

Figure 9.3.1: Eukaryotic Promoter

Many different genes and many different types of cells share the same transcription factors — not only those that bind at the core
promoter but even some of those that bind upstream. What turns on a particular gene in a particular cell is probably the unique
combination of promoter sites and the transcription factors that are chosen.

9.3.1 https://bio.libretexts.org/@go/page/4878
An Analogy
The rows of lock boxes in a bank provide a useful analogy. To open any particular box in the room requires two keys:
Your key, whose pattern of notches fits only the lock of the box assigned to you (= the upstream promoter), but which cannot
unlock the box without
A key carried by a bank employee that can activate the unlocking mechanism of any box (= the core promoter) but cannot by
itself open any box.

Hormones Effect

Figure 9.3.2: Enhancer

These loops are stabilized by a protein designated CTCF ("CCCTC binding factor"; named for the nucleotide sequence to which it
binds). The CTCF at one site on the DNA forms a dimer with the CTCF at another site on the DNA binding the two regions
together. CTCF has 11 zinc fingers. They can also be stabilized by cohesin — the same protein complex that holds sister
chromatids together during mitosis and meiosis.
Michael R. Botchan and his colleagues have produced visual evidence of this model of enhancer action. They created an artificial
DNA molecule with
several (4) promoter sites for Sp1 about 300 bases from one end. Sp1 is a zinc-finger transcription factor that binds to the
sequence 5' GGGCGG 3' found in the promoters of many genes, especially "housekeeping" genes.
several (5) enhancer sites about 800 bases from the other end. These are bound by an enhancer-binding protein designated E2.
1860 base pairs of DNA between the two.

Figure 9.3.3: Evidence of Enhancer Action courtesy Michael R. Botchan

Significance of "Looping"
The looping of chromosomes that brings enhancers close to promoters (and promoters close to other promoters) seems to be a
mechanism to ensure the expression (or inhibition) of groups of genes that must perform together. The response of a cell to the
arrival of a signal (e.g., a hormone) may involve turning on (or off) hundreds of different genes whose products must be produced
in a coordinated way for the cell to respond appropriately. The dynamic movement of portions of the chromosome carrying the
appropriate gene loci into a "transcription factory" may be a mechanism to accomplish this. If so, we are seeing the eukaryotic
equivalent of the coordinated gene expression provided by operons in bacteria.

Silencers
Silencers are control regions of DNA that, like enhancers, may be located thousands of base pairs away from the gene they control.
However, when transcription factors bind to them, expression of the gene they control is repressed.

9.3.2 https://bio.libretexts.org/@go/page/4878
Insulators
As you can see above, enhancers can turn on promoters of genes located thousands of base pairs away. Insulators prevent an
enhancer from inappropriately binding to and activating the promoter of some other gene in the same region of the chromosome..
Insulators are
stretches of DNA (as few as 42 base pairs may do the trick)
located between the
enhancer(s) and promoter(s) or
silencer(s) and promoter(s)
of adjacent genes or clusters of adjacent genes.

Figure 9.3.4 Insulator

The enhancer for the promoter of the gene for the delta chain of the gamma/delta T-cell receptor for antigen (TCR) is located
close to the promoter for the alpha chain of the alpha/beta TCR (on chromosome 14 in humans). A T cell must choose between
one or the other. There is an insulator between the alpha gene promoter and the delta gene promoter that ensures that activation of
one does not spread over to the other.
All insulators discovered so far in vertebrates work only when bound by the CTCF protein. Another example: In mammals (mice,
humans, pigs), only the allele for insulin-like growth factor-2 (IGF2) inherited from one's father is active; that inherited from the
mother is not — a phenomenon called imprinting.
The mechanism: the mother's allele has an insulator between the IGF2 promoter and enhancer. So does the father's allele, but in his
case, the insulator has been methylated. CTCF can no longer bind to the insulator, and so the enhancer is now free to turn on the
father's IGF2 promoter.
Many of the commercially-important varieties of pigs have been bred to contain a gene that increases the ratio of skeletal muscle to
fat. This gene has been sequenced and turns out to be an allele of IGF2, which contains a single point mutation in one of its
introns. Pigs with this mutation produce higher levels of IGF2 mRNA in their skeletal muscles (but not in their liver). This tells us
that:
Mutations need not be in the protein-coding portion of a gene in order to affect the phenotype.
Mutations in non-coding portions of a gene can affect how that gene is regulated (here, a change in muscle but not in liver).

This page titled 9.3: Regulation of Gene Expression in Eukaryotes is shared under a CC BY 3.0 license and was authored, remixed, and/or curated
by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available
upon request.

9.3.3 https://bio.libretexts.org/@go/page/4878
9.4: Steroid Response Elements

Figure 9.4.1: Stereoscopic view of the glucocorticoid response element courtesy of P. B. Sigler. This image shows a stereoscopic
view of the glucocorticoid response element (DNA, the double helix shown in yellow at the left of each panel) with the
glucocorticoid receptor (a protein homodimer, right portion of each panel) bound to it.
The DNA sequence of the glucocorticoid response element is
5' AGAACAnnnTGTTCT 3'
3' TCTTGTnnnACAAGA 5'
where n represents any nucleotide. (Note the inverted repeats.) The glucocorticoid receptor, like all steroid hormone receptors, is a
zinc-finger transcription factor; the zinc atoms are the four yellow spheres. Each is attached to four cysteines.
For a steroid hormone to regulate (turn on or off) gene transcription, its receptor must:
bind to the hormone (cortisol in the case of the glucocorticoid receptor)
bind to a second copy of itself to form a homodimer
be in the nucleus, moving from the cytosol if necessary
bind to its response element
bind to other protein cofactors

Figure 9.4.2: Autoradiograph of Endometrial cell courtesy of Madhabananda Sar and Walter E. Stumpf
This autoradiograph shows the endometrial cells from the uterus of a guinea pig 15 minutes after an injection of radioactive
progesterone. The radioactivity has concentrated within the nuclei of the endometrial cells as shown by the dark grains
superimposed on the images of the nuclei. The same effect is seen when radioactive estrogens are administered.
The cells of the endometrium are target cells for both progesterone and estrogens, preparing the uterus for possible pregnancy.
Nontarget cells (e.g. liver cells or lymphocytes) show no accumulation of female sex hormones. Although their DNA contains the
response elements, their cells do not have the protein receptors needed.

The Nuclear Receptor Superfamily

The zinc-finger proteins that serve as receptors for glucocorticoids and progesterone are members of a large family of similar
proteins that serve as receptors for a variety of small, hydrophobic molecules. These include:
other steroid hormones like the mineralocorticoid aldosterone and estrogens
the thyroid hormone, T3
calcitriol, the active form of vitamin D

9.4.1 https://bio.libretexts.org/@go/page/4880
 retinoids: vitamin A (retinol) and its relatives
retinal
retinoic acid (tretinoin — also available as the drug Retin-A®); and its isomer
isotretinoin (sold as Accutane® for the treatment of acne).
bile acids
fatty acids. These bind members of the superfamily called peroxisome-proliferator-activated receptors (PPARs). They got their
name from their initial discovery as the receptors for drugs that increase the number and size of peroxisomes in cells.
In every case, the receptors consists of at least three functional modules or domains. From N-terminal to C-terminal, these are:
a domain needed for the receptor to activate the promoters of the genes being controlled
the zinc-finger domain needed for DNA binding (to the response element)
the domain responsible for binding the particular hormone as well as the second unit of the dimer

Contibutors
John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 9.4: Steroid Response Elements is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

9.4.2 https://bio.libretexts.org/@go/page/4880
9.5: Epigenetics
Epigenetics can be defined as a change in phenotype that is heritable but does not involve a change in the nucleotide sequence in
DNA; that is, a change in genotype. This definition is very broad encompassing a variety of phenomena.

Epigenetic changes during cellular differentiation

For example, a change in phenotype of a single cell that is then passed on to its descendants qualifies as an epigenetic phenomenon.
Thus it includes the various pathways of differentiation that are taken by cells during the embryonic development of an organism.
Examples:
X-inactivation — where one of the two X chromosomes in female mammals is inactivated in each cell early in development
and that same chromosome remains inactivated in all the descendants of that cell.
Imprinting — where whether a gene in a cell lineage is expressed or not depends on which parent contributed the gene.
The great stumbling block in converting differentiated cells into induced pluripotent stem cells (iPSCs) was to find ways of
reversing the epigenetic changes in the differentiated cell (e.g., a skin cell) to unlock its full developmental potential. Stable
changes in gene expression are brought about in two main ways:
DNA methylation — where its cytosines are methylated. This usually represses the activity of that DNA.
Histone modifications — where methyl, acetyl, and other groups are added to the histones in chromatin. Prominent examples:
adding methyl groups to the #4 lysine in histone H3 ("H3K4me"). This is associated with active genes in that region of the
chromatin.
adding methyl groups to the #27 lysine in histone H3 ("HeK27me"). This is associated with gene silencing.
Some definitions:
epigenetic "writers": enzymes that add chemical groups to histones or DNA.
epigenetic "erasers": enzymes that remove these groups.
epigenetic "readers": proteins that recognize specific epigenetic modifications of histones or DNA producing a change in gene
expression, e.g., increasing (or decreasing) gene transcription.

This page titled 9.5: Epigenetics is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

9.5.1 https://bio.libretexts.org/@go/page/4882
9.6: Visualization of Transcription and Translation in Bacteria

Figure 9.6.1: Transcition and Translationn of E. coli genes

The above figure is an Electron micrograph courtesy of O. L. Miller, Jr., B. A. Hamkalo, and C. A. Thomas, Jr. It shows
simultaneous transcription and translation of E. coli genes. The long fiber running from top to bottom (green arrow ) is a
segment of the E. coli chromosome. Extending from it are polysomes (red arrow), the size of which generally increases from top to
bottom. Each polysome consists of a backbone of messenger RNA (mRNA) to which the ribosomes are attached.
Each polysome is attached to the DNA fiber by a complex of proteins that includes a molecule of RNA polymerase. Thus the
DNA is transcribed by RNA polymerase molecules moving from top to bottom, and the growing mRNA molecules are
translated by ribosomes moving in a proximal -> distal direction. IIn E. coli, then, and probably in all bacteria, the transcription
of DNA into mRNA and the translation of mRNA into polypeptides (not visible here) are closely coordinated in both time and
space.
In eukaryotes, in contrast, while all transcription takes place in the nucleus, most (but not all) translation of mRNA occurs later in
the cytosol.

This page titled 9.6: Visualization of Transcription and Translation in Bacteria is shared under a CC BY 3.0 license and was authored, remixed,
and/or curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history
is available upon request.

9.6.1 https://bio.libretexts.org/@go/page/4884
9.7: Footprinting
Footprinting is a method for determining the exact DNA sequence to which a particular DNA-binding protein binds. Examples:
hormone-receptor complexes that bind to their hormone response elements
transcription factors that bind eukaryotic operators, enhancers, and silencers
the lac repressor that shuts down the lac operon in E. coli

Figure 9.7.1 Footprinting

Clone a piece of DNA that contains the operator site to which the repressor binds.
Label one end of the DNA molecules with a radioactive molecule, e.g. radioactive ATP.
Digest the DNA with DNase I.
DNase I cuts DNA molecules randomly (in contrast to restriction enzymes that cut where they find a particular sequence)
Choose such gentle conditions that most molecules will be cut only once.
The result will be a mixture of radioactive fragments of varying length, with the smallest increment in length represented by a
single nucleotide.
Separate the fragments by electrophoresis.
Binding of the lac repressor to the sequence of 24 base pairs in the operator prevents DNase I from attacking that region of the
molecule.
When the fragments are separated by electrophoresis, those representing the lengths covered by the repressor will be missing
from the autoradiogram.
The resulting gap is the "footprint".
The same sample of DNA (unprotected by the repressor) is subjected to normal DNA sequencing and the resulting ladder
aligned with the footprint autoradiogram.
The exact sequence of bases in the lac operator can then be read directly because they represent the rungs of the ladder missing
in the footprint.

This page titled 9.7: Footprinting is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

9.7.1 https://bio.libretexts.org/@go/page/4886
9.8: Chromatin Immunoprecipitation
Many DNA-binding proteins, such as transcription factors, bind to specific sequences of nucleotides in, for example, promoters and
enhancers of genes. Some examples:
a generalized eukaryotic promoter
multiple transcription factors bound to the Drosophila eve promoter
the glucocorticoid receptor (protein) bound to its response element (DNA)
the tryptophan repressor bound to its operator
The binding of protein to DNA is done by noncovalent forces and is easily reversible. In fact, as conditions in a cell change, there
is a dynamic coming and going of DNA-binding proteins throughout the genome. The identification of a specific site in DNA
bound by a particular protein at a particular time can be discovered by the technique of chromatin immunoprecipitation (ChIP).

The Procedure
1. Harvest your cell population at the desired time. Some examples:
yeast cells growing on a particular nutrient;
HeLa cells exposed to a particular cytokine;
salivary gland cells of Drosophila at the time of pupation.
2. Treat the cells with formaldehyde (HCHO) which creates covalent bonds between the proteins and nucleotides to which they
have been bound noncovalently.
3. Break open the cells releasing their contents.
4. Use ultrasound to break the DNA into fragments averaging about 500 bp long.
5. Add an antibody that specifically binds to the protein you are interested in.
6. Add beads coated with Protein A or Protein S — both proteins that bind to any antibody.
7. Centrifuge down the complexes of bead—antibody—target protein—DNA.
8. Heat the complexes to break the covalent crosslinks between the target protein and the DNA.
9. Digest the protein with a protease leaving purified DNA fragments.
10. Perform PCR on the fragments.
11. Use any of several methods to identify the amplified DNA, for example,
Southern blotting
DNA chip analysis ("ChIP on chip")
clone and sequence ("ChIP-Seq")

This page titled 9.8: Chromatin Immunoprecipitation is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

9.8.1 https://bio.libretexts.org/@go/page/4888
9.9: Isolating Transcription Factors
Transcription factors are extraordinarily diverse, and any one factor represents only a tiny fraction of the protein molecules present
in the cell. This page describes how one can isolate and purify such rare molecules.

Example: Isolating the lac Repressor

An E. coli cell contains only 10-20 copies of the lac repressor. This represents a ratio of only 1 molecule in 50,000 protein
molecules in the cell. However, the specificity of the lac repressor for the DNA sequence of the operator provides a mechanism for
fishing it out of the mixture.

Affinity Chromatography

Figure 9.9.1 Affinity Chromatography

The following procedure is carried out for an affinity chromatograph:
Learn the sequence to which the repressor binds (by footprinting).
Synthesize a segment of DNA containing the sequence.
Attach this artificial molecule to beads of an inert, solid medium (the matrix).
Pour an extract of E. coli cells over the beads.
Only molecules specific for the DNA sequence — in this case, molecules of the lac repressor — will bind to the beads.
After irrelevant protein molecules have passed through the column, wash the beads with a buffer that will release the lac
repressor molecules so they can be studied.

This page titled 9.9: Isolating Transcription Factors is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

9.9.1 https://bio.libretexts.org/@go/page/4890
9.10: Palindromes
A palindrome is a sequence of letters and/or words, that reads the same forwards and backwards. "able was I ere I saw elba" is a
palindrome. Palindromes also occur in a DNA. There are two types.

Palindromes that occur on opposite strands of the same section of DNA helix

Figure 9.10.1 Restriction Enzymes Palindrome

5' GGCC 3'
3' CCGG 5'
This type of palindrome serves as the target for most restriction enzymes. The graphic shows the palindromic sequences "seen" by
five restriction enzymes (named in blue) commonly used in recombinant DNA work.

Inverted Repeats
In these cases, two different segments of the double helix read the same but in opposite directions.
5' AGAACAnnnTGTTCT 3'
3' TCTTGTnnnACAAGA 5'
Inverted repeats are commonly found in
The DNA to which transcription factors bind.
The DNA sequence shown above is that of the glucocorticoid response element where n represents any nucleotide.
Transcription factors are often dimers of identical proteins homodimers so it is not surprising that each member of the pair
needs to "see" the same DNA sequence in the same orientation.
The DNA of many transposons is flanked by inverted repeats such as this one:
5' GGCCAGTCACAATGG..~400 nt..CCATTGTGACTGGCC 3'
3' CCGGTCAGTGTTACC..~400 nt..GGTAACACTGACCGG 5'
Inverted repeats at either end of retroviral gene sequences aid in inserting the DNA copy into the DNA of the host.
Duplicated Genes.
The human Y chromosome contains 7 sets of genes — each set containing from 2 to 6 nearly-identical genes — oriented back-
to-back or head-to-head; that is, they are inverted repeats like the portion shown here. (The dashes represent the thousands of
base pairs that separate adjacent palindromes.)
CTCCCACAACCCATGGGATTTGTG... 3'
GAGGGTGTTGGGTACCCTAAACAC... 5'
This orientation and redundancy may help ensure that a deleterious mutation in one copy of the set can be repaired using the
information in another copy of that set. All that is needed is to form a loop so that the two sequences line up side-by-side.
Repairs can then be made (probably by the mechanism of homologous recombination). Here, for example, the single
difference in the sequences can be eliminated (red for blue or vice versa).

9.10.1 https://bio.libretexts.org/@go/page/4892
This page titled 9.10: Palindromes is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

9.10.2 https://bio.libretexts.org/@go/page/4892
9.11: Cell-specific gene expression

Figure 9.11.2 Even-skipped gene courtesy of Peter A. Lawrence and Blackwell Scientific Publications
An example: Make Drosophila transgenic for recombinant DNA containing:
the Z gene for beta-galactosidase
even-skipped (eve), (another homeobox gene).
Any cell with the transcription factors for turning on the even-skipped promoter will begin to make beta-galactosidase. Given the
proper substrate, the enzyme produces a colored product.
The above photomicrograph shows 7 bands of this colored product identifying the cells that were expressing the even-skipped gene.
This event was "reported" by the lacZ gene. The 7 dark stripes reveal regions that alternate with the 7 bands formed by the cells
expressing fushi-tarazu.

Green fluorescent protein (GFP)

In nature, green fluorescent protein (GFP) is produced by, Aequorea victoria, the Pacific Northwest jellyfish. The protein has
become of great interest to cell and molecular biologists because it can reveal gene expression in living cells.
This is done by fusing the gene for GFP to the gene whose expression you are interested in. When that gene is turned on in a cell,
not only is its protein synthesized, but GFP is synthesized as well. Illuminating the cells with near-ultraviolet light causes them to
fluoresce a bright green. In this way, the experimenter can see when and where the gene is expressed in the living organism.

DNA Chips
All the methods described so far are limited to monitoring the expression of one or, at most, a few genes. But as conditions change
in a cell, the transcription and translation of literally hundreds of genes may be altered.
Thanks to the marriage of
semiconductor chip technology
automated synthesis of oligodeoxynucleotides
automated fluorescence scanners
computer software,
it is now possible to monitor the activity of literally thousands of genes in one kind of cell. For examples:
mammalian cells when they are transferred from a "minimal" culture medium to one enriched in growth factors;
the skeletal muscles of mice as they age.

The Chip

Figure 9.11.3 DNA chip

Examine published gene sequences.
For each gene, pick out ~20 different stretches of ~25 nucleotides that seem characteristic of that gene.
Synthesize oligodeoxynucleotides corresponding to these.
Also synthesize oligodeoxynucleotides for each of the above that have one nucleotide altered (usually near the middle). These
will provide a control.

9.11.1 https://bio.libretexts.org/@go/page/4893
 Using robotic chip-making machines, spot these oligonucleotides individually in arrays, each spot receiving millions of copies
that are fixed to the chip surface.
With the partial completion of the human genome project, three companies are now selling DNA chips containing from 36,000 to
50,000 pieces of DNA thought to represent different human genes.

The Assay
Harvest your cells. Presumably they are expressing a characteristic subset of their genes; that is, transcribing them into
messenger RNA (mRNA) molecules.
Extract the RNA.
Make complementary DNA (cDNA) by treating the RNA mixture with reverse transcriptase.
Transcribe the cDNA back into now much-amplified RNA.
Attach fluorescent tags to the RNA.
Flood the chip with this mixture.
RNAs finding their complementary sequences on the chip will bind to them. (They will bind less strongly to adjacent spots with
the single-nucleotide change if the binding is truly specific.
Illuminate the chip and automatically record the intensities of the color at each spot.
Use a computer to analyze the pattern.

Results of monitoring genome-wide expression

This work was reported by V. R. Iyer, et al in the 1 January 1999 issue of Science. It involved the monitoring the expression of
8613 different genes.
Mice raised on a restricted diet did not show such dramatic shifts in gene expression as they aged. This fits well with data that
mice on restricted diets age more slowly than those on rich diets.

This page titled 9.11: Cell-specific gene expression is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

9.11.2 https://bio.libretexts.org/@go/page/4893
9.12: Imprinted Genes
Imprinted genes are genes whose expression is determined by the parent that contributed them. Imprinted genes violate the usual
rule of inheritance that both alleles in a heterozygote are equally expressed.
Examples of the usual rule:
If a child inherits the gene for blood group A from either parent and the gene for group B from the other parent, the child's
blood group will be AB.
If a child inherits the gene encoding hemoglobin A from either parent and the gene encoding hemoglobin S from the other
parent, the child's red blood cells will contain roughly equal amounts of the two types of hemoglobin.
But there are a few exceptions to this rule. A small number of genes in mammals (~80 of them at a recent count) and in
angiosperms have been found to be imprinted. Because most imprinted genes are repressed, either
the maternal (inherited from the mother) allele is expressed exclusively because the paternal (inherited from the father) allele
is imprinted or
vice versa.
The process begins during gamete formation when
in males certain genes are imprinted in developing sperm and
in females, others are imprinted in the developing egg.
All the cells in a resulting child will have the same set of imprinted genes from both its father and its mother EXCEPT for those
cells ("germplasm") that are destined to go on to make gametes. All imprints — both maternal and paternal — are erased in them.

Examples
IGF2
— the gene encoding the insulin-like growth factor-2
In humans (and other mammals like mice and pigs) the IGF2 allele inherited from the father (paternal) is expressed; the allele
inherited from the mother is not.
If both alleles should begin to be expressed in a cell, that cell may develop into a cancer.

IGF2r
— the gene encoding the cell receptor for Igf-2
In mice the IGF2r allele inherited from the mother is expressed; that from the father is not. Differential imprinting accounts for
this, and the mechanism is described below.

XIST
— the gene encoding the RNA that converts one of the X chromosomes in a female cell into an inactive Barr body. This process is
random in the cells of the female fetus and thus is NOT an example of imprinting. However, all the cells of her extraembryonic
membranes (which form the amnion, placenta, and umbilical cord) have the father's X chromosome inactivated. Imprinting of the
XIST locus accounts for this.

Mechanism of parental imprinting

The process of imprinting starts in the gametes where the allele destined to be inactive in the new embryo (either the father's or the
mother's as the case may be) is "marked". The mark appears to be methylation of the DNA in the promoter(s) of the gene.
Methyl groups are added to cytosines (Cs) in the DNA. When this occurs at stretches of alternating Cs and Gs
called CpG sites in a promoter, it prevents binding of transcription factors to the promoter thus shutting down
expression of the gene.
Although methylation seems to be the imprinting signal, keeping the gene shut down may require the production of RNA.
Methylation — and thus inactivation — of the promoters of tumor suppressor genes is frequently found in cancer cells.

9.12.1 https://bio.libretexts.org/@go/page/4894
The IGF2r gene

Figure 9.12.1 the IGF2r gene

A report in Nature (16 October 1997) by Wutz et al, reveals that:

In the mother's (maternal) copy of the gene,

there is an upstream (left) promoter that is unmethylated and active
binding of transcription factors to this upstream promoter enables transcription of the sense strand of the gene to produce Igf2r
messenger RNA.
There is also a downstream set of CpG sites that are methylated
In the father's (paternal) copy of the IGF2r gene (the imprinted version)
the promoter for IGF2r transcription is methylated (and inactive),
but the downstream promoter is unmethylated and active.
Transcription of the antisense strand from the downstream promoter produces an antisense RNA (a long noncoding RNA) that
participates in shutting his gene down.

XIST
The XIST locus on the X chromosome encodes a long noncoding RNA that shuts down all (or almost all) of the other genes on the
chromosome, converting it into an inactive Barr body.

Is imprinting important?
Yes.
Deliberate (in mice) or accidental (in humans) inheritance of two copies of a particular chromosome from one parent and none
from the other parent is usually fatal (even though a complete genome is present).
Inheritance of two copies of one of mother's genes and no copy of the father's (or vice versa) can produce serious
developmental defects.
Failure to inherit several nonimprinted genes on the father's chromosome #15 causes a human congenital disorder called
Prader-Willi syndrome.
Absence or mutation of a nonimprinted gene (UBE3A) on the mother's chromosome #15 causes Angelman syndrome.
Failure of imprinting in somatic cells may lead to cancer.
The cancerous cells in some cases of a malignancy called Wilms´ tumor and many cases of colon cancer have both copies
of the IGF2 gene expressed (where only one, the father's, should be).
Reduced methylation — and hence increased expression — of proto-oncogenes can lead to cancer, while
increased methylation — and hence decreased expression — of tumor suppressor genes can also do so.

Imprinting and Parthenogenesis

Imprinting is the reason that parthenogenesis ("virgin birth") does not occur in mammals. Two complete female genomes cannot
produce viable young because of the imprinted genes. For example, the embryo needs the father's Igf2 gene because the mother's
copy has been imprinted and is inactive.
An insulator — with a bound protein designated CTCF ("CCCTC binding factor") (named for a nucleotide sequence found in
all insulators) — prevents her Igf2 gene from interacting with the enhancers needed to turn it ON.
The father's copy of the gene can be turned on because methylation of his insulator prevents binding by CTCF so the enhancers
can interact with the gene.

9.12.2 https://bio.libretexts.org/@go/page/4894
However, two healthy laboratory mice have been produced by parthenogenesis; that is, containing two female (haploid) genomes.
(See Kono, T. et al., Nature, 22 April 2004.)
This was done by fusing two oocytes (thus each cell haploid):
a normal oocyte with its imprinted (inactivated) Igf2 gene
an immature oocyte
harvested before imprinting occurs and
containing a deletion of the insulator that blocks enhancer activation of the Igf2 gene. Thus the Igf2 gene from this oocyte
could be expressed in the developing embryo.
Out of several hundred attempts, two resulting blastocysts not only implanted successfully in a surrogate mother but went on to be
born normally. One even grew up and had babies of her own.

Imprinting in Plants
Some genes in the endosperm of angiosperms are imprinted by the addition of methyl groups. For some, both maternal copies
(endosperm is 3n) are expressed (demethylated) while the male allele remains shut down. For other genes, it is the female alleles
that are imprinted and thus not expressed while the male allele is functional.

This page titled 9.12: Imprinted Genes is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

9.12.3 https://bio.libretexts.org/@go/page/4894
9.13: Ribozymes
Until about 20 years ago, all known enzymes were proteins. But then it was discovered that some RNA molecules can act as
enzymes; that is, catalyze covalent changes in the structure of substrates (most of which are also RNA molecules). Catalytic RNA
molecules are called ribozymes. Most classes of RNA, including transfer RNA (tRNA), ribosomal RNA (rRNA), and messenger
RNA (mRNA) are transcribed as precursors that are larger than the final product. These precursors often contain "head" (5') and
"tail" (3') sequences and intron sequences that must be removed to make the final product. Some of the processing steps employ
other RNA molecules (always associated with proteins).

Ribonuclease P
Almost all living things synthesize an enzyme — called Ribonuclease P (RNase P) — that cleaves the head (5') end of the
precursors of transfer RNA (tRNA) molecules. In bacteria, ribonuclease P is a heterodimer containing a molecule of RNA and one
of protein. Separated from each other, the RNA retains its ability to catalyze the cleavage step (although less efficiently than the
intact dimer), but the protein alone cannot do the job.

Figure 9.13.1: Crystal structure of a bacterial ribonuclease P holoenzyme in complex with tRNA (yellow), showing metal ions
involved in catalysis (pink spheres), PDB: 3Q1R. (CC BY SA 30; RNAMacGyver).

Group I Introns
Some ribosomal RNA (rRNA) genes, including those in the mitochondrial genome of certain fungi (e.g., yeast), in some
chloroplast genomes and in the nuclear genome of some "lower" eukaryotes (e.g., the ciliated protozoan Tetrahymena thermophila
and plasmodial slime moldPhysarum polycephalum) contain introns that must be spliced out to make the final product.
The splicing reaction is self-contained; that is, the intron — with the help of associated proteins — splices itself out of the
precursor RNA. Once excision of the intron and splicing of the adjacent exons are completed, the story is over. In other words,
although the action is catalyzed by the RNA, only a single molecule of substrate is involved (unlike protein enzymes that
repeatedly catalyze a reaction).
However, synthetic versions of Group I introns made in the laboratory can — in vitro — act repeatedly; that is, like true enzymes.
The DNA of some Group I introns includes an open reading frame (ORF) that encodes a transposase-like protein that can make a
copy of the intron and insert it elsewhere in the genome. All the Group I introns share a characteristic secondary structure and
mode of action that distinguishes them from the next group.

Group II Introns
Some messenger RNA (mRNA) genes in the mitochondrial genome of yeast and other fungi (encoding the proteins cytochrome b
and subunits of cytochrome c oxidase) and in some chloroplast genomes also contain self-splicing introns. Because their
secondary structure and the details of the splicing reaction differ from the rRNA introns discussed above, these are called Group II

9.13.1 https://bio.libretexts.org/@go/page/4895
introns. The DNA of some Group II introns also includes an open reading frame (ORF) that encodes a transposase-like protein that
can make a copy of the intron and insert it elsewhere in the genome.

Spliceosomes
Spliceosomes remove introns and splice the exons of most nuclear genes. They are composed of 5 kinds of small nuclear RNA
(snRNA) molecules and over 100 different protein molecules. It is the RNA — not the protein — that catalyzes the splicing
reactions. The molecular details of the reactions are similar to those of Group II introns, and this has led to speculation that this
splicing machinery evolved from them.

Viroids
Viroids are DNA molecules that infect plant cells as conventional viruses do, but are far smaller (one has only 246 nucleotides).
They are naked; that is, they are not encased in a capsi like viruses. Some viroidlike molecules get into the cell as passengers inside
a conventional plant virus. These are called virusoids or viroidlike satellite RNAs.
In both cases, the molecules consists of single-stranded RNA whose ends are covalently bonded to form a circle. There are several
regions where base-pairing occurs across adjacent portions of the molecule. New viroids and virusoids are synthesized by the host
cell as long precursors in which the viroid structure is tandemly repeated. These repeats must be cut out and ligated to form the
final product. Most virusoids and at least one viroid are self-splicing; that is, they can cut themselves out of the precursor and ligate
their ends without the aid of any host enzymes. Thus they represent another class of ribozyme.
Both viroids and virusoids are responsible for a number of serious diseases of economically important plants, e.g. the coconut palm
and chrysanthemums. (The problem is so severe with chrysanthemums that all growers in the U.S. now secure their stock from a
few companies that raise the plants in "clean" rooms using stringent precautions to prevent infection by the viroid.)

This page titled 9.13: Ribozymes is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

9.13.2 https://bio.libretexts.org/@go/page/4895
 CHAPTER OVERVIEW
Unit 10: Mutation
10.1: Mutations - Causes and Significance
10.2: Testing for Mutagenic Chemicals in Bacteria and Mice
10.3: Radiation and its effect on DNA
10.4: Transposons - "jumping genes"

This page titled Unit 10: Mutation is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1
10.1: Mutations - Causes and Significance
In the living cell, DNA undergoes frequent chemical change, especially when it is being replicated (in S phase of the eukaryotic
cell cycle). Most of these changes are quickly repaired. Those that are not result in a mutation. Thus, mutation is a failure of DNA
repair.

Single-base substitutions
A single base, say an A, becomes replaced by another. Single base substitutions are also called point mutations. (If one purine [A
or G] or pyrimidine [C or T] is replaced by the other, the substitution is called a transition. If a purine is replaced by a pyrimidine
or vice-versa, the substitution is called a transversion.)

Missense mutations
With a missense mutation, the new nucleotide alters the codon so as to produce an altered amino acid in the protein product.

 Deasese: Sickle Cell anemia

The replacement of A by T at the 17th nucleotide of the gene for the beta chain of hemoglobin changes the codon GAG (for
glutamic acid) to GTG (which encodes valine). Thus the 6th amino acid in the chain becomes valine instead of glutamic acid.

Figure 10.1.1 Sickle Cell Mutation

Nonsense mutations
With a nonsense mutation, the new nucleotide changes a codon that specified an amino acid to one of the STOP codons (TAA,
TAG, or TGA). Therefore, translation of the messenger RNA transcribed from this mutant gene will stop prematurely. The
earlier in the gene that this occurs, the more truncated the protein product and the more likely that it will be unable to function.

 Cystic Fibrosis
Here is a sampling of mutations that have been found in patients with cystic fibrosis. Each of these mutations occurs in a huge
gene that encodes a protein (of 1480 amino acids) called the cystic fibrosis transmembrane conductance regulator (CFTR).
The protein is responsible for transporting chloride and bicarbonate ions through the plasma membrane. The gene encompasses
over 188,000 base pairs on chromosome 7 embedded in which are 27 exons encoding the protein. The numbers in the mutation
column represent the number of the nucleotides affected. Defects in the protein cause the various symptoms of the disease.
Unlike sickle-cell disease, then, no single mutation is responsible for all cases of cystic fibrosis. People with cystic fibrosis
inherit two mutant genes, but the mutations need not be the same.

Figure 10.1.2 Cystic Fibrosis Mutation

10.1.1 https://bio.libretexts.org/@go/page/4896
 In one patient with cystic fibrosis (Patient B), the substitution of a T for a C at nucleotide 1609 converted a glutamine codon
(CAG) to a STOP codon (TAG). The protein produced by this patient had only the first 493 amino acids of the normal chain
of 1480 and could not function.

Silent mutations
Most amino acids are encoded by several different codons. For example, if the third base in the TCT codon for serine is changed
to any one of the other three bases, serine will still be encoded. Such mutations are said to be silent because they cause no change
in their product and cannot be detected without sequencing the gene (or its mRNA).

Splice-site mutations
The removal of intron sequences, as pre-mRNA is being processed to form mRNA, must be done with great precision. Nucleotide
signals at the splice sites guide the enzymatic machinery. If a mutation alters one of these signals, then the intron is not removed
and remains as part of the final RNA molecule. The translation of its sequence alters the sequence of the protein product.

Insertions and Deletions (Indels)

Extra base pairs may be added (insertions) or removed (deletions) from the DNA of a gene. The number can range from one to
thousands. Collectively, these mutations are called indels.

Figure 10.1.3: Frameshifting

Indels involving one or two base pairs (or multiples of two) can have devastating consequences to the gene because translation of
the gene is "frameshifted". This figure shows how by shifting the reading frame one nucleotide to the right, the same sequence of
nucleotides encodes a different sequence of amino acids. The mRNA is translated in new groups of three nucleotides and the
protein specified by these new codons will be worthless. Scroll up to see two other examples (Patients C and D).
Frameshifts often create new STOP codons and thus generate nonsense mutations. Perhaps that is just as well as the protein would
probably be too garbled anyway to be useful to the cell.
Indels of three nucleotides or multiples of three may be less serious because they preserve the reading frame (see the above figure).
However, a number of inherited human disorders are caused by the insertion of many copies of the same triplet of nucleotides.
Huntington's disease and the fragile X syndrome are examples of such trinucleotide repeat diseases.

 Disease: Fragile X Syndrome

Several disorders in humans are caused by the inheritance of genes that have undergone insertions of a string of 3 or 4
nucleotides repeated over and over. A locus on the human X chromosome contains such a stretch of nucleotides in which the
triplet CGG is repeated (CGGCGGCGGCGG, etc.). The number of CGGs may be as few as 5 or as many as 50 without
causing a harmful phenotype (these repeated nucleotides are in a noncoding region of the gene). Even 100 repeats usually
cause no harm. However, these longer repeats have a tendency to grow longer still from one generation to the next (to as many
as 4000 repeats).

Figure 10.1.4 Fragile X Syndrome

This causes a constriction in the X chromosome, which makes it quite fragile. Males who inherit such a chromosome (only
from their mothers, of course) show a number of harmful phenotypic effects including mental retardation. Females who inherit

10.1.2 https://bio.libretexts.org/@go/page/4896
 a fragile X (also from their mothers; males with the syndrome seldom become fathers) are only mildly affected.
The above image shows the pattern of inheritance of the fragile X syndrome in one family. The number of times that the
trinucleotide CGG is repeated is given under the symbols. The gene is on the X chromosome, so women (circles) have two
copies of it; men (squares) have only one. People with a gene containing 80–90 repeats are normal (light red), but this gene is
unstable, and the number of repeats can increase into the hundreds in their offspring. Males who inherit such an enlarged gene
suffer from the syndrome (solid red squares). (Data from C. T. Caskey, et al.).

Polyglutamine Diseases
In these disorders, the repeated trinucleotide is CAG, which adds a string of glutamines (Gln) to the encoded protein. These have
been implicated in a number of central nervous system disorders including
Huntington's disease (where the protein called huntingtin carries the extra glutamines). The abnormal protein increases the
level of the p53 protein in brain cells causing their death by apoptosis.
some cases of Parkinson's disease where the extra glutamines are in the protein ataxin-2.

Muscular Dystrophy
Some forms of muscular dystrophy that appear in adults are caused by tri- or tetranucleotide, e.g. (CTG)n and (CCTG)n, repeats
where n may run into the thousands. The huge RNA transcripts that result interfere with the alternative splicing of other transcripts
in the nucleus.

Amyotrophic Lateral Sclerosis (ALS)

ALS is a neurodegenerative disorder leading to dementia and muscle weakness. (ALS is often called "Lou Gehrig's disease" after
the baseball player who died from it.)
The most common mutation in ALS is an expansion of the number of repeats of the hexanucleotide GGGGCC in a gene on
chromosome 9 from the normal two, or at least fewer than three dozen, to hundreds or even several thousand. Translation of both
the sense and the antisense strands containing these repeats (and in all 3 reading frames; there is no ATG start codon) produces
polymers with long strings of gly-ala, gly-pro, gly-arg (from the sense strand) as well as pro-ala, another pro-gly, and pro-arg from
the antisense strand. These proteins, especially those containing arginine (arg) form aggregates that damage brain cells.

Duplications
Duplications are a doubling of a section of the genome. During meiosis, crossing over between sister chromatids that are out of
alignment can produce one chromatid with a duplicated gene and the other (not shown) with the two genes with deletions. In the
case shown here, unequal crossing over created a second copy of a gene needed for the synthesis of the steroid hormone
aldosterone.

Figure 10.1.5 Gene Duplication

However, this new gene carries inappropriate promoters at its 5' end (acquired from the 11-beta hydroxylase gene) that cause it to
be expressed more strongly than the normal gene. The mutant gene is dominant: all members of one family (through four
generations) who inherited at least one chromosome carrying this duplication suffered from high blood pressure and were prone to
early death from stroke.
Gene duplication has also been implicated in several human neurological disorders.
Gene duplication has occurred repeatedly during the evolution of eukaryotes. Genome analysis reveals many genes with similar
sequences in a single organism. Presumably these paralogous genes have arisen by repeated duplication of an ancestral gene.
Such gene duplication can be beneficial.
Over time, the duplicates can acquire different functions.

10.1.3 https://bio.libretexts.org/@go/page/4896
 The proteins they encode can take on different functions; for example, if the original gene product carried out two different
functions (see "pleiotropy"), each duplicated gene can now specialize at one function and do a better job at it than the
parental gene.
But even if they do not, changes in the regulatory sequences of the genes (promoters and enhancers) may cause the same
protein to be expressed at different times, at different levels, and/or in different tissues.
Either situation can provide the basis for adaptive evolution.
But even while two paralogous genes are still similar in sequence and function, their existence provides redundancy ("belt and
suspenders"). This may be a major reason why knocking out genes in yeast, "knockout mice", etc. so often has such a mild
effect on the phenotype. The function of the knocked out gene can be taken over by a paralog.
After gene duplication, random loss — or inactivation — of one of these genes at a later time in
one group of descendants
different from the loss in another group
could provide a barrier (a "post-zygotic isolating mechanism") to the two groups interbreeding. Such a barrier could cause
speciation: the evolution of two different species from a single ancestral species.

Translocations
Translocations are the transfer of a piece of one chromosome to a nonhomologous chromosome. Translocations are often
reciprocal; that is, the two nonhomologues swap segments.

Figure 10.1.6 Translocations

Translocations can alter the phenotype is several ways:
the break may occur within a gene destroying its function
translocated genes may come under the influence of different promoters and enhancers so that their expression is altered. The
t(8;14) translocation in Burkitt's lymphoma (figure) is an example.
the breakpoint may occur within a gene creating a hybrid gene. This may be transcribed and translated into a protein with an N-
terminal of one normal cell protein coupled to the C-terminal of another. The Philadelphia chromosome found so often in the
leukemic cells of patients with chronic myelogenous leukemia (CML) is the result of a translocation which produces a
compound gene (bcr-abl).

Frequency of Mutations
Mutations are rare events. This is surprising. Humans inherit 3 x 109 base pairs of DNA from each parent. Just considering single-
base substitutions, this means that each cell has 6 billion (6 x 109) different base pairs that can be the target of a substitution.
Single-base substitutions are most apt to occur when DNA is being copied; for eukaryotes that means during S phase of the cell
cycle.
No process is 100% accurate. Even the most highly skilled typist will introduce errors when copying a manuscript. So it is with
DNA replication. Like a conscientious typist, the cell does proofread the accuracy of its copy. But, even so, errors slip through. It
has been estimated that in humans and other mammals, uncorrected errors (= mutations) occur at the rate of about 1 in every 50
million (5 x 107) nucleotides added to the chain. (Not bad — I wish that I could type so accurately.) But with 6 x 109 base pairs in
a human cell, that means that each new cell contains some 120 new mutations.
Should we be worried? The evidence is not clear. Only 1.2% of our DNA encodes the exons of our proteome, and for a long time it
was thought that much of the rest was "junk" DNA. Mutations in it would most likely be harmless. And even in coding regions, the
existence of synonymous codons could result in the altered (mutated) gene still encoding the same amino acid in the protein. But it

10.1.4 https://bio.libretexts.org/@go/page/4896
now appears that as much as 80% of our DNA seems to participate in regulating which genes are expressed, and how strongly, in
each of the multitude of differentiated cell types in our body as each responds to the signals (nutrients, hormones, etc.) it receives.
So mutations in these regions might well have harmful, if subtle, effects.
As more vertebrate genomes are sequenced, it turns out that some of these stretches of DNA that do not encode proteins none-the-
less have been remarkably conserved during vertebrate evolution. Some of these regions have accumulated even fewer mutations
than protein-encoding genes have. This suggests that these sequences are extremely important to the welfare of the organism.
However, other regions of the genome seem able to sustain point mutations with no detectible harm.
Recent advances have enabled the coding portions of the genome of single cells to be sequenced. Preliminary results indicate that
each normal cell in an adult has accumulated ~20 somatic mutations, and that its collection of mutations differs from cell to cell.
Cancer cells accumulate many more mutations (often in the hundreds).
How can we measure the frequency at which phenotype-altering mutations occur? In humans, it is not easy.
First we must be sure that the mutation is newly-arisen. (Some populations have high frequencies of a particular mutation, not
because the gene is especially susceptible, but because it has been passed down through the generations from a early "founder".
Recessive mutations (most of them are) will not be seen except on the rare occasions that both parents contribute a mutation at
the same locus to their child.
This leaves us with estimating mutation frequencies for genes that are inherited as
autosomal dominants
X-linked recessives; that is, recessives on the X chromosome which will be expressed in males because they inherit only
one X chromosome.

Examples
Frequency is expressed as the frequency of mutations occurring at that locus in the gametes
Autosomal dominants
Retinoblastoma
in the RB gene: about 8 per million (8 x 10-6)
Osteogenesis imperfecta
in one or the other of the two genes that encode Type I collagen: about 1 per 100,000 (10-5)
Inherited tendency to polyps (and later cancer) in the colon.
in a tumor suppressor gene (APC): ~10-5
X-linked recessives
Hemophilia A
~3 x 10-5 (the Factor VIII gene)
Duchenne Muscular Dystrophy (DMD)
>8 x 10-5 (the dystrophin gene)
Why should the mutation frequency in the dystrophin gene be so much larger than most of the others? It's probably a matter
of size. The dystrophin gene stretches over 2.4 x 106 base pairs of DNA. This is almost 0.1% of the entire human genome!
Such a huge gene offers many possibilities for damage.

Measuring Mutation Rate

The frequency with which a given mutation is seen in a population (e.g., the mutation that causes cystic fibrosis) provides only a
rough approximation of mutation rate — the rate at which fresh mutations occur — because of historical factors at work such as
natural selection (positive or negative), drift, and founder effect. In addition, most methods for counting mutations require that the
mutation have a visible effect on the phenotype. Thus
many (but not all) mutations in noncoding DNA
mutations that produce
synonymous codons (encode the same amino acid)
or, sometimes, new codons that encode a chemically-similar amino acid
mutations which disrupt a gene whose functions are redundant; that is, can be compensated for by other genes

10.1.5 https://bio.libretexts.org/@go/page/4896
will not be seen. But now these problems have been largely solved. The story is told in a report by D. R. Denver, et al. in the 5
August 2004 issue of Nature.

 C. elegans

The Procedure
Their organism = C. elegans
Its advantages
compact genome
hermaphroditic — it fertilizes its own eggs and any new germline mutation will soon be either lost or appear on both
homologous chromosomes.
rapid generation time (4 days)
They created 198 different experimental lines of worms.
They grew them under optimum conditions to minimize any effects of natural selection.
Only one offspring was kept at each new generation.
Each line was maintained for several hundred generations.
At the end of this time, random stretches of DNA
derived from multiple locations on each of the six C. elegans chromosomes and
totalling an average of ~21 thousand base pairs for each line
were sequenced from each of the 198 lines and the sequences compared with the same loci in natural populations of C.
elegans.
Results
Examining the DNA sequences from their experimental animals (a total of over 4 million base pairs!), and comparing them
with the controls, turned up a total of 30 mutations.
17 of these were insertions or deletions ("indels')
7 in exons — all but 2 of which produced frameshifts and a premature STOP codon.
10 in introns or between genes
13 of these were single base substitutions ("point" mutations)
3 in exons : one "silent" producing a synonymous codon; two that changed the encoded amino acid.
10 in introns or between genes
Calculating Mutation Rate
From these results I have pooled their data to calculate an approximate rate at which spontaneous mutations occur throughout
the genome.
Mutation Rate = # of mutations observed [30] ÷ (# of experimental lines [198]) x (average # of generations [339]) x (average #
of base pairs sequenced [~21,000])
yielding a rate of 2.1 x 10-8 mutations per base pair per generation.
The total C. elegans genome contains some 108 base pairs so this tells us that two new germline mutations occur somewhere
in each of C. elegans's two haploid genomes in each generation.
A similar analysis for Drosophila (whose genome is about the same size as that of C. elegans) showed a similar mutation rate:
~10-8 mutations per base pair per generation. As for the green plant Arabidopsis thaliana, its spontaneous mutation rate is
slightly lower: ~7 x 10-9 mutations per base pair per generation.
In the 30 April 2010 issue of Science, Roach, J. C., et al., reported that the rate for humans is in the same range: ~1.1 x 10-8
mutations per base pair in the haploid genome. With a diploid genome of 6 x 109 base pairs, that works out to some 70 new
mutations in each child. They derived these numbers from comparing the complete genome sequence of two children and their
parents.
In the 20 July 2012 issue of Cell, Wang, J., et al. reported the results of sequencing 8 individual sperm cells from a 40-year-old
man. They found a mutation rate ranging from 2.0 x 10-8 to 3.8 x 10-8.

10.1.6 https://bio.libretexts.org/@go/page/4896
 Should we be worried about such spontaneous mutation rates? Probably not too much. With our high proportion of noncoding
DNA, many mutations will occur in regions that will have no effect on our phenotype. Evidence: out of a total of 251
mutations found in the 8 sperm cells, only 3 were missense mutations altering a gene product. However, even in noncoding
DNA, point mutations may affect the expression of genes, so perhaps as many as 10% of the point mutations a child inherits
may have harmful, if subtle, effects.

Males Contribute More Mutations Than Females

If most mutations occur during S phase of cell division, then males should be more at risk. This is because only two dozen (24) or
so mitotic divisions occur from the fertilized egg that starts a little girl's embryonic development and the setting aside of her future
eggs (which is done long before she is even born). Furthermore, the sperm of a 30-year old man, in contrast, are the descendants of
at least 400 mitotic divisions since the fertilized egg that formed him.
So, fathers are more likely than mothers to transmit newly-formed mutations to their children. The sperm of a 25-year-old man
might carry some 45 new mutations. This number rises at a rate of about 1 per year, so the sperm of a 40-year-old man may
transmit some 60 new mutations to his children (about 20 of these in coding regions). No matter what the age of the mother, she
transmits only about 15 new mutations to her offspring. (But chromosomal aberrations, like aneuploidy, are more apt to arise in
eggs than in sperm, and the incidence of these increases with maternal age.) These data explain why the children of aged fathers
suffer more genetic disorders than those of young fathers.

Somatic vs. Germline Mutations

The significance of mutations is profoundly influenced by the distinction between germline and soma. Mutations that occur in a
somatic cell, in the bone marrow or liver for example, may
damage the cell
make the cell cancerous
kill the cell
Whatever the effect, the ultimate fate of that somatic mutation is to disappear when the cell in which it occurred, or its owner,
dies.
Germline mutations, in contrast, will be found in every cell descended from the zygote to which that mutant gamete contributed.
If an adult is successfully produced, every one of its cells will contain the mutation. Included among these will be the next
generation of gametes, so if the owner is able to become a parent, that mutation will pass down to yet another generation.

This page titled 10.1: Mutations - Causes and Significance is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by
John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

10.1.7 https://bio.libretexts.org/@go/page/4896
10.2: Testing for Mutagenic Chemicals in Bacteria and Mice
Ames test

Figure 10.2.2 Blue Mouse

Big Blue mice are transgenic for a segment of DNA that contains the DNA of bacteriophage lambda, a virus that infects E. coli,
and which serves here as the vector for 3 genetic elements from the lac operon of E. coli:
the lacI gene
the operator of the operon
the beta-galactosidase (lacZ) gene

The Assay
The transgenic mice are given repeated doses of the suspected carcinogen for a week or two. If the chemical is mutagenic, it will
cause random mutations throughout the genome of each mouse cell. If a mutation occurs in either the lacI gene (which encodes the
lac repressor) or the operator,
the gene (lacZ) for beta-galactosidase will no longer be repressed. To detect this,
The DNA is extracted from the tissues of the treated mouse.
The vector is isolated and used to make functional bacteriophages.
E. coli cells are mixed with the bacteriophage and spread on a solid culture medium.
The bacteriophages infect and destroy ("lyze") the E. coli cells.
This causes clear circular zones, called plaques, to appear in a "lawn" of bacteria.
Before they die, cells that have been infected by bacteriophages carrying a mutated lacI or operator will produce beta-
galactosidase.
This reacts with a substrate in the culture medium turning it blue.
Bacteriophages with unmutated genes produce colorless plaques because no beta-galactosidase is synthesized.
Count both colorless and blue plaques.
The number of blue plaques divided by the total number of plaques gives the mutation frequency.

Figure 10.2.4 Blue Plaque courtesy of Stratagene

This photograph shows one mutant (blue) plaque on a lawn of E. coli containing many non-mutant (clear) plaques.

This page titled 10.2: Testing for Mutagenic Chemicals in Bacteria and Mice is shared under a CC BY 3.0 license and was authored, remixed,
and/or curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history
is available upon request.

10.2.1 https://bio.libretexts.org/@go/page/4897
10.3: Radiation and its effect on DNA
For biologists, the most significant forms of radiation are light, heat, and ionizing radiation. Ionizing radiation can penetrate cells and create ions in the cell contents. These, in turn, can cause
permanent alterations in DNA (i.e., mutations). Ionizing radiation includes X rays, gamma rays, neutrons, electrons ("beta" particles), and alpha particles (helium nuclei).

Units of measurement
rad: The rad represents a certain dose of energy absorbed by 1 gram of tissue. It is a unit of concentration. So if we could uniformly expose the entire body to radiation, the number of rads received
would be the same whether we were speaking of a single cell, an organ (e.g., an ovary) or the entire body (just as the concentration of salt in sea water is the same whether we consider a cupful or
an entire ocean).
rem: Some forms of radiation are more efficient than others transferring their energy to the cell. To have a level playing field, it is convenient to multiply the dose in rads by a quality factor (Q)
for each type of radiation. The resulting unit is the rem ("roentgen-equivalent man"). Thus, rem = rad x Q. X rays and gamma rays have a Q about 1, so the absorbed dose in rads is the same
number in rems. Neutrons have a Q of about 5 and alpha particles have a Q of about 20. An absorbed dose of, say, 1 rad of these is equivalent to 5 rem and 20 rem respectively.
The sievert (Sv) and gray (Gy): Despite the years of high-quality research reported in rems and millirems (mrem, 10-3 rem), the International Commission on Radiation Units and Measurements
wants us to give up the rad in favor of the gray (Gy), a unit 100 times larger. Similarly, the rem is to be replaced by the sievert (Sv), again so that 100 rem = 1 Sv. So I will try to express all
radiation doses in a single unit, the millisievert (mSv).
Table 10.2.1: An assortment of typical radiation doses (in mSv)
Used to destroy the bone marrow in preparation for a marrow transplant (given over several days)

Approximate lethal dose ("LD50") if no treatment and given to the entire body in a short period

Causes radiation sickness (when absorbed in a short period)

When delivered in a single dose, increases the risk of developing cancer by 1%

Increase in lifetime dose to most heavily exposed people living near Chernobyl

Annual dose (excluding natural background) permitted for U.S. radiation workers

Average annual dose (excluding natural background) for medical X-ray technicians

Maximum permissible annual dose (excluding natural background and medical exposure) to general public

Average annual dose of natural background radiation, worldwide

Natural background, Boston, MA, USA (per year)(excluding radon)

Natural background, Denver, CO, USA (per year)(excluding radon)

Additional annual dose if you live in a brick rather than a wood house

Annual dose in some houses in Ramsar, Iran

Average dose to person living within 10 miles of Three-Mile Island (TMI) caused by the accident of 28 March 1979

Most heavily exposed person (a fisherman) near TMI

Approximate dose received by a person spending 1 year at the fence surrounding a nuclear power station

Average dose to each person in the U. S. population from nuclear power plants (per year)

Received by the brain during a set of dental x rays

Received by the colon during a barium enema

Received by the lungs during a chest x ray

Screening mammogram

Total dose received by the people living near the Fukushima Daiichi Nuclear Power Station in Japan during the first year after the reactors were damaged by a devastating tsunami.

Dose from a typical set of full-body computed tomography (CT) scans

Cardiac stress test using radioactive thallium

Typical dose received by the abdomen during a CT scan to diagnose appendicitis

Typical PET scan

Airline passenger crossing the U.S.

Flight crew flying regularly between New York and Tokyo (per year)

Hourly dose to skin holding piece of the original "Fiesta Ware" (a brand of pottery)

Annual dose to each person in the U. S. population from fallout (former weapons testing plus Chernobyl)

Estimated average annual radiation exposure from various sources (in millisieverts) of an inhabitant of the United States (total = 5.86 mSv). Individual exposures, especially to radon and medical
sources, vary widely from these average values. The use of medical imaging in the United States (some 67 million CT scans were performed here in 2006) has increased greatly in recent years. As for
radon, only the lungs are exposed as the alpha particles emitted by radon cannot penetrate other tissues. (Data from the National Council on Radiation Protection and Measurements, Bethesda, MD.)

Background Radiation
About 27% of our annual exposure to radiation is from background radiation (Figure 10.3.1) and originate from three primary sources:
1. Cosmic radiation (0.27 mSv). The value increases with altitude, so the dose for people in Denver, Colorado is about 0.50 mSv.
2. Rocks and soil (0.28 mSv). This value varies with the geology of a region: people in Louisiana get as little as 0.15 mSv/yr; people on the Colorado plateau (incl. Denver!) get 1.4 mSv/yr.
3. From within the body (0.4 mSv). Most of this comes from potassium-40. About 0.02% of the potassium in nature is in the form of the radioactive isotope 40K. Living tissue cannot discriminate
between radioactive and nonradioactive versions, so the same 0.02% of the total potassium in the body (about 1.7 g in a 70-kg person) is radioactive.

Figure 10.3.1 Radiation Pie Chart

10.3.1 https://bio.libretexts.org/@go/page/4898
This page titled 10.3: Radiation and its effect on DNA is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source content that was edited to the style and standards of the
LibreTexts platform; a detailed edit history is available upon request.

10.3.2 https://bio.libretexts.org/@go/page/4898
10.4: Transposons - "jumping genes"
Transposons are segments of DNA that can move around to different positions in the genome of a single cell. In the process, they
may cause mutations and increase (or decrease) the amount of DNA in the genome of the cell, and if the cell is the precursor of a
gamete, in the genomes of any descendants. These mobile segments of DNA are sometimes called "jumping genes" and there are
two distinct types. Class II transposons consist of DNA that moves directly from place to place. Class I transposons are
retrotransposons that first transcribe the DNA into RNA and then use reverse transcriptase to make a DNA copy of the RNA to
insert in a new location.

Class II Transposons
Class II transposons move by a "cut and paste" process: the transposon is cut out of its location (like command/control-X on your
computer) and inserted into a new location (command/control-V). This process requires an enzyme — a transposase — that is
encoded within some of these transposons.

Fig.10.4.1 Transposons
Transposase binds to both ends of the transposon, which consist of inverted repeats; that is, identical sequences reading in
opposite directions. They also bind to a sequence of DNA that makes up the target site. Some transposases require a specific
sequence as their target site; others can insert the transposon anywhere in the genome.
The DNA at the target site is cut in an offset manner (like the "sticky ends" produced by some restriction enzymes). After the
transposon is ligated to the host DNA, the gaps are filled in by Watson-Crick base pairing. This creates identical direct repeats at
each end of the transposon. Often transposons lose their gene for transposase. However, as long as somewhere in the cell there is a
transposon that can synthesize the enzyme, their inverted repeats are recognized and they, too, can be moved to a new location.

Miniature Inverted-repeat Transposable Elements (MITEs)

The recent completion of the genome sequence of rice and C. elegans has revealed that their genomes contain thousands of copies
of a recurring motif consisting of almost identical sequences of about 400 base pairs flanked by characteristic inverted repeats of
about 15 base pairs such as
5' GGCCAGTCACAATGG..~400 nt..CCATTGTGACTGGCC 3'
3' CCGGTCAGTGTTACC..~400 nt..GGTAACACTGACCGG 5'
MITEs are too small to encode any protein. Just how they are copied and moved to new locations is still uncertain. Probably larger
transposons that do encode the necessary enzyme and recognize the same inverted repeats are responsible. There are over 100,000
MITEs in the rice genome (representing some 6% of the total genome). Some of the mutations found in certain strains of rice are
caused by the insertion of a MITE in the gene. MITEs have also been found in the genomes of humans, Xenopus, and apples.

Transposons in Maize
The first transposons were discovered in the 1940s by Barbara McClintock who worked with maize (Zea mays, called "corn" in the
U.S.). She found that they were responsible for a variety of types of gene mutations, usually insertions and deletions (indels) and

10.4.1 https://bio.libretexts.org/@go/page/4899
translocations. Some of the mutations (c, bz) used as examples of how gene loci are mapped on the chromosome were caused by
transposons. In developing somatic tissues like corn kernels, a mutation (e.g., c) that alters color will be passed on to all the
descendant cells. This produces the variegated pattern which is so prized in "Indian corn". (Photo courtesy of Whalls Farms.) It
took about 40 years for other scientists to fully appreciate the significance of Barbara McClintock's discoveries. She was finally
awarded a Nobel Prize in 1983.

Figure 10.4.2: Transposons in Maize

Transposons in Drosophila
P elements are Class II transposons found in Drosophila. They do little harm because expression of their transposase gene is
usually repressed. However, when male flies with P elements mate with female flies lacking them, the transposase becomes active
in the germline producing so many mutations that their offspring are sterile. In nature this is no longer a problem. P elements seem
to have first appeared in Drosophila melanogaster about 50 years ago. Since then, they have spread through every population of the
species. Today flies lacking P elements can only be found in old strains maintained in the laboratory. P elements have provided
valuable tools for Drosophila geneticists. Transgenic flies containing any desired gene can be produced by injecting the early
embryo with an engineered P element containing that gene. Other transposons are being studied for their ability to create transgenic
insects of agricultural and public health importance.

Transposons in bacteria
Some transposons in bacteria carry — in addition to the gene for transposase — genes for one or more (usually more) proteins
imparting resistance to antibiotics. When such a transposon is incorporated in a plasmid, it can leave the host cell and move to
another. This is the way that the alarming phenomenon of multidrug antibiotic resistance spreads so rapidly. Transposition in these
cases occurs by a "copy and paste" mechanism. This requires an additional enzyme — a resolvase — that is also encoded in the
transposon itself. The original transposon remains at the original site while its copy is inserted at a new site.

Retrotransposons
Retrotransposons also move by a "copy and paste" mechanism but in contrast to the transposons described above, the copy is
made of RNA, not DNA. The RNA copies are then transcribed back into DNA — using a reverse transcriptase — and these are
inserted into new locations in the genome. Many retrotransposons have long terminal repeats (LTRs) at their ends that may
contain over 1000 base pairs in each. Like DNA transposons, retrotransposons generate direct repeats at their new sites of insertion.
In fact, it is the presence of these direct repeats that often is the clue that the intervening stretch of DNA arrived there by
retrotransposition. Some 50% of the entire human genome consists of retrotransposons.

LINEs (Long interspersed elements)

The human genome contains over one million LINEs (representing 19% of the genome). The most abundant of these belong to a
family called LINE-1 (L1). These L1 elements are DNA sequences that range in length from a few hundred to as many as 9,000
base pairs. Only about 50 L1 elements are functional "genes"; that is, can be transcribed and translated. The functional L1 elements
are about 6,500 bp in length and encode three proteins, including an endonuclease that cuts DNA and a reverse transcriptase that
makes a DNA copy of an RNA transcript.

 L1 activity

L1 activity proceeds as follows:

1. RNA polymerase II transcribes the L1 DNA into RNA.
2. The RNA is translated by ribosomes in the cytoplasm into the proteins.

10.4.2 https://bio.libretexts.org/@go/page/4899
 3. The proteins and RNA join together and reenter the nucleus.
4. The endonuclease cuts a strand of "target" DNA, often in the intron of a gene.
5. The reverse transcriptase copies the L1 RNA into L1 DNA which is inserted into the target DNA forming a new L1
element there.

Through this copy-paste mechanism, the number of LINEs can increase in the genome. The diversity of LINEs between individual
human genomes make them useful markers for DNA "fingerprinting". Variation occurs in the length of L1 elements: Transcription
of an active L1 element sometimes continues downstream into additional DNA producing a longer transposed element. Reverse
transcription of L1 RNA often concludes prematurely and produces a shortened transposed element.
While L1 elements are not functional, they may play a role in regulating the efficiency of transcription of the gene in which they
reside. Occasionally, L1 activity makes and inserts a copy of a cellular mRNA (thus a natural cDNA). Lacking introns as well as
the necessary control elements like promoters, these genes are not expressed. They represent one category of pseudogene.

SINEs (Short interspersed elements)

SINEs are short DNA sequences (100–400 base pairs) that represent reverse-transcribed RNA molecules originally transcribed
by RNA polymerase III; that is, molecules of tRNA, 5S rRNA, and some other small nuclear RNAs. The most abundant SINEs are
the Alu elements. There are over one million copies in the human genome (representing 9% of our total DNA). Alu elements
consist of a sequence averaging 260 base pairs that contains a site that is recognized by the restriction enzyme AluI. They appear to
be reverse transcripts of 7S RNA, part of the signal recognition particle. Most SINEs do not encode any functional molecules and
depend on the machinery of active L1 elements to be transposed; that is, copied and pasted in new locations.

HIV-1
HIV-1 — the cause of AIDS — and other human retroviruses (e.g., HTLV-1, the human T-cell leukemia/lymphoma virus) behave
like retrotransposons. The RNA genome of HIV-1 contains a gene for reverse transcriptase and one for integrase. The integrase
serves the same function as the transposases of DNA transposons. The DNA copies can be inserted anywhere in the genome.
Molecules of both enzymes are incorporated in the virus particle.

Transposons and Mutations

Transposons are mutagens and can cause mutations in several ways. If a transposon inserts itself into a functional gene, it will
probably damage it. Insertion into exons, introns, and even into DNA flanking the genes (which may contain promoters and
enhancers) can destroy or alter the gene's activity. Faulty repair of the gap left at the old site (in cut and paste transposition) can
lead to mutation there. The presence of a string of identical repeated sequences presents a problem for precise pairing during
meiosis. How is the third, say, of a string of five Alu sequences on the "invading strand" of one chromatid going to ensure that it
pairs with the third sequence in the other strand? If it accidentally pairs with one of the other Alu sequences, the result will be an
unequal crossover — one of the commonest causes of duplications.

 Note

The insertion of a retrotransposon in the DNA flanking a gene for pigment synthesis is thought to have produced white grapes
from a black-skinned ancestor. Later, the loss of that retrotransposon produced the red-skinned grape varieties cultivated today.

SINEs (mostly Alu sequences) and LINEs cause only a small percentage of human mutations. (There may even be a mechanism by
which they avoid inserting themselves into functional genes.) However, they have been found to be the cause of the mutations
responsible for some cases of human genetic diseases, including:
Hemophilia A (Factor VIII gene) and Hemophilia B [Factor IX gene]
X-linked severe combined immunodeficiency (SCID) [gene for part of the IL-2 receptor]
porphyria
predisposition to colon polyps and cancer [APC gene]
Duchenne muscular dystrophy [dystrophin gene]

10.4.3 https://bio.libretexts.org/@go/page/4899
What good are transposons?
Transposons have been called "junk" DNA and "selfish" DNA. They are "selfish" because their only function seems to make more
copies of themselves and "junk" because there is no obvious benefit to their host. Because of the sequence similarities of all the
LINEs and SINEs, they also make up a large portion of the "repetitive DNA" of the cell. Retrotransposons cannot be so selfish
that they reduce the survival of their host. And it now appears that many, at least, confer some benefit. The ENCODE project found
that some 75% of our repetitive DNA occurs within, or overlaps with, sequences, like enhancers, that regulate gene expression.
Some other possibilities:
Retrotransposons often carry some additional sequences at their 3' end as they insert into a new location. Perhaps these
occasionally create new combinations of exons, promoters, and enhancers that benefit the host.
Example:

Figure 10.4.3 Retrotransposons

Thousands of our Alu elements occur in the introns of genes.
Some of these contain sequences that when transcribed into the primary transcript are recognized by the
spliceosome.
These can then be spliced into the mature mRNA creating a new exon, which will be transcribed into a new
protein product.
Alternative splicing can provide not only the new mRNA (and thus protein) but also the old.
In this way, nature can try out new proteins without the risk of abandoning the tried-and-true old one.
L1 elements inserted into the introns of functional genes reduce the transcription of those genes without harming the gene
product — the longer the L1 element, the lower the level of gene expression. Some 79% of our genes contain L1 elements, and
perhaps they are a mechanism for establishing the baseline level of gene activity.
Telomerase, the enzyme essential for maintaining chromosome length, is closely related to the reverse transcriptase of LINEs
and may have evolved from it.
RAG-1 and RAG-2. The proteins encoded by these genes are needed to assemble the repertoire of antibodies and T-cells
receptors (TCRs) used by the adaptive immune system. The mechanism resembles that of the cut and paste method of Class II
transposons , and the RAG genes may have evolved from them. If so, the event occurred some 450 million years ago when the
jawed vertebrates evolved from jawless ancestors. Only jawed vertebrates have the RAG-1 and RAG-2 genes.
In Drosophila, the insertion of transposons into genes has been linked to the development of resistance to DDT and
organophosphate insecticides.

Transposons and the C-value Paradox

The genome of Arabidopsis thaliana contains ~1.2 x 108 base pairs (bp) of DNA. About 14% of this consists of transposons; the
rest functional genes (25,498 of them). The maize (corn) genome contains 20 times more DNA (2.4 x 109 bp) but surely has no
need for 20 times as many genes. In fact, 60% of the corn genome is made up of transposons (the figure for humans is 42%). So it
seems likely that the lack of an association between size of genome and number of functional genes — the C-value paradox — is
caused by the amount of transposon DNA accumulated in the genome.

This page titled 10.4: Transposons - "jumping genes" is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

10.4.4 https://bio.libretexts.org/@go/page/4899
 CHAPTER OVERVIEW
Unit 11: Genomics
11.1: Recombinant DNA and Gene Cloning
11.2: Polymerase Chain Reaction
11.3: Gene Therapy - Methods and Prospects
11.4: Recent Advances in Gene Therapy
11.5: Transgenic Animals
11.6: Transgenic Plants
11.7: Restriction Fragment Length Polymorphisms
11.8: Gel Blotting
11.9: Genetic Screening for Phenylketonuria
11.10: Antisense RNA
11.11: Antisense Oligodeoxynucleotides and their Therapeutic Potential
11.12: Forward and Reverse genetics
11.13: Metagenomics

Thumbnail: A DNA microarray. (CC BY-SA 3.0; Guillaume Paumier).

This page titled Unit 11: Genomics is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1
11.1: Recombinant DNA and Gene Cloning
Recombinant DNA is DNA that has been created artificially. DNA from two or more sources is incorporated into a single
recombinant molecule.

Making Recombinant DNA (rDNA) - An Overview

Treat DNA from both sources with the same restriction endonuclease (BamHI in this case).
BamHI cuts the same site on both molecules
5' GGATCC 3'
3' CCTAGG 5'
The ends of the cut have an overhanging piece of single-stranded DNA.
These are called "sticky ends" because they are able to base pair with any DNA molecule containing the complementary sticky
end.
In this case, both DNA preparations have complementary sticky ends and thus can pair with each other when mixed.
A DNA ligase covalently links the two into a molecule of recombinant DNA.

Figure 11.1.1 Making a rDNA

To be useful, the recombinant molecule must be replicated many times to provide material for analysis, sequencing, etc. Producing
many identical copies of the same recombinant molecule is called cloning. Cloning can be done in vitro, by a process called the
polymerase chain reaction (PCR). Here, however, we shall examine how cloning is done in vivo.
Cloning in vivo can be done in
unicellular microbes like E. coli
unicellular eukaryotes like yeast and
in mammalian cells grown in tissue culture.
In every case, the recombinant DNA must be taken up by the cell in a form in which it can be replicated and expressed. This is
achieved by incorporating the DNA in a vector. A number of viruses (both bacterial and of mammalian cells) can serve as vectors.
But here let us examine an example of cloning using E. coli as the host and a plasmid as the vector.

Plasmids
Plasmids are small (a few thousand base pairs), usually carry only one or a few genes, are circular and have a single origin of
replication. Plasmids are replicated by the same machinery that replicates the bacterial chromosome. Some plasmids are copied at
about the same rate as the chromosome, so a single cell is apt to have only a single copy of the plasmid. Other plasmids are copied
at a high rate and a single cell may have 50 or more of them.
Genes on plasmids with high numbers of copies are usually expressed at high levels. In nature, these genes often encode proteins
(e.g., enzymes) that protect the bacterium from one or more antibiotics. Plasmids enter the bacterial cell with relative ease. This
occurs in nature and may account for the rapid spread of antibiotic resistance in hospitals and elsewhere. Plasmids can be
deliberately introduced into bacteria in the laboratory transforming the cell with the incoming genes.

11.1.1 https://bio.libretexts.org/@go/page/4918
 Figure 11.1.2 Electron micrograph of an E. coli cell ruptured to release its DNA Courtesy of Huntington Potter and David Dressler,
Harvard Medical School
In the above figure, the tangle is a portion of a single DNA molecule containing over 4.6 million base pairs encoding
approximately 4,300 genes. The small circlets are plasmids.

Examples of Plasmids

Figure 11.1.3 pAMP/ pKAN

pAMP
4539 base pairs
a single replication origin
a gene (ampr)conferring resistance to the antibiotic ampicillin (a relative of penicillin)
a single occurrence of the sequence
5' GGATCC 3'
3' CCTAGG 5'that, as we saw above, is cut by the restriction enzyme BamHI
a single occurrence of the sequence
5' AAGCTT 3'
3' TTCGAA 5'that is cut by the restriction enzyme HindIII
Treatment of pAMP with a mixture of BamHI and HindIII produces:
a fragment of 3755 base pairs carrying both the ampr gene and the replication origin
a fragment of 784 base pairs
both fragments have sticky ends

pKAN
4207 base pairs
a single replication origin
a gene (kanr) conferring resistance to the antibiotic kanamycin.
a single site cut by BamHI
a single site cut by HindIII
Treatment of pKAN with a mixture of BamHI and HindIII produces:
a fragment of 2332 base pairs
a fragment of 1875 base pairs with the kanr gene (but no origin of replication)
both fragments have sticky ends

11.1.2 https://bio.libretexts.org/@go/page/4918
These fragments can be visualized by subjecting the digestion mixtures to electrophoresis in an agarose gel. Because of its
negatively-charged phosphate groups, DNA migrates toward the positive electrode (anode) when a direct current is applied. The
smaller the fragment, the farther it migrates in the gel.

Ligation Possibilities
If you remove the two restriction enzymes and provide the conditions for DNA ligase to do its work, the pieces of these plasmids
can rejoin (thanks to the complementarity of their sticky ends).
Mixing the pKAN and pAMP fragments provides several (at least 10) possibilities of rejoined molecules. Some of these will not
produce functional plasmids (molecules with two or with no replication origin cannot function).

Fig.11.1.4 Recombinant Plasmid

One interesting possibility is the joining of
the 3755-bp pAMP fragment (with ampr and a replication origin) with the
1875-bp pKAN fragment (with kanr)
Sealed with DNA ligase, these molecules are functioning plasmids that are capable of conferring resistance to both ampicillin and
kanamycin. They are molecules of recombinant DNA.
Because the replication origin, which enables the molecule to function as a plasmid, was contributed by pAMP, pAMP is called the
vector.

Transforming E. coli

Figure 11.1.5 Colonies of E. coli

Treatment of E. coli with the mixture of religated molecules will produce some colonies that are able to grow in the presence of
both ampicillin and kanamycin.
A suspension of E. coli is treated with the mixture of religated DNA molecules.
The suspension is spread on the surface of agar containing both ampicillin and kanamycin.
The next day, a few cells — resistant to both antibiotics — will have grown into visible colonies containing billions of
transformed cells.
Each colony represents a clone of transformed cells.
However, E. coli can be simultaneously transformed by more than one plasmid, so we must demonstrate that the transformed cells
have acquired the recombinant plasmid.

11.1.3 https://bio.libretexts.org/@go/page/4918
Electrophoresis of the DNA from doubly-resistant colonies (clones) tells the story.

Figure 11.1.6 Cloning

Plasmid DNA from cells that acquired their resistance from a recombinant plasmid only show only the 3755-bp and 1875-bp
bands (Clone 1, lane 3).
Clone 2 (Lane 4) was simultaneous transformed by religated pAMP and pKAN. (We cannot tell if it took up the recombinant
molecule as well.)
Clone 3 (Lane 5) was transformed by the recombinant molecule as well as by an intact pKAN.

Cloning other Genes

The recombinant vector described above could itself be a useful tool for cloning other genes. Let us assume that within its
kanamycin resistance gene (kanr) there is a single occurrence of the sequence
5' GAATTC 3'
3' CTTAAG 5'
This is cut by the restriction enzyme EcoRI, producing sticky ends.
If we treat any other sample of DNA, e.g., from human cells, with EcoRI, fragments with the same sticky ends will be formed.
Mixed with EcoRI-treated plasmid and DNA ligase, a small number of the human molecules will become incorporated into the
plasmid which can then be used to transform E. coli.
But how to detect those clones of E. coli that have been transformed by a plasmid carrying a piece of human DNA?
The key is that the EcoRI site is within the kanr gene, so when a piece of human DNA is inserted there, the gene's function is
destroyed.

Figure 11.1.7 Screening Clones

All E. coli cells transformed by the vector, whether it carries human DNA or not, can grow in the presence of ampicillin. But E.
coli cells transformed by a plasmid carrying human DNA will be unable to grow in the presence of kanamycin. So,
Spread a suspension of treated E. coli on agar containing ampicillin only
grow overnight
with a sterile toothpick transfer a small amount of each colony to an identified spot on agar containing kanamycin

11.1.4 https://bio.libretexts.org/@go/page/4918
 (do the same with another ampicillin plate)
Incubate overnight
All those clones that continue to grow on ampicillin but fail to grow on kanamycin (here, clones 2, 5, and 8) have been transformed
with a piece of human DNA.

Some recombinant DNA products being used in human therapy

Using procedures like this, many human genes have been cloned in E. coli or in yeast. This has made it possible — for the first
time — to produce unlimited amounts of human proteins in vitro. Cultured cells (E. coli, yeast, mammalian cells) transformed with
a human gene are being used to manufacture more than 100 products for human therapy. Some examples:
insulin for diabetics
factor VIII for males suffering from hemophilia A
factor IX for hemophilia B
human growth hormone (HGH)
erythropoietin (EPO) for treating anemia
several types of interferons
several interleukins
granulocyte-macrophage colony-stimulating factor (GM-CSF) for stimulating the bone marrow after a bone marrow
transplant
granulocyte colony-stimulating factor (G-CSF) for stimulating neutrophil production (e.g., after chemotherapy) and for
mobilizing hematopoietic stem cells from the bone marrow into the blood.
tissue plasminogen activator (TPA) for dissolving blood clots
adenosine deaminase (ADA) for treating some forms of severe combined immunodeficiency (SCID)
parathyroid hormone
many monoclonal antibodies
hepatitis B surface antigen (HBsAg) to vaccinate against the hepatitis B virus
C1 inhibitor (C1INH) used to treat hereditary angioedema

This page titled 11.1: Recombinant DNA and Gene Cloning is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by
John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

11.1.5 https://bio.libretexts.org/@go/page/4918
11.2: Polymerase Chain Reaction
The polymerase chain reaction is a technique for quickly "cloning" a particular piece of DNA in the test tube (rather than in living
cells like E. coli). Thanks to this procedure, one can make virtually unlimited copies of a single DNA molecule even though it is
initially present in a mixture containing many different DNA molecules.

Procedure
To perform PCR, you must know at least a portion of the sequence of the DNA molecule that you wish to replicate. You must then
synthesize primers: short oligonucleotides (containing about two dozen nucleotides) that are precisely complementary to the
sequence at the 3' end of each strand of the DNA you wish to amplify. The DNA sample is heated to separate its strands and mixed
with the primers. If the primers find their complementary sequences in the DNA, they bind to them; synthesis begins (as always 5' -
> 3') using the original strand as the template.
The reaction mixture must contain all four deoxynucleotide triphosphates (dATP, dCTP, dGTP, dTTP), and a DNA polymerase. It
helps to use a DNA polymerase that is not denatured by the high temperature needed to separate the DNA strands. Polymerization
continues until each newly-synthesized strand has proceeded far enough to contain the site recognized by the other primer. Now
you have two DNA molecules identical to the original molecule. You take these two molecules, heat them to separate their strands,
and repeat the process. Each cycle doubles the number of DNA molecules.
Using automated equipment, each cycle of replication can be completed in less than 5 minutes. After 30 cycles, what began as a
single molecule of DNA has been amplified into more than a billion copies (2 = 1.02 × 10 ).
30 9

Figure 11.2.1: Schematic drawing of the Polymerase Chain Reaction (PCR) cycle. (CC-SA-BY-3.0; Enzoklop)
With PCR, it is routinely possible to amplify enough DNA from a single hair follicle for DNA typing. Some workers have
successfully amplified DNA from a single sperm cell. The PCR technique has even made it possible to analyze DNA from
microscope slides of tissue preserved years before. However, the great sensitivity of PCR makes contamination by extraneous DNA
a constant problem.

This page titled 11.2: Polymerase Chain Reaction is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

11.2.1 https://bio.libretexts.org/@go/page/4920
11.3: Gene Therapy - Methods and Prospects
Many human diseases are caused by defective genes. A few common examples are tabulate in Table 11.3.1; all of these diseases
are caused by a defect at a single gene locus. (The inheritance is recessive so both the maternal and paternal copies of the gene
must be defective.) Is there any hope of introducing functioning genes into these patients to correct their disorder? Probably. Other
diseases also have a genetic basis, but it appears that several genes must act in concert to produce the disease phenotype. The
prospects of gene therapy in these cases seems far more remote.
Table 11.3.1 : Human Diseases cause by defective gene
Disease Genetic defect

hemophilia A absence of clotting factor VIII

cystic fibrosis defective chloride channel protein

muscular dystrophy defective muscle protein (dystrophin)

sickle-cell disease defective beta globin

hemophilia B absence of clotting factor IX

any one of several genes fail to make a protein essential for T and B cell
severe combined immunodeficiency (SCID)
function

 Severe Combined Immunodeficiency (SCID)

SCID is a disease in which the patient has neither cell-mediated immune responses nor is able to make antibodies. It is a
disease of young children because, until recently, the absence of an immune system left them prey to infections that ultimately
killed them. About 25% of the cases of SCID are the result of the child being homozygous for a defective gene encoding the
enzyme adenosine deaminase (ADA). The normal catabolism of purines is deficient, and this is particularly toxic for T cells
and B cells.
Treatment Options for SCID include:
1. Raise the child in a strictly germfree environment: all food, water, and air to be sterilized. David, the "bubble boy" from
Houston, survived this way until he was 12 years old.
2. Give the child a transplant of bone marrow from a normal, histocompatible, donor. Ideally, this would give the child a
continuous source of ADA+ T and B cells. However, even though the child cannot reject the transplant (the child has no
immune system), T cells in the transplant (unless the donor was an identical twin) can attack the cells of the child
producing graft-versus-host disease. Moreover, the donor cells may be infected with a virus which could overwhelm the
recipient before his or her immune system was restored. (David received a bone marrow transplant from his sister, but she,
like many people, had been infected earlier with the Epstein-Barr virus (the cause of "mono")). The virus was still present
in the cells she donated, and killed her brother.
3. Give injections of ADA (the enzyme is currently extracted from cows). When conjugated with polyethylene glycol (PEG)
to delay its breakdown in the blood, ADA-PEG injections have kept SCID patients reasonably healthy. But just like the
insulin injections of a diabetic, they must be repeated at frequent intervals. So,
4. Giving the patient functioning ADA genes - gene therapy

Gene Therapy Requirements

The gene must be identified and cloned. This has been done for the ADA gene. It must be inserted in cells that can take up long-
term residence in the patient. So far, this means removing the patient's own cells, treating them in tissue culture, and then returning
them to the patient. It must be inserted in the DNA so that it will be expressed adequately; that is, transcribed and translated with
sufficient efficiency that worthwhile amounts of the enzyme are produced. All these requirements seem to have been met for SCID
therapy using a retrovirus as the gene vector. Retroviruses have several advantages for introducing genes into human cells.

Figure 11.3.1 : (left) ADA vector and (right) Retroviral Genome crippled
Their envelope protein enables the virus to infect human cells.

11.3.1 https://bio.libretexts.org/@go/page/4939
 RNA copies of the human ADA gene can be incorporated into the retroviral genome using a packaging cell.
Packaging cells are treated so they express an RNA copy of the human ADA gene along with a packaging signal (P) needed for
the assembly of fresh virus particles. They also needs inverted repeats ("R") at each end to aid insertion of the DNA copies into
the DNA of the target cell. They need an RNA copy of the retroviral gag, pol, and env genes but with no packaging signal (so
these genes cannot be incorporated in fresh viral particles).

Figure 11.3.2 : Packaging Cell

Treated with these two genomes, the packaging cell produces a crop of retroviruses with:
the envelope protein needed to infect the human target cells
an RNA copy of the human ADA gene, complete with R sequences at each end
reverse transcriptase, needed to make a DNA copy of the ADA gene that can be inserted into the DNA of the target cell
none of the genes (gag, pol, env) that would enable the virus to replicate in its new host.
Once the virus has infected the target cells, this RNA is reverse transcribed into DNA and inserted into the chromosomal DNA of
the host.

Target Cells: T cells

The first attempts at gene therapy for SCID children (in 1990), used their own T cells (produced following ADA-PEG therapy) as
the target cells. The T cells were:
placed in tissue culture
stimulated to proliferate (by treating them with the lymphokine, Interleukin 2 (IL-2)
infected with the retroviral vector
returned, in a series of treatments, to the child
The children developed improved immune function but the injections had to be repeated because T cells live for only 6–12 months
in the blood. Moreover, the children also continued to receive ADA-PEG so the actual benefit of the gene therapy was unclear

Target Cells: Stem cells

Blood ("hematopoietic") stem cells:
produce (by mitosis) all the types of blood cells, including T and B lymphocytes
produce (by mitosis) more stem cells, thus ensuring an inexhaustible supply
In June of 2002, a team of Italian and Israeli doctors reported on two young SCID patients that were treated with their own blood
stem cells that had been transformed in vitro with a retroviral vector carrying the ADA gene. After a year, both children had fully-
functioning immune systems (T, B, and NK cells) and were able to live normal lives without any need for treatment with ADA-

11.3.2 https://bio.libretexts.org/@go/page/4939
PEG or immune globulin (IG). The doctors attribute their success to first destroying some of the bone marrow cells of their patients
to "make room" for the transformed cells. Nine years later (August 2011) these two patients are still thriving and have been joined
by 28 other successfully-treated children most of whom no longer need to take ADA-PEG.

 Gene Therapy for X-linked SCID

Gene therapy has also succeeded for 20 baby boys who suffered from another form of severe combined immunodeficiency
called X-linked SCID because it is caused by a mutated X-linked gene encoding a subunit — called γc (gamma-c) — of the
receptor for several interleukins, including interleukin-7 (IL-7). IL-7 is essential for converting blood stem cells into the
progenitors of T cells. Boys with X-linked SCID can make normal B cells, but because B cells need T-helper cells to function,
these boys could make neither cell-mediated nor antibody-mediated immune responses and had to live in a sterile bubble
before their treatment.
Their doctors
isolated blood stem cells from the bone marrow of each infant
treated the cells with a retroviral vector containing the normal gene for the γc interleukin receptor subunit
returned the treated cells to each donor
The results: Now after as long as 11 years, 19 of these boys
are able to live normal lives at home instead of inside a sterile "bubble"
have normal (with some exceptions*) numbers of T cells of both the CD4 and CD8 subsets
have responded to several childhood immunizations, including diphtheria, tetanus and polio by producing both T cells
and antibodies specific for these agents
Antibody production is sufficiently good that most of the boys have no need for periodic infusions of immune globulin (IG)
Five of the little boys developed leukemia (one has died):
in one case caused by a proliferating clone of γδ T cells in which the vector has inserted itself in a gene (on chromosome
11) implicated in some cases of acute lymphoblastic leukemia (ALL)
in a second case, the leukemia was of αβ T cells

Gene Therapy for β-thalassemia

β-thalassemia is an inherited disease. The most severe cases result from mutations in both copies of the gene encoding the beta
chain of hemoglobin. Many causative mutations have been identified, and most lead to a failure to make any beta chains. The
resulting hemoglobin functions poorly and the person requires frequent blood transfusions. In 2010, Cavazzana-Calvo (and many
colleagues) report a single case of successful gene therapy for this disorder; their patient was an 18-year old male. Their procedure
involve harvesting blood stem cells from the patient and exposing him to a retroviral vector that contained
a human gene for beta-hemoglobin complete with its promoter, enhancer, and other control elements;
alterations to the vector to make it safe.
After sufficient chemotherapy to "make room" for them, the patient was injected with these cells.
The result: Almost three years later, the patient is well and no longer requires periodic blood transfusions. One-third of his
hemoglobin is now manufactured by the red-cell precursors descended from the gene-altered stem cells. A similar procedure was
used on several babies born with an inherited lysosomal storage disease or Wiskott-Aldrich syndrome (another type of immune
deficiency). Up to two years after treatment with a retroviral vector containing the intact gene, these babies shown any signs of
their disorders (reported in the 23 August 2013 issue of Science).

Adenovirus Vectors
Adenoviruses are human pathogens responsible for some cases of the human "cold". Modified versions of two strains are currently
being used as vectors in gene therapy trials. Advantages of adenovirusus: Unlike retroviral vectors, they do not integrate into the
host genome and thus should not be able to disrupt host genes (It was such disruption that caused some X-linked SCID patients
treated with a retroviral vector to develop leukemia) and they can infect nondividing cells with high efficiency. Disadvantages are
that they elicit a powerful immune response, both by T cells and by B cells (antibodies) so repeated doses soon lose their
effectiveness. Moreoer, many people already have antibodies against the virus from earlier "colds", and these can inactivate the

11.3.3 https://bio.libretexts.org/@go/page/4939
vector at the outset. A recent trial of an HIV vaccine using an adenovirus as the vector was halted when it was found not only not to
be effective but, in people with preexisting high levels of anti-adenovirus antibodies, may have even increased their susceptibility
to HIV.

This page titled 11.3: Gene Therapy - Methods and Prospects is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by
John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

11.3.4 https://bio.libretexts.org/@go/page/4939
11.4: Recent Advances in Gene Therapy
Reaching the goal of effective gene therapies for human diseases has been a difficult one. Some of the problems that remain to be
solved include:
how to avoid an immune response in the patient, which can interfere with gene therapy in two ways:
The vector provokes inflammation.
The vector elicits antibodies that destroy the vector when it is administered again.
Both of these are serious problems with adenovirus vectors.
how to get the gene into non-dividing cells like liver, muscle, and neurons;
how to get the gene to be replicated (in dividing cells) and expressed indefinitely but
minimize the risk that it inserts near a proto-oncogene which it could activate producing a cancer. (This occurred in several little
boys treated with a retroviral vector based on the murine leukemia virus.
how to get the gene to be expressed as needed; that is, how to bring the gene under normal physiological controls so that its
product is produced where, when, and in the amounts needed.

Adeno-Associated Virus (AAV) — A possible solution?

Adeno-associated virus gets its name because it is often found in cells that are simultaneously infected with adenovirus. However,
by itself it seems to be harmless. Unlike adenovirus, AAV
does not stimulate inflammation in the host;
can enter non-dividing cells;
integrates successfully into one spot in the genome of its host — on chromosome 19 in humans.
(However, AAV vectors do elicit a strong immune response so they can be used only once.)
As for the problem of getting the transgene to be expressed appropriately, that may be solved by using two AAV vectors
simultaneously:
one carrying the desired gene (e.g., for factor VIII or adenosine deaminase, or in the case illustrated here, erythropoietin) into
the cells of the host;
the other carrying genes for the components of the transcription factors needed to turn that gene on.

Regulated production of erythropoietin (EPO)

Figure 11.3.2.1 AAV Vectors

Vector 1
This piece of DNA contained (among other things):
the DNA of adeno-associated virus (AAV)
a gene encoding a protein containing two domains:
a portion of the molecule ("p65") that is needed to activate gene transcription but that by itself cannot bind to DNA
a portion ("FRB") that binds the drug rapamycin.

11.4.1 https://bio.libretexts.org/@go/page/4940
 a gene encoding another protein with two domains:
a portion of molecule ("ZFHD1") that binds specifically to the DNA sequence in the promoter of the erythropoietin gene
but that by itself cannot activate transcription of the gene;
a portion ("FKBP12") that also binds to rapamycin.
promoters (not shown) that allow continuous expression (transcription and translation) of the two genes. But note that, by
themselves, the two gene products are inactive

Vector 2
This piece of DNA contained (among other things):
the DNA of adeno-associated virus (AAV)
12 identical promoters (green boxes) of the erythropoietin gene
the gene for erythropoietin (EPO) itself

The Experiment
The experimental animals were injected (in their skeletal muscles) with many copies of both vectors. Skeletal muscle was chosen
because muscle fibers are multinucleate. Once across the plasma membrane, there are many nuclei which the vectors can enter and
hence many opportunities to integrate into the DNA of the host.
Later the animals were injected with rapamycin. This small molecule is an immunosuppressant and is currently being tested in
transplant recipients to help them avoid rejection of the transplant. It was used here because of its ability to simultaneously bind to
the FRB and FKBP12 domains of the two gene products of vector 1. The resulting trimer is an active transcription factor for the
erythropoietin gene.

The Results
In mice
Injections of the two vectors had — by themselves — no effect on the production of EPO nor on the number of red blood cells
(hematocrit), but every time these animals were given an injection of rapamycin, they quickly began to produce EPO (with levels
increasing as much as 100 fold) and the number of red blood cells rose (hematocrits increasing from 42% to 60%). The amount of
EPO produced was directly related to the amount of rapamycin given. Even after 5 months, a single injection of rapamycin
produced a sharp rise in the level of EPO in the blood.
In monkeys
The results were similar to those in mice, but the effect wore off after 4 months. So here is a system where a gene introduced into
an animal can then be switched on by giving the animal a small molecule. (In humans, rapamycin can be given by mouth as a pill.)
and can have its output regulated by the amount of the small molecule administered.

Curing Insulin-Dependent Diabetes Mellitus (IDDM) in mice and rats

Researchers in Seoul, Korea reported in the 23 November 2000 issue of Nature that they have used an AAV-type vector to cure
mice with inherited IDDM (the animal equivalent of Type 1 diabetes mellitus in humans)
rats with IDDM induced by chemical destruction of their insulin-secreting beta cells
Both groups of animals were injected (in their hepatic portal vein) with billions of copies of a complex vector containing:
AAV
the complementary DNA (cDNA) encoding a synthetic version of insulin
a promoter that is active only in liver cells and is turned on by the presence of glucose
the DNA encoding a signal sequence (so that the insulin can be secreted)
an enhancer to elevate expression of this artificial gene
The results:
Both groups of animals gained control over their blood sugar level and kept this control for over 8 months. When given glucose,
they proceeded to synthesize the synthetic insulin which then brought their blood glucose back down to normal levels.

11.4.2 https://bio.libretexts.org/@go/page/4940
Curing hemophilia B in mice
Researchers at the Salk Institute reported (in the 30 March 1999 issue of the Proceedings of the National Academy of Sciences)
work with mice
whose genes for clotting factor IX had been "knocked out" and
thus were subject to uncontrolled bleeding like human patients with hemophilia B.
These mice were injected (also in the hepatic portal vein) with DNA containing
AAV
cDNA for factor IX (the dog gene)
liver-specific promoter and enhancer sequences
The mice proceeded to make factor IX and were no longer susceptible to uncontrolled bleeding.
In later work, injection of embryonic stem cells with functioning factor IX genes into the liver of mice without the genes cured
them.

Treating ALS
ALS (amyotrophic lateral sclerosis) is a human disease in which motor neurons degenerate. (It is often called "Lou Gehrig's
disease" after the baseball player who died from it.)
A similar disease can be created in transgenic mice carrying mutant human genes (for superoxide dismutase) associated with ALS.
Researchers at the Salk Institute have slowed up the progression of the disease in these mice by injecting their skeletal muscles
with an AAV vector containing the gene for insulin-like growth factor 1 (IGF-1). The vector
invaded the muscle cells
moved into the motor neurons attached to them and
through their axons up to the cell bodies
The results:
Destruction of motor neurons was reduced, and the mice lived longer than they otherwise would have.

The Outlook
It's a big jump from mice to humans, but these results indicate that the principle of gene therapy for single-gene disorders is valid.
And some early trials in humans look promising.
An intravenous injection of an AAV vector containing the cDNA of factor IX has produced functional levels of factor IX in
several men with hemophilia B.
On August 18, 2003, physicians in New York injected 3.5 x 109 copies of an AAV vector carrying a gene for the synthesis of
GABA into the brain of a patient with Parkinson's disease. He was the first of a phase I clinical trial of this procedure. By 2007,
several more Parkinson's patients had been treated with these injections with no harmful side effects and some improvement in
their symptoms.
Several patients with an inherited lack of a functional gene needed to synthesize 11-cis-retinal — and thus destined to be blind
— have had a useful level of vision temporarily restored in one eye injected with an AAV vector containing the gene (the other
eye was the untreated control). Probably the fact that
the vector was injected directly into the eye and so not diluted throughout the body as an intravenous injection would be;
retinal cells rarely divide so the vector would not be lost. (The vector used had the genes needed for integration into the host
cell's DNA removed so it could not be duplicated in S phase and, in dividing cells, would eventually disappear.)
the interior of the eye is an immunologically privileged site
contributed to this remarkable success.
Several children suffering from X-linked severe combined immunodeficiency have had their immune systems restored after
retroviral gene therapy.
A few patients with hemophilia A have shown modest improvement when injected with their own cells that had earlier been
harvested and transformed in vitro with a plasmid containing the factor VIII gene.
Several gene therapy agents — using adenoviral vectors — are in clinical trials and have shown some promise.

11.4.3 https://bio.libretexts.org/@go/page/4940
 Among these:
a recombinant adenovirus encoding p53, a tumor-suppressor protein missing in many cancers
a recombinant adenovirus that destroys cells lacking the p53 protein (as many cancer cells do)
People with the rare disorder lipoprotein lipase deficiency are unable to process the globules (chylomicrons) of fat and protein
that appear in the blood after a fat-containing meal because they lack functional copies of the gene encoding lipoprotein lipase.
Intramuscular injection of an AAV vector containing the functional gene provides sufficient improvement, with apparent safety,
that in October 2012, this agent (Glybera®) received approval for use in the European Union. It is the first gene therapy to receive
such approval.

This page titled 11.4: Recent Advances in Gene Therapy is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

11.4.4 https://bio.libretexts.org/@go/page/4940
11.5: Transgenic Animals
A transgenic animal is one that carries a foreign gene that has been deliberately inserted into its genome. The foreign gene is
constructed using recombinant DNA methodology. In addition to the gene itself, the DNA usually includes other sequences to
enable it to be incorporated into the DNA of the host and to be expressed correctly by the cells of the host. Transgenic sheep and
goats have been produced that express foreign proteins in their milk. Transgenic chickens are now able to synthesize human
proteins in the "white" of their eggs. These animals should eventually prove to be valuable sources of proteins for human therapy.

 Note
In July 2000, researchers from the team that produced Dolly reported success in producing transgenic lambs in which the
transgene had been inserted at a specific site in the genome and functioned well.

Transgenic mice have provided the tools for exploring many biological questions.

 Example
Normal mice cannot be infected with polio virus. They lack the cell-surface molecule that, in humans, serves as the receptor
for the virus. So normal mice cannot serve as an inexpensive, easily-manipulated model for studying the disease. However,
transgenic mice expressing the human gene for the polio virus receptor
can be infected by polio virus and even
develop paralysis and other pathological changes characteristic of the disease in humans.

Two methods of producing transgenic mice are widely used:

transforming embryonic stem cells (ES cells) growing in tissue culture with the desired DNA
injecting the desired gene into the pronucleus of a fertilized mouse egg

Fig.11.4.1 Methods to produce Transgenic mice

The Embryonic Stem Cell Method - Method 1

Embryonic stem cells (ES cells) are harvested from the inner cell mass (ICM) of mouse blastocysts. They can be grown in culture
and retain their full potential to produce all the cells of the mature animal, including its gametes.
1. Make your DNA
Using recombinant DNA methods, build molecules of DNA containing
the gene you desire (e.g., the insulin gene)
vector DNA to enable the molecules to be inserted into host DNA molecules
promoter and enhancer sequences to enable the gene to be expressed by host cells

11.5.1 https://bio.libretexts.org/@go/page/4924
2. Transform ES cells in culture
Expose the cultured cells to the DNA so that some will incorporate it.
3. Select for successfully transformed cells
4. Inject these cells into the inner cell mass (ICM) of mouse blastocysts.
5. Embryo transfer
Prepare a pseudopregnant mouse (by mating a female mouse with a vasectomized male). The stimulus of mating elicits the
hormonal changes needed to make her uterus receptive.
Transfer the embryos into her uterus.
Hope that they implant successfully and develop into healthy pups (no more than one-third will).
6. Test her offspring
Remove a small piece of tissue from the tail and examine its DNA for the desired gene. No more than 10–20% will have it, and
they will be heterozygous for the gene.
7. Establish a transgenic strain
Mate two heterozygous mice and screen their offspring for the 1 in 4 that will be homozygous for the transgene.
Mating these will found the transgenic strain.

The Pronucleus Method - Method 2

1. Prepare your DNA as in Method 1
2. Transform fertilized eggs
Harvest freshly fertilized eggs before the sperm head has become a pronucleus.
Inject the male pronucleus with your DNA.
When the pronuclei have fused to form the diploid zygote nucleus, allow the zygote to divide by mitosis to form a 2-cell
embryo.
3. Implant the embryos in a pseudopregnant foster mother and proceed as in Method 1.

 Example

This image (courtesy of R. L. Brinster and R. E. Hammer) shows a transgenic mouse (right) with a normal littermate (left). The
giant mouse developed from a fertilized egg transformed with a recombinant DNA molecule containing:
the gene for human growth hormone
a strong mouse gene promoter
The levels of growth hormone in the serum of some of the transgenic mice were several hundred times higher than in control
mice.

Random vs. Targeted Gene Insertion

The early vectors used for gene insertion could, and did, place the gene (from one to 200 copies of it) anywhere in the genome.
However, if you know some of the DNA sequence flanking a particular gene, it is possible to design vectors that replace that gene.
The replacement gene can be one that
restores function in a mutant animal or
knocks out the function of a particular locus.
In either case, targeted gene insertion requires
the desired gene

11.5.2 https://bio.libretexts.org/@go/page/4924
 neor, a gene that encodes an enzyme that inactivates the antibiotic neomycin and its relatives, like the drug G418, which is
lethal to mammalian cells
tk, a gene that encodes thymidine kinase, an enzyme that phosphorylates the nucleoside analog ganciclovir. DNA polymerase
fails to discriminate against the resulting nucleotide and inserts this nonfunctional nucleotide into freshly-replicating DNA. So
ganciclovir kills cells that contain the tk gene

Figure 11.4.2 Neo vector

Step 1
Treat culture of ES cells with preparation of vector DNA.
Results:
Most cells fail to take up the vector; these cells will be killed if exposed to G418.
In a few cells: the vector is inserted randomly in the genome. In random insertion, the entire vector, including the tk gene, is
inserted into host DNA. These cells are resistant to G418 but killed by gancyclovir.
In still fewer cells: homologous recombination occurs. Stretches of DNA sequence in the vector find the homologous
sequences in the host genome, and the region between these homologous sequences replaces the equivalent region in the host
DNA.
Step 2
Culture the mixture of cells in medium containing both G418 and ganciclovir.
The cells (the majority) that failed to take up the vector are killed by G418.
The cells in which the vector was inserted randomly are killed by gancyclovir (because they contain the tk gene).
This leaves a population of cells transformed by homologous recombination (enriched several thousand fold).
Step 3
Inject these into the inner cell mass of mouse blastocysts.

Knockout Mice: What do they teach us?

If the replacement gene (A* in the diagram) is nonfunctional (a "null" allele), mating of the heterozygous transgenic mice will
produce a strain of "knockout mice" homozygous for the nonfunctional gene (both copies of the gene at that locus have been
"knocked out"). Knockout mice are valuable tools for discovering the function(s) of genes for which mutant strains were not
previously available. Two generalizations have emerged from examining knockout mice:
Knockout mice are often surprisingly unaffected by their deficiency. Many genes turn out not to be indispensable. The mouse
genome appears to have sufficient redundancy to compensate for a single missing pair of alleles.
Most genes are pleiotropic. They are expressed in different tissues in different ways and at different times in development.

Tissue-Specific Knockout Mice

While "housekeeping" genes are expressed in all types of cells at all stages of development, other genes are normally expressed in
only certain types of cells when turned on by the appropriate signals (e.g. the arrival of a hormone).
To study such genes, one might expect that the methods described above would work. However, it turns out that genes that are only
expressed in certain adult tissues may nonetheless be vital during embryonic development. In such cases, the animals do not

11.5.3 https://bio.libretexts.org/@go/page/4924
survive long enough for their knockout gene to be studied. Fortunately, there are now techniques with which transgenic mice can be
made where a particular gene gets knocked out in only one type of cell.

The Cre/loxP System

Figure 11.4.3 The Cre/loxP System

One of the bacteriophages that infects E. coli, called P1, produces an enzyme — designated Cre — that cuts its DNA into lengths
suitable for packaging into fresh virus particles. Cre cuts the viral DNA wherever it encounters a pair of sequences designated loxP.
All the DNA between the two loxP sites is removed, and the remaining DNA ligated together again (so the enzyme is a
recombinase). Using "Method 1" above, mice can be made transgenic for
the gene encoding Cre attached to a promoter that will be activated only when it is bound by the same transcription factors that
turn on the other genes required for the unique function(s) of that type of cell;
a "target" gene, the one whose function is to be studied, flanked by loxP sequences.
In the adult animal,
those cells that
receive signals (e.g., the arrival of a hormone or cytokine)
to turn on production of the transcription factors needed
to activate the promoters of the genes whose products are needed by that particular kind of cell
will also turn on transcription of the Cre gene. Its protein will then remove the "target" gene under study.
All other cells will lack the transcription factors needed to bind to the Cre promoter (and/or any enhancers) so the target gene
remains intact.
The result: a mouse with a particular gene knocked out in only certain cells.

Knock-in Mice
The Cre/loxP system can also be used to
remove DNA sequences that block gene transcription. The "target" gene can then be turned on in certain cells or at certain times
as the experimenter wishes.
replace one of the mouse's own genes with a new gene that the investigator wishes to study.
Such transgenic mice are called "knock-in" mice.

Transgenic Sheep and Goats

Until recently, the transgenes introduced into sheep inserted randomly in the genome and often worked poorly. However, in July
2000, success at inserting a transgene into a specific gene locus was reported. The gene was the human gene for alpha1-

11.5.4 https://bio.libretexts.org/@go/page/4924
antitrypsin, and two of the animals expressed large quantities of the human protein in their milk.
This is how it was done.
Sheep fibroblasts (connective tissue cells) growing in tissue culture were treated with a vector that contained these segments of
DNA:
1. 2 regions homologous to the sheep COL1A1 gene. This gene encodes Type 1 collagen. (Its absence in humans causes the
inherited disease osteogenesis imperfecta.)
This locus was chosen because fibroblasts secrete large amounts of collagen and thus one would expect the gene to be easily
accessible in the chromatin.
2. A neomycin-resistance gene to aid in isolating those cells that successfully incorporated the vector.
3. The human gene encoding alpha1-antitrypsin.
Some people inherit two non- or poorly-functioning genes for this protein. Its resulting low level or absence produces the
disease Alpha1-Antitrypsin Deficiency (A1AD or Alpha1). The main symptoms are damage to the lungs (and sometimes to
the liver).
4. Promoter sites from the beta-lactoglobulin gene. These promote hormone-driven gene expression in milk-producing cells.
5. Binding sites for ribosomes for efficient translation of the beta-lactoglobulin mRNAs.
Successfully-transformed cells were then
Fused with enucleated sheep eggs and implanted in the uterus of a ewe (female sheep)
Several embryos survived until their birth, and two young lambs lived over a year.
When treated with hormones, these two lambs secreted milk containing large amounts of alpha1-antitrypsin (650 µg/ml; 50
times higher than previous results using random insertion of the transgene).
On June 18, 2003, the company doing this work abandoned it because of the great expense of building a facility for purifying the
protein from sheep's milk. Purification is important because even when 99.9% pure, human patients can develop antibodies against
the tiny amounts of sheep proteins that remain.
However, another company, GTC Biotherapeutics, has persevered and in June of 2006 won preliminary approval to market a
human protein, antithrombin, in Europe. Their protein — the first made in a transgenic animal to receive regulatory approval for
human therapy — was secreted in the milk of transgenic goats.

Transgenic Chickens
Chickens grow faster than sheep and goats and large numbers can be grown in close quarters. They also synthesize several grams
of protein in the "white" of their eggs.Two methods have succeeded in producing chickens carrying and expressing foreign genes.
Infecting embryos with a viral vector carrying
the human gene for a therapeutic protein
promoter sequences that will respond to the signals for making proteins (e.g. lysozyme) in egg white
Transforming rooster sperm with a human gene and the appropriate promoters and checking for any transgenic offspring.
Preliminary results from both methods indicate that it may be possible for chickens to produce as much as 0.1 g of human protein
in each egg that they lay.
Not only should this cost less than producing therapeutic proteins in culture vessels, but chickens will probably add the correct
sugars to glycosylated proteins — something that E. coli cannot do.

Transgenic Pigs
Transgenic pigs have also been produced by fertilizing normal eggs with sperm cells that have incorporated foreign DNA. This
procedure, called sperm-mediated gene transfer (SMGT) may someday be able to produce transgenic pigs that can serve as a source
of transplanted organs for humans.

Transgenic Primates
In the 28 May 2009 issue of Nature, Japanese scientists reported success in creating transgenic marmosets. Marmosets are
primates and thus our closest relatives (so far) to be genetically engineered. In some cases, the transgene (for green fluorescent

11.5.5 https://bio.libretexts.org/@go/page/4924
protein) was incorporated into the germline and passed on to the animal's offspring. The hope is that these transgenic animals will
provide the best model yet for studying human disease and possible therapies.

This page titled 11.5: Transgenic Animals is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

11.5.6 https://bio.libretexts.org/@go/page/4924
11.6: Transgenic Plants
Progress is being made on several fronts to introduce new traits into plants using recombinant DNA technology. The
genetic manipulation of plants has been going on since the dawn of agriculture, but until recently this has required the
Page ID
slow and tedious process of cross-breeding varieties. Genetic engineering promises to speed the process and broaden the
4926 scope of what can be done.

There are several methods for introducing genes into plants, including infecting plant cells with plasmids as vectors
carrying the desired gene and physically shooting microscopic pellets containing the gene directly into the cell. In contrast to
animals, there is no real distinction between somatic cells and germline cells. Somatic tissues of plants (e.g., root cells grown in
culture) can be transformed in the laboratory with the desired gene and can grow into mature plants with flowers. If all goes well,
the transgene will be incorporated into the pollen and eggs and passed on to the next generation. In this respect, it is easier to
produce transgenic plants than transgenic animals.

Figure 11.6.1 : A gene gun is used for injecting cells with genetic information, it is also known as biolistic particle delivery system.
Gene guns can be used effectively on most cells but are mainly used on plant cells. Step 1 The gene gun apparatus is ready to fire.
Step 2 When the gun is turned on and the helium flows through. Step 3 The helium moving the disk with DNA coated particles
toward the screen. Step 4 The helium having pushed the particles moving through the screen and moving to the target cells to
transform the cells. (CC-SA-BY-4.0; RachelBrooks15)

Achievements
Improved Nutritional Quality
Milled rice is the staple food for a large fraction of the world's human population. Milling rice removes the husk and any beta-
carotene it contained. Beta-carotene is a precursor to vitamin A, so it is not surprising that vitamin A deficiency is widespread,
especially in the countries of Southeast Asia. The synthesis of beta-carotene requires a number of enzyme-catalyzed steps. In
January 2000, a group of European researchers reported that they had succeeded in incorporating three transgenes into rice that
enabled the plants to manufacture beta-carotene in their endosperm.

Insect Resistance
Bacillus thuringiensis is a bacterium that is pathogenic for a number of insect pests. Its lethal effect is mediated by a protein toxin
it produces. Through recombinant DNA methods, the toxin gene can be introduced directly into the genome of the plant where it is
expressed and provides protection against insect pests of the plant.

Disease Resistance
Genes that provide resistance against plant viruses have been successfully introduced into such crop plants as tobacco, tomatoes,
and potatoes.

11.6.1 https://bio.libretexts.org/@go/page/4926
  Example 11.6.1

Tomato plants infected with tobacco mosaic virus (which attacks tomato plants as well as tobacco). The plants in the back row
carry an introduced gene conferring resistance to the virus. The resistant plants produced three times as much fruit as the
sensitive plants and the same as control plants.

Herbicide Resistance
Questions have been raised about the safety — both to humans and to the environment — of some of the broad-leaved weed killers
like 2,4-D. Alternatives are available, but they may damage the crop as well as the weeds growing in it. However, genes for
resistance to some of the newer herbicides have been introduced into some crop plants and enable them to thrive even when
exposed to the weed killer.

 Example 11.6.2

Effect of the herbicide bromoxynil on tobacco plants transformed with a bacterial gene whose product breaks down
bromoxynil (top row) and control plants (bottom row). "Spray blank" plants were treated with the same spray mixture as the
others except the bromoxynil was left out. (Courtesy of Calgene, Davis, CA.)

Salt Tolerance
A large fraction of the world's irrigated crop land is so laden with salt that it cannot be used to grow most important crops.
However, researchers at the University of California Davis campus have created transgenic tomatoes that grow well in saline soils.
The transgene was a highly-expressed sodium/proton antiport pump that sequestered excess sodium in the vacuole of leaf cells.
There was no sodium buildup in the fruit.

"Terminator" Genes
This term is used (by opponents of the practice) for transgenes introduced into crop plants to make them produce sterile seeds (and
thus force the farmer to buy fresh seeds for the following season rather than saving seeds from the current crop). The process
involves introducing three transgenes into the plant:
A gene encoding a toxin which is lethal to developing seeds but not to mature seeds or the plant. This gene is normally inactive
because of a stretch of DNA inserted between it and its promoter.
A gene encoding a recombinase — an enzyme that can remove the spacer in the toxin gene thus allowing to be expressed.
A repressor gene whose protein product binds to the promoter of the recombinase thus keeping it inactive.
How they work
When the seeds are soaked (before their sale) in a solution of tetracycline
Synthesis of the repressor is blocked.
The recombinase gene becomes active.
The spacer is removed from the toxin gene and it can now be turned on.
Because the toxin does not harm the growing plant — only its developing seeds — the crop can be grown normally except that its
seeds are sterile. The use of terminator genes has created much controversy. Farmers — especially those in developing countries —
want to be able to save some seed from their crop to plant the next season. However, Seed companies want to be able to keep
selling seeds.

11.6.2 https://bio.libretexts.org/@go/page/4926
Transgenes Encoding Antisense RNA
Messenger RNA (mRNA) is single-stranded. Its sequence of nucleotides is called "sense" because it results in a gene product
(protein). Normally, its unpaired nucleotides are "read" by transfer RNA anticodons as the ribosome proceeds to translate the
message.

Figure 11.6.2 : Sense Strand

The second strand is called the antisense strand because its sequence of nucleotides is the complement of message sense. When
mRNA forms a duplex with a complementary antisense RNA sequence, translation is blocked. This may occur because the
ribosome cannot gain access to the nucleotides in the mRNA or duplex RNA is quickly degraded by ribonucleases in the cell. With
recombinant DNA methods, synthetic genes (DNA) encoding antisense RNA molecules can be introduced into the organism.

Biopharmaceuticals
The genes for proteins to be used in human (and animal) medicine can be inserted into plants and expressed by them.
Advantages:
Glycoproteins can be made (bacteria like E. coli cannot do this).
Virtually unlimited amounts can be grown in the field rather than in expensive fermentation tanks.
It avoids the danger from using mammalian cells and tissue culture medium that might be contaminated with infectious agents.
Purification is often easier.
Corn is the most popular plant for these purposes, but tobacco, tomatoes, potatoes, rice and carrot cells grown in tissue culture are
also being used.
Some of the proteins that have been produced by transgenic crop plants:
human growth hormone with the gene inserted into the chloroplast DNA of tobacco plants
humanized antibodies against such infectious agents as
HIV
respiratory syncytial virus (RSV)
sperm (a possible contraceptive)
herpes simplex virus, HSV, the cause of "cold sores"
Ebola virus, the cause of the often-fatal Ebola hemorrhagic fever
protein antigens to be used in vaccines
An example: patient-specific antilymphoma (a cancer) vaccines. B-cell lymphomas are clones of malignant B cells
expressing on their surface a unique antibody molecule. Making tobacco plants transgenic for the RNA of the variable
(unique) regions of this antibody enables them to produce the corresponding protein. This can then be incorporated into a
vaccine in the hopes (early trials look promising) of boosting the patient's immune system — especially the cell-mediated
branch — to combat the cancer.
other useful proteins like lysozyme and trypsin
However, as of April 2012, the only protein to receive approval for human use is glucocerebrosidase, an enzyme lacking in
Gaucher's disease. It is synthesized by transgenic carrot cells grown in tissue culture.

Controversies
The introduction of transgenic plants into agriculture has been vigorously opposed by some. There are a number of issues that
worry the opponents. One of them is the potential risk of transgenes in commercial crops endangering native or nontarget species.
Examples:
A gene for herbicide resistance in, e.g. maize (corn), escaping into a weed species could make control of the weed far more
difficult.

11.6.3 https://bio.libretexts.org/@go/page/4926
 The gene for Bt toxin expressed in pollen might endanger pollinators like honeybees.
To date, field studies on Bt cotton and maize show that the numbers of some nontarget insects are reduced somewhat but not as
much as in fields treated with insecticides.
Another worry is the inadvertent mixing of transgenic crops with nontransgenic food crops. Although this has occurred
periodically, there is absolutely no evidence of a threat to human health. Despite the controversies, farmers around the world are
embracing transgenic crops. Currently in the United States over 80% of the corn, soybeans, and cotton grown are genetically
modified (GM) — principally to provide resistance to the herbicide glyphosate ("Roundup Ready®") thus making it practical to
spray the crop with glyphosate to kill weeds without harming the crop and resistance to insect attack (by expressing the toxin of
Bacillus thuringiensis).

This page titled 11.6: Transgenic Plants is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

11.6.4 https://bio.libretexts.org/@go/page/4926
11.7: Restriction Fragment Length Polymorphisms
Restriction enzymes cut DNA at precise points producing a collection of DNA fragments of precisely defined length. These can be
separated by electrophoresis, with the smaller fragments migrating farther than the larger fragments. One or more of the fragments
can be visualized with a "probe" — a molecule of single-stranded DNA that is complementary to a run of nucleotides in one or
more of the restriction fragments and is radioactive (or fluorescent). If probes encounter a complementary sequence of nucleotides
in a test sample of DNA, they bind to it by Watson-Crick base pairing and thus identify it. Polymorphisms are inherited differences
found among the individuals in a population.
Restriction Fragment Length Polymorphisms (RFLPs) have provided valuable information in many areas of biology, including
screening human DNA for the presence of potentially deleterious genes ("Case 1") and providing evidence to establish the
innocence of, or a probability of the guilt of, a crime suspect by DNA "fingerprinting" ("Case 3").

Case 1: Screening for the sickle-cell gene

Sickle-cell disease is a genetic disorder in which both genes in the patient encode the amino acid valine (Val) in the sixth position
of the beta chain (betaS) of the hemoglobin molecule. "Normal" beta chains (betaA) have glutamic acid at this position. The only
difference between the two genes is the substitution of a T for an A in the middle position of codon 6. This converts a GAG codon
(for Glu) to a GTG codon for Val and abolishes a sequence (CTGAGG, which spans codons 5, 6, and 7) recognized and cut by one
of the restriction enzymes.

Figure 11.7.1 : Sickle-cell Mutation. Data provided by S. E. Antonarakis

When the normal gene (betaA) is digested with the enzyme and the fragments separated by electrophoresis, the probe binds to a
short fragment (between the red arrows). However, the enzyme cannot cut the sickle-cell gene at this site, so the probe attaches to
a much larger fragment (between the blue arrows).
Figure 11.7.1 shows the pedigree of a family whose only son has sickle-cell disease. Both his father and mother were heterozygous
(semifilled box and circle respectively) as they had to be to produce an afflicted child (solid box). The electrophoresis patterns for
each member of the family are placed directly beneath them. Note that the two homozygous children (1 and 3) have only a single
band, but these are more intense because there is twice as much DNA in them. In this example, a change of a single nucleotide
produced the RFLP. This is a very common cause of RFLPs and now such polymorphisms are often referred to as single
nucleotide polymorphisms or SNPs. (However, not all RFLPs arise from SNPs.

 How can these tools be used?

By testing the DNA of prospective parents, their genotype can be determined and their odds of producing an afflicted child can
be determined. In the case of sickle-cell disease, if both parents are heterozygous for the genes, there is a 1 in 4 chance that
they will produce a child with the disease. Amniocentesis and chorionic villus sampling make it possible to apply the same
techniques to the DNA of a fetus early in pregnancy. The parents can learn whether the unborn child will be free of the disease
or not. They may choose to have an abortion rather than bring an afflicted child into the world.
Three problems:

11.7.1 https://bio.libretexts.org/@go/page/4928
 The mutations that cause most human genetic diseases are more varied than the single mutation associated with sickle-cell
disease. Over a thousand different mutations in the cystic fibrosis gene can cause the disease. A probe for one will probably
fail to identify a second. A mixture of probes, one for each of the more common mutations, can be used. But there remains
the problem of "false negatives": people who are falsely told they do not carry a mutant gene.
There are many diseases which result from several mutant genes working together to produce the disease phenotype.
There are still genetic diseases for which no gene has yet been discovered. Until the gene can be located, cloned, and
sequenced, no probe can be made to detect it directly. However, it is sometimes possible to find a genetic "marker" that can
serve as a surrogate for the gene itself. Let's see how.

Case 2: Screening for a RFLP "marker"

If a particular RFLP is usually associated with a particular genetic disease, then the presence or absence of that RFLP can be used
to counsel people about their risk of developing or transmitting the disease. The assumption is that the gene they are really
interested in is located so close to the RFLP that the presence of the RFLP can serve as a surrogate for the disease gene itself. But
people wanting to be tested cannot simply walk in off the street. Because of crossing over, a particular RFLP might be associated
with the mutant gene in some people, with its healthy allele in others. Thus it is essential to examine not only the patient but as
many members of the patient's family as possible.

Figure 11.7.2 : RFLP Marker

The most useful probes for such analysis bind to a unique sequence of DNA; that is, a sequence occurring at only one place in the
genome. Often this DNA is of unknown, if any, function. This can actually be helpful as this DNA has been freer to mutate without
harm to the owner. The probe will hybridize (bind to) different lengths of digested DNA in different people depending on where the
enzyme cutting sites are that each person has inherited. Thus a large variety of alleles (polymorphisms) may be present in the
population. Some people will be homozygous and reveal a single band; others (e.g., all the family members shown below) will be
heterozygous with each allele producing its band.
The pedigree in Figure 11.7.2 shows the inheritance of a RFLP marker through three generations in a single family. A total of 8
alleles (numbered to the left of the blots) are present in the family. The RFLPs of each member of the family are placed directly
below his (squares) or her (circles) symbol and RFLP numbers.
If, for example, everyone who inherited RFLP 2 also has a certain inherited disorder, and no one lacking RFLP 2 has the disorder,
we deduce that the gene for the disease is closely linked to this RFLP. If the parents decide to have another child, prenatal testing
could reveal whether that child was apt to come down with the disease. But note, that crossing over during gamete formation could
have moved the RFLP to the healthy allele. So the greater the distance between the RFLP and the gene locus, the lower the
probability of an accurate diagnosis.

Case 3: DNA "typing"

Each human cell contains 6 x 109 base pairs of DNA. Some of this represents protein-encoding genes (e.g., for the beta chain of
hemoglobin) that are identical in a large proportion of people. But long stretches of DNA do not encode for anything and are free to
mutate extensively. It seems certain that if we could read the entire sequence of DNA in each human, we would never find two that
were identical (unless the samples were from identical siblings; i.e., derived from a single zygote).

11.7.2 https://bio.libretexts.org/@go/page/4928
So each person's DNA is as unique as a fingerprint. This truth has not escaped the law enforcement and legal professions. Analysis
of DNA, called DNA typing, is widely used to identify rapists and other criminals, determine paternity; that is, who the father of
the child really is, determine whether a hopeful immigrant is, as he or she claims, really a close relative of already established
residents.

 Example 11.7.1: Rape Suspect

Figure 11.7.3 shows the test results in a rape case. Two probes were used: one revealing the bands at the top, the other those at
the bottom.

3
Figure 11.7.3 : DNA typing courtesy of Lifecodes Corporation
DNA was tested from
semen removed from the vagina of the rape victim (EVIDENCE #2);
a semen stain left on the victim's clothing (EVIDENCE #1);
the DNA of the victim herself (VICTIM) to be sure that the DNA didn't come from her cells;
DNA from two suspects (SUSPECT #1, SUSPECT #2);
a set of DNA fragments of known and decreasing length (MARKER). They provide a built-in ruler for measuring the exact
distance that each fragment travels.
the cells of a previously-tested person to be sure the probes are performing properly (CONTROL).
One the basis of this test, suspect #2 can clearly be ruled out. None of his bands matches the bands found in the semen.
Is suspect #1 guilty?
We can never be certain. The best we can do is to estimate the probability that another person, picked at random, could provide
the same DNA fingerprint. As a conservative estimate, a given allele (band) might be found in 25% of the people tested. The
probability of a random match of two alleles is (0.25)2 or 1 in 16. The probability that 6 alleles match, as in this case, is
(0.25)6 or 1 in 4096. However, the suspect was not picked at random, so you may feel that the evidence of guilt is strong.
The more probes you use, the more confident you can be that you have gotten the right man. If, for example, a set of probes
revealed 14 bands in a suspect's DNA identical to those in the semen sample, the probability that you have the wrong man
14

11.7.3 https://bio.libretexts.org/@go/page/4928
 drops to less than 1 in 268 million (0.25)14 = 1/268,435,456, which is almost as great as the entire population, males and
females, in the United States.

Starting in 1999, law enforcement agencies in both Great Britain and the United States began switching to a new version of RFLP
analysis using shorter sequences called STRs ("Short Tandem Repeats"). STRs are repeated sequences of a few (usually four)
nucleotides, e.g., TCATTCATTCATTCAT. They often occur in the untranslated parts of known genes (whose sequence can be used
for the PCR primers). The exact number of repeats (6, 7, 8, 9, etc.) varies in different people (and, often, in the gene on each
chromosome; that is, people are often heterozygous for the marker).
When 13 STR loci — scattered over different chromosomes — are examined, the chance that two people picked at random have
the same pattern is less than 1 in 1 trillion. The U.S. Federal Bureau of Investigation (FBI) wants to increase the number of loci
examined to 20 further eliminating the possibility of false positives.

This page titled 11.7: Restriction Fragment Length Polymorphisms is shared under a CC BY 3.0 license and was authored, remixed, and/or
curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is
available upon request.

11.7.4 https://bio.libretexts.org/@go/page/4928
11.8: Gel Blotting
Gel blotting is a technique for visualizing a particular subset of macromolecules — proteins, or fragments of DNA or RNA —
initially present in a complex mixture. The steps:
1. Separate the molecules by electrophoresis. This is done in a gel which allows the molecules to migrate under the influence of
the electric field.
2. "Blot" them with a nitrocellulose filter. For unknown reasons, the molecules stick tightly to the filter and will retain their
relative positions when flooded with fluid at the next step.
3. Bathe the filter with a solution containing a "probe": a molecule that will combine specifically with the target molecules; that is,
the one(s) you are looking for and carries a mean of visualization, e.g. a radioactive or fluorescent marker.

Southern Blot
The diagram illustrates the procedure for detecting DNA fragments containing a particular sequence. DNA is extracted from the
cell and is partially digested by a restriction endonuclease. The resulting DNA fragments are separated by electrophoresis and then
denatured to form single-stranded molecules (ssDNA). Without altering their positions, the separated bands of ssDNA are
transferred to a nitrocellulose filter and exposed to radiolabeled cDNA or RNA. If the probe detects complementary DNA
sequences, it will bind to them. The presence of the probe in a particular band is revealed by autoradiography.

Figure 11.8.1 : Southern Blotting

This procedure was developed by E. M. Southern and the finished product is called a "Southern blot". The same basic procedure
can also be used to separate and visualize RNA molecules and protein molecules. As a humorous extension of the term "Southern
blot", these have been dubbed "Northern" and "Western" blots, respectively (Table 11.8.1).
Table 11.8.1 : Summary or Common Gel Blots
Type of Blot Molecules separated by electrophoresis Probe

Southern ssDNA cDNA or RNA

Northern denatured RNA RNA or cDNA

Western Protein Antibodies

This page titled 11.8: Gel Blotting is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

11.8.1 https://bio.libretexts.org/@go/page/4930
11.9: Genetic Screening for Phenylketonuria
Phenylketonuria is one of the commonest inherited disorders — occurring in approximately 1 in 10,000 babies born in the U. S. It
occurs in babies who inherit two mutant genes for the enzyme phenylalanine hydroxylase (PAH — "1" in the figure on the left).
This enzyme normally starts the process of breaking down molecules of the amino acid phenylalanine that are in excess of the
body's needs for protein synthesis.

Figure 11.8.1 Phenylalanine pathways

The complete pathway is shown in the above figure. Phenylalanine that is in excess of the body's needs for protein synthesis is
broken down as shown here and used in cellular respiration and to synthesize melanin as needed. Carbon atoms are shown in color,
nitrogen atoms in black, and hydrogen atoms as short dashes.
Because we inherit two copies of the gene for the enzyme, both must be defective to produce the disease. A laboratory test that
measures how quickly an injection of phenylalanine is removed from the blood can distinguish a person who has one PKU gene
from a person who has none, but the person with one is perfectly healthy because the unmutated allele produces enough of the
enzyme. However, these heterozygous individuals are "carriers" of the disease.

The Phenylalanine Tolerance Test

A short time after administering a measured amount of phenylalanine to the subject, the concentration of phenylalanine in the blood
plasma is measured. The level is usually substantially higher in people who carry one PKU gene (even though they show no signs
of disease) than in individuals who are homozygous for the unmutated gene. Both parents must be heterozygous (i.e., must be
"carriers" of the trait) to produce a child with PKU. The chance of their doing so is 1 in 4.

11.9.1 https://bio.libretexts.org/@go/page/4932
 Figure 11.8.2 Phenylaline Tolerance test
Inability to remove excess phenylalanine from the blood during infancy and early childhood produces a variety of problems
including mental retardation. Fortunately, a simple test (needing only a drop of blood) done shortly after birth can identify the
genetic defect and, with close attention to the amount of phenylalanine in their diet, the children can develop normally.
Alcaptonuria is another inherited disease involving this pathway. It results from the inheritance of two mutant genes for the
enzyme ("4") that converts homogentisic acid to maleylacetoacetic acid. When step 4 is blocked, homogentisic acid accumulates in
the blood. The kidney excretes this excess in the urine, and oxidation of homogentisic acid by the air turns the urine black. Diseases
like PKU and alcaptonuria are called "inborn errors of metabolism" because they are inherited and each is characterized by a
distinct metabolic defect.

Genetic Screening
In the United States, approximately 1 person in 50 has inherited a PKU allele. This means that some 5 million people in the U.S.
are "carriers". Should they be tested before they decide to become parents? By testing the DNA of prospective parents, their
genotype can be determined and their odds of producing an afflicted child calculated. In the case of PKU, if both parents are
heterozygous for the gene, there is a 1 in 4 chance that they will produce a child with the disease.
Problems:
Scores of different mutations in the PAH gene can cause the disease. A probe for one will probably fail to identify a second. A
mixture of probes, one for each of the more common mutations, can be used. But there remains the problem of "false
negatives": people who are falsely told they do not carry a mutant gene.
With an effective treatment for PKU available, should heterozygous parents forego having children?
Do they want their health insurance company to know their status?

Genetic Screening Example

Figure 11.8.3 PKU. Genetic screening for "a" (NOTE: not "the" — many different mutations in the PKU gene have been
identified) PKU allele.
Top: schematic of a portion of the gene encoding the enzyme phenylalanine hydroxylase (PAH) showing the sites cut by the
restriction enzyme HindIII ("H") and the region to which the radioactive probe binds a mutant version of the gene with a
deletion that destroys its function. The deletion eliminates the HindIII site in Exon 2, lengthening the DNA fragment to which
the probe binds from 3.3 to 4.2 thousand base pairs (kb) (and thus revealing a RFLP).
Middle: The daughter (solid circle) with PKU inherited one PKU allele from each of her parents (half-filled symbols). Her
brother (open square) beat the odds (0.5) of inheriting at least one PKU allele and thus of being a carrier. If he had been a
carrier, would he have wanted to know?

11.9.2 https://bio.libretexts.org/@go/page/4932
 Bottom: The blot shows the fragments to which the probe binds directly beneath each individual in the pedigree. It reveals only
the 3.3 kb fragment for the brother, only the 4.2 kb fragment for the sister, and both for each parent.
The particular mutation in this family is only one of many mutant PAH alleles that cause PKU, and testing with this particular
enzyme and probe would not necessarily detect the others.

Phenylalanine hydroxylase (PAH) is made in the liver

The evidence:
A child with PKU was cured when he received a transplanted liver (needed for reasons unrelated to his PKU). (Described by
Vajro, P., et. al., in the New England Journal of Medicine 329:363, 29 July 1993.)
Hepatic Nuclear Factor 1 (HNF1) is a transcription factor that is strongly expressed in the cells of the liver (called
hepatocytes). In these cells, it binds to and activates the promoters of many genes expressed in the liver. "Knockout" mice were
created from embryonic stem (ES) cells carrying two mutant PAH genes.Among other problems, these mice produced no PAH
and had severe PKU. (Described by Pontoglio, M., et. al., in Cell 84:575, 23 February 1996.)

Dominant or recessive
The disease PKU is clearly inherited as a recessive trait. Only if one inherits a mutant allele from each parent will one develop the
disease. However, heterozygous people are easily distinguished from homozygotes by the phenylalanine tolerance test. So using the
test as the criterion, the PKU allele shows partial dominance. So, the relationship between genotype and phenotype is not always
straightforward. What is the criterion of phenotype in this case? the disease? the results of the tolerance test?

This page titled 11.9: Genetic Screening for Phenylketonuria is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by
John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

11.9.3 https://bio.libretexts.org/@go/page/4932
11.10: Antisense RNA
Messenger RNA (mRNA) is single-stranded. Its sequence of nucleotides is called "sense" because it results in a gene product
(protein). Normally, its unpaired nucleotides are "read" by transfer RNA anticodons as the ribosome proceeds to translate the
message.

Figure 11.9.1 Sense Strand

However, RNA can form duplexes just as DNA does. All that is needed is a second strand of RNA whose sequence of bases is
complementary to the first strand.
Example
5´ C A U G 3´ mRNA
3´ G U A C 5´ Antisense RNA
The second strand is called the antisense strand because its sequence of nucleotides is the complement of message sense.

Figure 11.9.2 Antisense RNA

When mRNA forms a duplex with a complementary antisense RNA sequence, translation is blocked. This may occur because the
ribosome cannot gain access to the nucleotides in the mRNA or because the duplex RNA is quickly degraded by ribonucleases in
the cell. With recombinant DNA methods, synthetic genes (DNA) encoding antisense RNA molecules can be introduced into the
organism.

Examples
The Flavr Savr tomato
Most tomatoes that have to be shipped to market are harvested before they are ripe. Otherwise, ethylene synthesized by the tomato
causes them to ripen and spoil before they reach the customer. Transgenic tomatoes have been constructed that carry in their
genome an artificial gene (DNA) that is transcribed into an antisense RNA complementary to the mRNA for an enzyme involved in
ethylene production. These tomatoes make only 10% of the normal amount of the enzyme.
The goal of this work was to provide supermarket tomatoes with something closer to the appearance and taste of tomatoes
harvested when ripe. However, these tomatoes often became damaged during shipment and handling and have been taken off the
market.

Transgenic Tobacco

Fig.11.9.3 tobacco flower

11.10.1 https://bio.libretexts.org/@go/page/4934
Flower of a tobacco plant carrying a transgene whose transcript is antisense to one of the mRNAs needed for normal flower
pigmentation.

Transgenic Flower

Figure 11.9.4 Transgenic flower

Flower of another transgenic plant that failed to have its normal pigmentation altered.

Making transgenic plants

There are several methods for introducing genes into plants, including
infecting plant cells with plasmid vectors carrying the desired gene
shooting microscopic pellets containing the gene directly into the cell
In contrast to animals, there is no real distinction between somatic cells and germline cells. Somatic tissues of plants, e.g., root cells
grown in culture,
can be transformed in the laboratory with the desired gene
grown into mature plants with flowers.
If all goes well, the transgene will be incorporated into the pollen and eggs and passed on to the next generation.
In this respect, it is easier to produce transgenic plants than transgenic animals.

Antisense RNA also occurs naturally

Do cells contain genes that are naturally translated into antisense RNA molecules capable of blocking the translation of other genes
in the cell? The answer is yes, and these seem to represent another method of regulating gene expression. In both mice and
humans, the gene for the insulin-like growth factor 2 receptor (Igf2r) that is inherited from the father synthesizes an antisense
RNA that appears to block synthesis of the mRNA for Igf2r. An inherited difference in the expression of a gene depending on
whether it is inherited from the mother or the father is called genomic or parental imprinting.

RNA interference (RNAi)

In testing the effects of antisense RNA, one should use sense RNA of the same coding region as a control. Surprisingly,
preparations of sense RNA often turn out to be as effective an inhibitor as antisense RNA.
Why? It seems that the preparations of sense RNA often are contaminated with hybrids: sense and antisense strands that form a
double helix of double-stranded RNA (dsRNA). Double-stranded RNA corresponding to a particular gene is a powerful
suppressant of that gene. In fact, the suppressive effect of antisense RNA probably also depends on its ability to form dsRNA
(using the corresponding mRNA as a template).
The ability of dsRNA to suppress the expression of a gene corresponding to its own sequence is called RNA interference (RNAi).
It is also called post-transcriptional gene silencing or PTGS.

Mechanism of RNAi
The only RNA molecules normally found in the cytoplasm of a cell are molecules of single-stranded RNA. If the cell finds
molecules of double-stranded RNA (dsRNA), it uses an enzyme called Dicer to cut them into fragments containing ~21 base
pairs (~2 turns of a double helix). The two strands of each fragment then separate — releasing the antisense strand. With the aid
of a protein, it binds to a complementary sense sequence on a molecule of mRNA. If the base-pairing is exact, the mRNA is
destroyed. Because of their action, these fragments of RNA have been named "small (or short) interfering RNA" (siRNA). The
complex of siRNA and protein is called the "RNA-induced silencing complex" (RISC).

11.10.2 https://bio.libretexts.org/@go/page/4934
siRNAs can also interfere with transcription
There is growing evidence that siRNAs can also inhibit the transcription of genes
perhaps by binding to complementary sequences on DNA or
perhaps by binding to the nascent RNA transcript as it is being formed.
In fission yeast, at least, the siRNA is complexed with one molecule of each of three different proteins. The entire complex is
called the RITS complex ("RNA-induced initiation of transcriptional gene silencing")
How these siRNAs — synthesized in the cytosol — gain access to the DNA in the nucleus is unknown.
Synthetic siRNA molecules that bind to gene promoters can — in the laboratory — repress transcription of that gene. The
repression is mediated by methylation of the DNA in the promoter and, perhaps, methylation of histones in the vicinity.
There is a strain of rice (LGC-1) that produces abnormally low levels of proteins called glutelins. It turns out that of several
glutelin genes found in rice
two closely-similar glutelin genes are located back to back on the same chromosome.
In LGC-1, a deletion has occurred between the two genes which removes the signal that would normally stop transcription after
the first gene.
Thus RNA polymerase II transcribes right past the first gene and on into the second.
The result is a messenger RNA with almost-identical sequences running in opposite directions.
This causes the mRNA to fold up into a molecule of double-stranded RNA (dsRNA).
A Dicer-like enzyme cuts up the dsRNA into small interfering RNAs (siRNAs) that suppress further transcription of those
genes as well as other glutelin genes.

Why RNAi?
RNAi has been found to operate in such diverse organisms as plants, fungi, and animals such as Drosophila melanogaster,
Caenorhabditis elegans, and even mice and the zebrafish. Such a universal cell response must have an important function. What
could it be?
Some possibilities:
Some viruses of both plants and animals have a genome of dsRNA. And many other viruses of both plants and animals have an
RNA genome that in the host cell is briefly converted into dsRNA. So RNAi may be a weapon to counter infections by these
viruses by destroying their mRNAs and thus blocking the synthesis of essential viral proteins.
Transposons may be transcribed into RNA molecules with regions that are double-stranded. RNAi could then destroy these.
RNA interference may be the unexpected dividend of another basic process of controlling gene expression.

RNAi as a tool
In any case, the discovery of RNAi adds a promising tool to the toolbox of molecular biologists. Introducing dsRNA corresponding
to a particular gene will knock out the cell's own expression of that gene. (Feeding C. elegans on E. coli manufacturing the dsRNA
will even do the trick.)
Heroic Example
In the 24 March 2005 issue of Nature, Sönnichsen et al reported that they have injected dsRNAs corresponding to 20,326 of C.
elegans's genes (98% of the total!) and monitored the effect of each on embryonic development from the completion of meiosis
(following fertilization) through the second mitotic division that produces the 4-cell embryo.
They found that at least 661 different genes altered some process during this period:
about half of them involved in cell division and
half in general cell metabolism.
(Another thousand genes produced phenotypic effects that were seen at later stages of development.)
Because RNAi can be done in particular tissues at a chosen time, it often provides an advantage over conventional gene
"knockouts" where the missing gene is carried in the germline and thus whose absence may kill the embryo before it can be
studied.

11.10.3 https://bio.libretexts.org/@go/page/4934
Another Example: screening genes for their effect on drug sensitivity
Distribute your cells in thousands of wells and add — from a "library" of thousands of siRNAs representing the entire genome
— siRNA molecules targeting the expression of one gene to each well
Add the drug to all the wells
See which wells have cells that respond
Some other promising applications of RNAi
In mammalian cells
In mammalian cells, introducing dsRNA fragments only reduces gene expression temporarily. However, mammalian cells can be
infected with a DNA vector that encodes an RNA molecule of 50–80 nucleotides called a "small hairpin RNA" (shRNA)
containing a sequence corresponding to the gene that one wishes to suppress. As the shRNA is synthesized, dicer converts it into a
typical siRNA molecule. Because the cell can continuously synthesize shRNA, the interference is long-lasting. In fact, with vectors
that become integrated in the host genome, RNAi can be passed on to the descendants.
In plants
The 19 June 2003 issue of Nature reported on coffee plants that were engineered to express a transgene that makes siRNA that
interferes — by RNAi — with the expression of a gene needed to make caffeine. So perhaps "decaf" coffee will one day no longer
require the chemical removal of caffeine from coffee beans.
Monsanto is developing a transgenic corn (maize) that expresses a dsRNA corresponding to the sequence of an essential gene in the
western corn rootworm, a devastating pest of the crop. After ingesting this dsRNA, the insect's own cells process it into an siRNA
that targets the gene's mRNA for destruction and kills the worm in a few days.

Amplification of RNAi
In C. elegans, plants, and Neurospora, the introduction of a few molecules of dsRNA has a potent and long-lasting effect. In plants,
the gene silencing spreads to adjacent cells (through plasmodesmata) and even to other parts of the plant (through the phloem).
RNAi within a cell can continue after mitosis in the progeny of that cell. Triggering of RNAi in C. elegans can even pass through
the germline into its descendants.
Such amplification of an initial trigger signal suggests a catalytic effect. It turns out that these organisms have RNA-dependent
RNA polymerases (RdRPs) that uses the mRNA targeted by the initial antisense siRNA as a template for the synthesis of more
siRNAs. Synthesis of these "secondary" siRNAs even occurs in adjacent regions of the mRNA. So not only can these secondary
siRNAs target additional areas of the original mRNA, but they are potentially able to silence mRNAs of other genes that may carry
the same sequence of nucleotides.
This phenomenon, called "transitive RNAi",
may complicate the interpretation of gene suppression experiments as the expression of other genes may be suppressed in
addition to the target gene;
raises a warning flag for the use of RNAi to suppress single genes in human therapy (although RdRPs and amplification have
not been observed in mammalian cells).

RNAi in human therapy

Because its target is so specific, the possibility of using RNAi to shut down the expression of a single gene has created great
excitement that a new class of therapeutic agents is on the horizon. Many clinical trials are underway exploring the use of siRNA
molecules in the treatment of a wide variety of diseases. To date, the most promising results have been using RNAi to target an
inherited disease in which the liver secretes a mutant form of transthyretin leading to the accumulation of amyloid deposits in
neurons and elsewhere.

MicroRNAs (miRNAs)
In C. elegans, successful development through its larval stages and on to the adult requires the presence of at least two
"microRNAs" ("miRNAs") — single-stranded RNA molecules containing about 22 nucleotides and thus about the same size as
siRNAs.
These small single-stranded transcripts are generated by the cleavage of larger precursors using the C. elegans version of Dicer.

11.10.4 https://bio.libretexts.org/@go/page/4934
They act by either destroying or inhibiting translation of several messenger RNAs in the worm (usually by binding to a region of
complementary sequence in the 3' untranslated region [3'-UTR] of the mRNA).
The microRNAs (miRNAs) in C. elegans (which were first called "small temporal RNAs") turn out to be representatives of a large
class of RNAs that are encoded by the organism's own genes.
The initial product of gene transcription is a large molecule called pri-miRNA.
While still within the nucleus an enzyme called Drosher cuts the pri-miRNA into a shorter molecule (~70 nucleotides) called
pre-miRNA.
The pre-miRNA is exported into the cytosol where it is cleaved (by Dicer in animals) into the miRNA.
MicroRNAs
are found in all animals (humans generate some 1000 miRNAs) and plants but not in fungi.
contain 19–25 nucleotides;
are encoded in the genome
some by stand-alone genes (that may encode several miRNAs)
some by portions of an intron of the gene whose mRNA they will regulate.
may be expressed in
only certain cell types and
at only certain times in the differentiation of a particular cell type.
While direct evidence of the function of many of these newly-discovered gene products remains to be discovered, they regulate
gene expression by regulating messenger RNA (mRNA), either
destroying the mRNA when the sequences match exactly (the usual situation in plants) or
repressing its translation when the sequences are only a partial match. In this latter case, it probably requires several miRNAs
to bind simultaneously in the 3'-UTR.
MicroRNAs have two traits ideally suited for this:
Being so small, they can be rapidly transcribed from their genes.
They do not need to be translated into a protein product to act (in contrast, e.g., to transcription factors).
MicroRNAs regulate (repress) expression of genes in mammals as well. Genome analysis has revealed thousands of human genes
whose transcripts (mRNAs) contain sequences to which one or more of our miRNAs might bind. Probably each miRNA can bind
to as many as 200 different mRNA targets while each mRNA has binding sites for multiple miRNAs. Such a system provides many
opportunities for coordinated mRNA translation.
A study reported in Nature (Lim, et al., 433: 769, 17 Feb 2005) used DNA chip analysis to show that when a particular miRNA
was expressed in HeLa cells,
a miRNA normally expressed in the brain repressed mRNA production by 174 different genes while
a miRNA normally expressed in cardiac and skeletal muscle repressed mRNA production by 96 genes — all but 8 of them
different from the those repressed by the brain miRNA.
As work proceeds rapidly in this field, the pattern that begins to emerge is that:
Many genes — especially those involved in such housekeeping activities (e.g., cellular respiration) common to all cells — do
not have 3'-UTRs that can be blocked by any of the miRNAs encoded in the genome.
The genes that must be expressed in a particular type of differentiated cell and/or at a particular time in the life of that cell
do not express any of the miRNA genes that could block their expression but
do express miRNA genes that block the expression of other genes for specialized functions that would not be appropriate in
that cell at that time.
Rather than being simple switches that turn gene expression on or off, miRNAs seem to exert a more subtle effect — raising or
lowering the level of gene expression (much as protein transcription factors do).
Thus repression of gene expression by miRNAs appears to be a mechanism to ensure regulated and coordinated gene expression as
cells differentiate along particular paths. For example, when zygote genes begin to be turned on in the zebrafish blastula, one of
them encodes a miRNA that triggers the destruction of the maternal mRNAs that have been running things up to then.

11.10.5 https://bio.libretexts.org/@go/page/4934
So miRNAs may play as important role as transcription factors in regulating and coordinating the expression of multiple genes in a
particular type of cell at particular times.

Therapeutic miRNAs?
The ease with which miRNAs can be introduced into cells and their widespread effects on gene expression have given rise to hopes
that they might be useful in controlling genetic disorders, e.g., cancer.
To date, some laboratory studies have been quite promising.
A miRNA that blocks the expression of G1 and S-phase cyclins — and thus stops the cell cycle in its tracks — protects mice
from liver cancer.
a miRNA that inhibits genes needed for metastasis suppresses the metastasis of treated human breast cancer cells.

Summary
In addition to protein transcription factors, eukaryotes use small RNA molecules to regulate gene expression — almost always by
repressing it — so the phenomenon is called RNA silencing.
There are two sources of small RNA molecules:
small interfering RNAs (siRNAs)
Plant cells make these from the double-stranded RNA (dsRNA) of invading viruses.
Scientists and pharmaceutical companies make these as agents to turn off the expression of specific genes (called RNA
interference or RNAi).
micro RNAs (miRNAs)
These are encoded in the genomes of all plants and animals.
Both siRNAs and miRNAs are processed in the same way in the cytosol of the cell.
Both are generated by Dicer.
Both are incorporated into an RNA-induced silencing complex (RISC).
If the nucleotide sequence of the small RNA exactly matches that of the mRNA, the mRNA is cut and destroyed.
If there is only a partial match (usually in its 3' UTR), translation (i.e., protein synthesis) is repressed. Both of these
activities take place in the cytosol — perhaps in P bodies.
However, for some small RNAs, the RISC complex enters the nucleus and turns off transcription of the corresponding
gene(s) by
binding to the unwound DNA sequence (or perhaps the RNA transcript as it is being formed)
converting euchromatin to heterochromation
methylating of lysine-9 histone H3 in the nucleosomes around the gene(s)
Aside from their use as laboratory — and perhaps therapeutic — tools, small RNAs are clearly essential to the organisms that make
them.
Some examples:
Plants and animals use them to defend themselves against viruses.
Example: When human cells are infected by hepatitis C virus (HCV), they produce miRNAs that interfere with gene
expression by this RNA virus and thus its ability to replicate.
Some herpesviruses use them to keep their host cell alive long enough to complete viral replication (by blunting a host immune
response against the infected cell and preventing its premature death by apoptosis).
Of the 46 miRNAs expressed in the Drosophila embryo, 25 have been shown to be essential to normal development.
Correct embryonic development in other animals (e.g., C. elegans, zebrafish, mice) also requires them.
They protect against the danger of mutations caused by transposons moving around in the genome.
They are also needed to regulate the size of the pool of at least some types of stem cells.
Transgenic mice with a single miRNA gene knocked out develop severe immunodeficiency affecting dendritic cells, helper T
cells, and B cells.
Reduced, or no, expression of certain miRNAs are characteristic of several different cancers in humans.

11.10.6 https://bio.libretexts.org/@go/page/4934
This page titled 11.10: Antisense RNA is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

11.10.7 https://bio.libretexts.org/@go/page/4934
11.11: Antisense Oligodeoxynucleotides and their Therapeutic Potential
Antisense oligonucleotides are synthetic polymers. The monomers are chemically-modified deoxynucleotides like those in DNA
or ribonucleotides like those in RNA. There are usually only 15–20 of them, hence "oligo". Their sequence (3′ → 5′) is antisense;
that is, complementary to the sense sequence of a molecule of mRNA.

Figure 11.10.1 Antisense oligonucleotides

Antisense oligonucleotides are synthesized in the hope that they can be used as therapeutic agents — blocking disease processes by
altering the synthesis of a particular protein. This would be achieved by the binding of the antisense oligonucleotide to the mRNA
from which that protein is normally synthesized. Binding of the two may
physically block the ability of ribosomes to move along the messenger RNA preventing synthesis of the protein;
hasten the rate at which the mRNA is degraded within the cytosol;
prevent splicing errors that would otherwise produce a defective protein.
To be useful in human therapy, antisense oligonucleotides must be able to enter the target cells; avoid digestion by nucleases; and
not cause dangerous side-effects. To achieve these goals, antisense oligonucleotides are generally chemically modified to resist
digestion by nucleases and attached to a targeting device such as the ligand for the type of receptors found on desired target cells or
antibodies directed against molecules on the surface of the desired target cells.

Antisense Oligonucleotides Uses

A variety of antisense oligonucleotides are being tested as possible weapons against:
Hepatitis C virus (HCV). Successful infection of the liver by this virus requires that the liver produce a particular microRNA
(miRNA-122). Injections of HCV-infected humans with an ODN ("miravirsen") complementary to miRNA-122 suppresses the
virus.
HIV-1, the most frequent cause of AIDS in the United States
Ebola virus, the cause of the often-fatal Ebola hemorrhagic fever
human cytomegalovirus (HCMV); which frequently causes serious complications in AIDS patients
asthma; inhalation of an antisense oligonucleotide targeting the mRNA of GATA3 (a transcription factor that promotes Th2
responses) provides relief to patients with allergic asthma.
certain cancers, e.g., chronic myelogenous leukemia (CML)
certain types of inflammation caused by cell-mediated immune reactions
Duchenne muscular dystrophy (DMD)
familial hypercholesterolemia — targets the mRNA for apolipoprotein B-100. On 31 January 2013, the antisense ODN
mipomersen (Kynamro®) received regulatory approval for use in humans with familial hypercholesterolemia.

This page titled 11.11: Antisense Oligodeoxynucleotides and their Therapeutic Potential is shared under a CC BY 3.0 license and was authored,
remixed, and/or curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed
edit history is available upon request.

11.11.1 https://bio.libretexts.org/@go/page/4936
11.12: Forward and Reverse genetics
The Zebrafish
The zebrafish, Danio rerio, has become another popular "model" organism with which to study fundamental biological questions. It
is a small (1–1.5 inches)(2.5–3.8 cm) freshwater fish that grows easily in aquaria (it is available at many pet stores). Some of its
advantages for biologists:
It breeds early and often (daily).
It is a vertebrate, like us, and thus can provide clues to human biology that invertebrates like Drosophila and Caenorhabditis
elegans may not.
Its embryos, like those of most fishes, develop outside the body where they can be easily observed (unlike mice).
Its embryos are transparent so defects in development can be seen easily.
Individual cells in the embryo can be labeled with a fluorescent dye and their fate followed.
Embryonic development is quick (they hatch in two days).
They can absorb small molecules, such as mutagens, from the aquarium water.
Individual cells — or clusters of cells — can be transplanted to other locations in the embryo (as Mangold did with newt
embryos).
They can be forced to develop by parthenogenesis to produce at will homozygous animals with either:
a male-derived or
female-derived genome.
They can be cloned from somatic cells.
They can be made transgenic (like mice and Drosophila)
Its genome (1.4 x 109 base pairs) has been sequenced revealing 26,606 protein-coding genes.

Forward Genetics
Since Mendel's time, most genetics has involved observing an interesting phenotype and tracking down the gene responsible for it.
So this "forward" genetics proceeds from phenotype -> genotype. Some examples in these pages:
Mendel's work
RFLP analysis of large families
the one gene - one enzyme theory
These methods have been called "forward" genetics to distinguish them from a more recent approach, which has become an urgent
priority with the successes of genome sequencing.

Reverse Genetics
Rapid methods of DNA sequencing has generated a vast amount of data. Thousands of suspected genes have been revealed (e.g.,
finding open reading frames — ORFs), but the function of many of them is still unknown. But now with a knowledge of the DNA
sequence of a gene of unknown function, one can use methods for suppressing that particular gene ("knockdown"), and then
observe the effect on the phenotype.
So this "reverse" genetics proceeds from genotype -> phenotype. Reverse genetics has been applied successfully to plants; mice; C.
elegans; and can also be used with the zebrafish. For example, the function of a mysterious gene sequence in Danio can be studied
by
synthesizing a short antisense oligonucleotide complementary to a section of the gene.
The oligonucleotide is chemically-modified to make it more stable than a fragment of RNA.
Binding to its complementary sequence on the messenger RNA (mRNA) produced by transcription of the animal's gene, blocks
("knocks down") gene expression by preventing translation or disrupting normal splicing of the mRNA.
Because we share so many similar gene sequences (orthologous genes) with Danio, if one can discover the function of the gene in
Danio, then we have a better idea of the role of its ortholog in humans.

This page titled 11.12: Forward and Reverse genetics is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

11.12.1 https://bio.libretexts.org/@go/page/4937
11.13: Metagenomics
All the genomes listed on my page Genome Sizes describe the complete genome of a single species. For bacteria and archaeons,
this means that the organism was grown in pure culture to provide the DNA for sequencing. But it is now clear that the microbial
world contains vast numbers of both groups that have never been grown in the laboratory and thus have escaped study. Soil, water,
and the contents of our large intestine are examples of habitats that teem with unknown microorganisms.
Thanks to the recent development of sequencing machines capable of rapidly (and inexpensively) sequencing huge amounts of
DNA, it is now practical to sequence the DNA extracted from complex microbial ecosystems like that found in a soil sample.
Several different approaches are used, but all depend on a first step of extracting the microbial DNA from the sample (and
separating it from the far more complex DNA of any eukaryotes that may be present).

Assessing Microbial Diversity

The DNA encoding the small subunit (16S) of the ribosomes of both bacteria and archaeons contain some highly conserved
regions; that is, regions of identical or almost identical sequence. Using primers that target these regions, one can then produce
enough material by the polymerase chain reaction PCR to sequence the entire 16S rRNA gene.
Comparing the various sequences to a database of sequences from known organisms, one can estimate how many different types of
microbes are present. Because of the substantial genetic diversity found between "strains" of a single species (e.g., E. coli K-12 and
E.coli O157:H7), closely-related (> 97% identity) 16S rDNA sequences are assigned to a single "phylotype" because we cannot be
sure whether they belong to separate species or to two strains of the same species. In either case, the collection of 16S rDNA
sequences can be arranged to form a phylogenetic tree to show the patterns of relatedness.

Cataloging the Genes in a Microbial Ecosystem

Analyzing the 16S rDNA genes in a sample tells us who is there, but, of course, is not a complete genome and tells us nothing
about the other genes present in the various members of the population. This information can be gained by "shotgun" sequencing of
the environmental DNA sample.
The Steps:
Break the DNA in short fragments.
Insert these into a vector, e.g. a plasmid capable of growing in E. coli K-12.
Expose E. coli cells to this random mix and grow the individual bacterial cells into colonies.
The result: a library containing millions of random DNA fragments from the original sample.
Isolate the plasmids and sequence them. Sequence "reads" average around 100 nucleotides — far shorter than a gene but often
enough to move on to the next step.
Use a powerful computer to attempt to assemble the fragments into a linear sequence of DNA. The computer looks for identical
stretches of nucleotides in different fragments and uses the overlap to assemble them into a "contig".

Look (have the computer look) for open reading frames (ORFs) of protein-encoding genes.
Compare the ORFs with those of known microbes already in databases to see if a function can be deduced.
The sheer diversity of organisms in most microbial ecosystems makes it virtually impossible to find enough contigs to assemble a
complete genome for any one organism like those listed in Genome Sizes. What you get instead is a window into the many kinds of
genes present in one inhabitant or another of that ecosystem. For example, you may discover genes that encode proteins able to
degrade environmental pollutants or genes able to synthesize a new antibiotic.

Finding New Functions in Microbial Populations

Another way of exploiting metagenomics is to look for new functions in the host (e.g. E. coli) if it can express the new gene with
which it was transformed. For example, screening the library of E. coli clones for the ability to resist an antibiotic can reveal genes
involved in antibiotic resistance — a worrisome development in recent years.

11.13.1 https://bio.libretexts.org/@go/page/4938
Some Applications of Metagenomics
The Sargasso Sea
Metagenomic analysis of the DNA extracted from sea water in the Sargasso Sea revealed the presence of over a thousand different
16S rDNA genes (and thus approximately that number of different species) and over a million protein-encoding genes.

The Human Colon

0.3 g fecal samples from two healthy humans produced 78 million base pairs of sequence. Each subject produced some 25 thousand
open reading frames (ORFs) of which about half could be recognized as already-known bacterial or archaeal genes. Included were
genes encoding enzymes for the synthesis of vitamins (e.g., vitamin B1), amino acids, and enzymes for the digestion of complex
polysaccharides in our diet which would otherwise be indigestible. Perhaps as much as 10% of the energy we extract from our food
is made available to us by the activity of these microorganisms.

Acid Mine Drainage

Metagenomic analysis of the acidic water (pH ~0.5) flowing from an abandoned metal mine in California revealed a much simpler
ecosystem than those described above: only 3 species of bacteria and 2 of archaea. With such limited diversity, it was possible to
assemble almost-complete genomes for two of these organisms.

A South African Gold Mine

Simpler still was the ecosystem found in water 2.8 km (1.7 miles) down in a gold mine. Only one organism turned up: an
autotrophic bacterium capable of extracting energy from inorganic substances in its environment and synthesizing all the molecules
needed for its life from them.

This page titled 11.13: Metagenomics is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

11.13.2 https://bio.libretexts.org/@go/page/4938
 CHAPTER OVERVIEW
Unit 12: Cancer
A cancer is an uncontrolled proliferation of cells. In some the rate is fast; in others, slow; but in all cancers the cells never stop
dividing. This distinguishes cancers — malignant tumors — from benign growths like moles where their cells eventually stop
dividing (usually). Even more important, benign growths differ from malignant ones in not producing metastases; that is, they do
not seed new growths elsewhere in the body.
12.1: Cancer in General
12.2: Cancer Cells in Culture
12.3: Oncogenes
12.4: Tumor Suppressor Genes
12.5: BCL-2
12.6: Burkitt's Lymphoma
12.7: Chronic Myelogenous Leukemia (CML)
12.8: Fighting Cancer with Inhibitors of Angiogenesis
12.9: Immunotherapy of Cancer
12.10: Cancer- The Causes and Prevention of Cancer
12.11: Estimating Cancer Risks
12.12: The LD50 test
12.13: Dioxin
12.14: Magnetic Fields and Cancer

Thumbnail: This is a photograph of a basal cell carcinoma on the back taken by me. Basal cell carcinoma is the most common skin
cancer. (Public Domain; John Hendrix).

This page titled Unit 12: Cancer is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1
12.1: Cancer in General
A cancer is an uncontrolled proliferation of cells. In some the rate is fast; in others, slow; but in all cancers the cells never stop
dividing. This distinguishes cancers — malignant tumors — from benign growths like moles where their cells eventually stop
dividing (usually). Even more important, benign growths differ from malignant ones in not producing metastases; that is, they do
not seed new growths elsewhere in the body.
Cancers are clones. No matter how many trillions of cells are present in the cancer, they are all descended from a single ancestral
cell. Evidence: Although normal tissues of a woman are a mosaic of cells in which one X chromosome or the other has been
inactivated, all her tumor cells — even if from multiple sites — have the same X chromosome inactivated.
Cancers begin as a primary tumor. Most (maybe all) solid tumors shed cells into the lymph and blood. Most of these lack the
potential to develop into tumors. However, some of the shed cells are able to take up residence and establish secondary tumors —
metastases — in other locations of the body. These metastases, not the primary tumor, are what usually kills the patient.
Cancer cells are usually less differentiated than the normal cells of the tissue where they arose. Many people feel that this reflects a
process of dedifferentiation, but I doubt it. Rather, evidence is accumulating that cancers arise in precursor cells — stem cells or
"progenitor cells" — of the tissue: cells that are dividing by mitosis producing daughter cells that are not yet fully differentiated.

A cancer is an uncontrolled proliferation of cells.

Cancer is a Genetic Disease

Figure 12.1.1 Cancer Gene Mutation

What probably happens is:
A single cell — perhaps an adult stem cell or progenitor cell — in a tissue suffers a mutation (red line) in a gene involved in the
cell cycle, e.g., an oncogene or tumor suppressor gene.
This results in giving that cell a slight growth advantage over other dividing cells in the tissue.
As that cell develops into a clone, some if its descendants suffer another mutation (red line) in another cell-cycle gene.
This further deregulates the cell cycle of that cell and its descendants.
As the rate of mitosis in that clone increases, the chances of further DNA damage increases.
Eventually, so many mutations have occurred that the growth of that clone becomes completely unregulated.
The result: full-blown cancer. (Genetic analysis reveals an average of 63 mutations in pancreatic cancers; almost as many in one
type of adult brain cancer, but only 11 somatic mutations in a case of brain cancer in a child.)
Sequencing samples from several areas in a primary tumor, as well as from some of its metastases, reveals a different collection
of mutations from sample to sample. This finding is reinforced by the sequencing of the genome of individual cells from a
single tumor each of which shows a unique pattern of shared and unique mutations. (The ability to sequence the genome of a
single cell reveals that even normal cells in an adult have accumulated a suite of somatic mutations that differs from cell to cell.
However, the rate of somatic mutations in these normal cells is only a fourth of that in cancer cells.)
So even though all the malignant cells in a cancer are descended from a single original cell — and thus are members of a single
clone — they are no longer genetically-identical. As the tumor develops, its various cells develop a variety of additional mutations,
and these give rise to "subclones" of varying degrees of malignancy with varying
propensity to metastasize;
susceptibility to treatment by anticancer drugs;
propensity to relapse after apparently-successful therapy.
These findings should stimulate a reexamination of the use of chemotherapy.

12.1.1 https://bio.libretexts.org/@go/page/5076
 While chemotherapy may wipe out dominant subclones in a tumor, there is evidence that is also exerts a selective pressure for
the expansion of more malignant, previously-minor, subclones.
Most chemotherapeutic agents damage DNA so while killing off some cells, they will raise the mutation rate in any surviving
cells perhaps encouraging the outgrowth of even more malignant subclones.
Evidence: In a group of patients with chronic lymphocytic leukemia, those receiving chemotherapy survived for shorter periods
than those that did not.

Cancer Stem Cells

Stem cells are cells that divide by mitosis to form either two stem cells, thus increasing the size of the stem cell "pool", or one
daughter that goes on to differentiate, and one daughter that retains its stem-cell properties. There is growing evidence that most of
the cells in leukemias, breast, brain, skin, ovarian, and colon cancers are not able to proliferate out-of-control (and to metastasize).
Only those members of the clone that retain their stem-cell-like properties (~2.5% of the cells in a tumor of the colon) can do so.
There is a certain logic to this. Most terminally-differentiated cells have limited potential to divide by mitosis and, seldom passing
through S phase of the cell cycle, are limited in their ability to accumulate the new mutations that predispose to becoming
cancerous. Furthermore, they often have short life spans — being eliminated by apoptosis (e.g., lymphocytes) or being shed from
the tissue (e.g., epithelial cells of the colon). The adult stem cell pool, in contrast, is long-lived, and its members have many
opportunities to acquire new mutations as they produce differentiating daughters as well as daughters that maintain the stem cell
pool.

Colon cancer
Begins with the development of polyps in the epithelium of the colon. Polyps are benign growths.
As time passes, the polyps may get bigger.
At some point, nests of malignant cells may appear within the polyps
If the polyp is not removed, some of these malignant cells will escape from the primary tumor and metastasize throughout the
body.

Figure 12.1.2 Colon Cancer

Examination of the cells at the earliest, polyp, stage, reveals that they contain one or two mutations associated with cancer.
Frequently these include
the deletion of a healthy copy of the APC (adenomatous polyposis coli) gene on chromosome 5 leaving behind a mutant copy
of this tumor suppressor gene
Two results:
1. One of the functions of the APC gene product is to destroy the transcription factor β-catenin thus preventing it from turning
on genes that cause the cell to divide. With no, or a defective, APC protein, the normal brakes on cell division are lifted.

12.1.2 https://bio.libretexts.org/@go/page/5076
 2. Another function of the APC protein is to help attach the microtubules of the mitotic spindle to the kinetochores of the
chromosomes. With no, or a defective, APC product available, chromosomes are lost from the spindle producing aneuploid
progeny.
a mutant oncogene (often RAS).
deletion and/or mutation of the tumor suppressor gene p53

Figure 12.1.3 Death Rate due to cancer in the USA

The graph also explains why cancer has become such a common cause of death during the twentieth century. It probably has very
little to do with exposure to the chemicals of modern living and everything to do with the increased longevity that has been such a
remarkable feature of the 20th century. A population whose members increasingly survive accidents and infectious disease is a
population increasingly condemned to death from such "organic" diseases as cancer.

Causes of Cancer
Cancers are caused by
anything that damages DNA; that is anything that is mutagenic
radiation that can penetrate to the nucleus and interact with DNA
chemicals that can penetrate to the nucleus and damage DNA. Chemicals that cause cancer are called carcinogens.
anything that stimulates the rate of mitosis. This is because a cell is most susceptible to mutations when it is replicating its
DNA during the S phase of the cell cycle.
certain hormones (e.g., hormones that stimulate mitosis in tissues like the breast and the prostate gland)
chronic tissue injury (which increases mitosis in the stem cells needed to repair the damage)
agents that cause inflammation (which generates DNA-damaging oxidizing agents in the cell)
certain other chemicals; some the products of technology
certain viruses
(Considering that from conception to death, an estimated 1016 mitotic cell divisions occur in humans, it is remarkable that
cancer is not more common than it is.)

Viruses and Cancer

Many viruses have been studied that reliably cause cancer when laboratory animals are infected with them. What about humans?
The evidence obviously is indirect but some likely culprits are:
two papilloma viruses that can cause cancer of the cervix and other regions of the genitals (male as well as female).
the hepatitis B and hepatitis C viruses, which infect the liver and are closely associated with liver cancer (probably because of
the chronic inflammation they produce)
some herpes viruses such as the Epstein-Barr virus (implicated in Burkitt's lymphoma) and KSHV that is associated with
Kaposi's sarcoma (a malignancy frequently seen in the late stages of AIDS)
two human T-cell lymphotropic viruses, HTLV-1 and HTLV-2
But note that the viral infection only contributes to the development of cancer.
Many people are infected by these viruses and do not develop cancer.
When cancers do arise in infected people, they still follow our rule of clonality. Many cells have been infected, but only one
(usually) develops into a tumor.

12.1.3 https://bio.libretexts.org/@go/page/5076
So again it appears that only if an infected cell is unlucky enough to suffer several other types of damage will it develop into a
tumor.Nevertheless, widespread vaccination against these viruses should not only prevent disease but lower the incidence of the
cancers associated with them. A vaccine against hepatitis B is available as are two vaccines (Gardasil® and Cervarix®) against the
most dangerous papilloma viruses.

Are Cancers Contagious?

The short answer is NO.
The reason: Cancer cells, like all cells in the body, express histocompatibility molecules on their surface. So like any organ or
tissue transplant between two people (other than identical twins), they are allografts and are recognized and destroyed by the
recipient's immune system.
However, there are some exceptions.
1. Although tumors are not transmissible, viruses are. So any of the viruses described in the previous section can be spread from
person to person and predispose them to the relevant cancers.
2. There have been a number of cases where, unbeknownst to the surgeon, an organ (e.g., a kidney) from a donor with melanoma
has allowed the growth of the same melanoma in the recipient. Transplant recipients must have their immune system suppressed
if the transplant is not to be rejected, but their immunosuppression also prevents their immune system from attacking the
melanoma cells. Stopping immune suppression cures the recipient (but also causes loss of the kidney).
3. Canine transmissible venereal tumor (CTVT). This tumor spreads from dog to dog during copulation. Although the MHC
alleles on the tumor cells are only weakly expressed, they do eventually cause the tumor to be rejected.
4. Devil facial tumor disease (DFTD). The carnivorous Tasmanian devil is a marsupial living in Tasmania, Australia. The
population is threatened by a facial cancer that is spread through bites. The population is highly inbred, thus closely-related
genetically, and the MHC alleles on the tumor are only weakly expressed. So it may be these factors that allow the tumor to
grow unchecked.
5. The soft-shell clam, Mya arenaria, along the North Atlantic coast of North America is being devastated by a leukemia that
spreads from animal to animal perhaps as these filter feeders ingest sea water in which leukemic cells have been shed. These
mollusks are invertebrates and lack powerful tissue rejection molecules like the MHC of vertebrates.
6. There are extremely rare cases where a pregnant woman with cancer (a leukemia or melanoma) has transmitted the cancer
across the placenta to her fetus (whose immune system has yet to develop).

The Hallmarks of Cancer

In the year 2000 Douglas Hanahan and Robert Weinberg published a paper — The Hallmarks of Cancer — outlining 6
characteristics that are acquired as a cell progresses toward becoming a full-blown cancer. In the 4 March 2011 issue of Cell, they
add 4 other features.
1. Uncontrolled proliferation.
2. Evasion of growth suppressors. Among the many mutations found in cancers, one or more inactivate tumor suppressor genes.
3. Resistance to apoptosis (programmed cell death).
4. Develop replicative immortality; i.e., avoid the normal process of cell senescence.
5. Induce angiogenesis; that is, promote the development of a blood supply.
6. Invasion and metastasis — the ability of tumor cells to invade underlying tissue and then to be carried to other parts of the body
where secondary tumors develop (metastasis). During this process, the normal adhesion of cells to each other and to the
underlying extracellular matrix (ECM) are disrupted.
7. Genomic instability. Cancer cells develop chromosomal aberrations and many (hundreds) of mutations. Most of the latter are
"passenger" mutations, but as many as 10 may be "drivers" of the cancerous transformation.
8. Inflammation. Tumors are invaded by cells of the immune system, which promote inflammation. One effect of inflammation is
the production of reactive oxygen species (ROS). These damage DNA and other molecules.
9. Changed energy metabolism. Even if well-supplied with oxygen, cancer cells get most of their ATP from glycolysis not cellular
respiration.
10. Evade the immune system.

This page titled 12.1: Cancer in General is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

12.1.4 https://bio.libretexts.org/@go/page/5076
12.2: Cancer Cells in Culture

Figure 12.2.2 Cells not showing contact inhibition

The photographs (courtesy of G. Steven Martin) show mouse fibroblasts (connective tissue cells) growing in culture. The cells in
the top photo show contact inhibition. Those below do not. The cells below are said to be transformed. These cells (called 3T3
cells) were not derived from a mouse cancer but were produced by laboratory treatment of normal cells. Radiation, certain
chemicals, and certain viruses are capable of transforming cells. Although transformed cells are not derived from cancers, they can
often develop into malignant tumors when injected into an appropriate test animal (like a nude mouse).
Normal cells are exceedingly fussy about the nutrients that must be supplied to them in their tissue culture medium.
Cancer cells (and transformed cells) can usually grow on much simpler culture medium.
Normal cells ordinarily have the normal set of chromosomes of the species; that is, have a normal karyotype.
Cancer cells almost always have an abnormal karyotype with
abnormal numbers of chromosomes (polyploid or aneuploid)
chromosomes with abnormal structure:
translocations
deletions
duplications
inversions

This page titled 12.2: Cancer Cells in Culture is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

12.2.1 https://bio.libretexts.org/@go/page/5078
12.3: Oncogenes
An oncogene is a gene that when mutated or expressed at abnormally-high levels contributes to converting a normal cell into a
cancer cell. Cancer cells are cells that are engaged in uncontrolled mitosis.

The signals for normal mitosis

Normal cells growing in culture will not divide unless they are stimulated by one or more growth factors present in the culture
medium (e.g, Epidermal Growth Factor (EGF)). The growth factor binds to its receptor, an integral membrane protein embedded in
the plasma membrane with its ligand-binding site exposed at the surface of the cell. Examples:
the Epidermal Growth Factor Receptor (EGFR). The gene encoding it, EGFR, is also known as HER1.
another growth factor receptor is encoded by the gene ERBB2 (also known as HER2.)
Binding of a growth factor to its receptor triggers a cascade of signaling events within the cytosol. Many of these involve
kinases — enzymes that attach phosphate groups to other proteins. Examples: the proteins encoded by SRC, RAF, ABL, and
the fusion protein encoded by BCR/ABL found in chronic myelogenous leukemia (CML).
or molecules that turn on kinases. Example: RAS. RAS molecules reside on the inner surface of the plasma membrane
where they serve to link receptor activation to "downstream" kinases like RAF.
In most cases, phosphorylation activates the protein and eventually transfers the signal into the nucleus.
Here phosphorylation activates transcription factors that bind to promoters and enhancers in DNA, turning on their associated
genes. Examples: AP-1, a heterodimer of the proteins encoded by jun and fos. Some of the genes turned on by these transcription
factors encode other transcription factors (e.g., myc).
Some of the genes turned on by these downstream transcription factors encode cyclins that prepare the cell to undergo mitosis.
Genes that participate in any one of the steps above can become oncogenes if they become mutated so that their product becomes
constitutively active (that is, active all the time even in the absence of a positive signal) or they produce their product in excess.
Possible causes include if their promoter and/or enhancer has become mutated (e.g., the oncomouse: a transgenic mouse that has
both copies of its myc gene under the influence of extra-powerful promoters) or loss (e.g., by a translocation) of the 3'-UTR of their
mRNA so that a microRNA (miRNA) that normally represses translation can no longer do so.
All these oncogenes act as dominants; if the cell has one normal gene (called a proto-oncogene) and one mutated gene (the
oncogene) at a pair of loci, the abnormal product takes control. No single oncogene can, by itself, cause cancer. It can, however,
increase the rate of mitosis of the cell in which it finds itself. Dividing cells are at increased risk of acquiring mutations, so a clone
of actively dividing cells can yield subclones of cells with a second, third, etc. oncogene. When a clone loses all control over its
mitosis, it is well on its way to developing into a cancer.

Figure 12.3.1 Synergistic effect of two Oncogenes. Three groups are shown: those mice transgenic for a hyperactive myc alone
(blue), those transgenic for ras alone (green), those transgenic for both myc and ras (red)
This graph (based on the work of E. Sinn et al, Cell 49:465,1987) shows the synergistic effect of two oncogenes. The fraction (%)
of transgenic mice without tumors is shown as a function of age.

12.3.1 https://bio.libretexts.org/@go/page/5080
Other types of potential cancer-promoting genes
Genes that inhibit apoptosis: The suicide of damaged cells — apoptosis — provides an important mechanism for ridding the
body of cells that could go on to form a cancer. It is not surprising then that inhibiting apoptosis can promote the formation of a
cancer. Example: Bcl-2. The product of this gene inhibits apoptosis. Overexpression of the gene is a hallmark of B-cell cancers.
Genes involved in repairing DNA or stopping mitosis if they fail: Mutations arise from an unrepaired error in DNA. So any
gene whose product participates in DNA repair probably can also behave as an oncogene when mutated. For example: ATM.
ATM (="ataxia telangiectasia mutated") gets its name from a human disease of that name, whose patients — among other things
— are at increased risk of cancer. The ATM protein is also involved in detecting DNA damage and interrupting the cell cycle
when damage is found. It is estimated that fully 1% of the ~21,000 genes in the human genome are proto-oncogenes.
Tumor-Suppressor Genes: The products of some genes inhibit mitosis. These genes are called tumor suppressor genes. In
contrast to oncogenes, these behave as recessives — both alleles must be defective to lose their braking effect on mitosis.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and made
possible by funding from The Saylor Foundation.

This page titled 12.3: Oncogenes is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

12.3.2 https://bio.libretexts.org/@go/page/5080
12.4: Tumor Suppressor Genes
Some genes suppress tumor formation.
Their protein product inhibits mitosis.
When mutated, the mutant allele behaves as a recessive; that is, as long as the cell contains one normal allele, tumor
suppression continues. (Oncogenes, by contrast, behave as dominants; one mutant, or overly-active, allele can predispose the
cell to tumor formation).

RB - the retinoblastoma gene

Retinoblastoma is a cancerous tumor of the retina. It occurs in two forms:
Familial retinoblastoma: Multiple tumors in the retinas of both eyes occurring in the first weeks of infancy.
Sporadic retinoblastoma: A single tumor appears in one eye sometime in early childhood before the retina is fully developed
and mitosis in it ceases.

Familial retinoblastoma
Familial retinoblastoma occurs when a baby inherits from one of its parents a chromosome (number 13) that has its RB locus
deleted (or otherwise mutated). The normal Rb protein controls the cell cycle. It integrates the signals reaching the cell to determine
whether it is safe for the cell to complete the passage from G1 of the cell cycle to mitosis.
Mechanism
The unphosphorylated Rb protein prevents cells from entering S phase of the cell cycle. It does this by binding to transcription
factors called E2F. This prevents the E2Fs from binding to the promoters of such proto-oncogenes as c-myc and c-fos.
Transcription of c-myc and c-fos is needed for mitosis so blocking the transcription factors needed to turn on these genes prevents
cell division. However, if conditions are adequate for the cell to successfully complete mitosis, the Rb protein becomes
phosphorylated, releases the E2Fs, and the cell can proceed through the cell cycle.
The Rb protein also plays a role in mitosis itself: it is needed for proper chromosome condensation starting in prophase, as well as
their proper attachment to the spindle. Failure of Rb function during mitosis can lead to aneuploidy and chromosome breakage.

Figure 12.4.1 RB schematic

A random mutation of the remaining RB locus in any retinal cell — which are nondividing cells and should not enter the cell cycle
— completely removes the inhibition provided by the Rb protein, and the affected cell grows into a tumor. So, in this form of the
disease, a germline mutation plus a somatic mutation of the second allele leads to the disease.

Sporadic retinoblastoma
In this disease, both inherited RB genes are normal and a single cell must be so unlucky as to suffer a somatic mutation (often a
deletion) in both in order to develop into a tumor. Such a double hit is an exceedingly improbable event, and so only rarely will
such a tumor occur. (In both forms of the disease, the patient's life can be saved if the tumor(s) is detected soon enough and the
affected eye(s) removed.)

p53
The product of the tumor suppressor gene p53 is a protein of 53 kilodaltons (hence the name). (You will find that the human gene is
variously designated as P53, TP53 ["tumor protein 53"], and TRP53 ["transformation-related protein 53"])
The p53 protein prevents a cell from completing the cell cycle if its DNA is damaged or the cell has suffered other types of
damage.

12.4.1 https://bio.libretexts.org/@go/page/5082
When
the damage is minor, p53 halts the cell cycle — hence cell division — until the damage is repaired.
the damage is major and cannot be repaired, p53 triggers the cell to commit suicide by apoptosis.
These functions make p53 a key player in protecting us against cancer; that is, it is an important tumor suppressor gene. More than
half of all human lung, ovarian, and colorectal cancers harbor p53 mutations and have no functioning p53 protein.
Mice have been cured of cancer by treating them with a peptide that turns on production of the p53 protein in the tumor cells.
However, there may be a tradeoff involved: excess production of the p53 protein leads to accelerated aging in mice.
Elephants are very long-lived but seldom develop cancers. It turns out that their cells contain 40 copies of the p53 gene (TP53)
compared with the two that we and other mammals have.

p16INK4a
The product of the tumor suppressor gene INK4a is a protein of 16 kilodaltons (hence the name).
Like p53, it blocks progression through the cell cycle — in this case by inhibiting the action of the cyclin-dependent kinase Cdk4.
As an animal ages, its cells produce increasing amounts of p16INK4a. This is probably a good thing in that it reduces the risk of the
cell entering uncontrolled mitosis, i.e., becoming a cancer. However, again like p53, there is a tradeoff. As levels of p16INK4a rise in
adult stem cells and progenitor cells, their ability to reproduce and thus replace lost or damaged tissue diminishes.
p16INK4a is not simply a reflection of an aging cell but is actively involved in the process.
Mice expressing higher-than-normal levels of p16INK4a show earlier replicative senescence while
mice in which p16INK4a activity is blocked continue to repair damaged tissue efficiently but run a higher risk of getting cancer.
In mice, eliminating senescent cells (they are high in p16INK4a) prevents (in young mice) and partially reverses (in older mice)
some of the signs of aging such as cataracts, and loss of adipose tissue and skeletal muscle mass.
In humans, deletions and other mutations of p16INK4a are found in a variety of cancers.

Loss Of Heterozygosity (LOH)

Because tumor suppressor genes are recessive, cells that contain one normal and one mutated gene — that is, are heterozygous —
still behave normally. (Exception: one X-linked tumor suppressor gene [WTX] has been found. In males, having only one X
chromosome, a damaging point-mutation in WTX or its deletion is all that is needed to eliminate tumor-suppression. Females are
also at risk if the mutation or deletion occurs on the X chromosome that is not inactivated.)
However, there are several mechanisms which can cause a cell to lose its normal gene and thus be predisposed to develop into a
tumor. These may result in a "loss of heterozygosity" or "LOH".
Mechanisms of LOH:
1. Deletion of
the normal allele;
the chromosome arm containing the normal allele;
the entire chromosome containing the normal allele (resulting in aneuploidy).
2. In females, X-inactivation of the X chromosome carrying the normal allele.
3. Loss of the chromosome containing the normal allele followed by duplication of the chromosome containing the mutated
allele.
4. Mitotic recombination. The study of tumor suppressor genes revealed (for the first time) that crossing over — with genetic
recombination — occasionally occurs in mitosis (as it always does in meiosis).
In #3 and #4, the resulting cell now carries two copies of the "bad" gene. This is called "reduction to homozygosity".
LOH can work both ways.
When LOH occurs by mitotic recombination (process #4 above), one daughter cell becomes homozygous for the mutant allele but
the other becomes homozygous for the normal ("wild-type") allele. This is of no help when tumor-suppressor genes are involved
but in other situations it can be.

12.4.2 https://bio.libretexts.org/@go/page/5082
A rare skin disease of humans called ichthyosis with confetti is an example. It is caused by the inheritance of a dominant mutation
in one of the keratins (which make intermediate filaments). At birth, infants with the disease have uniformly reddened skin whose
cells are heterozygous for the dominant mutant allele and a normal keratin allele. But as the years go by, an increasing number of
patches of normal, whitened, skin appear (like "confetti"). Genomic analysis reveals that each patch develops from a skin stem cell
that by mitotic recombination has undergone "reduction to homozygosity". In this case, the daughter cell that inherits two normal
keratin alleles goes on to generate a patch of normal skin. This work is described in Choate, K.A., et al., Science 330:94-97 (1
October 2010).

Mutation is not the only way to inactivate tumor suppressor genes.

Their function can also be blocked by methylation of their promoter.
Cancer cells often contain a methylated promoter on one tumor suppressor gene accompanied by
a similarly blocked promoter on the other allele (producing the same effect as #2 above);
a loss of that locus on the other chromosome (like the LOH in #1 above);
an inactivating mutation in the other allele.

Tumor suppressor genes = anti-oncogenes

Figure 12.4.2 Cell Colonies

Genes like RB and p53 are also called anti-oncogenes. They were first given this name because they reverse, at least in cell culture,
the action of known oncogenes. This image (courtesy of Moshe Oren, from Cell 62:671, 1990) shows petri dishes which were
seeded with the same number of mouse cells that had been transformed by two oncogenes: myc and ras. Many of those on the left
have grown into colonies of cells. However, the cells plated on the right also contained the tumor suppressor p53 gene. Only a few
have been able to grow into colonies.

Human Papilloma Viruses (HPV)

The name anti-oncogene may be even more appropriate than originally thought. Both the Rb protein and the p53 protein turn out to
complex directly in the cell with a gene product of some human papilloma viruses.
Once inside the cells of their host, these viruses synthesize a protein designated E7 and another designated E6.

Figure 12.4.3 HPV

Of the >30 strains of HPV that infect humans, several, especially HVP-16 and HPV-18, have been implicated as a risk factor for
cervical cancer and also cancers of the throat. Their E7 protein binds to the Rb protein preventing it from binding to the host
transcription factor E2F.
Result: E2F is now free to bind to the promoters of genes (like c-myc) that cause the cell to enter the cell cycle (right). Thus this
version of E7 is an oncogene product.

12.4.3 https://bio.libretexts.org/@go/page/5082
The E6 protein binds the p53 protein targeting it for destruction by proteasomes and thus removing the block on the host cell's
entering the cell cycle.
Although the figure shows the "off" promoters as empty, it is now clear that being "off" involves both
the absence of activators of transcription and
the presence of repressors of transcription.
A cell cannot remain in G0 of the cell cycle without these repressors. Perhaps mutant versions of them are another cause of cancer
(cancer cells are never in G0).

This page titled 12.4: Tumor Suppressor Genes is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

12.4.4 https://bio.libretexts.org/@go/page/5082
12.5: BCL-2
BCL-2 is a human proto-oncogene located on chromosome 18. Its product is an integral membrane protein (called Bcl-2) located in
the membranes of the endoplasmic reticulum (ER), nuclear envelope, and in the outer membranes of mitochondria. The gene was
discovered as the translocated locus in a B-cell leukemia (hence the name). This translocation is also found in some B-cell
lymphomas.

Figure 12.5.1 : BCL - 2

In the cancerous B cells, the portion of chromosome 18 containing the BCL-2 locus has undergone a reciprocal translocation with
the portion of chromosome 14 containing the antibody heavy chain locus. This t(14;18) translocation places the BCL-2 gene close
to the heavy chain gene enhancer. This enhancer is very active in B cells (whose job it is to synthesize large amounts of antibody).
So it is not surprising to find that the Bcl-2 protein is expressed at high levels in these t(14;18) cells.

What makes BCL-2 a proto-oncogene?

B cells, like all activated lymphocytes, die a few days after they have had a chance to do their job. This ensures that they do not
linger around after the threat has been dealt with and turn their attack against self components. Aging B cells kill themselves by
apoptosis. However, high levels of the Bcl-2 protein protect the cells from early death by apoptosis. The Bcl-2 protein suppresses
apoptosis by preventing the activation of the caspases that carry out the process. So genes encoding inhibitors of apoptosis must be
added to the list of genes that can act as oncogenes. In this case the effect is not achieved by increasing the rate of cell proliferation
but by reducing the rate of cell death.
Although the t(14:18) translocation is found in B-cell lymphomas and leukemias, something else must contribute to creating the
cancer because over 50% of us have small numbers of B-cells with that translocation that never progress to cancer. The antibody
gene loci are dangerous places for proto-oncogenes to take up residence. Translocation of the proto-oncogene c-myc close to the
enhancer of the antibody heavy chain genes also produces cancerous B cells resulting in Burkitt's lymphoma. The translocation of
the BCL-2 locus is just one of many mutations that can give rise to a malignant clone of B cells. All of the resulting leukemias are
designated chronic lymphocytic leukemia or CLL.

This page titled 12.5: BCL-2 is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

12.5.1 https://bio.libretexts.org/@go/page/5084
12.6: Burkitt's Lymphoma
Burkitt's lymphoma is a solid tumor of B lymphocytes, the lymphocytes that the immune system uses to make antibodies. The
genes for making antibodies are located on chromosomes 14 (the heavy [H] chains), 2 (kappa light chains), and 22 (lambda light
chains). These genes are expressed only in B lymphocytes because only B cells have the necessary transcription factors for the
promoters and enhancers needed to turn these antibody genes "on". In most (approximately 90%) of the cases of Burkitt's
lymphoma, a reciprocal translocation (designated t(8;14) has moved the proto-oncogene c-myc from its normal position on
chromosome 8 to a location close to the enhancers of the antibody heavy chain genes on chromosome 14.

Figure 12.6.1 : Chromosome 14

In all the other cases, c-myc has been translocated close to the antibody genes on chromosome 2 or 22. In every case, c-myc now
finds itself in a region of vigorous gene transcription, and it may simply be the overproduction of the c-myc product (a transcription
factor essential for mitosis of mammalian cells) that turns the lymphocyte cancerous. Uncontrolled mitosis of this cell results in a
clone of cancer cells, Burkitt's lymphoma. Many other human cancers involve chromosome aberrations, such as translocations, at
the loci of known proto-oncogenes.

Figure 12.6.2 : Karyotype of a cell with Burkitt's lymphoma

Figure 12.6.2 is an actual karyotype (courtesy of Janet Finan and C. M. Croce) of a cell from the tumor of a patient with Burkitt's
lymphoma. The long (q) arm of the resulting chromosome 8 is shorter (8q−) than its normal homologue; the long arm of
translocated chromosome 14 longer (14q+). The heavy chain gene locus on chromosome 14 is a dangerous place. Several other
proto-oncogenes produce cancerous B cells — leukemias, lymphomas, and multiple myelomas — when translocated into this
locus. The risk of translocations involving the heavy chain gene locus is probably especially high because breaks in its DNA occur
naturally during the synthesis of antibodies.

This page titled 12.6: Burkitt's Lymphoma is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

12.6.1 https://bio.libretexts.org/@go/page/5086
12.7: Chronic Myelogenous Leukemia (CML)
Leukemia is an uncontrolled proliferation of one kind of white blood cell (or leukocyte). Like all cancers (probably), all the
leukemic cells are descended from a single cell that lost the ability to maintain normal control over the cell cycle. There are a
number of types of leukemia, as you would expect from the number of types of white blood cells (5) and the number of stages they
pass through as they mature. One of the most common is chronic myelogenous leukemia or CML.
Chronic Myelogenous Leukemia (CML) arises in a bone marrow stem cell that is the precursor to all the types of blood cells.
However, it usually affects the so-called myeloid lineage (hence the name) that produces granulocytes and macrophages. As the
name suggests, the disease often exists for years with only moderately elevated numbers of leukemic cells (descended from the
stem cells) and few symptoms. At some point, however, the patient goes through a "blast crisis" when the leukemic granulocyte-
macrophage progenitors begin to divide by themselves — increasing their numbers enormously while failing to continue their
differentiation.

The Philadelphia Chromosome (Ph ) 1

In most cases of CML, the leukemic cells share a chromosome abnormality not found in any nonleukemic white blood cells, nor in
any other cells of the patient's body. This abnormality is a reciprocal translocation between one chromosome 9 and one
chromosome 22. This translocation is designated t(9;22). It results in one chromosome 9 longer than normal and one chromosome
22 shorter than normal. The latter is called the Philadelphia chromosome and designated P h . 1

Figure 12.7.1 : Translocation between chromosome 9 and 22. Reciprical translations between one # 9 and one #22 chromosomes
forms an extra long chromosome ("der 9") and the Philadelphia chromosome (P h ) containting the fused abl-bcr gene. This is a
1

schematic view representating metaphase chromosomes.

The DNA removed from chromosome 9 contains most of the proto-oncogene designated c-ABL. The break in chromosome 22
occurs in the middle of a gene designated BCR. The resulting Philadelphia chromosome has the 5' section of BCR fused with most
of c-ABL.

Figure 12.7.1 : FISH image of bcr/abl positive rearranged metaphase (CC-SA-BY-3.0);

The micrograph in Figure 12.7.2 uses fluorescence in situ hybridization (FISH) to reveal the ABL DNA (red) and the BCR DNA
(green) in the interphase nuclei of the leukemic cells of a patient with CML. The red dot at left center reveals the location of ABL
on the normal chromosome 9; the green dot (top center) shows BCR on the normal chromosome 22. The combined dots (red +
green = yellow) at the lower right reveal the fused BCR-ABL gene on the Philadelphia chromosome. Figure 12.7.3 is a schematic
which can help you interpret the micrograph.

12.7.1 https://bio.libretexts.org/@go/page/5088
 Figure 12.7.3 : Schematic of ABL DNA
Transcription and translation of the hybrid BCR-ABL gene produces an abnormal ("fusion") protein that activates constitutively
(all the time) a number of cell activities that normally are turned on only when the cell is stimulated by a growth factor, such as
platelet-derived growth factor (PDGF).
This unrestrained activation increases the rate of mitosis and protects the cell from apoptosis. The outcome is an increase in the
number of Ph1-containing cells. During the chronic phase of the disease, these are still able to exit the cell cycle and to differentiate
into mature cells that perform their normal functions. At some point, however, another mutation in a proto-oncogene (RAS, for
example) or in a tumor-suppressor gene (p53, for example), will occur in one of these cells. The additional mutation causes the
rate of mitosis in that cell and its descendants to rise sharply. The daughter cells fail to differentiate and the patient enters the crisis
phase of the disease.

 A Promising Treatment

Until recently, the only successful treatment of CML was to destroy the patient's bone marrow and then restore blood-cell
production by infusing stem cells from the bone marrow of a healthy donor. But now treatment with the drug imatinib mesylate
(Gleevec® also known STI571) appears to be able to cure the disease. This molecule fits into the active site of the ABL
protein preventing ATP from binding there. Without ATP as a phosphate donor, the ABL protein cannot phosphorylate its
substrate(s). A phase 2 study, found that almost 90% of the CML patients treated with the drug showed no further progression
of their disease.
Gleevec also shows promise against one type of stomach cancer (gastrointestinal stromal tumors = GIST), which is a life-
threatening excessive production of eosinophils. In this disease, Gleevec inhibits a different overactive tyrosine kinase. This
one also results from the fusion of parts two different genes (because of the deletion of the DNA between them):
the first 233 codons of a gene designated FIP1L1 fused to
the final 523 codons of the gene (PDGFRα) encoding the tyrosine kinase domain of a receptor for platelet-derived growth
factor. The fusion protein produced, like BCR-ABL, is hyperactive.

This page titled 12.7: Chronic Myelogenous Leukemia (CML) is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by
John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

12.7.2 https://bio.libretexts.org/@go/page/5088
12.8: Fighting Cancer with Inhibitors of Angiogenesis
Once a nest of cancer cells reaches a certain size (1–2 mm in diameter), it must develop a blood supply in order to grow larger.
Diffusion is no longer adequate to supply the cells with oxygen and nutrients and to take away wastes. Cancer cells (probably like
all tissues) secrete substances that promote the formation of new blood vessels — a process called angiogenesis. Over a dozen
substances have been identified that promote angiogenesis. A few examples are angiopoietin-1, the basic fibroblast growth factor
(bFGF) and the vascular endothelial growth factor (VEGF).
Curiously, some tumors also secrete substances that inhibit angiogenesis. This explains a clinical phenomenon that has been
known for decades:
A patient has a tumor, the so-called primary tumor.
There is no evidence that the primary tumor has metastasized.
A surgeon removes the primary tumor.
Some weeks later metastases of the tumor appear throughout the patient's body
The speed of their appearance indicates that they were present all along, but too small to be detected.
This phenomenon caused Dr. Judah Folkman of Children's Hospital and the Harvard Medical School in Boston to hypothesize that
a large primary tumor secretes not only stimulators of its own angiogenesis but angiogenesis inhibitors that are released into the
circulation and inhibit angiogenesis — and thus further growth — of any metastases of the primary tumor. A number of inhibitors
of angiogenesis have been discovered.

Angiostatin
Angiostatin is a polypeptide of approximately 200 amino acids. It is produced by the cleavage of plasminogen, a plasma protein
that is important for dissolving blood clots. Angiostatin binds to subunits of ATP synthase exposed at the surface of the cell
embedded in the plasma membrane. (Before this recent discovery, ATP synthase was known only as a mitochondrial protein.)

Endostatin
Endostatin is a polypeptide of 184 amino acids. It is the globular domain found at the C-terminal of Type XVIII (18) collagen (a
collagen found in blood vessels) cut off from the parent molecule.

Figure 12.8.1 : Endostatin monomer, basic amino acid residues shown in red (source: pdb.org, 1KOE).

Effects of angiostatin and endostatin in mice

Injections of angiostatin inhibit the metastasis of certain (mouse) primary tumors. Injections of endostatin (made by recombinant
DNA technology) cause the primary tumor to regress. In time, the primary tumor reappears, but a repeat injection causes it to
regress again. Each time it reappears, the tumor is just as susceptible to treatment as before. After a few cycles of growth,
treatment, and regression, the primary tumor finally stops growing (at least in the cases examined) and remains dormant at a small
size.
Some human tumors can be grown in immunodeficient mice. (Being immunodeficient, they cannot reject this foreign tissue).
Treatment with endostatin caused these human tumor masses to shrink in their mouse host. Combined treatment with both
angiostatin and endostatin has caused some primary mouse tumors to disappear entirely.

12.8.1 https://bio.libretexts.org/@go/page/5090
This is not seen with conventional chemotherapy. Repeated exposure to chemotherapeutic drugs selects for the appearance of drug-
resistant tumor cells. Eventually, further drug treatment is worthless. Why the difference in response? Chemotherapy works directly
on tumor cells which mutate easily. Angiogenesis inhibitors don't work on the tumor cells but on normal cells involved in the
formation of blood vessels.

Other Angiogenesis Inhibitors

Epithelial cells express transmembrane proteins on their surface — called integrins — by which they anchor themselves to the
extracellular matrix. It turns out that the new blood vessels in tumors express a vascular integrin — designated alpha-v/beta-3 —
that is not found on the old blood vessels of normal tissues.
Vitaxin®, a humanized monoclonal antibody directed against the alpha-v/beta-3 vascular integrin, shrinks tumors in mice without
harming them. In Phase II clinical trials in humans, Vitaxin has shown some promise in shrinking solid tumors without harmful
side effects.

What does the future hold for angiogenesis inhibitors?

Clinical trials of endostatin (manufactured by recombinant DNA technology), in combination with standard chemotherapy have
shown some benefit in one type of lung cancer.
Bevacizumab (Avastin®). This is a humanized monoclonal antibody that binds to VEGF thus keeping it from binding to its
receptors. Approved by the US FDA in February 2004 for the treatment of colorectal cancers.
Ranibizumab (Lucentis®) is a modified version of Avastin® that is showing great promise in inhibiting the formation of new blood
vessels in the retina — the cause "wet" macular degeneration.
Trials are also scheduled to begin on a synthetic ribozyme that blocks synthesis of the VEGF receptor. These are only a few
examples of the ~50 antiangiogenesis drugs now in clinical trials.

But proceed with caution.

In animal studies, some cancers — notably pancreatic cancer — have turned out to resist chemotherapy because of their poor blood
supply. Perhaps such cancers need to have angiogenesis promoted; inhibiting it could make a bad problem worse.

This page titled 12.8: Fighting Cancer with Inhibitors of Angiogenesis is shared under a CC BY 3.0 license and was authored, remixed, and/or
curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is
available upon request.

12.8.2 https://bio.libretexts.org/@go/page/5090
12.9: Immunotherapy of Cancer
Most cancer patients are treated with some combination of surgery, radiation, and chemotherapy. Radiation and chemotherapy have
the disadvantage of destroying healthy as well as malignant cells and thus can cause severe side-effects. What is needed are more
precisely-targeted therapies. One long-held dream is that the specificity of immune mechanisms could be harnessed against tumor
cells. This might use the patient's own immune system or the transfer of antibodies or T cells from an outside source (i.e. passive
immunization). Ideally, these agents would be targeted to molecules expressed on the cancer cells but not on healthy cells.
However, such tumor-specific antigens have been hard to find, and so many of the immune agents now in use do target healthy
cells as well.

Immunostimulants
There is considerable evidence that cancer patients have T cells that are capable of attacking their tumor cells. In fact, it may be
that the appearance of cancer is a failure of immune surveillance: the ability of one's own immune system to destroy cancer cells
as soon as they appear. But what to do if they fail? Immunostimulants are nonspecific agents that tune-up the body's immune
defenses. There have been some successes with
injecting adjuvant-like agents directly into the tumor. The only one that succeeds often enough to remain in use is the bacterial
preparation BCG. Introduced into the bladder, it can help eradicate early-stage bladder tumors.
Oral therapy with levamisole, a drug widely-used for deworming (people as well as animals), has been used to treat a variety of
cancers but with inconsistent results.
interleukin-2 (IL-2), a potent growth factor for T cells;
alpha-interferon (IFN-α)

Cancer Therapy with Monoclonal Antibodies

A number of monoclonal antibodies show promise against cancer, especially cancers of white blood cells (leukemias, lymphomas,
and multiple myeloma). Some examples:
Rituximab (trade name = Rituxan®). Used to treat B-cell lymphomas. The CD20 molecule to which it binds is present on most
B-cells, healthy as well as malignant, but over the months following treatment, new healthy B cells are formed from precursors
that do not have CD20 and thus were not destroyed by the treatment.
Trastuzumab (trade name = Herceptin®). Binds HER2, a growth factor receptor found on some tumor cells (some breast
cancers, lymphomas). The only monoclonal so far that seems to be effective against solid tumors.
Alemtuzumab (MabCampath®). Binds to CD52, a molecule found on white blood cells. Has produced remission of chronic
lymphocytic leukemia.
Lym-1 (Oncolym®). Binds to the HLA-DR-encoded histocompatibility antigen that can be expressed at high levels on
lymphoma cells.
Bevacizumab (Avastin®). Binds to vascular endothelial growth factor (VEGF) thus blocking its action and depriving the tumor
of its blood supply.
Cetuximab (Erbitux®). Used to treat colorectal cancers.
A monoclonal antibody against CD47. CD47 is a cell-surface protein expressed at high levels in many different human cancers.
CD47 blocks any effort that macrophages and dendritic cells might make to phagocytose the cancer cells; that is, CD47 is a
"don't eat me" signal. A variety of human cancers transplanted into immunodeficient mice have their growth suppressed and
metastases prevented when the mice are given a monoclonal antibody against CD47 thus unleashing the ability of phagocytes to
destroy the cancer cells. The success in mice will soon lead to clinical trials in humans.
Ipilimumab (Yervoy®). Unlike the other monoclonals listed here, ipilimumab acts as an immunostimulant. It does so by
binding to the CTLA-4 molecules on the T cell so that they cannot bind to the B7 molecules on the antigen-presenting cell. This
frees the T cell's CD28 molecules to bind B7 thus receiving the stimulatory "signal 2" from the antigen-presenting cell.
Ipilimumab was approved by the U.S. Food and Drug Administration on 25 March 2011 for use against metastatic melanoma.
Because its double-negative effect works to enhance the body's overall T-cell responses, it may well turn out to be useful against
other cancers as well (and explains some of the autoimmune-like side effects it produces). It also provides perhaps the best
evidence yet for the existence of immune surveillance; that is, the presence in the patient's body of an innate population of T
cells specific for the tumor.
Pembrolizumab and nivolumab

12.9.1 https://bio.libretexts.org/@go/page/5092
 Figure 12.9.1 : Tumor cell Inhibits and Antibodies

Blinatumomab is a synthetic monoclonal antibody each arm of which carries a binding site with a different specificity:
one arm binds to CD19, an antigen found on the surface of B cells and B-cell lymphomas
the other arm binds to CD3, a cell-surface molecule on T cells, including cytotoxic T lymphocytes (CTLs)
By forming a bridge between CD3 and CD19, blinatumomab is able to attach T cells to B cells and activate the T cells to kill the B
cells. Early clinical trials with blinatumomab on a small number of patients appear quite promising. Modest doses of the drug
produced partial and, in a few cases, complete regression of their lymphoma.

Immunotoxins
A major problem with chemotherapy is the damage the drugs cause to all tissues where rapid cell division is going on. What is
needed is a "magic bullet", a method of delivering a cytotoxic drug directly and specifically to tumor cells, sparing healthy cells.
Such a magic bullet would have two parts - a monoclonal antibody specific for the cancer cell attached to a cytotoxic drug or toxin
that kills the cell once it gets inside.
Some two dozen immunotoxins are in clinical trials. Two that have already received FDA approval:
1. Adcetris®. The vedotin is attached to the monoclonal antibody by a bridge that is cleaved once the conjugate is safely inside
the tumor cell releasing the toxin to do its work there. In one trial, 73% of the patients with Hodgkin's lymphoma went into
remission.
a monoclonal antibody that binds CD30, a cell-surface molecule expressed by the cells of some lymphomas but not found
on the normal stem cells needed to repopulate the bone marrow.
vedotin, a drug that blocks mitosis by preventing the polymerization of tubulin (needed to form the mitotic spindle).
2. Kadcyla® The DM1 is attached to the monoclonal antibody by a bridge that is cleaved once the conjugate is safely inside the
tumor cell releasing the toxin to do its work there. Kadcyla® prolongs survival in women whose breast cancer over-expresses
HER2 (about 20% of breast cancer cases).
Trastuzumab (Herceptin®), the monoclonal antibody against HER2 listed above;
DM1, another drug that inhibits mitosis by preventing the polymerization of tubulin (needed to form the mitotic spindle).

Radioimmunotherapy
Monoclonal antibodies against tumor antigens can also be coupled to radioactive atoms. The goal with these agents is to limit the
destructive power of radiation to those cells (cancerous) that have been "fingered" by the attached monoclonal antibody. Examples:
Zevalin®. This is a monoclonal antibody against the CD20 molecule on B cells (and lymphomas) conjugated to either
the radioactive isotope indium-111 (111In) or
the radioactive isotope yttrium-90 (90Y)
Both are given to the lymphoma patient, the 111In version first followed by the 90Y version (in each case supplemented with
Rituxan®).
Bexxar® (tositumomab). This is a conjugate of a monoclonal antibody against CD20 and the radioactive isotope iodine-131
(131I). It, too, is designed as a treatment for lymphoma. Although both Bexxar® and Zevalin® kill normal B cells, they don't
harm the B-cell precursors because these do not express CD20. So, in time, the precursors can repopulate the body with healthy
B cells.
On 3 February 2005, the New England Journal of Medicine reported that 59% of patients with a B-cell lymphoma were disease-
free 5 years after a single treatment with 131I-tositumomab (a treatment that was relatively free of the nasty side-effects, e.g.,
hair loss, of conventional chemotherapy).

12.9.2 https://bio.libretexts.org/@go/page/5092
Adoptive Cell Therapy (ACT)
Tumor destruction is done by cells. Antibodies may help, but only by identifying the cells to be destroyed, e.g., by macrophages.
But T cells, e.g., cytotoxic T lymphocytes (CTL), are designed to destroy target cells. What about enlisting them in the fight?

Tumor-Infiltrating Lymphocytes (TIL)

Solid tumors contain lymphocytes that are specific for antigens expressed by the tumor. For many years, Steven A. Rosenberg and
his associates at the U. S. National Cancer Institute have tried to enlist these cells in cancer therapy.
On September 19, 2002, he reported his most promising results at that time. The procedure:
Isolate T cells — both CD4+ T-helper cells and CD8+ cytotoxic T lymphocytes (CTL) from samples of the tumor (melanoma)
Test them in vitro to find the most efficient killers of the melanoma cells.
Grow large numbers of them in culture (using the powerful T-cell growth factor IL-2).
Treat the patient with modest doses of cytotoxic drugs to reduce — but not destroy — the bone marrow (called
nonmyeloablative conditioning).
Reintroduce the mix of Th cells (CD4+) and CTL (CD8+) into the patient (along with IL-2).
The results:
The infused cells usually took up long-term residence.
In 10 of 13 patients, their melanoma cells — including all metastases — regressed either partially or completely.
In a few cases, the TIL seemed to be reacting to tumor-specific antigens, but in most the target seems to have been antigens
expressed by all melanin-containing cells. Evidence:
Four patients lost normal melanocytes from their skin leaving white patches.
One patient developed inflammation of the uvea, the coat of melanin-containing cells within the eye.

Adoptive transfer of a clone of the patient's own tumor-antigen-specific T cells

The 19 June 2008 issue of the New England Journal of Medicine (Naomi Hunder et al) carried a report describing the successful
treatment of a man with metastasized melanoma using his own T cells. The procedure:
His leukocytes were harvested and a mixed culture was prepared containing
antigen-presenting dendritic cells.
a peptide from the antigen NY-ESO-1. NY-ESO-1 is a protein that is produced by several types of tumors (e.g., melanoma,
lung and breast cancers) but is not expressed by normal cells (except those in the testis).
The patient's own T cells.
After repeated stimulation with the antigen, responding cells were cloned by limiting dilution.
One (of four) antigen-reactive cells was then expanded in culture until
5 billion (5 x 109) identical anti-NY-ESO-1 CD4+ T cells were available to infuse into the patient.
The result: complete regression of each metastatic clump of melanoma cells, and the patient has remained free of this lethal cancer
for two years since this treatment.

Adoptive transfer of genetically-modified T cells

Genetically engineered with a T-cell Receptor
On April 20, 2006, the Rosenberg group reported some success with melanoma patients using a modification of the TIL procedure.
The patient's T cells were removed and treated with a retroviral vector containing the αβ T-cell receptor (TCR) specific for a
melanoma antigen.
Large numbers of these were grown in culture.
After nonmyeloablative conditioning to "make room" for them, the genetically-modified lymphocytes were infused into the
patient.
This application of gene therapy succeeded in eliminating the metastases and providing a disease-free period of two years in
two patients.

12.9.3 https://bio.libretexts.org/@go/page/5092
Genetically engineered with a Chimeric Antigen Receptor (CAR)
The 10 August 2011 online version of the New England Journal of Medicine carried a report by Porter, D., et al. on their results
with one (of three) patients treated for chronic lymphocytic leukemia (CLL) with an infusion of his own genetically-modified T
cells.
The patient's malignant B cells expressed the surface antigen CD19 just as normal B cells do.
T cells were harvested from his blood and later treated with a vector encoding the antigen-binding site of an anti-CD19 antibody
along with two other costimulatory molecules. The result: some 5% of these T cells expressed this synthetic antibody (called a
chimeric antigen receptor or CAR) and were activated when they bound CD19 with it (rather than with their T cell receptor (TCR)
which they would normally use).
Injected back into the patient, they proliferated by some 1000-fold and persisted for months. During this period, they eliminated all
his malignant B cells (as well as his normal B cells). At the time of the report (10 months after treatment), he continued to be free
of his cancer. Lacking normal B cells as well, he needed periodic infusions of immune globulin to keep infections at bay.
"One swallow does not make a summer", but these results give hope that in time immunotherapy will become an effective weapon
against cancer.

Cancer Vaccines
Any response of the patient's own immune system – immune surveillance – has clearly failed in cancer patients. The purpose of
cancer vaccines is to elicit a more powerful active immunity in the patient. Several approaches are being explored.

Patient-Specific Cancer Vaccines

Patient-Specific Dendritic-Cell Vaccines
Dendritic cells are the most potent antigen-presenting cells. They engulf antigen, process it into peptides, and "present" these to T
cells.
To make a dendritic-cell vaccine,
Harvest dendritic cells from the patient.
Expose these in vitro to antigens associated with the type of tumor in the patient.
The antigens are found in normal – as well as cancerous – cells of that tissue (e.g., tyrosinase in melanocytes, prostatic acid
phosphatase [PAP] in prostate cells).
They may be fused with a stimulatory molecule such as granulocyte-macrophage colony-stimulating factor (GM-CSF)
Inject these "pulsed" dendritic cells back into the patient.
Hope that they elicit an strong cell-mediated immune response, e.g. by cytotoxic T lymphocytes (CTL).
On 29 April 2010 the U.S. Food and Drug Administration approved the first anti-cancer vaccine: a patient-specific dendritic-cell
vaccine for use against advanced prostate cancer. The vaccine, called sipuleucel-T (Provenge®), is produced by pulsing the
patient's dendritic cells with a fusion protein coupling prostatic acid phosphatase [PAP] with GM-CSF.
Patient-Specific Tumor-Antigen Vaccines
The antigens in these vaccines are taken from the patient's own tumor cells.
Harvest some tumor cells from the patient.
Ship them to a company that will use them to make complexes with adjuvant materials.
The complexes are returned to be injected into the patient.
Several of such vaccines are currently in clinical trials.

Tumor-Antigen-Specific Vaccines
These vaccines are used to immunize the patient with an antigen universally expressed by tumors of that type (but not by normal
cells) mixed with some form of adjuvant that will enhance the response.
Examples:
Many cancer patients mount an immune response — both antibody-mediated and cell-mediated — against the tumor (and testis)
antigen NY-ESO-1. Deliberate immunization with this protein (plus an adjuvant) boosts this response and has shown some

12.9.4 https://bio.libretexts.org/@go/page/5092
 promise in early clinical trials. (Cells in the testis do not express HLA antigens, so are not at risk from attack by NY-ESO-1-
specific cytotoxic T lymphocytes).
MAGE-A3 is another protein common on cancer cells. A vaccine using MAGE-A3 — along with an adjuvant — is in Phase III
clinical trials to assess its effectiveness against melanoma and lung cancer.
HER2 is a protein over-expressed on 20–30% of breast cancers. NeuVax® is a vaccine that contains a peptide of HER2 along
with recombinant GM-CSF as an adjuvant. It stimulates the formation of cytotoxic T lymphocytes (CTLs) that attack cells
expressing HER2 and has shown promise in clinical trials.
Unlike patient-specific vaccines, these vaccines can be mass-produced for use in anyone with the appropriate tumor.

Combining Procedures #3 and #4

While tumors are immunogenic in the patient who carries them, they are only weakly so. In the hopes of improving cancer
immunotherapy, clinical trials are now proceeding to test the efficacy of combining potent patient-specific cancer immunization
with treating the patient with large numbers of cultured cancer-antigen-specific T cells that result.
The patient is repeatedly immunized with his or her own cancer cells along with a strong adjuvant (e.g., GM-CSF) followed by
harvesting the patient's leukocytes and growing large numbers of them in the laboratory before infusing them into the patient along
with interleukin-2. This combined approach — which generates large numbers of patient-cancer-specific killer T cells — has been
tested against kidney and one type of brain cancer with promising results.

Blood Cancers
Cancers of blood cells, leukemias and lymphomas, arise in the bone marrow — the source of all blood cells.
One approach to curing leukemia is to treat the patient with such high doses of chemotherapy and radiation that not only are the
leukemic cells killed, but the patient's bone marrow is destroyed. If the patient is to survive the treatment, called "myeloablative
conditioning", he or she must be given a transplant of hematopoietic stem cells — the cells from which all blood cells are formed.
The stem cells can be
an autograft; that is, from bone marrow harvested from the patient and stored before treatment begins. In this case, however, the
marrow must also be treated to purge it of all cancer cells it may contain before it is returned to the patient. This sometimes
fails.
an allograft; that is, cells harvested from another person, usually a family member sharing the same major histocompatibility
molecules.
Allografted hematopoietic stem cells also sometimes fail to cure, but in that case it is because not all of the patient's leukemic cells
were destroyed. However, an infusion of T lymphocytes from the blood of the same donor that provided the cells can finish off the
job.
This effect is called the graft-versus-leukemia effect.
However, most (if not all) of the donor T cells are probably attacking normal cell surface molecules, not tumor-specific ones. (Even
if the donor and recipient are matched for the major histocompatibility molecules, there will be minor ones that elicit a rejection
response.)
So the patient may also suffer life-threatening graft-versus-host disease (GVHD).
The graft-versus-leukemia effect lays the foundation for an approach that has shown considerable promise against various blood
cancers and even some solid (e.g., kidney) tumors.
The patient is treated to kill some — but not all — of the bone marrow cells (nonmyeloablative conditioning).
Instead of using high doses of radiation to the entire body and chemotherapy, only the lymphoid organs (spleen, thymus, lymph
nodes) are irradiated (called "total lymphoid irradiation").
Antithymocyte globulin can also be given.
Even though this leaves some cancer cells, it makes it possible for allogeneic bone marrow stem cells to take up long-term
residence in the recipient (just as immunosuppression allows kidney transplants, etc. to avoid rejection by the recipient).
This is followed by an infusion of T cells from the same donor. These can then go to work against the cancer cells without being
threatened with rejection by the host.

12.9.5 https://bio.libretexts.org/@go/page/5092
 Once again, though, they will also attack normal cells of the recipient usually causing graft-versus-host disease (GVHD).
However, this promises to be milder than that following myeloablative conditioning — perhaps because repeated small doses of
radiation favors the survival of natural killer (NK) cells, and these appear to protect against GVHD.
In mice, the graft-versus-leukemia effect can be enjoyed without the downside of GVHD by including extra-large numbers of
regulatory T cells (Treg cells) in the bone marrow infusion. Whether this approach could be helpful for humans remains to be seen.

Virotherapy
It has long been known that viral infections can occasionally (and unpredictably) cause tumors to regress. A number of viruses
have been studied in the hope of developing a reliable therapy. On 27 October 2015, the U.S. FDA approved T-VEC (Imlygic®) for
the treatment of melanoma. T-VEC is a mutated and engineered Herpes Simplex Virus (HSV-1 — the cause of cold sores). The
alterations in the virus include incorporating the gene for GM-CSF and a mutation that prevents the virus from infecting non-
dividing cells while preserving its ability to infect and replicate in cancer cells. Replication kills the cells and causes them to
release:
more viruses which spread the infection;
tumor antigens, and
GM-CSF which attracts dendritic cells to the site. These take up the tumor antigens and present them to T cells that go on to
mount an attack against surviving tumor cells.
(Tumor cell death by HSV does not qualify it as immunotherapy, but the T-cell response that results certainly does.)

This page titled 12.9: Immunotherapy of Cancer is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

12.9.6 https://bio.libretexts.org/@go/page/5092
12.10: Cancer- The Causes and Prevention of Cancer
As described by Bruce N. Ames, Professor of Biochemistry & Molecular Biology, Director of the National Institute of
Environmental Health Sciences Centerm, University of California at Berkeley
Aging is in good part due to the oxidants produced as by-products of normal metabolism. These oxidants, such as superoxide and
hydrogen peroxide, are the same mutagens produced by radiation, and cause damage to DNA, proteins, and lipids.
The DNA in each cell of a normal rat receives on average about 100,000 oxidative lesions per day. DNA repair enzymes constantly
remove this damage, but they do not keep up: a young rat has about one million oxidative lesions in the DNA of each cell, which
increases to about two million in an old rat. A human cell receives about ten times less damage than a rat cell, in agreement with
the higher cancer rate and shorter lifespan of a rat.
The degenerative diseases of aging such as cancer, cardiovascular disease, cataracts, and brain dysfunction, are increasingly found
to have, in good part, an oxidative origin. It is argued that dietary antioxidants, such as Vitamins C and E and carotenoids, play a
major role in minimizing this damage and that most of the world's population is receiving inadequate amounts of them, at a great
cost to health.
The main source of dietary antioxidants is fruits and vegetables. Humans should eat 5 portions of fruits and vegetables per day, yet
only 9% of the U.S. population eats that much. Epidemiological studies show that the incidence of most types of cancer is double
among people who eat few fruits and vegetables as compared to those who eat about five portions per day. Considerable evidence
indicates that oxidative damage is important in cardiovascular disease, cataracts, and brain and immune system dysfunction, and
that adequate dietary antioxidants can minimize their incidence.
Men with low Vitamin C intake have low vitamin C in their seminal fluid and much more oxidative damage to the DNA in their
sperm. Male smokers are particularly at risk as they have depleted antioxidant pools (cigarette smoke is extremely high in
oxidants). A smoker must eat two to three times as much Vitamin C as a non-smoker to maintain an equal plasma level, yet
smokers tend to eat worse diets than non-smokers. Indeed, male smokers have a considerably higher risk of having children with
birth defects and childhood cancer.
The three main causes of cancer are smoking, dietary imbalances (excess fat and calories; inadequate intake of fruits,
vegetables, fiber, and calcium), and chronic infections leading to chronic inflammation (hepatitis B and C viruses, Helicobacter
pylori infection, schistosomiasis, etc.). Chronic inflammation is a major cause of cancer in the world because it releases powerful
oxidants which both stimulate cell division and are mutagens.
Past occupational exposures might cause about 2% of current human cancer, a major part being asbestos exposure in smokers, and
industrial or synthetic chemical pollution causes less than 0.1 %, in my view. The age-adjusted cancer death rate in the U.S. for all
cancers combined (excluding those attributable to smoking) has been remaining steady since 1950, while life expectancy increases
every year.
We are the healthiest we have ever been in human history.
Two factors are critical in the formation of mutations: lesions in DNA, formed when DNA is damaged, and cell division, which
converts DNA lesions to mutations. Agents increasing either lesions or cell division increase mutations and as a consequence
increase cancer incidence. Hormones stimulating cell division increase cancer incidence (e.g., levels of estrogen in breast cancer
and testosterone in prostate cancer); hormones may be a risk factor in about 20% of human cancer.
Animal cancer tests, which are done at the maximum tolerated dose (MTD), are being misinterpreted to mean that low doses of the
chemicals tested and found positive are thereby relevant to human cancer. Animal cancer tests are mainly done on synthetic
chemicals and industrial pollutants, yet half of all natural chemicals that have been tested at the MTD are rodent carcinogens.
It is argued that the explanation for the high frequency of positive results in animal cancer tests is that high dose animal cancer tests
are mainly measuring increases in cell division due to cell killing and compensatory cell division; this is a high dose effect that
does not occur at low doses.
In any case 99.9% or more of the chemicals we eat are natural. For example, 99.99% of the pesticides we eat are natural
chemicals that are present in plants to ward off insects and other predators. More than half of those natural pesticides tested in
high dose animal tests are rodent carcinogens. There are about 10,000 or so different natural pesticides in our diet, and they are
usually present at enormously higher levels than synthetic pesticides.

12.10.1 https://bio.libretexts.org/@go/page/5094
Cooking food also generates thousands of chemicals. There are over 1000 chemicals reported in a cup of coffee. Only 26 have been
tested in animal cancer tests and more than half are rodent carcinogens; there are still a thousand chemicals left to test. The amount
of potentially carcinogenic pesticide residues consumed in a year is less than the amount known of rodent carcinogens in a cup of
coffee.
The reason we can eat the tremendous variety of natural chemical rodent carcinogens in our food is that animals are extremely well
defended against all chemicals by many general defense systems. These enzymes, e.g., DNA repair and glutathione transferases
which defend against reactive compounds such as mutagens, are all inducible (more of them are made when they are in use). They
are equally effective against natural and synthetic reactive chemicals. Thus, animals are extremely well defended against low
doses of chemicals. One does not expect, nor does one find, a general difference between synthetic and natural chemicals in their
carcinogenicity, and though less well studied, the same would be expected for mutagenicity, teratogenicity, and acute toxicity.
The effort to eliminate synthetic pesticides because of unsubstantiated fears about residues in food will make fruits and vegetables
more expensive, decrease consumption, and thus increase cancer rates. The levels of synthetic pesticide residues are trivial in
comparison to natural chemicals, and thus their potential for cancer causation is extremely low.

This page titled 12.10: Cancer- The Causes and Prevention of Cancer is shared under a CC BY 3.0 license and was authored, remixed, and/or
curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is
available upon request.

12.10.2 https://bio.libretexts.org/@go/page/5094
12.11: Estimating Cancer Risks
Is there a safe dose of any mutagen or carcinogen?
We live surrounded by radiation and by chemicals that cause mutations in test organisms (like bacteria, yeast, and mice) and cause
an increase in the rate of cancers in experimental animals (rats and mice). Is there any safe dose for humans of these agents (which
include oxygen!) The question is exceedingly difficult to answer and, I believe, at low doses, unanswerable. Why?

Figure 12.11.1: Dose - Response relationship

Figure 12.11.1 shows several theoretical dose-response relationships. There is considerable evidence that at moderate doses of a
mutagen or carcinogen, the response is linear (A). However, at very low doses of some chemicals, there may be a threshold below
which the agent has no effect (B). Many workers believe that for some agents, it is likely that even the tiniest doses will have an
effect (C), but the population exposed must be large enough to observe it. This is called the linear no-threshold (LNT) model. Note
that even at zero dose, the line does not intercept the origin. This is because even unexposed animals (including people) show a
spontaneous level of response (e.g., tumors).
There is also evidence that for some agents in some circumstances, increasing the dose (at relatively low levels) actually reduces
the response below control levels (G). This phenomenon is called hormesis. At very high doses, the rate of response may increase
faster than the dose (E) as, for example, the probability of a single cell suffering two mutations increases. On the other hand, very
high doses may kill off damaged cells before they can develop into tumors (F).

Radiation and cancer

High doses of radiation cause cancer. Various studies, including excellent ones on the survivors of Hiroshima and Nagasaki, show
that a population exposed to a dose of 100 millisieverts (mSv) will have a measurable increase (about 1%) in the incidence of
cancer. Note that the measurements are made on a population, not on individuals. We can never say that a particular individual
exposed to a particular dose of radiation will develop cancer. The induction of cancer is a chance ("stochastic") event unlike the
induction of radiation sickness which is completely predictable. The element of chance arises because cancer is an event that occurs
in a single cell unlucky enough to suffer damage to several specific genes. However, the energy needed to cause mutations is very
low. So if you expose a sufficiently large number of cells to even tiny doses of radiation, some cell is going to be unlucky. How can
we evaluate the risk?

Collective Dose
100 mSv causes a 1% increase in cancer in a population; i.e., it should cause an increase of 1 cancer in every 100 people in the
exposed population. But if our reasoning is correct, a population of 10,000 people exposed to 1 mSv should also yield one case of
radiation-induced cancer. In any population, where the product of radiation dose (in mSv) times population size equals 1 x 104, one
case of cancer will be induced. The product of exposure multiplied by the size of the exposed population is known as the collective
dose. Its units are (persons)x(mSv).

12.11.1 https://bio.libretexts.org/@go/page/5095
  Example 12.11.1

The population of the U.S. in 2009 was about 305 million. so anything that increases the annual exposure of the U.S.
population by as little as 0.01 mSv (a typical chest x ray is 0.02 mSv) per year would cause an additional 305 cases of cancer.
6
(305 × 10 persons)(0.01 mSv)
= 305 cancers (12.11.1)
4
1 × 10 person mSv/cancer

But consider:
The total number of cancer deaths in the United States that year was expected to exceed 560,000.
How can we possible detect an increase of 305 faced with these large numbers?

Hormesis?
The citizens of Colorado are exposed to background radiation of some 1.8 mSv per year; the figure for Massachusetts is only 1.02
mSv/year.
If the linear non-threshold model is correct, we would expect to find a higher incidence of cancer in Colorado than in
Massachusetts.
If the background radiation added to other sources keeps both groups below a threshold, then we would expect no difference in
cancer incidence.
If the modest increase in background radiation in Colorado has a protective effect (hormesis), then we would expect that their
cancer incidence would be lower than in Massachusetts.
What do we find? In 1999, when adjusted for the age of the population, the incidence of cancer averaged 16% higher in
Massachusetts than in Colorado. (If this truly is evidence of hormesis, the mechanism is unknown.)
Some other parts of the world have background radiation levels that dwarf those in Colorado. In some houses in Ramsar, Iran, the
inhabitants are exposed to an annual dose of background radiation of as much as 130 mSv per year — over 70 times that in
Colorado. Nevertheless, the inhabitants of Ramsar are just as healthy as — or even healthier than — control populations exposed to
far lower levels of radiation.

 Chernobyl

It has been estimated (in this case, using a collective dose value of 5 x 104 person mSv/cancer) that the radioactive fallout from
the nuclear accident at Chernobyl (now often spelled "Chornobyl") in 1986 will cause an increase of 17,000 cancers over the
lifetime of people living in the Northern Hemisphere.
Large those this estimate seems, it is dwarfed by the 513 million cancer deaths that will occur anyway in this population. Even
among those heavily exposed (rescue workers and people living in the region), the expected death toll from cancer is ~4,000 or
only 3% more than their death rate from cancer would have been anyway. This is why I say above that the answer to the
question of the dangers of low doses of radiation is unknowable.
As of September 2005, some 4000 children and adolescents who drank milk contaminated by the radioactive iodine [131I]
released in the accident had come down with thyroid cancer. In their case, the ability of the thyroid gland to concentrate iodine
within its cells resulted in those cells receiving a relatively high, not a low, dose. As of that date, however, only 15 of those
cancer patients had died.

Chemicals and cancer: dioxin

At one time it was found that the chemical dioxin, which can be produced as a contaminant in the manufacture of paper and
cardboard, was leaching from milk cartons into milk itself.
the concentration in the milk averaged 0.1 part per trillion (ppt) or 0.0001 µg in a liter (109 µg) of milk. Assuming:
0.1 µg per day given to rats increases their rate of tumors by 1%
the idea of collective dose applies to chemicals (that is, a single molecule in an unlucky cell can turn it cancerous)
people are 100 times more sensitive to dioxin than rats (probably not true) and
people are 100 times larger than rats

12.11.2 https://bio.libretexts.org/@go/page/5095
 we conclude that there is a risk of 10 additional cancers in every million people consuming a liter (about a quart) of milk a day
from cardboard containers.
And, in fact, this was the estimate made. The uncertainties in such assumptions helps explain the controversy that has so often
swirled around the test data on such chemicals as
the artificial sweeteners cyclamate and saccharin,
the pesticide Alar,
the hydrocarbons in a charcoal-broiled steak,
the chlorinated compounds in municipal water supplies.

Some chemicals appear to have a safety threshold

Cells have a number of different methods for detoxifying certain types of chemicals. So long as these mechanisms are not
overwhelmed, they should provide a threshold of safety.

This page titled 12.11: Estimating Cancer Risks is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

12.11.3 https://bio.libretexts.org/@go/page/5095
12.12: The LD50 test
The LD50 is a standardized measure for expressing and comparing the toxicity of chemicals. The LD50 is the dose that kills half
(50%) of the animals tested (LD = "lethal dose"). The animals are usually rats or mice, although rabbits, guinea pigs, hamsters, and
so on are sometimes used. In all these tests, the dose must be calculated relative to the size of the animal. The most common units
are milligrams of chemical per kilogram of test animal (mg/kg or ppm).
Table 12.12.1: LD50 values of common drugs
Chemical Category Oral LD50 in Rats (mg/kg)

Aldicarb ("Temik") Carbamate 1

Carbaryl ("Sevin") Carbamate 307

DDT Chlorinated hydrocarbon 87

Dieldrin Chlorinated hydrocarbon 40

Diflubenzuron ("Dimilin") Chitin inhibitor 10,000

Malathion Organophosphate 885

Methoprene JH mimic 34,600

Methoxychlor Chlorinated hydrocarbon 5,000

Parathion Organophosphate 3

Piperonyl butoxide Synergist 7,500

Pyrethrins Plant extract 200

Rotenone Plant extract 60

Table 12.12.1 gives the LD50 values for some insecticides. In each case, the chemical was fed to laboratory rats. Note that the
lower the LD50, the more toxic the chemical. Even adjusting for the test animal's weight, the LD50 for one species is often quite
different from that for another. Thus any LD50 value gives only a rough estimate of the risk to humans. The way in which the
chemical is administered also has a marked effect on LD50 values. The chemical may be fed, injected, applied to the animal's skin,
etc., and each method usually generates a different LD50.

Because a single test may kill as many as 100 animals, the United States and other members of the Organization for Economic
Cooperation and Development agreed in December 2000 to phase out the LD50 test in favor of alternatives that greatly reduce
(or even eliminate) deaths of the test animals.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 12.12: The LD50 test is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

12.12.1 https://bio.libretexts.org/@go/page/5096
12.13: Dioxin
Name given members of a family of closely-related chemicals. The term dioxin is often used for one of these: 2,3,7,8-
tetrachlorodibenzo-p-dioxin or TCDD. This substance was present as a contaminant in the herbicide agent orange, which was so
widely used during the Vietnam war.

Figure 12.13.1: Structure of 2,3,7,8-tetrachlorodibenzo-p-dioxin.

When ingested or injected, TCDD is extremely poisonous to laboratory animals. At sub-lethal concentrations, it causes cancer and
birth defects in them. Exposure to high levels of dioxins causes a severe skin disease (chloracne) in humans as well as damage to
the liver and nervous system. While the evidence is still hotly debated, the U.S. Environmental Protection Agency (EPA) is
convinced that dioxins cause cancer in humans. They base this conclusion on extrapolating from dose-response studies done in
animals (rats) and following the health of industrial workers who were exposed to dioxins in the U.S., Germany, and the
Netherlands.
Thanks to the development of delicate analytical techniques, it is possible to detect trace amounts in everyone's blood. Most of us
have a few parts per trillion (ppt) of TCDD in our serum. TCDD (and other dioxins) are produced when organic matter is burned.
Measurable levels are found in soot from wood-burning stoves and the ash of municipal incinerators. However, the amounts to
which we are exposed have dropped some threefold since the mid-80s, and the cancer risk dioxins pose for most of us is probably
close to zero.
Dioxin can prevent disease! (in mice). Experimental allergic encephalomyelitis (EAE) is a disease in experimental animals (e.g.,
mice, guinea pigs) that closely mimics multiple sclerosis, an autoimmune disease of humans in which the myelin sheaths of
neurons are destroyed. In the 1 May 2008 issue of Nature, F. J. Quintana and colleagues reported that they could strongly suppress
the induction of EAE in mice by pretreating them with 1 µg of TCDD. The protection appeared to be mediated by regulatory T
cells (Treg) whose numbers rose sharply following TCDD treatment.

This page titled 12.13: Dioxin is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

12.13.1 https://bio.libretexts.org/@go/page/5097
12.14: Magnetic Fields and Cancer
The Background
Late in the 1970s, researchers investigating a cluster of cancers in children in Colorado found an association with living near high-
voltage power lines. The cancers, a form of leukemia called acute lymphoblastic leukemia (ALL), had long been associated with
exposure to ionizing radiation. But power lines do not generate ionizing radiation. What they do generate is a weak magnetic field
that oscillates at the frequency of the alternating current (60 hertz in the U.S.; 50 hertz in Europe). Follow-up studies elsewhere
continued to find a weak association between living near power lines and the incidence of ALL in children. Note that the
association was with the proximity to power lines; not to the strength of the magnetic fields. The nature of the wiring (e.g., voltage,
proximity) was used as a surrogate to the actual agent under suspicion (the magnetic field).

The National Cancer Institute (NCI) Study

On July 3, 1997, The New England Journal of Medicine published the largest and best study of the question (Martha S. Linet, et al,
"Residential Exposure to Magnetic Fields and Acute Lymphoblastic Leukemia in Children").
Their conclusion: "Our results provide little support for the hypothesis that living in homes with high time-weighted average
magnetic fields or in homes close to electrical transmission or distribution lines is related to the risk of childhood ALL."

How the NCI study differed from earlier studies

The NCI study differed from the earlier studies in 4 important ways:
It involved a much larger sample size (624 children with ALL and 615 children chosen at random to compare their homes with
those of the patients.
The strength of the magnetic fields in the homes were actually measured (including continuous measurement for 24 hours under
the child's bed). They also evaluated the nearby power lines as the earlier studies had done.
The collection of data was "blinded"; that is, the people doing the measurements did not know whether they were in the house
of an ALL patient or in the house of a control.
The investigators had no axe to grind. None had any connection to the power industry or to grieving parents seeking to find an
explanation for the tragedy that had struck their family.

The Magnetic Field Results

Patients and controls were grouped in 7 classes ranging from a magnetic field of less than 0.065 microteslas (µT) to greater than
0.5 µT. The tesla is a unit of magnetic field strength; the earth's magnetic field, which makes a compass needle turn, is about 50
microteslas (but does not fluctuate at 60 hertz as the much smaller fields near alternating current lines do). The Odds Ratio is a
calculation of how likely it is that the results for the patient group differ from that of the control group. The total number of patients
and controls in each class is shown within each bar. The blue lines show the 95% confidence limits; that is, that there is a 95%
probability that the "true" mean (the height of the bar) is somewhere within the range shown in blue.

Figure 12.14.1: Odds Ratio

Interpreting the results

Only one class of exposure (0.400 - 0.499 µT) showed a statistically significant difference between patients and controls. Is it truly
significant? Perhaps. But note that only 19 children of the 1,239 enrolled in the study lived in homes with this level of magnetic
field.

12.14.1 https://bio.libretexts.org/@go/page/5098
How do this and the earlier studies meet the 5 standards of epidemiology?
1. High Relative Risk
Not met. Every group but one had a relative risk whose 95% confidence limit included 1.00; that is, no relative risk at all.
2. Consistency
Not met.
The earlier studies did not measure magnetic fields.
Most of the earlier studies, which simply evaluated the nature of the nearby power lines, showed a 2–3 fold increase in
relative risk whereas this study showed no increase.
3. A graded response to a graded dose
Not met. There is no steady increase in ALL with increasing exposure to magnetic fields. The possible increased risk of ALL
with exposure to 0.400 - 0.499 µT is followed by no increase at exposures above 0.5 µT.
4. Temporal relationship
Met. In fact, built into the design of the study. All the patients were selected after they had developed ALL.
5. A plausible mechanism Not met. In vitro studies have failed to reveal any mechanism to explain how such weak magnetic
fields could produce oncogenic changes in cells. (Note that the Y axis of this graph of representative magnetic fields is
logarithmic: the magnetic field directly under a high-voltage power line is only 1/10 that of the earth's own magnetic field.)
Two papers published in 1992 claimed that weak magnetic fields increase the flow of calcium ions into lymphocytes. Such a
response may trigger mitosis and thus provide a plausible mechanism for a tumor-promoting effect. However, in June 1999 the
author was censured by the Office of Research Integrity for falsifying his data, and the author retracted the papers.

The Bottom Line

In the words of Edward W. Campion, M.D. (New England Journal of Medicine, 337:44, July 3, 1997):
"there is no convincing evidence that high-voltage power lines are a health hazard or a cause of cancer...18 years of research have
produced considerable paranoia, but little insight and no prevention. It is time to stop wasting our research resources. We should
redirect them to research that will be able to discover the true biologic causes of the leukemic clones that threaten the lives of
children."

This page titled 12.14: Magnetic Fields and Cancer is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

12.14.2 https://bio.libretexts.org/@go/page/5098
 CHAPTER OVERVIEW
Unit 13: Aging
13.1: Aging
13.2: Telomeres

This page titled Unit 13: Aging is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1
13.1: Aging
What is Aging?
Aging is the progressive loss of physiological functions that increases the probability of death. This table gives some data.

Loss of structure and function in aging. Figures represent percentage of a given function remaining in an average 75-year-old man compared The
with that found in an average 30-year-old man, the latter value taken as 100%. dec
Weight of brain 56% line
in
Blood supply to brain 80
fun
Output of heart at rest 70 ctio
Number of glomeruli in kidney 56 n
cert
Glomerular filtration rate 69
ainl
Speed of return to normal pH of blood after displacement 17 y
Number of taste buds 36 occ
urs
Vital capacity 56
wit
Strength of hand grip 55 hin
Maximum O2 uptake during exercise 40 cell
s.
Number of axons in spinal nerve 63
Thi
Velocity of nerve impulse 90 s is
Body weight 88
esp
ecia
lly
true of cells that are no longer in the cell cycle:
neurons in the brain;
skeletal and cardiac muscle;
kidney cells.
Tissue and organs made of cells that are replenished by mitosis throughout life. Blood and intestinal epithelium show far fewer
signs of aging.
In the natural world, very few animals live long enough to show signs of aging. Random mortality from starvation, predation,
infectious disease and a harsh environment (e.g., cold) kills off most animals long before they begin to show signs of aging. Even
for humans, aging has only become common in recent decades.
At the start of the 20th century, infectious diseases such as pneumonia and influenza caused more deaths in the United States than
"organic" diseases like cancer. Now the situation is reversed. The availability of effective weapons against infectious disease (e.g.,
sanitation, antibiotics, and immunization) has greatly increased the average life span (but not maximum life span) and resulted in
"organic" diseases like cardiovascular disease and cancer becoming the most common cause of death.
In 1900, a newborn child in the U.S. could look forward to an average life expectancy of only 47 years. Infectious diseases were
the major causes of death, killing most people before they reached an age when aging set in. Three-quarters of a century later, life
expectancy had risen to 73 years and "organic" diseases, including all the diseases of aging, had replaced infectious diseases as the
major cause of death. Today, the life expectancy has risen to 80 for women (74 for men), and coping with an aging population has
become a major economic and social challenge in the U.S.

13.1.1 https://bio.libretexts.org/@go/page/5133
 Figure 13.1.1 Survival curves
The above graph shows four representative survival curves. The vertical axis represents the fraction of survivors at each age (on the
horizontal axis).
Curve A is characteristic of organisms that have low mortality until late in life. Then mortality increasingly becomes the
endpoint of the aging process.
Curve B is typical of populations in which such environmental factors as starvation and disease obscure the effects of aging
(and infant mortality in high).
Curve C is a theoretical curve for organisms for which the chance of death is equal at all ages. This might be the case for
organisms that show few, if any, signs of aging (some fishes) or those (e.g., songbirds in the wild) that suffer severe random
mortality from environmental causes throughout life.
Curve D is typical of organisms, oysters for example, that produce huge numbers of offspring accompanied by high rates of
infant mortality.
Organisms with survivorship curves between C and D have no opportunity to show the signs of aging.

Aging in Invertebrates
Invertebrate animals have provided some important clues about the aging process.
Colonial invertebrates like sponges and corals don't show signs of aging. Even individual cnidarians, like the sea anemone that
lived for 78 years, show little or no sign of aging. In all these cases, this is probably because there is constant replacement of old
cells by new ones as the years go by.
Lobsters also can live to a very old age with no obvious sign of a decline in fecundity or any other physiological process. But
lobsters never stop growing, so once again it may be the continuous formation of new cells that keeps the animal going.
In culture vessels, Drosophila does have a limited life span and shows signs of aging before it dies. Two factors have been
found to influence the aging process and thus life span:
Calorie restriction, that is, a semi-starvation diet. In fact, restricting food intake has been shown to increase life span (and
slow aging) in all animals — including mammals — that have been tested.
Single genes have been identified that extend life span in Drosophila (and also in the invertebrate Caenorhabditis elegans).

Aging in Vertebrates
Some cold-blooded vertebrates fishes, amphibians, reptiles have long life spans if they can survive environmental hazards (giant
tortoises are known to have reached 177 years of age). These animals are cold-blooded and grow so slowly that they will probably
succumb to environmental hazards before they stop growing and begin to show signs of aging. The situation is different for birds
and mammals. They are warm-blooded, grow rapidly to adult size and, if protected from environmental hazards, will show signs
of aging.

Why Do We Age?
Programmed in our genes
The pros
Single genes have been found that increase life span in Drosophila, C. elegans, and mice. Genes that suppress signaling by
insulin and insulin-like growth factor-1 (Igf-1) increase life span in these animals. Examples:
Mice with one of their Igf-1 receptor genes "knocked out" live 25% longer than normal mice.

13.1.2 https://bio.libretexts.org/@go/page/5133
 Klotho. Cells in the kidney and brain release the extracellular portion of a cell surface transmembrane protein into the
blood. This "hormone", called Klotho, binds to receptors on many target cells reducing their ability to respond to insulin and
Igf-1 signaling.
Mice homozygous for a mutant klotho gene show many signs of premature aging while
mice expressing extra-high levels of the Klotho protein live 20–30% longer than normal.
Long life spans clearly run in human families.
Aging often appears sooner in animals that suffer high death rates from external causes (e.g. predation) early in life.
Why should this be? Three (interrelated) possibilities:
The accumulation of harmful mutations (in the germline). Few individuals survive long enough for these to be selected
against.
Antagonistic pleiotropy. Genes that promote survival early in life at the expense of maintaining the body will be selected
for.
Some examples:
p53. By forcing cells with damaged DNA to stop dividing and become senescent or even to die by apoptosis, it protects
the organism from the threat of those cells becoming cancerous but at the expense of reducing cell renewal (e.g., by
decreasing the size of the pools of stem cells). Mice that are forced to produce higher-than-normal levels of the p53
protein show many signs of premature aging while female mice that are deficient in p53 have reduced fecundity
(blastocysts fail to implant). So here is a tradeoff by a gene that promotes evolutionary success at an early age but at the
expense of accelerated aging.
In both Drosophila and C. elegans, some mutations that increase life span do so at the cost of decreased fecundity and
vice versa.
Disposable soma. Early death from external causes will select for genes that increase the chances of passing germplasm on
(i.e. reproduction) at the expense of genes that might delay aging.
There is no way that natural selection can select for genes whose only beneficial effect appears after the age of reproduction is
over. But
any genes that extend the reproductive period or
any genes that promote fitness in youth as well as longevity
would be selected for.
The cons
High early mortality from external causes (e.g. predators) has been linked to early aging (in the survivors) in some animals, but the
reverse has been found in others. These contradictory results do not negate the role of genes in aging, but indicate that other
environmental factors (e.g. more food left for the survivors) may skew the outcome.

The Inevitable Consequence of an Active Life

The pros
Many cold-blooded vertebrates (e.g., many fishes and reptiles) do not show signs of aging.
Transgenic mice whose "thermostat" in the hypothalamus has been reset to give a lower body temperature (reduced by 0.3 –
0.5°C) live 12% (males) to 20% (females) longer than their nontransgenic littermates. This translates into adding some 3
months to the average life span of 27 months for these mice. (See Conti, B., et al., Science, 3 November 2006).)
The effects of Calorie Restriction (CR). The life span of yeast, C. elegans, Drosophila, birds, and mammals (mice, rats, and
probably monkeys) can be extended, and signs of aging delayed, if they are maintained on a semi-starvation diet. Calorie
restriction in mice causes
a drop in
the level of circulating insulin and insulin-like growth factor-1 (Igf-1);
the level of glucose and triglycerides in the blood;
the level of NADH (produced by cellular respiration) within cells;
an increase in the production of sirtuins — deacetylases that remove acetyl groups from proteins.
apoptosis of cells to be inhibited;

13.1.3 https://bio.libretexts.org/@go/page/5133
 formation of adipose tissue to be suppressed;
increased production of nitric oxide (NO) which is essential for the benefits of CR to take effect.
greatly increased physical activity and
lower body weight.
The life-extending and other effects of CR on rats and mice may not be as significant as they seem. All the studies have been
done on laboratory rats and mice. Control animals are normally fed ad libitum, which means that they have food available all
the time. But this would not likely be the case in the wild so it may be that the physiology and life span of these animals are
already compromised and that the effects of CR are mainly restoring normal conditions for these species.
The problem of proper controls may also explain the divergent results in studies of CR in rhesus monkeys.
In the 10 July 2009 issue of Science, researchers at the Wisconsin National Primate Research Center reported the status of
rhesus monkeys that had been on CR for 20 years compared with a control group allowed to feed ad libitum on the same diet
during that time. The results: the CR animals showed markedly fewer signs of aging (none showed any signs of diabetes),
and the few that died from age-related causes did so at only one-third the rate of the controls.
However, a 25-year study of CR in rhesus monkeys carried out at the National Institute of Aging (NIA) (and reported in
Nature in August 2012) showed no increased longevity in the CR monkeys.
The difference may have arisen because the control monkeys in Wisconsin were fed ad libitum while the controls at the NIA
were fed a fixed amount. Furthermore, the diet used in the Wisconsin study were much higher in sugar than the diet at the NIA,
and the NIA diets also included omega-3 fatty acids and other healthy components absent from the Wisconsin diet. So perhaps
the positive effect seen in the Wisconsin study resulted from the CR animals simply getting less of an unhealthy diet than the
controls.

Resveratrol
Resveratrol, is a small molecule found in red wine which appears to activate sirtuins mimicking the effects of calorie restriction.
Mice given daily doses of resveratrol while indulging in a high-fat diet get fat but avoid the degenerative changes and shortened
life span that normally accompany a high-fat diet. But before rushing out to buy red wine, realize that the doses of resveratrol given
to the mice were far higher than could be supplied by drinking it. Studies on the effect of resveratrol on extending life span in yeast,
Drosophila and C. elegans have produced mixed results.
No one knows for certain why calorie restriction delay aging, but some mechanisms might be because it lowers the level of glucose
in the blood and thus the speed with which lipids and proteins suffer from glycation. Advanced glycation end products (AGEs) are
molecules that have reduced function because of the haphazard addition of sugars to them. For proteins like collagens and elastin,
this results is increasing stiffness of the extracellular matrix (ECM) of blood vessels, joints, heart, kidney, etc. Reducing calorie
intake reduces female fecundity (at least in C. elegans, Drosophila, rats and mice). The energy that would have been devoted to
producing offspring can be devoted instead to tissue repair and maintenance. Calorie restriction raises the level of sirtuins:
The SIRT1 protein CR in knockout mice lacking SIRT1 gain no increase in life span.
plays a key role in repairing DNA damage and so helps protect the integrity of the genome which appears to be essential to
longevity.
It also inhibits the nutrient sensor TOR ("target of rapamycin") which accelerates aging in mice.
SIRT1 also inhibits p53 activation thus protecting against mitochondrial damage.
The SIRT3 protein is found in mitochondria where it inhibits the production of free radicals.

The Free Radical Theory of Aging

A major aspect of metabolism is the oxidation of foodstuffs by the mitochondria. Electron transport in the mitochondria generates
reactive oxygen species ("ROS") such as the superoxide anion (O2−), which generates hydrogen peroxide (H2O2). Although cells
contain enzymes for detoxifying these reactive substances (e.g., catalase which breaks down H2O2), they eventually and inevitably
damage macromolecules in the cell: proteins; lipids; and probably most important of all, DNA.
Damaged proteins and lipids accumulate in the cell, especially nondividing cells like neurons and muscle, producing aggregates of
denatured proteins and an "aging pigment" called lipofuscin (a principal component of ear wax). The accumulation of protein
aggregates in striated muscles reduces muscle strength. Protein aggregates accumulate more slowly in the cells of animals on a
calorie restricted diet — perhaps as a result of more-efficient autophagy. However, it may be damage to DNA that is the crucial
factor in the decline in cell function with age.

13.1.4 https://bio.libretexts.org/@go/page/5133
The DNA of the mitochondria (mtDNA) may be at special risk. ROS are produced as an inevitable byproduct of electron transport
in the mitochondria and thus are generated close to the mtDNA. But the products of these genes are essential for electron transport.
So perhaps a positive feedback loop is generated: ROS -> mutations in electron transport genes reducing their efficiency -> more
ROS production.
Supporting evidence:
mtDNA accumulates mutations faster than nuclear DNA, and these show the chemical characteristics of damage by ROS.
Transgenic mice containing the human gene for catalase (but with the targeting signal that would normally send the protein to
peroxisomes replaced with that for mitochondria) live 20% longer than normal for their strain. [See Schriner, S. E. et al.,
Science, 24 June 2005.]
Transgenic mice whose DNA polymerase for copying mtDNA genes (DNA polymerase gamma) is defective, and introduces an
elevated number of mutations in mtDNA, show many signs of premature aging — both cellular and in various organ systems —
and die early.
The cons
Neither mice genetically engineered to overproduce free radicals, nor those engineered to produce lower amounts of free
radicals, have any change in their lifespan.
Bats and mice are similar in size and metabolic rate, but bats can live ten times as long.
Although glucose-starved yeast do live longer, they have an increased — not decreased — rate of cellular respiration.
The metabolic rate of mice on a CR diet is no lower than that of mice on a normal diet.
The beneficial effects of CR take hold at any time, at least in Drosophila. Even after three weeks on a rich diet (in the second
half of the normal life span of adult flies), switching to a CR diet reduces mortality to the same degree as flies maintained on
CR throughout their adult lives. The reverse is also true — switching from a CR diet to a rich diet quickly undoes the good
work of the former. These results suggest that if a rich diet does produce irreversible and accumulating damage, its harmful
effects on life span can be blunted at any time.

The Accumulation of Senescent Cells

Chronological Senescence

Once formed, some cells in a mouse or human are never replaced. A neuron formed during embryonic development may still be
functioning at the end of life. However, during its life span, damage to its organelles and DNA may accumulate resulting in a loss
of function. This is called chronological senescence. In other tissues, e.g., blood and epithelia, new cells replace old ones
throughout life. But even though new, they may have reduced function because of replicative senescence.
Replicative Senescence
One might expect that cells removed from a mouse or human and placed in tissue culture could be cultured indefinitely, but that is
not the case. When human fibroblasts, for example, are placed in culture, they proliferate at first, but eventually a time comes when
their rate of mitosis slows and finally stops. The cells continue to live for a while, but cannot pass from G1 to the S phase of the
cell cycle. This phenomenon is called replicative senescence. Fibroblasts taken from a young human pass through some 60–80
doublings before they reach replicative senescence.
Why should this be? Cells — unless they retain the enzyme telomerase — lose DNA from the tips of their chromosomes
(telomeres) with each cell division. In general, the telomeres in the cells of old animals are much shorter than those in young
animals. A recent study of short-lived versus long-lived birds showed that telomere shortening was faster in the short-lived species.
And one species, a petrel which lives four times as long as other birds of its size, actually has telomeres that grew longer with age.
Most somatic cells of the body cease to express telomerase. However, cells genetically manipulated to express telomerase long
after they should have stopped, avoid replicative senescence. Germline cells, e.g., spermatogonia, and some stem cells continue to
express the enzyme. Some 95% of cancer cells express telomerase. If telomeres get too short (less than 13 repeats in human cells),
chromosome abnormalities — a hallmark of cancer — occur. Cancer can be avoided if the cell senses this dangerous condition and
ceases to divide. So telomere shortening may protect against cancer at the price of cell senescence.
Two proteins encoded by tumor suppressor genes p53 and p16INK4a play pivotal roles in stopping the cell cycle. The result:
replicative senescence. So replicative senescence may be the price we pay for removing cells from the cell cycle before they can
accumulate the mutations that would turn them into cancer cells.
The role of the tumor suppressor proteins in replicative senescence is mirrored in the intact animal, at least in mice.

13.1.5 https://bio.libretexts.org/@go/page/5133
 Mice engineered to express abnormally-high levels of p53 activity show many signs of premature aging including premature
reduction in the length of their telomeres.
Mice
that express abnormally-high levels of p16INK4a have a reduced ability to regenerate tissue while
mice whose activity of p16INK4a is suppressed continue to repair damaged tissue as efficiently as young animals do.
In mice, eliminating senescent cells (they are high in p16INK4a) prevents (in young mice) and partially reverses (in older mice)
some of the signs of aging such as cataracts, and loss of adipose tissue and skeletal muscle mass.
Mice genetically-engineered to express high levels of
telomerase and
tumor suppressor genes (e.g., p53 and p16INK4a)
have substantially-increased life spans and show fewer of the degenerative changes characteristic of aging in their skin and
other epithelia. (The need to make these transgenic mice with increased tumor suppressor activity in addition to increased
telomerase activity arises because an increased level of telomerase alone elevates the incidence of cancer — killing the animals
before any anti-aging effects of telomerase can be measured reliably.)
The role of telomerase deficiency in mammalian aging
Mice whose genes for telomerase have been "knocked out" (either Tert−/− or Terc −/−) show many of the degenerative changes
associated with aging.
The number of mitochondria in their cells decreases as does the function of those that remain.
Oxygen consumption and ATP production declines.
The efficiency of the electron transport chain decreases.
This leads to an increased generation of reactive oxygen species (ROS).
The level of p53 activity increases.
mitosis declines
apoptosis of cells increases
replicative senescence increases
The anatomy and function of organs such as the liver and heart show the degenerative changes of age.
In the 6 January 2011 issue of Nature, Mariela Jaskelioff and her colleagues (many of the same team that found the results
described in the previous section) report that reactivation of telomerase in aged mice reverses many signs of aging.
Their experimental animals were another telomerase-deficient strain of mice; that is, mice that couldn't produce telomerase even in
those cells — "adult" stem cells and cells of the germline — that normally retain telomerase activity. The mice were made by
"knocking-in" a gene that prevents any expression of telomere reverse transcriptase (TERT) unless an activating drug is given to
the animal. Without the drug, these mice live half as long as normal, and as they get older, they display many signs of aging:
their telomeres get shorter leading to chromosome aberrations;
their cells undergo early replicative senescence;
almost all their organs — testes, spleen, intestine, brain — show degenerative changes typical of aging.
BUT, if given the activating drug over a four-week period at a time when degenerative changes were already apparent (25-30
weeks), their deterioration stopped and even partially reversed.
the length of their telomeres increased;
replicative senescence was delayed;
their life span was substantially increased;
their brain, testes, liver, spleen, and intestine escaped the degenerative changes seen in untreated telomerase-deficient mice;
they produced larger litters than untreated mice;
there was reduced activation of p53, indicating
reduced damage to their genome and
reduced apoptosis in their tissues
How would replicative senescence of cells lead to the deterioration in structure and function of the aging tissues (e.g., skin) in
which they reside? In tissues, e.g., skin and other epithelia, where mitosis must continue throughout life to replace the cells that are

13.1.6 https://bio.libretexts.org/@go/page/5133
lost, the accumulation of senescent cells — incapable of further mitosis — could leading to the characteristic changes of aging in
that tissue.
One mechanism could be simply the inability of senescent cells to repair the tissue by mitosis.
However, senescent cells remain active although the genes they express change. Perhaps the proteins they secrete (e.g.,
collagen-digesting enzymes) cause the aging changes in the tissue where they reside.
Perhaps it is the senescence of adult stem cells that has the greatest effect on tissue aging. In knockout mice that cannot make
the Klotho protein, stem cells and progenitor cells in various tissues undergo senescence and decline in numbers.
An unavoidable tradeoff?
Some of the data so far suggests that efforts to avoid the degenerative changes that come with age (e.g., by increasing cell renewal
by means of increased telomerase activity) in the hope of increasing longevity may instead hasten death from cancer while efforts
to prevent cancer (e.g., by increasing the activity of tumor suppressor genes) may hasten aging. However, other evidence paints a
less-gloomy picture. Mice heterozygous for the p53 tumor suppressor gene (p53+/−) develop many cancers when exposed to
ionizing radiation. With only a single copy of this tumor suppressor, a single cell is at great risk of losing the remaining copy ("loss
of heterozygosity") and starting the growth of a malignant clone. However, if before being irradiated the mice are given resveratrol
— to stimulate the production of the anti-aging SIRT1 protein — the incidence of some cancers is reduced and the mice live longer
before succumbing to their tumors.

The Accumulation of Genetic Errors

The pros
Mice given ionizing radiation that damages DNA show early aging.
Transgenic mice with a defect in the "proofreading" function of the DNA polymerase responsible for copying mitochondrial
DNA
accumulate many mutations in their mitochondrial genes;
show marked signs of premature aging.
Cells taken from old mice (and old humans) show slightly elevated levels of somatic mutations and chromosome abnormalities
like translocations and aneuploidy. Many of these changes also cause cancer so it is no accident that the incidence of cancer
rises with advancing age (graph).
The hematopoietic stem cells of "knockout" mice deficient in any one of these enzymes needed for genome maintenance
XPD for nucleotide excision repair (NER)
Ku80 for nonhomologous end joining (NHEJ)
TR (telomerase RNA) needed for telomere maintenance
lose their ability to supply the various progenitor cells that produce the white blood cells.
Most of the hematopoietic stem cells in aged mice show evidence of double-stranded breaks (DSBs) in their chromatin.
As DSBs form, SIRT1 proteins move from their original locations (at gene promoters) to the locations of the DSBs (where they
recruit DNA repair proteins). This shifts the pattern of gene expression to one typical of aging cells.
Cells taken from old people (and people with premature aging syndromes) show marked reductions in the transcription of some
genes, increases in others.
Clues from the Transcriptome of Aging Brains
A group of Harvard researchers reported (in the 26 June 2004 issue of Nature) the results of their study of gene expression in the
human brain. They extracted the RNA from autopsied brain tissue of 30 people who had died at ages ranging from 26 to 106. They
analyzed the RNA with DNA chips looking for the level of activity of some 11,000 different genes (the transcriptome). A clear
pattern emerged.
The level of activity of some 400 genes changed over time.
Gene expression declined in old age for many genes. Some examples:
genes encoding proteins involved in synaptic activity in the brain (e.g., learning, memory)
NMDA, AMPA, GABAA receptors
calcium-calmodulin-dependent kinase II (CaMKII)
genes involved in mitochondrial functions, such as
production of ATP (needed for DNA repair)

13.1.7 https://bio.libretexts.org/@go/page/5133
 production of damaging reactive oxygen species (ROS)
Detailed examination of some of these down-regulated genes showed that they had suffered DNA damage — more often in
their promoters than in their coding regions.
Gene expression increased in old age for other genes. Some examples:
genes involved in inflammation and other immune defenses;
genes encoding proteins involved in defense against reactive oxygen species (ROS);
genes encoding proteins involved in DNA repair.
The transition from the youthful transcriptome to the transcriptome of the aged brain occurred at varying times from as young as 42
to as old at 73.
A study of individual heart muscle cells in young and old mice (Bahar, R. et al., Nature, 22 June 2006) showed that the
transcriptome of young cells was quite uniform from cell to cell but that of aged cells was highly variable from one cell to another.
Variable gene expression from one cell to the next in a single tissue might well lead to defects in the functioning of that tissue.
Clues from Premature Aging Syndromes

Humans suffer from a number of rare genetic diseases that, among other things, produce signs of premature aging, e.g., gray hair,
wrinkled skin, and shortened life span. In several cases, the mutated genes are ones that have roles to play in maintaining the
integrity of the genome, that is, in DNA repair.
Werner's syndrome. The hair of patients turns gray in their 20s and most die in their late 40s with such signs of age as
osteoporosis, cataracts, and atherosclerosis. Even when young, their cells undergo replicative senescence after only ~20
doublings instead of the normal 70 or more. Caused by mutations in WRN, which encodes a helicase needed for DNA repair and
maintenance of telomeres.
Cockayne syndrome (CS). Caused by mutations in genes needed for DNA repair, especially transcription-coupled DNA
repair. While these people show only some of the signs of aging, they do have a sharply-reduced life span.
Ataxia telangiectasia (AT). These patients show signs of premature aging. They lack a functioning gene (ATM) product needed
to detect DNA damage and initiate a repair response.
Hutchinson-Gilford progeria syndrome. Children with this rare disorder show many signs of severe aging by their second
birthday and die in their early teens. Caused by mutations in the gene (LMNA) for lamin the intermediate filament protein that
stabilizes the inner membrane of the nuclear envelope. The machinery for DNA replication, transcription, and repair is located
at the inner surface of the nuclear envelope, and the cells of these patients have increased DNA damage and other defects in
gene expression.
So these syndromes suggest that aging may be the consequence not so much of mutations in general, but of mutations in those
genes whose products are essential for the error-free replication, repair and transcription of all genes.
Why is a mouse as old at 2 years as a human at 70
If aging represents the inevitable consequence of a failure of DNA repair, why does it occur so much sooner in some mammals
(e.g., mice) than in others (e.g., elephants and humans)?
The answer probably lies in the risk of death from external factors (e.g., predation, starvation, cold) in that species.
As noted above, few small mammals ever age because they die early of external causes. These animals are r-strategists, putting
their energy into quickly
reaching sexual maturity
producing large numbers of offspring that can soon live independently
There is no selective advantage for them to invest in the machinery of efficient DNA repair because they are going to die before
mutations become a problem.
Humans, in contrast, are K-strategists. They take a long time to reach sexual maturity. They also produce small numbers of young
that must be cared for over a long period. Small wonder, then, that evolution in humans (and other long-lived mammals) has
selected for genes promoting efficient DNA repair.
The table shows that the efficiency of DNA repair is directly correlated with life span in a variety of mammals.

13.1.8 https://bio.libretexts.org/@go/page/5133
 Correlation between life span and the relative effectiveness of DNA repair in cells of certain mammals. In each case, cells growing in tissue Inte
rrel
culture were irradiated with ultraviolet light and then the efficiency with which they repaired their DNA was determined. (From the work of R. W.
atio
Hart and R. B. Setlow, 1974.) nshi
ps
Species Average life span, yr Relative effectiveness of DNA repair

Human 70 50 Exa
Elephant 60 47 min
ing
Cow 30 43
the
Hamster 4 26 vari
Rat 3 13 ous
fact
Mouse 2 9
ors
Shrew 1 8 that
hav
e been implicated in the aging process suggests that most —perhaps all — are interrelated.
Mitochondria disfunction with the production of
reactive oxygen species (ROS) with their damaging effect on
DNA and other cell constituents coupled with the
onset of replicative senescence so that damaged cells can no longer be replaced
may all play important roles. So the factors described above are by no means mutually exclusive.

Figure 13.1.2 Factors involved in aging

The above figure attempts to show how various factors involved in aging interact. Key players are
The gradual shortening of telomeres with repeated cell divisions.
p53.
the enzyme designated TOR ("target of rapamycin"). TOR is a kinase that participates in many metabolic pathways in the cell.
(It is inhibited by the antibiotic rapamycin that is used as an immunosuppressant).
Stimulatory interactions are shown with blue arrows; inhibitory interactions are shown in red.
Interactions:
Telomere shortening activates p53 which leads to damaged mitochondria.
The inefficient electron transport chain in damaged mitochondria produces ROS.
Abundant nutrients (e.g. amino acids) as well as other growth stimulants activate TOR which promotes anabolism (protein and
lipid synthesis) with attendant production of reactive oxygen species (ROS) and aging.
Calorie restriction, working through SIRT1 inhibits TOR and its downstream effects.
Inhibition of TOR relieves its inhibition of autophagy allowing the cells to scavenge, for example, damaged mitochondria.
SIRT1 inhibits p53 activation thus protecting against mitochondrial damage.
Because of the association between telomere shortening and aging, two companies have begun (in 2011) to offer tests of telomere
length. How such tests might be useful to the people asking for them remains to be seen.

13.1.9 https://bio.libretexts.org/@go/page/5133
The Hallmarks of Aging
In the 6 June 2013 issue of Cell, an international group of scientists developed a list of 9 features that characterize aging in animals.
(This effort to bring order to such a complex subject is reminiscent of earlier papers in the same journal, The Hallmarks of Cancer.)
They expected that each hallmark would meet at least two of three criteria.
It should be characteristic of normal aging.
Increased expression of the hallmark should result in faster aging.
Efforts to reduce expression of the hallmark should prolong a healthy lifespan ("healthspan").
The 9 hallmarks.
1. Genomic Instability
Meeting the criteria:
Aged cells contain more DNA damage than young ones.
Agents that increase unrepaired damage to DNA, including chromosomal damage (e.g., aneuploidy), hasten aging.
Limited evidence that treatments that reduce, for example, chromosome missegregation, prolong healthspan.
2. Telomere Attrition
Meeting the criteria:
The chromosomes of aged cells have shorter telomeres than those of young cells.
Telomerase-deficient mice show premature aging.
Treatments that reactivate telomerase in normal mice delay aging.
3. Epigenetic Alterations
Meeting the criteria:
The patterns of DNA methylation and histone modifications changes as a mammal ages.
Mice that are deficient in the sirtuin SIRT6, an enzyme that deacetylates histones, age more rapidly than normal.
Treatments that increase the activity of sirtuins increase healthspan in mice.

 Note

As we humans age, the DNA in our cells accumulates an ever-increasing number of epigenetic changes as measured by the
methylation of CpGs. This is true for a wide variety of cell types even those that have been formed recently; that is, the number
of epigenetic changes reflects the age of the donor not the age of the cell. The correlation is so good that analysis of these
changes in a cell can predict the donor's age sometimes within a matter of months.

4. Loss of Proteostasis
Proteostasis is the homeostasis of the proteome — the proper balance of the synthesis and degradation of proteins in the cell.
Meeting the criteria:
The clearance of denatured (unfolded) proteins by autophagy and proteasomes, as well as the ability to refolded them with
chaperones, all decline with age. The result: toxic protein aggregates that accumulate in aged cells.
Mutant mice with defective chaperone activity age more quickly.
Transgenic Drosophila and C. elegans that overexpress chaperones have increased life spans.
5. Derugulated Nutrient Sensing
Meeting the criteria:
The nutrient sensor TOR ("target of rapamycin"), which promotes anabolism, increases during normal aging (and produces
obesity, at least in mice).
Increased activity of TOR accelerates aging in mice.
Examples:
Genetic suppression of TOR signaling extends lifespan in Drosophila and C. elegans.
Calorie Restriction (CR), which inhibits TOR, increases healthspan in all animals in which it has been tested.
Rapamycin, which inhibits TOR, extends lifespan in Drosophila, C. elegans, and mice.

13.1.10 https://bio.libretexts.org/@go/page/5133
6. Mitochondrial Dysfunction
Meeting the criteria:
The production and efficiency of mitochondria decreases in aging, otherwise normal, mice.
Deleterious mutations in mitochondrial DNA and other defects in mitochondrial function all accelerate aging in mice.
No compelling evidence yet that treatments to improve mitochondrial function increase life span.
7. Cellular Senescence
Meeting the criteria:
Replicative senescence (cells no longer able to enter the cell cycle) sets in much sooner in the cells of aged animals than it does
in young animals.
Mice engineered to express abnormally-high levels of p53, a protein that blocks entry into the cell cycle, show many signs of
premature aging.
In mice, eliminating senescent cells prevents (in young mice) and partially reverses (in older mice) some of the signs of aging
such as cataracts, and loss of adipose tissue and skeletal muscle mass.
8. Stem Cell Exhaustion
Meeting the criteria:
The proliferative capacity of adult stem cells declines with age in the tissues that have been examined.
Deliberately exhausting the pool of stem cells in the Drosophila intestine leads to premature aging.
Transplantation of stem cells from young mice into aged mice improves the degenerative changes of aging and prolongs their
life.
9. Altered Intercellular Communication
All cells respond to chemical signals in their environment. These include cytokines secreted by nearby cells (paracrine stimulation).
Meeting the criteria:
Inflammation in various tissues — mediated by the secretion of a variety of cytokines — increases in the aged.
Genetically engineered mice that are unable to down-regulate the mRNAs synthesizing pro-inflammatory cytokines show
accelerated aging.
Inhibition of the pro-inflammatory cytokine NF-κB delays aging in mice. Even such a simple anti-inflammatory agent as aspirin
seems to prolong life in mice.

Relationships of the Hallmarks

The first 4 hallmarks appear to represent the initiating events leading to aging.
Hallmarks 5, 6, and 7 appear to represent damage produced as the cell attempts to respond to the damage caused by the first 4
hallmarks.
Taken together, hallmarks 1 through 7 produce the aging phenotype seen in hallmarks 8 and 9, which are ultimately responsible
for the decline with age in the function of cells and the organism of which they are a part.

An Elixir of Youth?
Despite years of research, only three interventions have been discovered that slow the aging process and/or prolong life.
Calorie Restriction (CR). Works in all animals tested.
Rapamycin. Extends lifespan in mice, Drosophila, and C. elegans but does not appear to reverse or even halt the degenerative
changes of aging.
Parabiosis. When the circulatory system of a young mouse is joined to that of an old mouse (the technique is called parabiosis),
various tissues in the old mouse, e.g., its skeletal muscle, cardiac muscle, liver, and central nervous system, become
rejuvenated. A promising candidate for mediating this effect is a protein called GDF11 ("Growth Differentiation Factor 11").
(GDF11 is also known as BMP-11). Injections of recombinant GDF11 are almost as effective as parabiosis. GDF11 probably
acts by stimulating the activity of stem cells. However, there is no evidence yet that it increases the lifespan of the mice.

13.1.11 https://bio.libretexts.org/@go/page/5133
Aging in Unicellular Organisms
It used to be thought that many unicellular organisms, such as yeast and bacteria, were immortal; that is, they
never aged but simply kept dividing to produce new individuals;
did not have the distinction between germline (immortal) and soma (mortal) that multicellular organisms have.
If true, every time a cell divides, the two daughter cells would be identical in all respects to the parent (symmetrical division).
But at least for yeast and E. coli, this is not the case.
Yeast cells do age and, as discussed above, have proved useful for studying the aging process. Placing a single yeast cell on solid
medium and removing its daughter (the bud) each time one is produced, it turns out that the number of times the mother cell can
form a new bud by mitosis is limited. After producing a bud some 20–30 times, the mother cell shows a number of harmful cellular
changes (e.g., defective mitochondria) and dies.
But, at least early in her life, the buds are born with the potential of a full life span. So the mitotic division must be asymmetrical
with the properties of the bud different from those of its parent. Several mechanisms by which this occurs have now been
demonstrated.
A diffusion barrier is formed at the neck between the mother cell and her bud. This barrier prevents the passage from the mother
into the bud of damaged nuclear components, e.g., plasmid-like fragments of DNA produced during the life of the mother. In
contrast to the situation in most eukaryotes, in yeast there is no breakdown of the nuclear envelope during mitosis. During
anaphase, the nuclear envelope grows and the portion enclosing the daughter chromosomes enters the bud. However, the barrier
at the neck keeps all the preexisting nuclear pore complexes (NPCs) within the mother cell and these retain the DNA fragments
and perhaps other damaged nuclear components.
Most of any damaged cytoplasmic components, such as proteins denatured by reactive oxygen species (ROS) resulting in the
formation of nonfunctional aggregates, become attached to aged mitochondria and the endoplasmic reticulum both of which are
retained in the mother cell. Any protein aggregates that do get through are either dissolved by chaperones in the bud or, if that
fails, actin filaments in the bud move the aggregates back into the mother cell. This latter mechanism requires the presence of a
number of proteins, including a sirtuin found in yeast called Sir2 ("Silent information regulator 2").

 Asymmetric division in stem cells.

Stem cells are cells that divide asymmetrically to produce a daughter cell that goes on to differentiate and a daughter cell that
remains a stem cell. A number of examples have been found — in Drosophila and in mammals — where aging stem cells
preferentially deposit their damaged cellular components, e.g. aggregated proteins, in the daughter that will go on to
differentiate while keeping undamaged components in the daughter that will remain a stem cell. So like yeast, these stem cells
have a mechanism that preferentially protects the "immortal" cell from the inevitable effects of aging.

Aging in E. coli

Figure 13.1.3 Formation of new poles during cell division

A similar aging phenomenon has been found in E. coli. When E. coli divides, a septum forms in the middle of the dividing cell and
then the two daughter cells are pinched apart. As the cell wall seals the break, the two daughter cells end up with one "old" end and
one newly-formed end. When the two daughters go on to divide, the process is repeated. The original old ends gets passed on from
generation to generation (rather like immortal strands of DNA).
The diagram shows how during cell division, two new poles are formed, one in each of the progeny cells (new poles shown in
green for the first generation; magenta for the second). The other ends of those cells were formed during a previous division.

13.1.12 https://bio.libretexts.org/@go/page/5133
It has been shown (Stewart EJ, Madden R, Paul G, Taddei F (2005) Aging and Death in an Organism That Reproduces by
Morphologically Symmetric Division. PLoS Biol 3(2): e45 doi:10.1371/journal.pbio.0030045) that the cells that inherit an
increasingly old pole exhibit a diminished growth rate, decreased offspring production, and an increased incidence of death.
So it appears that the phenomenon — characteristic of all multicellular organisms — of an aging and mortal soma producing
germplasm (sperm and eggs) that starts a new youthful generation may have its counterpart in unicellular organisms. Perhaps no
single cell can escape the ravages of time on the integrity of its organelles and the molecules.

Aging in Plants
Annuals and Biennials
Annuals, such as many grasses and "weeds"
grow vigorously for a period;
then form flowers followed by fruits.
Fruiting is followed by a slowing of growth accompanied by physiological and morphological changes such as
an increase in the rate of respiration (catabolism)
loss of chlorophyll
These changes constitute aging and end in the death of the plant. Biennials follow the same pattern, but take two years to do it.
This pattern in clearly programmed in the genes. Even with plentiful moisture, soil minerals, sunlight, and warm temperatures,
the plants age and die.

Perennials
The situation is quite different in perennials. Throughout their lives, woody perennials (trees) produce new vascular tissue, leaves,
and flowers each year. They do not show marked signs of aging, although their rate of growth may decline over the years. Finally,
disease or inability to support their ever-increasing size against wind or snow load lead to their death.

Figure 13.1.4 Bristlecone Pine

This picture (courtesy of Walter Gierasch) is of bristlecone pines (Pinus longaeva) growing in the White Mountains of eastern
California. Tree-ring analysis shows that some of these trees are almost 5000 years old. But note that no living cells in the tree are
more than a few years old.
Even so, how have long-lived plants like these avoided the accumulation — over years of DNA replication as their cells divided —
of deleterious mutations that would reduce fitness and life span? Perhaps it is because the cells in plant meristems, where all
growth begins are stem cells which divide slowly and like all stem cells, asymmetrically; that is, producing one daughter that will
remain a stem cell and one that will begin a phase of rapid mitosis and eventually differentiate into the mature tissues of the plant.
If (and this is as yet only a speculation) the division of a meristematic stem cell is asymmetric with respect to the segregation of
DNA strands; that is, the stem cell retains the immortal strands of DNA while the cell destined to produce more tissues receives the
newly-replicated strands, this would provide an additional mechanism to protect the genome as the years go by.

13.1.13 https://bio.libretexts.org/@go/page/5133
Contributors and Attributions
John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 13.1: Aging is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

13.1.14 https://bio.libretexts.org/@go/page/5133
13.2: Telomeres
Each eukaryotic chromosome consists of a single molecule of DNA associated with a variety of proteins. The DNA molecules in
eukaryotic chromosomes are linear; i.e., have two ends. (This is in contrast to such bacterial chromosomes as that in E. coli that is a
closed circle, i.e. has no ends.)

Figure 13.2.1 : Telomeres are found at the termini of chromosomes. The end of a telomere inserts back into the main body of the
telomere to form a T-loop. (CC BY-SA 3.0; Samulili).
The DNA molecule of a typical chromosome contains a linear array of genes (encoding proteins and RNAs) interspersed with
much noncoding DNA. Included in the noncoding DNA are long stretches that make up the centromere and long stretches at the
ends of the chromosome, the telomeres. Telomeres are crucial to the life of the cell. They keep the ends of the various
chromosomes in the cell from accidentally becoming attached to each other. The telomeres of humans consist of as many as 2000
repeats of the sequence 5' GGTTAG 3'
5'...GGTTAG GGTTAG GGTTAG GGTTAG GGTTAG GGTTAG..3'
3'...CCAATC CCAATC CCAATC CCAATC CCAATC CCAATC..5'

Replication of linear chromosomes presents a special problem

DNA polymerase can only synthesize a new strand of DNA as it moves along the template strand in the 3' –> 5' direction. This
works fine for the 3' –> 5' strand of a chromosome as the DNA polymerase can move uninterruptedly from an origin of replication
until it meets another bubble of replication or the end of the chromosome. However, synthesis using the 5' –> 3' strand as the
template has to be discontinuous. When the replication fork opens sufficiently, DNA polymerase can begin to synthesize a section
of complementary strand — called an Okazaki fragment — working in the opposite direction. Later, a DNA ligase ("DNA ligase
I") stitches the Okazaki fragments together.

Figure 13.2.2 : Okazaki fragments

In Figure 13.2.3, the horizontal black arrows show the direction that the replication forks are moving. Wherever the replication
fork of a strand is moving towards the 3' end, the newly-synthesized DNA (red) begins as Okazaki fragments (red dashes). This
continues until close to the end of the chromosome. Then, as the replication fork nears the end of the DNA, there is no longer
enough template to continue forming Okazaki fragments. So the 5' end of each newly-synthesized strand cannot be completed.
Thus each of the daughter chromosomes will have a shortened telomere.

13.2.1 https://bio.libretexts.org/@go/page/5134
 Figure 13.2.3 : Direction of Replication fork
It is estimated that human telomeres lose about 100 base pairs from their telomeric DNA at each mitosis. This represents about 16
GGTTAG repeats. At this rate, after 125 mitotic divisions, the telomeres would be completely gone. Is this why normal somatic
cells are limited in the number of mitotic divisions before they die out?

Telomeres and Cellular Aging

Telomeres are important so their steady shrinking with each mitosis might impose a finite life span on cells. This, in fact, is the
case. Normal (non-cancerous) cells do not grow indefinitely when placed in culture. Cells removed from a newborn infant and
placed in culture will go on to divide almost 100 times. Well before the end, however, their rate of mitosis declines (to less than
once every two weeks). Were my cells to be cultured (I am 81 years old), they would manage only a couple of dozen mitoses
before they ceased dividing and died out. This phenomenon is called replicative senescence. Could shrinkage of telomeres be a
clock that determines the longevity of a cell lineage and thus is responsible for replicative senescence?

Evidence
Some cells do not undergo replicative senescence:
the cells of the germline (the germplasm)
unicellular eukaryotes like Tetrahymena thermophila
stem cells, including "adult" stem cells and cancer stem cells.
It turns out that these cells are able to maintain the length of their telomeres. They do so with the aid of an enzyme telomerase.

Telomerase
Telomerase is an enzyme that adds telomere repeat sequences to the 3' end of DNA strands. By lengthening this strand, DNA
polymerase is able to complete the synthesis of the "incomplete ends" of the opposite strand. Telomerase is a ribonucleoprotein. Its
single snoRNA molecule — called TERC ("TElomere RNA Component") — provides an CCAAUC (in mammals) template to
guide the insertion of GGTTAG. Its protein component — called TERT ("TElomere Reverse Transcriptase") — provides the
catalytic action. Thus telomerase is a reverse transcriptase; synthesizing DNA from an RNA template.
Telomerase is generally found only in the cells of the germline, including embryonic stem (ES) cells; unicellular eukaryotes like
Tetrahymena thermophila; and some, perhaps all, "adult" stem cells (including cancer stem cells) and "progenitor" cells enabling
them to proliferate. When normal somatic cells are transformed in the laboratory with DNA expressing high levels of telomerase,
they continue to divide by mitosis long after replicative senescence should have set in. And they do so without any further
shortening of their telomeres. This remarkable demonstration (reported by Bodnar et. al. in the 16 January 1998 issue of Science)
provides the most compelling evidence yet that telomerase and maintenance of telomere length are the key to cell immortality.

Telomere Deficiency Syndromes

A number of rare human diseases are caused by mutations in TERT or TERC or several other genes involved in telomere
maintenance. The severity of the disease, the organs it affects, and the age of onset vary widely. But all are characterized by
abnormally short telomeres. Patients with telomere deficiency are also at increased risk of developing cancer.

13.2.2 https://bio.libretexts.org/@go/page/5134
Telomerase and Cancer
The crucial feature that distinguishes a cancer from normal tissue is its ability to grow indefinitely. Most (85–90%) cancers express
telomerase — at least in the population of cancer stem cells that divide uncontrollably causing the tumor to grow. Perhaps agents
that prevent the expression of the gene for telomerase — or prevent the action of the enzyme — will provide a new class of
weapons in the fight against cancer. But if telomerase activity — however brief — is essential for all cells, we had better be careful,
and if lack of telomerase hastens replicative senescence, it may also hasten the aging of the tissues that depend on newly-formed
cells for continued health — a tradeoff that may not be worth making.

Telomerase and Transplanted Cells

One approach to gene therapy it to remove cells from the patient, transform them with the gene for the product that the patient has
been unable to synthesize, return them to the patient. One problem with this approach is that the cells — like all normal somatic
cells — are mortal. After a series of mitotic divisions, they die out. That is the reason the children described in the link above
required periodic fresh infusions of their transformed T cells.
What if their cells could be transformed not only with the therapeutic gene, but also with an active telomerase gene? This should
give them an unlimited life span. But if cancer cells regain the ability to make telomerase, might not the reverse be true; that cells
transformed with an active telomerase gene might become cancerous? Perhaps not. The cells described by Bodnar et. al. in the 16
January 1998 issue of Science have continued to grow in culture and have been subjected to a number of tests to see if they have
acquired any properties of cancer cells in culture.
The results are encouraging. While these cells continue to divide indefinitely as cancer cells do,
They still show contact inhibition as normal cells do when grown in culture.
They do not grow into tumors when injected into immunodeficient mice (as cancer cells do).
They are still fussy about their diet — unable to grow on the simple media that supports cancer cells in culture.
They still retain a normal karyotype; something that cancer cells seldom do.
However, studies with whole animals — transgenic mice that express abnormally high levels of TERT — reveal that they do suffer
an elevated incidence of cancer.

 Telomeres and Cloning

The now-famous sheep Dolly was cloned using a nucleus taken from an adult sheep cell that had been growing in culture. The
cell donor was 6 years old, and its cells had been growing in culture for several weeks. What about Dolly's telomeres? Analysis
of telomere length in Dolly's cells reveals that they were only 80% as long as in a normal one-year-old sheep. Not surprising,
since the nucleus that created Dolly had been deprived of telomerase for many generations. Two other sheep — cloned from
embryonic, not adult, cells — also had shortened telomeres although not as short as Dolly's. Perhaps the length of time the
cells spent in culture before they were used accounts for this.

Dolly. (Cc BY-SA 2.0 Toni Barros).

Does this mean that Dolly is doomed to a shortened life? She seemed healthy at first and even had babies of her own. But
medical problems — probably unrelated to her telomeres — ended with her being euthanized at a relatively young age. But her
short telomeres do add another question to the debate about cloning mammals from adult cells.

This page titled 13.2: Telomeres is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

13.2.3 https://bio.libretexts.org/@go/page/5134
 CHAPTER OVERVIEW
Unit 14: Embryonic Development and its Regulation
Embryogenesis is the process by which the embryo forms and develops. In mammals, the term refers chiefly to early stages of
prenatal development, whereas the terms fetus and fetal developmentdescribe later stages. Embryogenesis starts with the
fertilization of the egg cell (ovum) by a sperm cell, (spermatozoon).
14.1: Embryonic Development
14.2: Frog Embryology
14.3: Cleavage
14.4: The Organizer
14.5: Segmentation - Organizing the Embryo
14.6: Homeobox Genes
14.7: Stem Cells
14.8: Embryonic Stem Cells
14.9: Germline vs. Soma
14.10: Regeneration

Thumbnail: Human embryo, 8-9 weeks, 38 mm. (CC BY-SA 3.0; Anatomist90).

This page titled Unit 14: Embryonic Development and its Regulation is shared under a CC BY 3.0 license and was authored, remixed, and/or
curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is
available upon request.

1
14.1: Embryonic Development
In animals, one can usually distinguish 4 stages of embryonic development.
Cleavage
Patterning
Differentiation
Growth

Cleavage
Mitosis and cytokinesis of the zygote, an unusually large cell, produces an increasing number of smaller cells, each with an exact
copy of the genome present in the zygote. However, the genes of the zygote are not expressed at first. The early activities of
cleavage are controlled by the mother's genome; that is, by mRNAs and proteins she deposited in the unfertilized egg. In humans,
the switch-over occurs after 4–8 cells have been produced; in frogs not until thousands of cells have been produced. Cleavage ends
with the formation of a blastula.

Patterning
During this phase, the cells produced by cleavage organize themselves in layers and masses, a process called gastrulation. The
pattern of the future animal appears:
front to rear (the anterior-posterior axis)
back side and belly side (its dorsal-ventral axis)
left and right sides.

Figure 14.1.1 Zygote Mitosis

The genome of the zygote contains all the genes needed to make the hundreds of different types of cells that will make up the
complete animal. There are two major categories of these genes:
"housekeeping" genes = those that encode the RNAs and proteins needed by all kinds of cells. Examples:
genes for tRNAs, rRNAs
genes encoding the enzymes of glycolysis.
tissue-specific genes = those that encode mRNAs and hence proteins that are used by one or a few specific kinds of cell.
Examples:
genes for hemoglobin expressed in the precursors of red blood cells
the gene for insulin expressed in the beta cells of the islets of Langerhans
However, every cell descended from the zygote has been produced by mitosis and thus contains the complete genome of the
organism (with a very few exceptions).
Two pieces of evidence:
Dolly - Dolly is the sheep that was formed by inserting a nucleus from a single cell of an adult sheep into an enucleated sheep
egg. She proves that the cell from the adult had lost none of the genes needed to build all the tissues of a sheep.
Spemann's egg-tying experiments - Many years earlier, the German embryologist Hans Spemann demonstrated the same truth.
He used strands of baby hair to tie loops around fertilized salamander eggs. Although the egg half with the nucleus began
cleaving normally, the other side did not begin cleavage until a nucleus finally slipped through the knot. So long as the egg was
tied so that both halves contained some of the gray crescent, the second half began normal cleavage and ultimately produced a
second tadpole (right). Even after 5 mitotic division of the zygote nucleus (the 32-cell stage), the entire genome was still
available in each descendant nucleus.

14.1.1 https://bio.libretexts.org/@go/page/5135
 Figure 14.1.3 Frog embryo courtesy L. M. Beidler
1. A fertilized egg is much larger than the normal cells of an animal's body. Some (e.g., a hen's egg) are truly huge. The frog egg
has a volume 1.6 millions times larger than a typical frog cell. The photo is of a 16-cell frog embryo. This mass of cells is no
larger than the original egg. The eggs of mammals are smaller, but even they are larger than their descendant cells will be.
2. The cytoplasm of the fertilized egg is not homogeneous. It contains gradients of mRNAs and proteins. These are the products
of the mother's genes and were deposited in the egg by her.
3. Cleavage of the fertilized egg partitions it into thousands of cells of normal size. Each contains a nucleus descended from the
zygote nucleus.
4. But each nucleus finds itself partitioned off in cytoplasm containing a particular mix of mRNAs and proteins.
5. When the frog blastula has produced some 4,000 cells, transcription and translation of its nuclear genes begins (and the mother's
mRNA molecules, that up to now have been the source of all protein synthesis, are destroyed).
6. The genes that are expressed by the nucleus in a given cell are regulated by the molecules, mostly protein transcription factors
and microRNAs (miRNAs), found in the cytoplasm surrounding that nucleus.
7. Once a cell-specific pattern of gene expression is launched, that cell may release molecules that regulate the genes of nearby
cells.
8. In this way, the foundation is laid for the building of an organism with hundreds of types of differentiated cells — each in its
correct location and performing its correct functions.

Xenopus

Figure 14.1.4 Vegetal Pole

During egg formation, molecules of mRNA encoding the protein VegT are deposited at the vegetal pole of the cell.
Cells that form there during cleavage translate the mRNA into the VegT protein.
VegT is a transcription factor that turns on genes that produce members of the transforming growth factor-beta (TGF-β) family
(e.g., activin).
These proteins are needed for cells to start down the path to becoming mesoderm.

14.1.2 https://bio.libretexts.org/@go/page/5135
 Some of those cells will, in turn, become the Spemann organizer.
Later, the Spemann organizer will secrete molecules that induce the ectodermal cells above them to develop into the tissues of
the brain and spinal cord.

Demonstration

Figure 14.1.7 Double posterior larva

Inject the anterior of the fertilized egg with nanos mRNA. The result: another double-posterior larva.
Make female fruit flies that are transgenic for a recombinant gene containing:
the gene for nanos
coupled to the 3´ anterior-directing signal of the bicoid gene.

Figure 14.1.8 Larva images Elizabeth Gavis and Ruth Lehmann

A normal larva is shown on the right. The bright object at the right end of the normal larva and at both ends of the double posterior
larva is the tip of the tail. These micrographs are courtesy of Elizabeth Gavis and Ruth Lehmann, in whose lab the third
demonstration was performed.

The Mud Snail

The mud snail, Ilyanassa obsoleta, is a small gastropod that lives in mud flats along the Atlantic coast.
Like other protostomes, cleavage of the zygote produces daughter cells that are already committed to their fate. In other words,
even as early as the two-cell stage, the cells are no longer totipotent. Unlike humans and other deuterostomes, then, identical twins
cannot form.
In the 12 December 2002 issue of Nature, J. David Lambert and Lisa Nagy reported another mechanism by which two daughter
cells become committed to different fates even though they have inherited the same genome.
They traced the distribution in the cells of early embryos of the messenger RNAs (mRNAs) encoding 3 proteins that are known to
be important in the development of other animals such as Xenopus and Drosophila.
IoEve, which is Ilyanassa obsoleta's version of even-skipped (eve) in Drosophila;
IoDpp, which is the snail's version of
decapentaplegic (dpp) in Drosophila and the genes encoding
bone morphogenic proteins (BMP2 and BMP4) in vertebrates
IoTld, which encodes the snail's version of a protein called tolloid in Drosophila.

14.1.3 https://bio.libretexts.org/@go/page/5135
 Figure 14.1.9 Duplication of centrosomes before mitosis
Lambert and Nagy found that
in interphase the messenger RNAs were distributed diffusely throughout the cytosol, but
as the cell got ready for cleavage, the mRNAs collected at only one of the now pair of centrosomes. They were collected there
by traveling along the microtubules that radiate out from the centrosome.
As cleavage continued, the mRNAs moved from the centrosome to a spot on the inner surface of the plasma membrane. They
got there by traveling along actin filaments.
At cytokinesis, this patch of accumulated mRNAs was incorporated exclusively into the smaller daughter cell.
Centrosome sorting (of proteins in this case) also plays a role in determining whether embryonic cells of Caenorhabditis elegans
remain in the germline or become the somatic cells of the worm.

What comes next?

Development in Xenopus and Drosophila passes through three rather different (although often overlapping) phases:
Establishing the main axes (anterior-posterior; dorsal-ventral; left-right). This is done by gradients of mRNAs and proteins
encoded by the mother's genes and placed in the egg by her. It has been discussed here.
Establishing the main body parts such as the notochord and central nervous system in vertebratesand the segments in
DrosophilaThese are run by genes of the zygote itself.
Filling in the details; that is, building the various organs of the animal.

This page titled 14.1: Embryonic Development is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

14.1.4 https://bio.libretexts.org/@go/page/5135
14.2: Frog Embryology
The Egg

Figure 14.2.1 Frog Egg

The frog egg is a huge cell; its volume is over 1.6 million times larger than a normal frog cell. During embryonic development, the
egg will be converted into a tadpole containing millions of cells but containing the same amount of organic matter.
The upper hemisphere of the egg — the animal pole — is dark.
The lower hemisphere — the vegetal pole — is light.
When deposited in the water and ready for fertilization, the haploid egg is at metaphase of meiosis II.

Fertilization

Figure 14.2.2 Frog Zygote

Entrance of the sperm initiates a sequence of events:
Meiosis II is completed.
The cytoplasm of the egg rotates about 30 degrees relative to the poles.
In some amphibians (including Xenopus), this is revealed by the appearance of a light-colored band, the gray crescent.
The gray crescent forms opposite the point where the sperm entered.
It foretells the future pattern of the animal: its dorsal (D) and ventral (V) surfaces; its anterior (A) and posterior (P); its left and
right sides.
The haploid sperm and egg nuclei fuse to form the diploid zygote nucleus.

Cleavage
The zygote nucleus undergoes a series of mitoses, with the resulting daughter nuclei becoming partitioned off, by cytokinesis, in
separate, and ever-smaller, cells. The first cleavage occurs shortly after the zygote nucleus forms. A furrow appears that runs
longitudinally through the poles of the egg, passing through the point at which the sperm entered and bisecting the gray crescent.
This divides the egg into two halves forming the 2-cell stage. The second cleavage forms the 4-cell stage. The cleavage furrow
again runs through the poles but at right angles to the first furrow. The furrow in the third cleavage runs horizontally but in a plane
closer to the animal than to the vegetal pole. It produces the 8-cell stage.

14.2.1 https://bio.libretexts.org/@go/page/5137
 Figure 14.2.3 Various stages of cleavage in a frog zygote
The next few cleavages also proceed in synchrony, producing a 16-cell and then a 32-cell embryo. However, as cleavage continues,
the cells in the animal pole begin dividing more rapidly than those in the vegetal pole and thus become smaller and more numerous.
By the next day, continued cleavage has produced a hollow ball of thousands of cells called the blastula. A fluid-filled cavity, the
blastocoel, forms within it.

Figure 14.2.4 Frog Bastula

During this entire process there has been no growth of the embryo. In fact, because the cells of the blastula are so small, the
blastula looks just like the original egg to the unaided eye. Not until the blastula contains some 4,000 cells is there any transcription
of zygote genes. All of the activities up to now have been run by gene products (mRNA and proteins) deposited by the mother
when she formed the egg.

Gastrulation
The start of gastrulation is marked by the pushing inward ("invagination") of cells in the region of the embryo once occupied by the
middle of the gray crescent.

Figure 14.2.5 Frog gastrula

This produces an opening (the blastopore) that will be the future anus. a cluster of cells that develops into the Spemann organizer
(named after one of the German embryologists who discovered its remarkable inductive properties).
As gastrulation continues, three distinct "germ layers" are formed:
ectoderm
mesoderm
endoderm
Each of these will have special roles to play in building the complete animal. Some are listed in the table.

14.2.2 https://bio.libretexts.org/@go/page/5137
 Germ-layer origin of various body tissues
Ectoderm Mesoderm Endoderm

skin notochord inner lining of gut, liver, pancreas

brain muscles inner lining of lungs

spinal cord blood inner lining of bladder

all other neurons bone thyroid and parathyroid glands

sense receptors sex organs thymus

Figure 14.2.6 Frog neural folds

The Spemann organizer (mostly mesoderm) will develop into the notochord, which is the precursor of the backbone and induce
the ectoderm lying above it to begin to form neural tissue instead of skin. This ectoderm grows up into two longitudinal folds,
forming the neural folds stage. In time the lips of the folds fuse to form the neural tube. The neural tube eventually develops into
the brain and spinal cord.

Differentiation
Although the various layers of cells in the frog gastrula have definite and different fates in store for them, these are not readily
apparent in their structure. Only by probing for different patterns of gene expression (e.g., looking for tissue-specific proteins) can
their differences be detected. In due course, however, the cells of the embryo take on the specialized structures and functions that
they have in the tadpole, forming neurons, blood cells, muscle cells, epithelial cells, etc., etc.

Growth
At the time the tadpole hatches, it is a fully-formed organism. However, it has no more organic matter in it than the original frog
egg had. Once able to feed, however, the tadpole can grow. It gains additional molecules with which it can increase the number of
cells that make up its various tissues.

This page titled 14.2: Frog Embryology is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

14.2.3 https://bio.libretexts.org/@go/page/5137
14.3: Cleavage
Cleavage refers to the early cell divisions that occur as a fertilized egg begins to develop into an embryo.

Holoblastic Cleavage
In eggs that contain no (mammals) or only moderate amounts (frog) of yolk, cytokinesis divides the cells completely. The figure
shows the results of the first two cleavages in the frog embryo.

Figure 14.3.1: First two cleavages in a frog embryo

Meroblastic Cleavage
In eggs that contain a large amount of yolk, cytokinesis does not divide the egg completely.

Figure 14.3.2: Bird cleavage

The hen's egg consists of just a tiny patch of cytoplasm resting on the surface of a large ball of yolk (the "white" of the egg is
noncellular accessory protein). When the first cleavages occur in the hen's egg, the cleavage furrows do not continue down through
the mass of yolk. Therefore, each of the cells produced in the earliest stages is bound on the top and on the sides by a plasma
membrane, but the bottom of the cell is in direct contact with yolk.

Figure 14.3.3: Zebrafish cleavage

This type of meroblastic cleavage is also found in the eggs of fish, reptiles, and 4 species of mammals — the monotremes. This
photo, courtesy of H. W. Beames and Richard G. Kessel, shows the zebrafish (Danio) embryo at the 32-cell stage. Note that the
cleavage furrows have not continued down through the yolk of the egg.
Insects use a different type of meroblastic cleavage.

14.3.1 https://bio.libretexts.org/@go/page/5139
 Figure 14.3.4: Insect cleavage
The yolk of the eggs of insects is concentrated in the center of the egg. The daughter nuclei produced by mitosis of the zygote
nucleus remain suspended within the single egg compartment. After several thousand nuclei have been produced, they migrate to
the cytoplasm-rich margin of the egg. Only then does a plasma membrane form around each one.
What does cleavage accomplish in the development of the organism? First, it provides a stockpile of cells out of which the embryo
will be constructed. Second, cleavage establishes a normal relationship between the nucleus and the volume of cytoplasm it
regulates (and which in turn regulates it). Even small eggs are enormous when compared with other kinds of cells. The volume of
the frog egg is about 1.6 million times larger than that of a normal frog cell. But it, too, contains only a single nucleus. During
cleavage, thousands of new nuclei are produced by mitosis all of which finally end up in a cell of normal dimensions. The frog
blastula, with its thousands of cells is no larger than the original fertilized egg.

This page titled 14.3: Cleavage is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

14.3.2 https://bio.libretexts.org/@go/page/5139
14.4: The Organizer
In the embryonic development of a zygote, gradients of mRNAs and proteins, deposited in the egg by the mother as she formed it,
give rise to cells of diverse fates despite their identical genomes. But is the embryo fully patterned in the fertilized egg? It is
difficult to imagine that the relatively simple gradients in the egg could account for all the complex migration and differentiation of
cells during embryonic development. And, in fact, the answer is no. However, once these gradients have sent certain cells along a
particular path of gene expression, the stage is set for those cells to begin influencing nearby cells to become increasingly
diversified.
In other words, cell-intrinsic signals (established between a nucleus and the particular cytoplasmic environment that cleavage has
placed it in) lay the foundation for cell-cell interactions to further guide the cells of the embryo to assume their proper position in
the embryo and to differentiate into their final specialized form and function.
Cell-cell interactions could — and probably do — occur in several ways:
diffusion of a signaling molecule out of one cell and into other cells in the vicinity;
diffusion of a signaling molecule from one cell into an adjacent cell that then secretes the same molecule to diffuse to the next
cell and so on (a "cell-relay" mechanism);
extension of projections from the plasma membrane of one cell until they make direct contact with nearby cells. This enables
proteins embedded in the plasma membrane to serve as signaling molecules.

The Spemann Organizer

In 1924, the Ph.D. student Hilde Mangold working in the laboratory of German embryologist Hans Spemann performed an
experiment that demonstrated that the pattern of development of cells is influenced by the activities of other cells and stimulated a
search, which continues to this day, for the signals at work. Spemann and Mangold knew that the cells that develop in the region of
the gray crescent migrate into the embryo during gastrulation and form the notochord (the future backbone; made of mesoderm).
She cut out a piece of tissue from the gray crescent region of one newt gastrula and transplanted it into the ventral side of a second
newt gastrula. To make it easier to follow the fate of the transplant, she used the embryo of one variety of newt as the donor and a
second variety as the recipient.

Figure 14.4.1 : Spemann Experiment

The remarkable results:
the transplanted tissue developed into a second notochord
neural folds developed above the extra notochord
these went on to form a second central nervous system (portions of brain and spinal cord) and eventually
a two-headed tadpole.
The most remarkable finding of all was that the neural folds were built from recipient cells, not donor cells. In other words, the
transplant had altered the fate of the overlying cells (which normally would have ended up forming skin [epidermis] on the side of
the animal) so that they produced a second head instead!
Spemann and Mangold used the term induction for the ability of one group of cells to influence the fate of another. And because of
the remarkable inductive power of the gray crescent cells, they called this region the organizer. Ever since then, vigorous searches
have been made to identify the molecules liberated by the organizer that induce overlying cells to become nerve tissue. One
candidate after another has been put forward and then found not to be responsible. Part of the problem has been that not until just
recently has it become clear that the organizer does NOT induce the central nervous system but instead it prevents signals
originating from the ventral side of the blastula from inducing skin (epidermis) there.

14.4.1 https://bio.libretexts.org/@go/page/5141
 Figure 14.4.2 : Spemann organizer
This is how it works:
Cells on the ventral side of the blastula secrete a variety of proteins such as bone morphogenetic protein-4 (BMP-4)
These induce the ectoderm above to become epidermis.
If their action is blocked, the ectodermal cells are allowed to follow their default pathway, which is to become nerve tissue of
the brain and spinal cord.
The Spemann organizer blocks the action of BMP-4 by secreting molecules of the proteins chordin and noggin
Both of these physically bind to BMP-4 molecules in the extracellular space and thus prevent BMP-4 from binding to receptors
on the surface of the overlying ectoderm cells.
This allows the ectodermal cells to follow their intrinsic path to forming neural folds and, eventually, the brain and spinal cord.
In the Spemann/Mangold experiment, transplanting an organizer to the ventral side provided a second source of chordin. This
blocked BMP-4 binding to the overlying ectoderm and thus changed the fate of those cells to forming a second central nervous
system rather than skin.

What Organizes the Organizer?

Protein synthesis by the cells of the organizer requires transcription of the relevant genes (e.g., chordin). Expression of organizer
genes depends first on Wnt transcription factors. Their messenger RNAs were deposited by the mother in the vegetal pole of the
egg. After fertilization and formation of the gray crescent, they migrated into the gray crescent region (destined to become the
organizer) where they were translated into Wnt protein.
Its accumulation on the dorsal side of the embryo unleashes the activity of Nodal — a member of the Transforming Growth Factor-
beta (TGF-β) family. Nodal induces these dorsal cells to begin expressing the proteins of Spemann's organizer.

A Tail Organizer
One of the distinguishing features of vertebrates is their tail, which extends out behind the anus. French researchers have reported
(in the 24 July 2003 issue of Nature) their discovery of a tail "organizer", that is, a cluster of cells in the embryo that induces
nearby cells to contribute to the formation of the tail. They worked with the zebrafish, Danio rerio (which also has a head organizer
like that of newts). They removed tiny clusters of cells from the ventral part of the blastula (a region roughly opposite where the
Spemann-like organizer forms) and transplanted this into a region of the host embryo that would normally form flank. The result: a
second tail.
Using a fluorescent label, they were able to show that the extra tail was made not only from descendants of the transplanted cells
but also from host cells that would normally have made flank. Three proteins were essential:
a Wnt protein (establishes the anterior-posterior axis in all bilaterians)
BMP (establishes the dorsal-ventral axis in all bilaterians)
Nodal (establishes the left-right axis in all bilaterians)

14.4.2 https://bio.libretexts.org/@go/page/5141
Patterning the central nervous system in Drosophila
Remarkably, it turns out that proteins similar in structure to the bone morphogenetic proteins and also to chordin are found in
Drosophila. The role of BMP-4 is taken by a related protein encoded by the decapentaplegic gene (dpp) and the role of chordin is
taken by a related protein called SOG encoded by the gene called short gastrulation.
In fact, these proteins and their mRNAs are completely interchangeable! An injection of the mRNAs for BMP-4 or chordin into the
blastoderm of the Drosophila embryo can replace the function of DPP and SOG respectively, and conversely, injections of mRNA
for DPP or SOG into the Xenopus embryo mimics the functions of BMP-4 and chordin respectively.
Table 14.4.1 : A selection of antagonistic pairs of proteins that guide the patterning of the embryo.
blocked by chordin
Xenopus
and also by noggin

blocked by short gastrulation (SOG)

Drosophila Decapentaplegic (DPP)
and also by a noggin homolog?

Dorsal vs Ventral Nerve Cords

Although their actions are similar, the distribution of these proteins in Drosophila differs from that in Xenopus (as well as in
mammals and other vertebrates). In Drosophila, DPP is produced in the dorsal region of the embryo and SOG is produced in the
ventral region.
However, their actions on overlying cells are the same as in Xenopus; that is, the SOG protein prevents the DPP protein from
blocking the formation of the central nervous system. The result in Drosophila is that its central nervous system forms on the
ventral side of the embryo, not on the dorsal! And, you may remember that one of the distinguishing traits of all arthropods
(insects, crustaceans, arachnids) as well as many other invertebrates, such as the annelid worms, is a ventral nerve cord.
Chordates, including all vertebrates, have a dorsal (spinal) nerve cord.

We're halfway done!

Xenopus development (and probably that of animals in general) passes through three rather different (although often overlapping)
phases:
establishing the main axes (dorsal-ventral; anterior-posterior; left-right). This is done by gradients of mRNAs and proteins
encoded by the mother's genes and placed in the egg by her.
establishing the main body parts such as
the notochord and central nervous system in vertebrates (discussed here and also described in Fro.g Embryology)
and the segments in Drosophila
These are run by genes of the zygote itself.
filling in the details; that is, building the various organs of the animal. (Our examples will include the wings, legs, and eyes of
Drosophila.)

This page titled 14.4: The Organizer is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

14.4.3 https://bio.libretexts.org/@go/page/5141
14.5: Segmentation - Organizing the Embryo
Insects, like all arthropods, are segmented. The body of Drosophila melanogaster is built from 14 segments:
3 segments make up the head with its antennae and mouth parts.
3 segments make up the thorax. Each thoracic segment has a pair of legs (insects are the six-legged creatures). In Drosophila
(and other flies), the middle thoracic segment carries a single pair of wings; the hind segment a pair of halteres.
8 abdominal segments.
What signals guide segment formation? The process begins with the gradients of messenger RNA (mRNA) that the mother
deposited in her egg before it was fertilized. Shortly after fertilization, these are translated into their proteins with a gradient of
bicoid diminishing from anterior to posterior and a gradient of nanos diminishing from posterior to anterior.

Figure 14.5.1 nanos graph

Bicoid protein is a transcription factor. It binds to the promoter of a gene called hunchback (hb), turning it ON (red arrow).
Nanos protein binds to hunchback mRNAs, inhibiting their translation (blue bar).
These effects combine to produce a high level of hunchback protein at the anterior of the embryo; with a sharp cut-off toward
the posterior.
The hunchback protein is also a transcription factor (as we shall see).
These concentration gradients regulate the turning on and off of other genes in sharply-defined regions of the embryo.
These establish the various segments of the body.

Eve stripe 2

Figure 14.5.2 Gene even skipped

The gene even-skipped (eve) is expressed in 7 bands or stripes corresponding to 7 of Drosophila's 14 segments (skipping the even-
numbered ones). The photo (courtesy of Peter A. Lawrence and Blackwell Scientific Publications) shows the 7 stripes of eve
activation.
At first the gene is expressed in fairly broad zones, but in time its expression becomes restricted to ever-narrower stripes. The
mechanism by which this occurs is known for the second stripe.

14.5.1 https://bio.libretexts.org/@go/page/5143
 Figure 14.5.4 Eve stripe
The eve promoter has binding sites for the proteins encoded by bicoid (bcd), hunchback (hb), giant (gt) and Krüppel (Kr).
Binding of bicoid and hunchback proteins stimulates transcription of eve.
Binding of giant and Krüppel represses transcription.
Trapped in a valley between high levels of the giant and Krüppel proteins, expression of eve in the second stripe finally becomes
limited to a band of cells only one cell thick. (A different set of promoter sites is used in the third eve stripe so expression is not
repressed there.)In principle, then, such a system of interacting gradients of transcription factors could act as on-off switches, which
in time partition the embryo into its future segments.
Drosophila development (and probably that of animals in general) passes through three rather different (although often
overlapping) phases:
establishing the main axes (dorsal-ventral; anterior-posterior; left-right). This is done by gradients of mRNAs and proteins
encoded by the mother's genes and placed in the egg by her.
establishing the main body parts such as the notochord and central nervous system in vertebrates.and the segments in
Drosophila (discussed here). These are run by genes of the zygote itself.
filling in the details; that is, building the various organs of the animal. (Our example will include the wings, legs, and eyes of
Drosophila.)

This page titled 14.5: Segmentation - Organizing the Embryo is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by
John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

14.5.2 https://bio.libretexts.org/@go/page/5143
14.6: Homeobox Genes
Insect (Drosophila) and frog (Xenopus) development passes through three rather different (although often overlapping) phases: (1)
establishing the main axes (dorsal-ventral; anterior-posterior; left-right). This is done by gradients of mRNAs and proteins encoded
by the mother's genes and placed in the egg by her. (2) Establishing the main body parts such as the notochord and central nervous
system in vertebrates and the segments in Drosophila These are run by genes of the zygote itself.
Now let us look for clues as to how the final working out of the embryo is done. We shall examine four examples:
1. the formation of wings (in Drosophila)
2. the formation of legs (also in Drosophila)
3. the formation of the bones (radius and ulna) of the front limb in mammals (mice)
4. the formation of eyes (probably in all animals)

Wings
The insect body plan consists of head, thorax, and abdomen. The thorax is built from three segments, T1, T2, and T3. Each carries
a pair of legs; hence insects are six-legged creatures. In most of the insect orders, T2 and T3 each carry a pair of wings (the
honeybee is an example). However, flies belong to the insect order diptera; they have only a single pair of wings (on T2). The
third thoracic segment, T3, carries instead a pair of balancing organs called halteres.

Figure 14.6.1 Flies with haltere Fig.14.6.2 Flies with haltere replaced by second pair of wings
In Drosophila, a gene called Ultrabithorax (Ubx) acts within the cells of T3 to suppress the formation of wings. By creating a
double mutation in the Ultrabithorax gene (in its introns, as it turned out), Professor E. B. Lewis of Caltech was able to produce
flies in which the halteres had been replaced by a second pair of wings. Ultrabithorax (Ubx) is an example of a "selector gene".
Selector genes are genes that regulate (turning on or off) the expression of other genes. Thus selector genes act as "master
switches" in development.
Wings and all their associated structures are complicated pieces of machinery. Nonetheless, mutations in a single gene, were able
to cause the reprogramming of the building of T3 (and deprived the flies of their ability to fly). Selector genes encode
transcription factors. Ultrabithorax encodes a transcription factor that is normally expressed at high levels in T3 (as well as in the
first abdominal segment) of Drosophila.
These photographs were taken by, and kindly supplied by, Professor Lewis. He has spent his entire career studying selector genes
in Drosophila. His life's work was honored when he shared the 1995 Nobel Prize for physiology or medicine.

Legs
Another selector gene, called Antennapedia (Antp), is normally turned "on" (expressed) in the thorax and turned "off" (repressed)
in the cells of the head. However, mutations in Antp can cause it to turn on in the head and form a pair of legs where the antennae
would normally be.
When you consider the many genes that must be involved in building a complex structure like an insect leg (or wing), it is
remarkable that a single gene can switch them all on. It is also clear that once a selector gene turns "on" in certain cells of the
embryo, it remains "on" in all the cells derived from those cells. Those cells become irrevocably committed to carrying out the
genetic program leading to the formation of a leg or wing.

14.6.1 https://bio.libretexts.org/@go/page/5145
Homeobox Genes
Most selector genes, including Antp and Ubx, are homeobox genes
Antp, Ubx, and a number of other selector genes have been cloned and sequenced. They all contain within their coding regions a
sequence of some 180 nucleotides called a homeobox. The approximately 60 amino acids encoded by the homeobox are called a
homeodomain. It mediates DNA binding by these proteins. Many proteins containing homeodomains have been shown to be
transcription factors; probably they all are.

Figure 14.6.3: Homeodomains

The table shows the sequence of 60 amino acids in the homeodomain of the protein encoded by the Drosophila homeobox gene
Antennapedia (Antp) compared with the homeodomain encoded by the mouse gene HoxB7; by bicoid (bcd), another homeobox
gene in Drosophila; by goosecoid, a homeobox gene in Xenopus; and by mab-5, a homeobox gene in the roundworm
Caenorhabditis elegans. A dash indicates that the amino acid at that position is identical to the one in the Antennapedia homeobox
domain. Note that the mouse homeobox in HoxB7 differs from the Antp homeobox by only two amino acids (even though some
700 millions years have passed since these animals shared a common ancestor). HoxB6, used in the experiment described in the
next section, differs from Antp in only 4 amino acids.

The Hox Cluster

Antp and Ubx are two of 8 homeobox genes that are linked in a cluster on one Drosophila chromosome. All of them encode
transcription factors, each with a DNA-binding homeodomain and act in sequential zones of the embryo in the same order that
they occur on the chromosome! The entire cluster is designated HOM-C with lab, Pb, Dfd, Scr, and Antp belonging to the ANT-C
complex and Ubx, Abd-A, and Abd-B designated the BX-C complex, All animals that have been examined have at least one Hox
cluster. Their genes show strong homology to the genes in Drosophila. Mice and humans have 4 Hox clusters (a total of 39 genes in
humans) located on four different chromosomes.
In mice: HoxA, HoxB (shown here), HoxC, HoxD
In humans: HOXA, HOXB, HOXC, HOXD
As in Drosophila, they act along the developing embryo in the same sequence that they occupy on the chromosome. All the genes
in the mammalian Hox clusters show some sequence homology to each other (especially in their homeobox) but very strong
sequence homology to the equivalent genes in Drosophila. HoxB7 differs from Antp at only two amino acids, HoxB6 at four. In
fact, when the mouse HoxB6 gene is inserted in Drosophila, it can substitute for Antennapedia and produce legs in place of
antennae just as mutant Antp genes do. This fascinating result indicates clearly that these selector genes have retained, through
millions of years of evolution, their function of assigning particular positions in the embryo, but the structures actually built depend
on a different set of genes specific for a particular species.

Figure 14.6.4 HOX

The Mammalian Skeleton

The foreleg of the mouse and the arm of humans contain a single upper bone, the humerus, and two lower bones, the radius and
ulna. The building of the entire arm, including carpals and the phalanges of the fingers, is controlled by Hox cluster genes.

14.6.2 https://bio.libretexts.org/@go/page/5145
When mice were bred with homozygous mutations for both HoxA11 and HoxD11, they were born with neither radius nor ulna in
the forelimbs. Here, then, is another example of the power of selector genes to initiate a whole program, perhaps involving
hundreds of other genes, to form a structure as complex as a forelimb. Mice that are homozygous for mutant HoxA10, C10, and
D10 genes fail to form a lumbar and sacrum region in their vertebral column ("backbone"). Instead these vertebrae develop ribs
like the thoracic vertebrae above them. However, if any one of these 6 Hox alleles is normal, the mice are much less severely
affected. This shows the high degree of redundancy of these Hox genes.

Eyes
The compound eye of Drosophila is a marvel of precisely-organized structural elements. No one knows how many genes it takes to
make the eye, but it must be a large number. Nevertheless, a single selector gene, eyeless (ey) (named, as is so often the case, for
its mutant phenotype) can serve as a master switch turning on the entire cascade of genes needed to build the eye. Through genetic
manipulation, it is possible to get the eyeless gene to be expressed in tissues where it is ordinarily not expressed. When eyeless is
turned on in cells destined to form
the insect's antennae, eyes form on the antennae
wings, extra eyes form on the wings
legs, eyes form on the legs.
Mice have a gene, small eyes (Sey; also known as Pax6) that is similar in sequence to the Drosophila eyeless gene. As its name
suggests, it, too, is involved in eye formation (even though the structure of the mouse eye is entirely different from the compound
eye of Drosophila).
However, the sequences of the mouse small eyes gene and the Drosophila eyeless genes are so similar that the mouse gene can
substitute for eyeless when introduced into Drosophila. So, like the genes of the Hox clusters, Drosophila eyeless and mouse small
eyes have retained, through millions of years of independent evolution, their function of assigning particular positions in the
embryo where certain structures should be built, but the structures actually built depend on a different set of genes specific for a
particular species.
Humans also have a gene that is homologous to small eyes and eyeless: it is called aniridia. Those rare humans who inherit a single
mutant version of aniridia lack irises in their eyes.

This page titled 14.6: Homeobox Genes is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

14.6.3 https://bio.libretexts.org/@go/page/5145
14.7: Stem Cells
Stem cells are cells that divide by mitosis to form either two stem cells, thus increasing the size of the stem cell "pool", or one
daughter that goes on to differentiate, and one daughter that retains its stem-cell properties. How the choice is made is still
unknown. However, several genes have been found whose activity prevents a daughter cell from differentiating.

Types of Stem Cells

Several adjectives are used to describe the developmental potential of stem cells; that is, the number of different kinds of
differentiated cell that they can become.
1. Totipotent cells. In mammals, totipotent cells have the potential to become any type in the adult body and any cell of the
extraembryonic membranes (e.g., placenta). The only totipotent cells are the fertilized egg and the first 4 or so cells produced
by its cleavage (as shown by the ability of mammals to produce identical twins, triplets, etc.). In mammals, the expression
totipotent stem cells is a misnomer — totipotent cells cannot make more of themselves.
2. Pluripotent stem cells. These are true stem cells, with the potential to make any differentiated cell in the body (but probably
not those of the placenta which is derived from the trophoblast).

Figure 14.7.1 : Human blastocyst showing inner cell mass (top right) and trophoblast. (J. Conaghan).
Three types of pluripotent stem cells occur naturally:
Embryonic Stem (ES) Cells. These can be isolated from the inner cell mass (ICM) of the blastocyst — the stage of embryonic
development when implantation occurs. For humans, excess embryos produced during in vitro fertilization (IVF) procedures are
used. Harvesting ES cells from human blastocysts is controversial because it destroys the embryo, which could have been
implanted to produce another baby (but often was simply going to be discarded).
Embryonic Germ (EG) Cells. These can be isolated from the precursor to the gonads in aborted fetuses.
Embryonic Carcinoma (EC) Cells. These can be isolated from teratocarcinomas, a tumor that occasionally occurs in a gonad
of a fetus. Unlike the other two, they are usually aneuploid.
All three of these types of pluripotent stem cells can only be isolated from embryonic or fetal tissue. They can be grown in culture,
but only with special methods to prevent them from differentiating.
In mice and rats, embryonic stem cells can also:
contribute to the formation of a healthy chimeric adult when injected into a blastocyst which is then implanted in a surrogate
mother;
enter the germline of these animals; that is, contribute to their pool of gametes;
develop into teratomas when injected into immunodeficient (SCID) mice. These tumors produce a wide variety of cell types
representing all three germ layers (ectoderm, mesoderm, and endoderm).
Using genetic manipulation in the laboratory, pluripotent stem cells can now be generated from differentiated cells. These induced
pluripotent stem cells (iPSCs) are described below.
3. Multipotent stem cells. These are true stem cells but can only differentiate into a limited number of types. For example, the
bone marrow contains multipotent stem cells that give rise to all the cells of the blood but not to other types of cells.
Multipotent stem cells are found in adult animals; perhaps most organs in the body (e.g., brain, liver, lungs) contain them where
they can replace dead or damaged cells. These adult stem cells may also be the cells that — when one accumulates sufficient
mutations — produce a clone of cancer cells.

14.7.1 https://bio.libretexts.org/@go/page/5147
Stem Cells for Human Therapy
The Dream
Many medical problems arise from damage to differentiated cells. Examples:
Type 1 diabetes mellitus where the beta cells of the pancreas have been destroyed by an autoimmune attack
Parkinson's disease; where dopamine-secreting cells of the brain have been destroyed
Spinal cord injuries leading to paralysis of the skeletal muscles
Ischemic stroke where a blood clot in the brain has caused neurons to die from oxygen starvation
Multiple sclerosis with its loss of myelin sheaths around axons
Blindness caused by damage to the cornea
The great developmental potential of stem cells has created intense research into enlisting them to aid in replacing the lost cells of
such disorders. While progress has been slow, some procedures already show promise. Using multipotent "adult" stem cells.
culturing human epithelial stem cells and using their differentiated progeny to replace a damaged cornea. This works best when
the stem cells are from the patient (e.g. from the other eye). Corneal cells from another person (an allograft) are always at risk
of rejection by the recipient's immune system.
the successful repair of a damaged left bronchus using a section of a donated trachea that was first cleansed of all donor cells
and then seeded with the recipient's epithelial cells and cartilage-forming cells grown from stem cells in her bone marrow. So
far the patient is doing well and needs no drugs to suppress her immune system.
Using differentiated cells derived from embryonic stem (ES) cells. Phase I clinical trials are underway to assess the safety of
injecting retinal cells derived from ES cells
into the eyes of young people with an inherited form of juvenile blindness;
into the eyes of adults with age-related macular degeneration.
injecting glial cells derived from ES cells into patients paralyzed by spinal cord injuries.

 The Immunological Problems

One major problem that must be solved before human stem cell therapy becomes a reality is the threat of rejection of the
transplanted cells by the host's immune system (if the stem cells are allografts; that is, come from a genetically-different
individual).

A Possible Solution
One way to avoid the problem of rejection is to use stem cells that are genetically identical to the host. This is already possible in
the rare situations when the patient has healthy stem cells in an undamaged part of the body (like the stem cells being used to
replace damaged corneas). But even where no "autologous" stems cells are available, there may be a solution: using somatic-cell
nuclear transfer .
In this technique,
1. An egg has its own nucleus removed and replaced by
2. a nucleus taken from a somatic (e.g., skin) cell of the donor.
3. The now-diploid egg is allowed to develop in culture to the blastocyst stage when
4. embryonic stem cells can be harvested and grown up in culture.
5. When they have acquired the desired properties, they can be implanted in the donor with no fear of rejection.
Using this procedure it possible to not only grow blastocysts but even have these go on to develop into adult animals — cloning —
with a nuclear genome identical to that of the donor of the nucleus. The first successful cloning by SCNT was with amphibians.
Later, mammals such as sheep (Dolly), cows, mice and others were successfully cloned. And in the 11 November 2007 issue of
Science, researchers in Oregon reported success with steps 1–4 in rhesus monkeys (primates like us).

14.7.2 https://bio.libretexts.org/@go/page/5147
 Figure 14.7.2 : Somatic cell transfer in rhesus monkeys
Their procedure:
Remove the spindle and thus all nuclear material from secondary oocytes at metaphase of meiosis II.
Fuse each enucleated egg with a skin cell taken from a male monkey.
Culture until the blastocyst stage is reached.
Extract embryonic stem cells from the inner cell mass.
Establish that they have the nuclear genome of the male (but mostly the mitochondrial genome of the female).
Culture with factors to encourage differentiation: they grew cardiac muscle cells (which contracted), and even neuron-like cells.
Inject into SCID mice and examine the tumors that formed. These contained cells of all three germ layers: ectoderm, mesoderm,
and endoderm.
However, even after more than 100 attempts, they have not been able to implant their monkey blastocysts in the uterus of a
surrogate mother to produce a cloned monkey.
This should reassure people who view with alarm the report in May 2013 by the same workers that they have finally succeeded in
producing embryonic stem cells (ESCs) using SCNT from differentiated human tissue. The workers assure us that they will not
attempt to implant these blastocysts in a surrogate mother to produce a cloned human. And their failure with monkeys suggests that
they would fail even if they did try.
While cloning humans still seems impossible, patient-specific ESCs
could be used in cell-replacement therapy or, failing that,
provide the material for laboratory study of the basis of — and perhaps treatment of — genetic diseases.
Whether they will be more efficient and more useful than induced pluripotent stem cells remains to be seen.

Questions that Remain to be Answered

Imprinted Genes. Sperm and eggs each contain certain genes that carry an "imprint" identifying them later in the fertilized egg
as being derived from the father or mother respectively. Creating an egg with a nucleus taken from an adult cell may not allow a
proper pattern of imprinting to be established. When the diploid adult nucleus is inserted into the enucleated egg (at least those
of sheep and mice), the new nucleus becomes "reprogrammed". What reprogramming actually means still must be learned, but
perhaps it involves the proper methylation and demethylation of imprinted genes. For example, the inactive X chromosome in
adult female cells must be reactivated in the egg, and this actually seems to happen.
Aneuploidy. In primates (in contrast to sheep, cattle, and mice), the process of removing the resident nucleus causes molecules
associated with the centrosome to be lost as well. Although injecting a donor nucleus allows mitosis to begin, spindle formation
may be disrupted, and the resulting cells fail to get the correct complement of chromosomes (aneuploidy).
Somatic Mutations. This procedure also raises the spectre of amplifying the effect(s) of somatic mutations. In other words,
mutations that might be well-tolerated in a single somatic cell of the adult (used to provide the nucleus) might well turn out to
be quite harmful when they become replicated in a clone of cells injected later into the patient.
Political Controversy. The goal of this procedure (which is often called therapeutic cloning even though no new individual is
produced) is to culture a blastocyst that can serve as a source of ES cells. But that same blastocyst could theoretically be
implanted in a human uterus and develop into a baby that was genetically identical to the donor of the nucleus. In this way, a
human would be cloned. And in fact, Dolly and other animals are now routinely cloned this way. The spectre of this is so
abhorrent to many that they would like to see the procedure banned despite its promise for helping humans. In fact, many are so
strongly opposed to using human blastocysts — even when produced by nuclear transfer — that they would like to limit stem
cell research to adult stem cells (even though these are only multipotent).

14.7.3 https://bio.libretexts.org/@go/page/5147
Possible Solutions to the Ethical Controversy
Induced pluripotent stem cells (iPSCs)
A promising alternative to the use of embryonic stem cells in human therapy are recently-developed methods of genetically
reprogramming the nuclei of differentiated adult cells so that they regain the pluripotency of embryonic stem (ES) cells.
In June 2007, three laboratories reported that introducing extra copies of only 4 genes into adult mouse skin cells (fibroblasts)
enables them to regain the properties of ES cells. When these cells, named induced pluripotent stem cells (iPSCs for short), were
placed in mouse blastocysts, they participated in building all the tissues of the chimeric mice that resulted. (When placed in
tetraploid (4n) blastocysts — unable by themselves to develop normally — embryos were formed that thus were clones of the skin
cell donor.) The four genes: c-Myc, Sox2, Oct3/4, Klf4.
By 2009, several labs had succeeded in producing fertile adult mice from iPSCs derived from mouse embryonic fibroblasts. This
shows that iPSCs are just a capable of driving complete development (pluripotency) as embryonic stem cells.
Reprogramming works in humans, too! Using the same four genes, the Yamanaka lab in Japan reported on 20 November 2007, that
they now had reprogrammed human skin cells to become induced pluripotent stem cells (iPSCs). And the Thomson lab in
Wisconsin accomplished the same thing using SOX2, OCT4, NANOG, and LIN28.
Further evidence of the remarkable role played by these few genes is the finding that during normal embryonic development of the
zebrafish, the same or similar genes (SoxB1, Oct4, Nanog) are responsible for turning on the genes of the zygote. Earlier in
development of the blastula, all the genes being expressed (including these) are the mother's — mRNAs and proteins that the
mother deposited in the unfertilized egg. It makes sense that the same proteins that can reprogram a differentiated cell into a
pluripotent state (iPSCs) are those that produce the pluripotent cells of the early embryo.
These achievements open the possibility of
creating cells for laboratory study of the basis of genetic diseases.
Examples: researchers have succeeded in deriving iPSCs from
patients with amyotrophic lateral sclerosis (ALS, "Lou Gehrig's disease"), and then causing them to differentiate into motor
neurons (the cells affected in the disease) for study of their properties;
the skin cells of a patient with an inherited heart disease (long QT syndrome) and causing these to differentiate into beating
heart cells for study in the laboratory.
The Jaenisch lab reported in the 6 March 2009 issue of Cell that they have succeeded in making iPSCs (they call them
hiPSCs) from fibroblasts taken from patients with Parkinson's disease. The cells were then differentiated into dopamine-
releasing cells — the cells lacking in this disease. What is particularly exciting is that they accomplished this after using the
Cre-lox system to remove all the genes (e.g., SOX2, OCT4, KLF4) needed for reprogramming the fibroblasts to an
embryonic-stem-cell-like condition.
Since that report, other laboratories — using other methods — have also created iPSCs from which all foreign DNA (vector
and transgenes) has been removed. Not only should such cells be safer to use in therapy, but these results show that the
stimulus to reprogram a differentiated cell into a pluripotent state need only be transitory.
creating patient-specific cell transplants — avoiding the threat of immunological rejection — that could be used for human
therapy.
Therapy with iPSCs has already been demonstrated in mice. Three examples:
1. The Jaenisch lab in Cambridge, MA reported (in Science, 21 December 2007) that they had successfully treated knock-in
mice that make sickle-cell hemoglobin with the human βS genes (and show many of the signs of sickle-cell disease in humans)
by
harvesting some fully-differentiated fibroblasts from a sickle-cell mouse;
reprogramming these to become iPSCs by infecting them with Oct4, Sox2, Klf4, and c-Myc;
then removing (using the Cre-lox system) the c-Myc to avoid the danger of this oncogene later causing cancer in the
recipient mice;
replacing the βS genes in the iPSCs with normal human βA genes;
coaxing, with a cocktail of cytokines, these iPSCs to differentiate in vitro into hematopoietic (blood cell) precursors;
injecting these into sickle-cell mice that had been irradiated to destroy their own bone marrow (as is done with human bone
marrow transplants). (Although the recipient mice were different animals from the fibroblast donor, they were of the same

14.7.4 https://bio.libretexts.org/@go/page/5147
 inbred strain and thus genetically the same — like identical human twins. So the procedure fully qualifies as "patient-
specific", i.e., with no danger of the injected cells being rejected by the recipient's immune system.)
The result: all the signs of sickle-cell disease (e.g., anemia) in the treated animals showed marked improvement.
2. In the 25 July 2013 issue of Nature, a team of Japanese scientists report that they were able to manufacture three-dimensional
buds of human liver cells. Their process:
create human iPSCs from human fibroblasts using the techniques described above;
treat these with the substances needed for them to differentiate in liver cell precursors;
culture these with a mixture of human endothelial cells and mesenchymal stem cells (to mimic the conditions that occur in
normal embryonic development of the liver);
implant the resulting solid masses (buds) of liver-like cells into immunodeficient mice.
The result: the implanted buds developed a blood supply and the mice began to secrete human albumin, human alpha-1-
antitrypsin, and to to detoxify injected chemicals just as human livers do.
3. Workers in the Melton lab at Harvard University reported in the 9 October 2014 issue of Cell that they had succeeded in
differentiating large numbers of human beta cells from human iPSCs (as well as from human ES cells). When transplanted into
diabetic mice, these cells brought their elevated blood sugar levels back down.
Let us hope that what works in mice can someday be developed into a safe therapy that will work in humans. (In the case of Type 1
diabetes mellitus, however, even patient-derived beta cells will still be at risk of the same autoimmune rejection that caused the
disease in the first place.)
Despite these successes, iPSCs may not be able to completely replace the need for embryonic stem cells and may even be
dangerous to use in human therapy. Several groups have found that human iPSCs contain mutations as well as epigenetic patterns
(e.g., methylation of their DNA) that are not found in embryonic stem cells. Some of the mutations are also commonly found in
cancer cells.

Other approaches being explored

ES cells can be derived from a single cell removed from an 8-cell morula. The success of preimplantation genetic diagnosis
(PGD) in humans shows that removing a single cell from the morula does not destroy it — the remaining cells can develop into
a blastocyst, implant, and develop into a healthy baby. Furthermore, the single cell removed for PGD can first be allowed to
divide with one daughter used for PGD and the other a potential source of an ES cell line.

Figure 14.7.1 : Preimplantation using ES cell

In altered nuclear transfer (ANT) — a modified version of SCNT (somatic-cell nuclear transfer) — a gene necessary for later
implantation (Cdx2 — encoding a homeobox transcription factor) is turned off (by RNA interference) in the donor nucleus
before the nucleus is inserted into the egg. The blastocyst that develops
has a defective trophoblast that cannot implant in a uterus
but the cells of the inner cell mass are still capable of developing into cultures of ES cells. (The gene encoding the
interfering RNA can then be removed using the Cre/loxP technique.)
Jose Cibelli and his team at Advanced Cell Technology reported in the 1 February 2002 issue of Science that they had
succeeded inIf this form of cloning by parthenogenesis works in humans [It does! — success with unfertilized human eggs was
reported in June 2007.], it would have
stimulating monkey oocytes to begin dividing without completing meiosis II (therefore still 2n)
growing these until the blastocyst stage, from which they were able to harvest
ES cells.
the advantage that no babies could be produced if the blastocyst should be implanted (two identical genomes cannot
produce a viable mammal — probably because of incorrect imprinting);

14.7.5 https://bio.libretexts.org/@go/page/5147
 the disadvantage that it will only help females (because only they can provide an oocyte!) (But men may have a procedure
that works for them next.)
On 24 March 2006, Nature published an online report that a group of German scientists had been able to derive pluripotent
stem cells from the stem cells that make spermatogonia in the mouse. Both in vitro and when injected into mouse blastocysts,
these cells differentiated in a variety of ways including representatives of all three germ layers. If this could work in humans, it
would
provide a source of stem cells whose descendants would be "patient-specific"; that is, could be transplanted back into the
donor (men only!) without fear of immune rejection.
avoid the controversy surrounding the need to destroy human blastocysts to provide embryonic stem cells.
The 7 January 2007 issue of Nature Biotechnology reports the successful production of amniotic fluid-derived stem cells
("AFS"). These are present in the amniotic fluid removed during amniocentesis. With the proper culture conditions, they have
been shown to be able to differentiate into a variety of cell types includingSo these cells are pluripotent. Although perhaps not
as versatile as embryonic stem cells, they are more versatile than adult stem cells.
ectoderm (neural tissue)
mesoderm (e.g., bone, muscle)
endoderm (e.g., liver)
Applied to humans, none of the above procedures would involve the destruction of a potential human life.

This page titled 14.7: Stem Cells is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

14.7.6 https://bio.libretexts.org/@go/page/5147
14.8: Embryonic Stem Cells
The other pages describe:
the properties and potential therapeutic applications of embryonic (and other types of) stem cells
how mouse embryonic stem cells can be used to make transgenic mice
how the fusion of a differentiated cell from an adult sheep with an enucleated sheep egg can produce a clone of the cell donor
("Dolly")
The techniques used in the early steps of each process have been achieved with human cells.
Thirteen years ago a research team led by James Thomson of the University of Wisconsin reported (in the 6 November 1998 issue
of Science) that they were able to grow human embryonic stem (ES) cells in culture.
At the time of implantation, the mammalian embryo is a blastocyst. It consists of the
trophoblast — a hollow sphere of cells that will go on to implant in the uterus and develop into the placenta and umbilical
cord.
inner cell mass (ICM) that will develop into the baby as well as the extraembryonic amnion and yolk sac.

Figure 14.8.1 Blastocyst

The cells of the inner cell mass are considered pluripotent; that is, each is capable of producing descendants representing all of the
hundreds of differentiated cell types in the newborn baby, including
ectodermal cells like neurons and skin (epithelial cells)
mesodermal cells like striated muscle, smooth muscle, cartilage, and bone
endodermal cells like the liver and the lining of the intestine

The Process
Remove the trophoblast cells from a human blastocyst (these were extras not needed for assisted reproductive technology).
Separate the cells of the inner cell mass and culture them on a plate of "feeder" cells (mouse fibroblasts were used).
Isolate single cells and grow them as clones.
Test the clones.

The Results
Each successful clone maintained a normal human karyotype (unlike most cultured human cells — HeLa cells, for example).
These cells had high levels of the enzyme telomerase, which maintains normal chromosome length and is characteristic of cells
with unlimited potential to divide ("immortal").
When injected into SCID mice, these cells formed teratomas; tumors containing a mix of differentiated human cell types,
including cells characteristic of
ectoderm
mesoderm
endoderm

 Note

SCID = severe combined immunodeficiency.

SCID mice lack a functioning immune system (have neither T cells nor B cells) and so cannot reject foreign tissue. Some rare
inherited diseases of humans are also called SCID. They produce a similar phenotype but involve different molecular defects.

Human embryonic stem cells have the potential to

teach us about the process of human embryonic development, its genetic control, etc.

14.8.1 https://bio.libretexts.org/@go/page/5149
 provide a source of replacement cells to repair damaged human tissue. As the proper signals are discovered, it will be possible
to cause these cells to differentiate along a particular pathway, e.g., to form insulin-secreting beta cells of the islets of
Langerhans. Such cells might be able to replace lost or non-functioning cells in a human patient (e.g., with Type 1 diabetes
mellitus).
However, there are problems that remain to be solved before this hope can be realized.
Production of human ES cells requires the destruction of the blastocyst, and this is morally-repugnant to many people.
Cell replacement therapy had better be "patient-specific"; that is, the donated cells should be genetically identical to the
recipient. Otherwise, the replaced cells are at risk of being rejected by the host's immune system. [Link to a discussion of
"therapeutic cloning" — a method to avoid this.
ES cells are pluripotent and might differentiate in unwanted ways when introduced into the patient.

This page titled 14.8: Embryonic Stem Cells is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

14.8.2 https://bio.libretexts.org/@go/page/5149
14.9: Germline vs. Soma
Could a mutation in one of your liver cells ever be passed on to your children?
No!
Why not?
The fusion of one sperm cell and one egg cell represents the only genetic link between the bodies of parents and the body of
their child and
the cells destined to produce sperm and eggs are set aside very early in embryonic life.
Example 1:
By the 15th week of gestation, the human female fetus has already set aside each and every cell that may someday develop into a
mature egg. (In fact, each of these cells has already entered its final meiotic division!)
Example 2:
Caenorhabditis elegans is a microscopic (~ 1 mm) nematode (roundworm) that normally lives in soil. Like all animals, it starts life
as a fertilized egg (zygote) which then undergoes the mitotic divisions needed to produce the
556 cells of the newly-hatched worm and, later,
the 959 somatic cells, and a variable number of germ cells, of the adult worm.

Figure 14.9.2 Germplasts

In Weismann's view, the somaplasm simply provides the housing for the germplasm, seeing to it that the germplasm is protected,
nourished, and conveyed to the germplasm of the opposite sex to create the next generation. The old riddle about which came first,
the chicken or the egg, would have been no puzzle to Weismann. In his view, the chicken is simply one egg's device for laying
another egg.
Weismann also understood the implications of his theory for aging. Once the opportunity to pass germplasm on has passed, there is
no need to maintain the integrity of the somaplasm ("disposable soma"); hence the decline in body function with aging .
Today we know that only the germplasm — the gametes and the cells that form them — continue to express high levels of the
enzyme telomerase. These cells are able to maintain the length of their chromosomes forever and are immortal. The cells of the
somaplasm, in contrast, stop producing telomerase, lose a portion of their chromosome tips at each mitosis, and eventually die.

Deciding between germline and soma

What determines
which of the early cells of the embryo will be destined to go on to form sperm or eggs, that is to become germline and
which are destined to develop into the body tissues (soma) of the animal?

14.9.1 https://bio.libretexts.org/@go/page/5151
 Figure 14.9.3 Mitotic division in a gall midge
At the 4th mitotic division in the gall midge (an insect) egg, 2 of the 16 nuclei become pinched off in a small amount of cytoplasm
at one end of the egg. At the 5th mitosis, these two nuclei divide normally, producing daughter cells with the full complement of
chromosomes (2n = 40) of the species. But not so for the other nuclei. When each of these reaches anaphase, only 8 of their 40
chromosomes (dyads) separate and move to opposite ends of the spindle. The remaining 32 chromosomes stay at the metaphase
plate and eventually disintegrate.
The descendants of the two "normal" nuclei ultimately differentiate to form sperm or eggs, i.e., the germline.
The descendants of the rest of the nuclei, those with the sharply-reduced chromosome number, go on to form all the other
tissues of the insect body, i.e., the soma.
The top row of this figure shows normal development in the gall midge. The gametes are descended from the two nuclei, each with
a full diploid set of 40 chromosomes, that were partitioned off in a mass of special cytoplasm (here called "germplasm"). The
remaining nuclei lose 32 chromosomes before going on to form the rest of the insect body (the somaplasm).
The bottom row shows that destruction of the germplasm causes the nuclei that move there to undergo chromosome elimination
also. The animal that develops is sterile but otherwise normal.

Mammals
In mammals (and birds), the decision to become germ cells is not intrinsic but is the result of cell-to-cell signaling during early
embryonic development.
In mice, the setting aside of the future germ cells begins at the start of gastrulation (6 days after fertilization in the mouse) as the
mesoderm is forming. Ectoderm cells of the future extraembryonic membranes secrete cytokines (including bone morphogenic
proteins) which signal cells in the developing mesoderm to differentiate into cells which — under the influence of other inter-
cellular chemical signals — will go on to form either
mesoderm of the extraembryonic membranes (amnion and allantois)
primordial germ cells (PGCs)
The PGCs migrate into the part of the developing embryo that will go on to form the gonads (ovaries or testes).

Exceptions to Weismann's Theory

The distinction between germline and soma exists only in animals.
In plants, cells destined to become gametes do arise from somatic tissues. In the flowering plants (angiosperms), for example,
certain signals cause meristems that had been making stem tissue to become converted into flower buds which go on to make the
gametes.
In microorganisms, all life's functions are embodied in a single cell. (However, some unicellular organisms, like the ciliated
protozoan Tetrahymena thermophila, have a complete genome in their micronuclei, which are passed on to the next generation,
as well as genes in a macronucleus, which is not. Thus, even here, there is the equivalent of a distinction between germline and
soma.)

Somatic vs. Germline Mutations

The significance of mutations is profoundly influenced by the distinction between germline and soma. Mutations that occur in a
somatic cell, in the bone marrow or liver for example, may
damage the cell

14.9.2 https://bio.libretexts.org/@go/page/5151
 make the cell cancerous
kill the cell
Whatever the effect, the ultimate fate of that somatic mutation is to disappear when the cell in which it occurred, or its owner,
dies.
Germline mutations, in contrast, will be found in every cell descended from the zygote to which that mutant gamete contributed.
If an adult is successfully produced, every one of its cells will contain the mutation. Included among these will be the next
generation of gametes, so if the owner is able to become a parent, that mutation will pass down to yet another generation.
Example 1:
More than 8000 people living in South Africa today carry a gene for the metabolic disease called porphyria. Every one of them
has acquired their gene through a chain of ancestors leading back to a single couple: Ariaantje Jacobs and Gerrit Jansz. This woman
and man emigrated from Holland to South Africa late in the seventeenth century and one or the other of them passed the gene —
through the germline — on to their descendants. Fortunately, the ailment is usually mild (unless the person is given a barbiturate
sedative, which triggers a violent reaction).
Example 2:
Retinoblastoma, a tumor that occurs in humans in
a sporadic form, which is caused by a somatic mutation in each of the two RB genes in a cell
a familial (inherited) form, which is caused by a somatic mutation to one RB gene in a cell that already has one mutant RB gene
inherited through the germline from a parent.

This page titled 14.9: Germline vs. Soma is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

14.9.3 https://bio.libretexts.org/@go/page/5151
14.10: Regeneration

Figure 14.10.2 Dugesia and Dugesia regenaration

When some species of flatworms (left) are decapitated, they can regenerate a new head. Double-amputees can regenerate both a
new head at the anterior surface and a new tail at the posterior surface (right). They do this by the proliferation and differentiation
of the pluripotent stem cells (called neoblasts) that it retains in its body throughout its life.
How do the cells know whether to develop into a head or a tail? Thanks to the ease with which individual genes can be knocked out
by RNA interference (RNAi), it has been shown that Wnt/β-catenin signaling dictates where the head and tail form.
Blocking Wnt/β-catenin signaling by RNAi causes a head to form where a tail should (producing a two-headed animal) while
blocking part of the β-catenin degradation complex (thus enhancing the pathway) causes a tail to develop where a head should
(producing a two-tailed animal).

Figure 14.10.4 Salamander

These amphibians can regenerate a missing tail, legs, even eyes. This remarkable ability is particularly pronounced in the larval
stage. For this reason, larval salamanders are favorites for doing research on regeneration. For example, cutting the tail off a larval
salamander initiates the following sequence of events:
A layer of epidermal cells grows over and covers the stump.
A mass of undifferentiated cells — called the blastema — develops just beneath.
Muscle and cartilage form in the regrowing tail.
The notochord and spinal cord grow out into the regrowing tail.
After a few weeks, a new, fully-functional and anatomically-correct tail is complete.
The Mechanism
For years, it has been unclear as to whether this regeneration depends on
a population of pluripotent stem cells that have resided in the animal body prepared for such an event (as occurs in the hydra) or
the dedifferentiation of specialized cells, e.g. muscle and cartilage cells, in the stump.
The answer appears to be both.
Stem cells in the spinal cord migrate into the regrowing tail and differentiate into several cell types, including muscle and
cartilage. Although the stem cells are ectoderm, they are able to develop into mesoderm.

14.10.1 https://bio.libretexts.org/@go/page/5153
 Muscle cells in the stump migrate into the blastema while
reentering the cell cycle to produce thousands of descendants;
dedifferentiate as they do so; that is, they lose the characteristic proteins, etc. of muscle cells.
Even though there is as yet no sign of a tail, its final pattern is established during this process for if the blastema is removed and
transplanted elsewhere, it will continue the process of regenerating a tail.
Finally the cells of the blastema differentiate into all the cell types — nerve, muscle, cartilage, skin — used to build the
regenerated tail.

Mammals
Don't we wish that we had the same powers of regeneration that salamanders do: able to regenerate a severed spinal cord or grow a
new heart! But unfortunately, we cannot. We can regenerate some skin, a large amount of liver, and the very tips of fingers and
toes. But that's about it. Just why we are so limited is not known (but is the subject of intense research). Much of the excitement
surrounding research on stem cells is because of the hope that they may provide a means of regrowing damaged or lost tissues or
even organs.
In contrast to the situation that appears to hold for salamanders, dedifferention of specialized cells does not appear to play a role in
the formation of a blastema in mice. Instead, the various tissues — epidermis, hair follicles, sweat glands, neurons (all ectoderm)
and muscle, bone, tendon, blood vessels (mesoderm) — that participate in regenerating the tip of an amputated mouse digit (finger
or toe) develop from a diverse population of "adult" stem cells in the stump that retain their restricted developmental potential. You
can read about the evidence for this in Rinkevich, Y., et al., Nature, 476, 409-413 (25 August 2011).

Genetic Control of Regeneration

A number of genes have been found to be implicated in regeneration. One of the most potent of these is Wnt.
Injection of agents (e.g. antisense RNA molecules) that interfere with the Wnt/β-catenin pathway
blocks limb regeneration in salamanders and, as we saw above,
promotes head formation in regenerating planarians, while
injection of agents that enhance the Wnt/β-catenin pathway
enable chicks (that, like mammals, are normally incapable of regenerating limbs) to regenerate a wing;
as well as enabling a regenerating planarian to form a tail where a head should go.

This page titled 14.10: Regeneration is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

14.10.2 https://bio.libretexts.org/@go/page/5153
CHAPTER OVERVIEW
Unit 15: The Anatomy and Physiology of Animals
15.1: Nutrition
15.1A: The Human Gastrointestinal Tract
15.1B: Metabolism
15.1C: Nutrition
15.1D: Recommended Dietary Allowances
15.2: Gas Exchange
15.2A: Human Respiratory System
15.2B: Control of Breathing
15.2C: Vertebrate Lungs
15.2D: Tracheal Breathing
15.3: Circulatory Systems
15.3A: Anatomy of Human Circulatory System
15.3B: How the Human Circulatory System Works
15.3C: The Heartbeat
15.3D: The Lymphatic System
15.3E: Blood
15.3F: Blood Groups
15.3G: The Transport of Heat
15.3H: Blood Clotting
15.3I: Sickle-Cell Disease
15.3J: Serine Proteases
15.3K: Animal Circulatory Systems
15.4: Immune System
15.4.1: 15.4T Allergies
15.4A: Clonal Selection and Immunological Memory
15.4B: Antibody-Antigen Binding
15.4C: B Cells and T Cells
15.4D: Antigen Receptors
15.4E: Histocompatibility Molecules
15.4F: Antigen Receptor Diversity
15.4G: Anatomy of the Immune System
15.4H: T Helper cells
15.4I: Cytotoxic T lymphocytes (CTL)
15.4J: Cell-Mediated Immunity
15.4K: Organ Transplants
15.4L: Bone Marrow Transplants
15.4M: Antigen Presentation
15.4N: The Immunological Synapse
15.4O: Dendritic Cells
15.4P: Passive Immunity
15.4Q: Innate Immunity
15.4R: The Complement System

1
 15.4S: Inflammation
15.4U: Asthma
15.4V: AIDS
15.4W: Vaccines
15.5: Excretion
15.5A: Human Kidneys
15.5B: Vertebrate Kidneys
15.5C: Urea Cycle
15.6: Hormones
15.6.1: Human Hormones
15.6.1.1: Thyroid and Parathyroids
15.6.1.2: Hormones of the Gut
15.6.1.3: Hormones of the Pancreas
15.6.1.4: Hormones of the Pituitary
15.6.1.5: Hormones of the Hypothalamus
15.6.1.6: Adrenal Glands
15.6.1.7: Sex Hormones
15.6.1.8: Progesterone
15.6.1.9: Melatonin and the Pineal Gland
15.6.1.10: Hormones of Kidney, Skin and Heart
15.6.1.11: Leptin - the Fat Hormone
15.6.1.12: Hormones of the Liver
15.6.1.13: Melanocyte Stimulating Hormone (MSH)
15.6.2: Insect Hormones
15.7: Sexual Reproduction
15.7A: Sexual Reproduction
15.7B: Asexual Reproduction in Animals
15.7C: Birth Control
15.7D: Prenatal Screening
15.7E: Extraembryonic Membranes and the Physiology of the Placenta
15.7F: Genetic Mosaics
15.7G: Human Cloning
15.8: Nervous System
15.8A: Neurons
15.8B: Synapses
15.8C: The Human Central Nervous System
15.8D: The Peripheral Nervous System
15.8E: Drugs and the Nervous System
15.8F: Nitric Oxide (NO)
15.8G: Prion Diseases
15.9: Senses
15.9A: Mechanoreceptors
15.9B: Hearing
15.9C: Vision
15.9D: Processing Visual Information
15.9E: Vision in Arthropods

2
 15.9F: Heat, Cold, and Pain Receptors
15.9G: Taste
15.9H: Olfaction - The Sense of Smell
15.9I: Electric Organs and Electroreceptors
15.9J: Magnetoreceptors
15.10: Muscles
15.10A: Bones
15.10B: Muscles
15.10C: Testing the Sliding-Filament Hypothesis
15.11: Behavior
15.11.1: Innate Behavior
15.11.2: Taxis
15.11.3: Learned Behavior
15.11.4: Long-Term Potentiation (LTP)
15.11.5: Honeybee Navigation
15.11.6: Avoiding Predation
15.11.7: Pheromones
15.11.8: Circadian Rhythms in Drosophila and Mammals

This page titled Unit 15: The Anatomy and Physiology of Animals is shared under a CC BY 3.0 license and was authored, remixed, and/or
curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is
available upon request.

3
 SECTION OVERVIEW
15.1: Nutrition
Topic hierarchy

15.1A: The Human Gastrointestinal Tract

15.1B: Metabolism

15.1C: Nutrition

15.1D: Recommended Dietary Allowances

This page titled 15.1: Nutrition is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.1.1 https://bio.libretexts.org/@go/page/5335
15.1A: The Human Gastrointestinal Tract
Strategy and Topology
Humans (and most animals) digest all their food extracellularly; that is, outside of cells. Digestive enzymes are secreted from cells
lining the inner surfaces of various exocrine glands. The enzymes hydrolyze the macromolecules in food into small, soluble
molecules that can be absorbed into cells.

Figure 15.1.1.1: Human Topology

Figure 15.1.1.1 shows the major topological relationships in the body. The linings of all
exocrine glands, including digestive glands
nasal passages, trachea, and lungs
kidney tubules, collecting ducts, and bladder
reproductive structures like the vagina, uterus, and fallopian tubes
are all continuous with the surface of the body. Anything placed within their lumen is, strictly speaking, outside the body. This
includes the secretions of all exocrine glands (in contrast to the secretions of endocrine glands, which are deposited in the blood)
and any indigestible material placed in the mouth which will appear, in due course, at the other end.

15.1A.1 https://bio.libretexts.org/@go/page/5381
 Figure 15.1A. 1 : Components of the Digestive System. All digestive organs play integral roles in the life-sustaining process of
digestion. (CC BY 3.0; OpenStax).

Ingestion
Food placed in the mouth is ground into finer particles by the teeth. It is then moistened and lubricated by saliva (secreted by three
pairs of salivary glands). Small amounts of starch are digested by the amylase present in saliva. The resulting bolus of food is
swallowed into the esophagus and carried by peristalsis to the stomach.

The Stomach
The wall of the stomach is lined with millions of gastric glands, which together secrete 400–800 ml of gastric juice at each meal.
Several kinds of cells are found in the gastric glands inlcuding parietal cells, chief cells, mucus-secreting cells, and hormone-
secreting (endocrine) cells.

Parietal cells
Parietal cells secrete hydrochloric acid and intrinsic factor.
Hydrochloric acid (HCl)
Parietal cells contain a H+/K+ ATPase. This transmembrane protein secretes H+ ions (protons) by active transport, using the
energy of ATP. The concentration of H+ in the gastric juice can be as high as 0.15 M, giving gastric juice a pH somewhat less than
1. With a concentration of H+ within these cells of only about 4 x 10-8 M, this example of active transport produces more than a
million-fold increase in concentration. No wonder that these cells are stuffed with mitochondria and are extravagant consumers of
energy.
Intrinsic factor is a protein that binds ingested vitamin B12 and enables it to be absorbed by the intestine. A deficiency of intrinsic
factor — as a result of an autoimmune attack against parietal cells — causes pernicious anemia.

15.1A.2 https://bio.libretexts.org/@go/page/5381
Chief cells
The chief cells synthesize and secrete pepsinogen, the precursor to the proteolytic enzyme pepsin. Pepsin cleaves peptide bonds,
favoring those on the C-terminal side of tyrosine, phenylalanine, and tryptophan residues. Its action breaks long polypeptide chains
into shorter lengths. Secretion by the gastric glands is stimulated by the hormone gastrin. Gastrin is released by endocrine cells in
the stomach in response to the arrival of food.

Absorption in the stomach

Very little occurs. However, some water, certain ions, and such drugs as aspirin and ethanol are absorbed from the stomach into the
blood (accounting for the quick relief of a headache after swallowing aspirin and the rapid appearance of ethanol in the blood after
drinking alcohol). As the contents of the stomach become thoroughly liquefied, they pass into the duodenum, the first segment
(about 10 inches [25 cm] long) of the small intestine. Most of our ingested vitamins and minerals are absorbed here. Two ducts
enter the duodenum:
1. one draining the gall bladder and hence the liver and
2. the other draining the exocrine portion of the pancreas.

The Liver
The liver secretes bile. Between meals it accumulates in the gall bladder. When food, especially when it contains fat, enters the
duodenum, the release of the hormone cholecystokinin (CCK) stimulates the gall bladder to contract and discharge its bile into the
duodenum. Bile contains:
bile acids. These amphiphilic steroids emulsify ingested fat. The hydrophobic portion of the steroid dissolves in the fat while
the negatively-charged side chain interacts with water molecules. The mutual repulsion of these negatively-charged droplets
keeps them from coalescing. Thus large globules of fat (liquid at body temperature) are emulsified into tiny droplets (about 1
µm in diameter) that can be more easily digested and absorbed.
bile pigments. These are the products of the breakdown of hemoglobin removed by the liver from old red blood cells. The
brownish color of the bile pigments imparts the characteristic brown color of the feces.

The Hepatic Portal System

The capillary beds of most tissues drain into veins that lead directly back to the heart. But blood draining the intestines is an
exception. The veins draining the intestine lead to a second set of capillary beds in the liver.

Figure 15.1.1.3 Hepatic portal system

Here the liver removes many of the materials that were absorbed by the intestine:
Glucose is removed and converted into glycogen.
Other monosaccharides are removed and converted into glucose.
Excess amino acids are removed and deaminated.
The amino group is converted into urea.
The residue can then enter the pathways of cellular respiration and be oxidized for energy.
Many nonnutritive molecules, such as ingested drugs, are removed by the liver and, often, detoxified.
The liver serves as a gatekeeper between the intestines and the general circulation. It screens blood reaching it in the hepatic portal
system so that its composition when it leaves will be close to normal for the body. Furthermore, this homeostatic mechanism works
both ways. When, for example, the concentration of glucose in the blood drops between meals, the liver releases more to the blood
by converting its glycogen stores to glucose (glycogenolysis) and converting certain amino acids into glucose (gluconeogenesis)

15.1A.3 https://bio.libretexts.org/@go/page/5381
The Pancreas
The pancreas consists of clusters of endocrine cells (the islets of Langerhans) and exocrine cells whose secretions drain into the
duodenum. Pancreatic fluid contains:
sodium bicarbonate (NaHCO3). This neutralizes the acidity of the fluid arriving from the stomach raising its pH to about 8.
pancreatic amylase. This enzyme hydrolyzes starch into a mixture of maltose and glucose.
pancreatic lipase. The enzyme hydrolyzes ingested fats into a mixture of fatty acids and monoglycerides. Its action is enhanced
by the detergent effect of bile.
4 "zymogens" — proteins that are precursors to active proteases. These are immediately converted into the active proteolytic
enzymes:
trypsin. Trypsin cleaves peptide bonds on the C-terminal side of arginines and lysines.
chymotrypsin. Chymotrypsin cuts on the C-terminal side of tyrosine, phenylalanine, and tryptophan residues (the same
bonds as pepsin, whose action ceases when the NaHCO3 raises the pH of the intestinal contents).
elastase. Elastase cuts peptide bonds next to small, uncharged side chains such as those of alanine and serine.
carboxypeptidase. This enzyme removes, one by one, the amino acids at the C-terminal of peptides.
nucleases. These hydrolyze ingested nucleic acids (RNA and DNA) into their component nucleotides.
The secretion of pancreatic fluid is controlled by two hormones: secretin, which mainly affects the release of sodium bicarbonate
and cholecystokinin (CCK), which stimulates the release of the digestive enzymes

The Small Intestine

Digestion within the small intestine produces a mixture of disaccharides, peptides, fatty acids, and monoglycerides. The final
digestion and absorption of these substances occurs in the villi, which line the inner surface of the small intestine. This scanning
electron micrograph shows the villi carpeting the inner surface of the small intestine.

Figure 15.1.1.4 Villi and electron micrograph of villi (courtesy of Keith R. Porter)
The crypts at the base of the villi contain stem cells that continuously divide by mitosis producing
More stem cells
Paneth cells, which secrete antimicrobial peptides that suppress the concentration of bacteria in the small intestine
Cells that migrate up the surface of the villus while differentiating into
columnar epithelial cells (the majority),which are responsible for digestion and absorption
goblet cells, which secrete mucus
endocrine cells, which secrete a variety of hormones
The continuous production of new epithelial cells replace older cells that after about 5 days die by apoptosis. The villi increase the
surface area of the small intestine to many times what it would be if it were simply a tube with smooth walls. In addition, the apical
(exposed) surface of the epithelial cells of each villus is covered with microvilli (also known as a "brush border"). Thanks largely
to these, the total surface area of the intestine is almost 200 square meters, about the size of the singles area of a tennis court and
some 100 times the surface area of the exterior of the body.

15.1A.4 https://bio.libretexts.org/@go/page/5381
 Figure 15.1.1.5: Microvilli
The electron micrograph (courtesy of Dr. Sam L. Clark) shows the microvilli of a mouse intestinal cell. Incorporated in the plasma
membrane of the microvilli are a number of enzymes that complete digestion:
aminopeptidases attack the amino terminal (N-terminal) of peptides producing amino acids
disaccharidases convert disaccharides into their monosaccharide subunits
maltase hydrolyzes maltose into glucose
sucrase hydrolyzes sucrose (common table sugar) into glucose and fructose
lactase hydrolyzes lactose (milk sugar) into glucose and galactose
Fructose simply diffuses into the villi, but both glucose and galactose are absorbed by active transport
fatty acids and monoglycerides. These become resynthesized into fats as they enter the cells of the villus. The resulting small
droplets of fat are then discharged by exocytosis into the lymph vessels, called lacteals, draining the villi.
Humans with a rare genetic inability to form microvilli die of starvation.

The Large Intestine (colon)

The large intestine receives the liquid residue after digestion and absorption are complete. This residue consists mostly of water as
well as any materials that were not digested. The colon contains an enormous (~413) population of microorganisms. Our bodies
consist of about the same number (~313) of cells. Most of the species live there perfectly harmlessly; that is, they are commensals.
Some are actually beneficial as they synthesize vitamins and digest polysaccharides for which we have no enzymes (providing an
estimated 10% of the calories we acquire from our food).
Most of the bacteria belong to the Firmicutes and Bacteroidetes (although used as an indicator of water pollution by feces, E. coli is
actually a minor component). In both obese mice (ob/ob) and humans, the relative proportion of Bacteroidetes declines and, in mice
at least, the efficiency with which residual food is absorbed increases. Putting humans on a diet causes them to regain the normal
proportion of Bacteroidetes. Why this relationships exists remains to be discovered. Bacteria flourish to such an extent that as much
as 50% of the dry weight of the feces may consist of bacterial cells.
Reabsorption of water is the chief function of the large intestine. The large amounts of water secreted into the stomach and small
intestine by the various digestive glands must be reclaimed to avoid dehydration. If the large intestine becomes irritated, it may
discharge its contents before water reabsorption is complete causing diarrhea. On the other hand, if the colon retains its contents
too long, the fecal matter becomes dried out and compressed into hard masses causing constipation.

This page titled 15.1A: The Human Gastrointestinal Tract is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

15.1A.5 https://bio.libretexts.org/@go/page/5381
15.1B: Metabolism
All living things must have an unceasing supply of energy and matter. The transformation of this energy and matter within the body
is called metabolism. Catabolism is destructive metabolism. Typically, in catabolism, larger organic molecules are broken down
into smaller constituents. This usually occurs with the release of energy (usually as ATP). Anabolism is constructive metabolism.
Typically, in anabolism, small precursor molecules are assembled into larger organic molecules. This always requires the input of
energy (often as ATP).

Autotrophic and Heterotrophic Nutrition

Green plants, algae, and some bacteria are autotrophs ("self-feeders"). Most of them use the energy of sunlight to assemble
inorganic precursors, chiefly carbon dioxide and water, into the array of organic macromolecules of which they are made. The
process is photosynthesis. Photosynthesis makes the ATP needed for the anabolic reactions in the cell.
All other organisms, including ourselves, are heterotrophs. We secure all our energy from organic molecules taken in from our
surroundings ("food"). Although heterotrophs may feed partially (as most of us do) or exclusively on other heterotrophs, all the
food molecules come ultimately from autotrophs. We may eat beef but the steer ate grass. Heterotrophs degrade some of the
organic molecules they take in (catabolism) to make the ATP that they need to synthesize the others into the macromolecules of
which they are made (anabolism).

How humans (and other animals) do it

Humans are heterotrophs. We are totally dependent on ingested preformed organic molecules to meet all our energy needs. We are
also dependent on preformed organic molecules as the building blocks to meet our anabolic needs.

Figure 15.1.2.1 Metabolic pathways

Ingestion: taking food within the body (although as the figure shows, it is still topologically in the external world, not the
internal).
Digestion.
The enzyme-catalyzed hydrolysis of
polysaccharides (e.g., starch) to sugars
proteins to amino acids
fats to fatty acids and glycerol
nucleic acids to nucleotides
Absorption into the body and transport to the cells.
Absorption into cells
Within cells, these molecules are further degraded into still simpler molecules containing two to four carbon atoms. These
fragments (acetyl-CoA for example) face one of two alternatives:
They may proceed up various metabolic pathways and serve as the building blocks of, for example, sugars and fatty acids. From
these will be assembled the macromolecules of the cell:
polysaccharides
fats

15.1B.1 https://bio.libretexts.org/@go/page/5382
 proteins
nucleic acids
Or the molecules in this pool of two- to four-carbon fragments may be still further degraded — ultimately to simple inorganic
molecules such as carbon dioxide (CO2), H2O, and ammonia (NH3). This phase of catabolism releases large amounts of energy
(in the form of ATP). One use to which this energy is put is to run the anabolic activities of the cell.

This page titled 15.1B: Metabolism is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.1B.2 https://bio.libretexts.org/@go/page/5382
15.1C: Nutrition
The human diet must provide the following:
calories - enough to meet our daily energy needs
amino acids - there are nine, or so, "essential" amino acids that we need for protein synthesis and that we cannot synthesize
from other precursors
fatty acids - there are three "essential" fatty acids that we cannot synthesize from other precursors
minerals - inorganic ions generally 18 different ones, calcium in relatively large amounts, zinc in "trace" amounts
vitamins - a dozen or so, small organic molecules that we cannot synthesize from other precursors in our diet
Determining what substances must be incorporated in the human diet and how much of each is incorporated even after years of
research still under active study. Why the uncertainty? Inadequate intake of some vitamins produces easily-recognized deficiency
diseases like However, it is so difficult to exclude some other possible vitamins from the diet that deficiency diseases are hard to
demonstrate.
scurvy: lack of ascorbic acid (vitamin C)
beriberi: lack of thiamine (vitamin B1)
pellagra: lack of niacin
Similarly, some minerals are needed is such vanishingly small amounts that it is practically impossible to prepare a diet that does
not include them. However, totally synthetic diets are now available for intravenous feeding of people who cannot eat. This so-
called total parenteral nutrition has revealed, unexpectedly, some additional trace element needs: chromium and molybdenum.
Despite some uncertainties, the Food and Nutrition Board of the U. S. National Academy of Sciences publishes guidelines. One of
the most useful of these is called recommended daily allowances or RDAs. These provide the basis for the nutrition labels on
food.

Carbohydrates
Carbohydrates provide the bulk of the calories (4 kcal/gram) in most diets and starches provide the bulk of that. Age, sex, size,
health, and the intensity of physical activity strongly affect the daily need for calories. Moderately active females (19–30 years old)
need 1500–2500 kcal/day, while males of the same age need 2500–3300 kcal/day. In some poor countries, too many children do not
receive enough calories to grow properly. In order to maintain blood sugar levels, they attack their own protein. This condition of
semi-starvation is known as marasmus.

Figure 1: Child suffering with Marasmus in India. (public domain; CDC/ Don Eddins )

Protein
Humans must include adequate amounts of 9 amino acids in their diet. These "essential" amino acids cannot be synthesized from
other precursors. However, cysteine can partially meet the need for methionine (they both contain sulfur), and tyrosine can partially
substitute for phenylalanine.

15.1C.1 https://bio.libretexts.org/@go/page/5383
 The Essential Amino Acids for Humans
Histidine
Isoleucine
Leucine
Lysine
Methionine (and/or cysteine)
Phenylalanine (and/or tyrosine)
Threonine
Tryptophan
Valine

Two of the essential amino acids, lysine and tryptophan, are poorly represented in most plant proteins. Thus strict vegetarians
should take special pains to ensure that their diet contains sufficient amounts of these two amino acids. Birds, mammals, and some
other animals are able to discriminate food that contains a nutrient, e.g., an essential amino acid, that they need from food that
doesn't. If offered a food lacking that nutrient, they quickly stop eating it. How is this done? In rats, at least, it turns out that certain
neurons in the brain detect the lack of an essential amino acid and signal the appetite centers of the brain to stop feeding on
deficient food. The neurons detect the lack by the failure of their transfer RNAs (tRNAs) for that amino acid to acquire it. Rats
whose tRNAs for threonine have been blocked from loading threonine cease feeding even if their food contains adequate
concentrations of it.

Fats
Ingested fats provide the precursors from which we synthesize our own fat as well as cholesterol and various phospholipids. Fat
provides our most concentrated form of energy. Its energy content (9 kcal/gram) is over twice as great as carbohydrates and
proteins (4 kcal/gram). Humans can synthesize fat from carbohydrates (as most of us know all too well). However, three essential
fatty acids cannot be synthesized this way and must be incorporated in the diet. These are
linoleic acid
linolenic acid
arachidonic acid
All are unsaturated; that is, have double bonds.

Types of fats
Saturated. No double bonds between the carbon atoms in the fatty acid chains. Most animal fats (e.g., butter) are highly
saturated.
Monounsaturated. Have a single double bond in the fatty acid chains. Examples are olive, peanut, and rapeseed (canola) oil.
Polyunsaturated. Have two or more double bonds in their fatty acid chains. Examples: corn, soy bean, cottonseed, sunflower,
and safflower oils.
Trans Fats. Have been partially hydrogenated producing fewer double bonds and of those that remain, converting them from a
cis to a trans configuration.
Omega-3 fats. Have at least one double bond three carbon atoms in from the end of the fatty acid molecule. Linolenic acid is an
example. Fish oils are a rich source of omega-3 fatty acids.
Many studies have examined the relationship between fat in the diet and cardiovascular disease. There is still no consensus, but the
evidence seems to indicate that Mono and polyunsaturated fats are less harmful than saturated ones, except that trans unsaturated
fats may be worse than saturated fats. Ingestion of omega-3 unsaturated fats may be protective. For this reason, 1.1 grams/day
for women (1.6 for men) is recommended.

Read the label

15.1C.2 https://bio.libretexts.org/@go/page/5383
 Figure 15.1.3.1 Nutrition label
At present, food labels in the U.S. list the total amount of fat in a serving of the product (5 g in the example shown here) with a
breakdown of the amounts of saturated (1 g), polyunsaturated (0.5 g), and monounsaturated fat (1.5 g).
What about trans fats? There is a proposal to have them included, but at present they are not. However, if you add the amounts of
saturated, polyunsaturated, and monounsaturated fat, and the total does not equal "Total Fat" , the discrepancy (2 g in this example)
represents the amount of trans fat. Baked goods (like the one whose label is shown here) tend to have quite a bit of trans fat.

Minerals
Calcium
Calcium is essential to almost every function in the body. Blood clotting, intracellular signaling and muscle contraction need only
trace amounts. However, large amounts of calcium are needed to make bone (which is 18% calcium), So substantial amounts are
needed in the diet, especially during infancy, childhood, and pregnancy. Three hormones parathyroid hormone (PTH), calcitonin
and calciferol (vitamin D) work together to regulate how much calcium
is absorbed from your food
is taken from, or added to, bone
is excreted in the urine.
A temporary deficit in the amount of calcium in the diet can be compensated for by its removal from the huge reserves in bone.

Iron (Fe)
Iron is incorporated in a number of body constituents, notably cytochromes, myoglobin and hemoglobin. Not surprisingly, an iron
deficiency shows up first as anemia.
In developed countries like the U.S., iron deficiency is the most common mineral deficiency. It is particularly common among
women because of the loss of blood during menstruation and the need for extra iron during pregnancy and breast feeding.
Marginal iron intake is so widespread that some nutritionists want to have iron added to common foods like bread and cereals, just
as some vitamins now are. However, excess iron in the body also leads to problems, and this has made the proposal controversial.
Even iron supplement tablets pose risks: thousands of children in the U.S. are accidentally poisoned each year by swallowing too
many iron tablets. In fact, iron is the most frequent cause of poisoning deaths among children in the U.S.

Iodine
Incorporated in the hormones thyroxine (T4) and triiodothyronine (T3).
In regions with iodine-deficient soils, food may not contain enough iodine to meet body needs. The result is goiter: a swelling
of the thyroid gland.
The use of iodized salt (table salt to which a small amount of sodium iodide, KI, is added) has reduced the incidence of goiter in
most developed countries.
Because iodine deficiency during pregnancy can lead to mental retardation of the infant, it is recommended that pregnant women
receive 150–250 µg of iodine daily during both pregnancy and lactation. Hundreds of supplements — both prescription and
nonprescription — are sold for this purpose. However, a study of 60 of them reported in the 2/26/09 issue of The New England
Journal of Medicine found that only 9 of the 60 contained an amount of iodine within 5% of the amount claimed on the label.
Others ranged from only 11% of the amount claimed to almost 3 times as much. Examples: one (prescription) preparation claiming

15.1C.3 https://bio.libretexts.org/@go/page/5383
a daily dose of 150 µg actually provided only 26 µg while another (nonprescription) preparation claiming 226 µg of iodine actually
contained 610 µg!

Fluoride
The value of fluoride (in ionized form, F−) was first recognized as a preventive for dental caries (cavities). This makes sense
because fluoride ions are incorporated along with calcium and phosphate ions in the crystalline structure of which both bones and
teeth are constructed. But it may have other functions.

Figure 15.1.3.2 Effect of fluoride on rats

In order to grow properly, a rat must consume 0.5 parts per million (ppm) of fluoride ions in its diet. The rat in the bottom photo
received the same diet as that in the top except that tin, vanadium, and fluorides were carefully excluded for 20 days. When tin and
vanadium were then given to the deprived rat, it still did not grow normally. But adding 0.5 ppm of potassium fluoride (KF) to its
diet restored normal growth and health. (Photos courtesy of Klaus Schwarz, VA Hospital, Long Beach, CA.)
Humans get most of their fluoride in drinking water. In regions where the natural amount is less than 1 ppm, many communities
add enough fluoride to bring the concentration up to 1 ppm. Perhaps because the range between optimum and excess is more
narrow for fluoride than for most minerals in the diet, water fluoridation has been controversial. Leaving aside the philosophical
and political questions raised by proponents and opponents of fluoridation, the safety and efficacy of this public health measure has
been thoroughly established.

Zinc
Zinc is incorporated in many enzymes and transcription factors. Zinc supplements are popular for their supposed antioxidant
properties and to hasten the recovery from colds. Excessive intake of zinc causes a brief illness. Its most frequent cause is from
ingested acidic food or drink that has been stored in galvanized (zinc-coated) containers.

Vitamins
Vitamin A (Retinol)
Functions: Multiple, including serving as the precursor to retinal, the prosthetic group of all four of the light-absorbing
pigments in the eye and regulating gene expression essential for the health of epithelia.
Sources: cream, butter, fish liver oils, eggs. Carrots and some other vegetables provide beta-carotene, which the liver can
convert into vitamin A.
Deficiency: night-blindness.
Excess: stored in the liver, but can be toxic in large doses, especially in children. Even in adults the range between too little and
too much is narrow: ingesting vitamin A in amounts not much greater than the recommended dietary allowance (RDA) leads to
an increase in bone fractures later in life. High doses taken early in pregnancy have been linked to a greater risk of birth defects.
(Its chemical relative isotretinoin — the acne treatment Accutane® — is such a notorious teratogen that it should not be used
when there is any chance of a pregnancy occurring).

Thiamine ( Vitamin B1)

Function: coenzyme in cellular respiration.
Sources: meat, yeast, unpolished cereal grains, enriched bread and breakfast cereals.
Deficiency: beriberi. Rarely found in developed countries except among alcoholics.

15.1C.4 https://bio.libretexts.org/@go/page/5383
 Excess: water soluble and any excess easily excreted.

Riboflavin ( Vitamin B2)

Function: prosthetic group of flavoprotein enzymes, e.g., flavin adenine dinucleotide (FAD) used in cellular respiration.
Sources: liver, eggs, cheese, milk, enriched bread and breakfast cereals.
Deficiency: damage to eyes, mouth, and genitals.
Excess: water soluble and any excess easily excreted.

Niacin (Nicotinic acid or Vitamin B3)

Function: this member of the B vitamins is a precursor of NAD and NADP.
Sources: meat, yeast, milk, enriched bread and breakfast cereals.
Deficiency: pellagra (producing skin lesions); a risk where corn (maize) is the staple carbohydrate.
Excess: accidental ingestion of very high doses produces a brief illness, but niacin is water-soluble and any excess is quickly
excreted.

Biotin (Vitamin B7)

Function: this member of the B vitamins is a cofactor in many essential metabolic enzymes.
Sources: liver, egg yolks, corn (maize), intestinal bacteria.
Deficiency: rare except perhaps during pregnancy.
Excess: none identified.

Vitamin B12
Function: needed for DNA synthesis.
Sources: liver, eggs, milk; needs intrinsic factor to be absorbed.
Deficiency: pernicious anemia; caused by lack of intrinsic factor or a vegan diet.
Excess: none identified.

Folic acid ( Folacin)

Function: synthesis of purines and pyrimidines.
Sources: green leafy vegetables, but destroyed by cooking.
Deficiency: anemia, birth defects. Women who expect to become pregnant should be extra careful that they receive adequate
amounts (400 µg/day). Starting 1 January 1998, any bread or breakfast cereal described as "enriched" must have enough folic
acid added to it so that a single serving will provide 10% of this requirement.
Excess: water soluble and any excess easily excreted.

Vitamin C (Ascorbic acid)

Functions: coenzyme in the synthesis of collagen.
Sources: citrus fruits, green peppers, tomatoes; destroyed by cooking.
Deficiency: scurvy.
Excess: Many people take huge amounts of vitamin C, hoping to ward off colds, cancer, etc. They seem to suffer no harm
except, perhaps, to their wallets.

Vitamin D
Functions: absorption of calcium from the intestine and bone formation.
Sources:
synthesized when ultraviolet light (mostly UV-B) strikes the skin (forms vitamin D3).
present in some fish (e.g., salmon), cod liver oil, eggs, and steroid-containing foods irradiated with ultraviolet light.
Deficiency:
rickets — inadequate conversion of cartilage to bone — in children;
osteomalacia — softening of the bones — in adults.
Until recently, rickets has been very rare in North America. But the combination of two growing trends
breast feeding and
protecting children from exposure to the sun

15.1C.5 https://bio.libretexts.org/@go/page/5383
 has caused cases to reappear especially in northern latitudes with their short winter days.
Breast milk provides less than 20% of the recommended daily dose for infants. Until the infant is old enough to eat foods
fortified with vitamin D, many pediatricians recommend vitamin supplements for breast-fed babies.
Excess: However, this fat-soluble vitamin is dangerous in very high doses, especially in infants, causing excessive calcium
deposits and mental retardation. So some pediatricians view the use of vitamin D supplements for infants with caution
(especially since certain preparations have been found to contain amounts far higher than that listed on the label).

Vitamin E (Tocopherol)
Function: acts as an antioxidant agent in cells.
Sources: vegetable oils, nuts, spinach.
Deficiency: anemia, damage to the retinas.
Excess: high doses may be toxic.

Vitamin K
Function: needed for the synthesis of blood clotting factors.
Sources: spinach and other green leafy vegetables; synthesized by intestinal bacteria.
Deficiency: slow clotting of blood. Because
little or no vitamin K crosses the placenta,
the colon of newborn babies has not yet been colonized by vitamin K-synthesizing bacteria,
breast milk is a poor source of the vitamin,
babies are routinely given vitamin K at birth to eliminate the risk of uncontrolled bleeding.
Excess: No risk from natural forms of the vitamin (K1 and K2).

 "Natural" versus "Synthetic" Vitamins

There is no scientific distinction between them. The thiamine molecule (or any other molecule) is the same entity whether
synthesized by a plant or by an organic chemist or whether it is still in plant or animal material or has been extracted and
incorporated in a pill.

Control of Food Intake

A complex web of signals controls appetite and the intake of food. These include both nerve signals and hormones - both of which
signal centers in the brain - chiefly in the hypothalamus. This table lists some of the hormonal signals that have been identified,
their effect on appetite and weight gain. Such complexity probably reflects the need for redundant circuits in such a vital activity as
acquiring food. But, it also frustrates the search for treatments to attack the increasing incidence of obesity.

Appetite Stimulants Appetite Suppressants

Ghrelin Leptin

Agouti-related protein (AgRP) α-MSH and β-MSH

Neuropeptide Y (NPY) β-endorphin

Melanin-concentrating hormone (MCH) Cholecystokinin (CCK)

Anandamide Incretins

Orexins (also called hypocretins) Insulin

Amylin

Pancreatic polypeptide

PYY3-36

Brain-derived neurotrophic factor (BDNF)

15.1C.6 https://bio.libretexts.org/@go/page/5383
 Figure 15.1.3.3 Interaction between hormones
This diagram presents a model of how some of the chief players interact.
After a period of fasting, secretion of ghrelin activates neurons ("X") in the hypothalamus. They release the excitatory
neurotransmitter glutamate where they synapse with AgRP/NPY-releasing neurons. These set in motion the signals that induce
feeding.
A positive feedback loop strengthens the response: AgRP and NPY inhibit the activity of proopiomelanocortin (POMC)
neurons whose function is to inhibit "X" neurons (a double-negative is a positive).
When satiety is finally reached, leptin activates the POMC neurons which release α-MSH and β-endorphin where they synapse
with the "X" neurons and the stimulus to continue feeding is stopped. (The precise identity of the "X" neurons remains to be
determined.)

This page titled 15.1C: Nutrition is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.1C.7 https://bio.libretexts.org/@go/page/5383
15.1D: Recommended Dietary Allowances
For many years the Food and Nutrition Board of the United States National Academy of Sciences has taken responsibility for
establishing guidelines on what quantities of the various nutrients should be eaten by human males and females at various ages.
These were called RDAs (for Recommended Dietary Allowances, and often referred to as Recommended Daily Allowances). They
provide the data on which food labels are based. In 1997, the Institute of Medicine of the National Academy published a report that
added three new categories, including:
adequate intake ("AI"), where no RDA has been established
tolerable upper intake levels ("UL"), to caution against excess intake of nutrients — like vitamin D — that can be harmful in
large amounts.
As their findings trickle in, here is a table of RDAs (or AIs) for young adult women and men.

Females Males Females Males

Protein 46 g 56 g Folacin 400 µg same

Vitamin A (retinol) 700 µg* 900 µg* Biotin 30 µg (AI) same

Thiamine (Vitamin
1.1 mg 1.2 mg Calcium 1000 mg (AI) same
B1)

Riboflavin (Vitamin
1.1 mg 1.3 mg Phosphorus 700 mg same
B2)

Niacin (Vitamin B3) 14 mg 16 mg Selenium 55 µg same

Pantothenic acid
5 mg (AI) same Iron 18 mg 8 mg
(Vitamin B5)

Vitamin B6 1.3 mg same Zinc 8 mg 11 mg

Vitamin B12 2.4 µg same Magnesium 310 mg 400 mg

Vitamin C 75 mg* 90 mg* Iodine 150 µg same

Vitamin D 15 µg ** same Fluoride 3 mg (AI) 4 mg (AI)

Vitamin E 15 mg** same Linoleic acid 12 g (AI) 17 g (AI)

Vitamin K 90 µg (AI) 120 µg α-Linolenic acid 1.1 g (AI) 1.6 g (AI)

*This value has been questioned following the publication of data indicating that a high intake of vitamin A in older people leads to
an increased risk of hip fractures. Vitamin A stimulates osteoclasts, the cells that degrade bone, and inhibits osteoblasts, the cells
that build bone. To the extent that the vitamin A requirement is met by ingested beta-carotene, these amounts should be multiplied
by 12. And that is probably the best way to get your vitamin A as the body only converts enough beta-carotene into vitamin A to
meet its needs. There is also evidence that beta-carotene has important functions besides being the precursor of vitamin A and
therefore should be ingested in amounts even greater than needed to meet the vitamin A requirement. In short, one should consume
vitamin tablets containing beta-carotene and not vitamin A.
*Smokers should add 35 mg to these values, and some nutritionists believe that 200 mg of vitamin C per day is probably optimal
for everyone. This is more than twice the current RDA, but far lower than the 2,000 mg/day that is the upper limit (UL) and that
some people exceed in the hope of warding off colds, cancer, etc.
**15 µg = 600 IU ("International Units").
**The upper limit (UL) is 1,000 mg/day.

This page titled 15.1D: Recommended Dietary Allowances is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by
John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

15.1D.1 https://bio.libretexts.org/@go/page/5384
 SECTION OVERVIEW
15.2: Gas Exchange
Topic hierarchy

15.2A: Human Respiratory System

15.2B: Control of Breathing

15.2C: Vertebrate Lungs

15.2D: Tracheal Breathing

This page titled 15.2: Gas Exchange is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.2.1 https://bio.libretexts.org/@go/page/5336
15.2A: Human Respiratory System
The Pathway

Figure 15.2.1.1: Human lungs. 1:Trachea 2:Pulmonary vein 3:Pulmonary artery 4:Alveolar duct 5:Alveoli 6:Cardiac notch
7:Bronchioles 8:Tertiary bronchi 9:Secondary bronchi 10:Primary bronchi 11:Hyoid bone. (CC-BY-SA-4.0; Credit: Rastrojo).

Breathing
In mammals, the diaphragm divides the body cavity into the abdominal cavity, which contains the viscera (e.g., stomach and
intestines) and the thoracic cavity, which contains the heart and lungs. The inner surface of the thoracic cavity and the outer
surface of the lungs are lined with pleural membranes which adhere to each other. If air is introduced between them, the adhesion
is broken and the natural elasticity of the lung causes it to collapse. This can occur from trauma. And it is sometimes induced
deliberately to allow the lung to rest. In either case, reinflation occurs as the air is gradually absorbed by the tissues. Because of this
adhesion, any action that increases the volume of the thoracic cavity causes the lungs to expand, drawing air into them.
During inspiration (inhaling), the external intercostal muscles contract, lifting the ribs up and out. This is accomplished by the
contraction of the diaphragm muscle, which draws it down. During expiration (exhaling), these processes are reversed and the
natural elasticity of the lungs returns them to their normal volume. At rest, we breath 15–18 times a minute exchanging about
500 ml of air.
In more vigorous expiration, the internal intercostal muscles draw the ribs down and inward and the the wall of the abdomen
contracts pushing the stomach and liver upward. Under these conditions, an average adult male can flush his lungs with about 4
liters of air at each breath. This is called the vital capacity. Even with maximum expiration, about 1200 ml of residual air
remain.
The table shows what happens to the composition of air when it reaches the alveoli. Some of the oxygen dissolves in the film of
moisture covering the epithelium of the alveoli. From here it diffuses into the blood in a nearby capillary. It enters a red blood cell
and combines with the hemoglobin therein. At the same time, some of the carbon dioxide in the blood diffuses into the alveoli from
which it can be exhaled.
Table 15.2.1.1: Composition of atmospheric air and expired air in a typical subject. Note that only a fraction of the oxygen inhaled is taken up
by the lungs.
Component Atmospheric Air (%) Expired Air (%)

N2 (plus inert gases) 78.62 74.9

O2 20.85 15.3

CO2 0.03 3.6

H2O 0.5 6.2

100.0% 100.0%

15.2A.1 https://bio.libretexts.org/@go/page/5385
 Figure 15.2.1.2: Alveoli(Reproduced with permission from Keith R. Porter and Mary A. Bonneville, An Introduction to the Fine
Structure of Cells and Tissues, 4th. ed., Lea & Febiger, 1973.)

Central Control of Breathing

The rate of cellular respiration (and hence oxygen consumption and carbon dioxide production) varies with level of activity.
Vigorous exercise can increase by 20–25 times the demand of the tissues for oxygen. This is met by increasing the rate and depth of
breathing. It is a rising concentration of carbon dioxide — not a declining concentration of oxygen — that plays the major role in
regulating the ventilation of the lungs. Certain cells in the medulla oblongata are very sensitive to a drop in pH. As the CO2 content
of the blood rises above normal levels, the pH drops
. Those rare people who inherit two defective genes for alpha-1 antitrypsin are particularly susceptible to developing emphysema.

This page titled 15.2A: Human Respiratory System is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.2A.2 https://bio.libretexts.org/@go/page/5385
15.2B: Control of Breathing

Figure 15.2.2.1 shows an experimental setup (a modification of a device invented by my grandfather, Francis Gano Benedict) with
which a human subject can inspire various precise gas mixtures. While the subject is inhaling the gas mixture, the rate and depth of
breathing can be recorded.
The subject begins by breathing pure air (21% oxygen, 0.03% carbon dioxide, and about 79% inert gases by volume), first from
the room and then from the tank. This control reveals what, if any, changes in response can be expected just by breathing from
the tank (because of an unpleasant taste or increased air resistance, for example). The two graphs show that no appreciable
change does occur when breathing air.
When 100% oxygen is used instead, no marked change in rate ("breaths/minute") or depth ("vital capacity") of breathing occurs
either, although there is a tendency for depth of breathing to decrease slightly.
When the subject inhales a gas mixture consisting of 92% oxygen and 8% carbon dioxide, however, a most dramatic increase in
the rate and depth of inspiration takes place. Note that there is no question of tissues lacking oxygen. The gas mixture contains
four times as much oxygen as air.

Figure 15.2.2.2 shows a setup with which this type of response can be studied. Movements of the subject's chest are detected by a
hollow bellows (the pneumograph) strapped around the chest. Expansion and contraction of the bellows causes decreases and
increases in the air within. These pressure changes are transmitted to a recording stylus, which writes on a slowly revolving drum
(the kymograph).
Note that after a period of breath-holding, the rate and depth of inspiration are markedly greater than before the breath-holding
began (1). This can be explained by the build-up of CO2 during the breath-holding period.
Vigorous, forced hyperventilation reduces the CO2 content of the alveolar air and blood to below its normal value, leading to a
period of shallow breathing before its concentration builds back up to normal (2).
The length of time that one can hold his or her breath to the breaking point can be substantially increased by hyperventilating
just prior to the period of breath-holding (3).
It may seem curious that the rate at which one breathes and thus supplies oxygen to the body is controlled by carbon dioxide rather
than oxygen. But cellular respiration produces CO2 as fast as oxygen is consumed, so the CO2 given off by active muscles triggers
increased ventilation of the lungs and thus automatically supplies additional oxygen. While CO2 is the major stimulus for

15.2B.1 https://bio.libretexts.org/@go/page/5386
controlling breathing, the carotid body in the carotid arteries does have receptors that respond to a drop in oxygen. Their activation
is important in situations (e.g., at high altitude in the unpressurized cabin of an aircraft) where oxygen supply is inadequate, but
there has been no increase in the production of CO2. People who live at high altitudes, e.g., in the Andes, have enlarged carotid
bodies.

This page titled 15.2B: Control of Breathing is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.2B.2 https://bio.libretexts.org/@go/page/5386
15.2C: Vertebrate Lungs
Terrestrial vertebrates (amphibians, reptiles, birds, and mammals) use a pair of lungs to exchange oxygen and carbon dioxide
between their tissues and the air.

Frog Lungs

Figure 15.2.3.1 Frog lungs

The frog's lungs are a pair of thin-walled sacs connected to the mouth through an opening, the glottis. The surface area of the lungs
is increased by inner partitions which are richly supplied with blood vessels. The frog inflates its lungs by
filling its mouth with air
then closing its mouth
closing the internal openings to its nostrils
opening its glottis
raising the floor of its mouth thus forcing air into the lungs.
The frog's skin serves as a supplementary organ of gas exchange. However, it must remain moist to do this, which is one reason
that frogs, like other amphibians, live in moist places. The frog's circulatory system, which brings oxygen-depleted blood to its
lungs (and skin) and takes oxygen-enriched blood away is described in a separate page.

Reptile Lungs

Figure 15.2.3.2 Reptile lungs

The skin of reptiles is dry and scaly, so they can live in arid locations (although many do not). However, they cannot use their skin
as an organ of gas exchange. Reptiles depend entirely on their lungs for this. Their lungs are considerably more efficient than those
of amphibians.
They have a much greater surface area for the exchange of gases.
They are inflated and deflated by the bellowslike expansion and contraction of the rib cage.
While fresh air flows in and stale air out of the lizard's lungs, another reptile, the American alligator, uses a more efficient
mechanism similar to that described below in birds.)
The lizard's circulatory system, which brings oxygen-depleted blood to its lungs and takes oxygen-enriched blood away is
described in a separate page.

Bird Lungs

15.2C.1 https://bio.libretexts.org/@go/page/5387
 Figure 15.2.3.3 Bird lungs
Unlike reptiles, birds are homeothermic ("warm blooded"), maintaining a constant body temperature (usually around 40°C) despite
wide fluctuations in the temperature of their surroundings. They maintain their body temperature with the heat produced by
muscular activity. This depends, in turn, on a high rate of cellular respiration. So the demands on the gas-exchange efficiency of the
lungs of a small, active bird are great.
Although the ventilation of bird lungs is similar to that of reptiles, their effectiveness is increased by the presence of air sacs.
Although no gas exchange occurs in the air sacs, their arrangement increases the efficiency of lung ventilation by enabling fresh air
to pass in one direction through the lungs during both inhalation and exhalation. The air sacs also aid in reducing the density of the
body by substituting air for tissue or fluid in many places. Even some of the bird's bones are penetrated by air sacs.

Mammalian Lungs
Ventilation of mammalian lungs is assisted by the diaphragm - a muscular partition that divides the thoracic cavity from the
abdominal cavity.

This page titled 15.2C: Vertebrate Lungs is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.2C.2 https://bio.libretexts.org/@go/page/5387
15.2D: Tracheal Breathing

Figure 15.2.4.1 Insect trachea

Tracheae open to the outside through small holes called spiracles. In the grasshopper, the first and third segments of the thorax
have a spiracle on each side. Another 8 pairs of spiracles are arranged in a line on either side of the abdomen. The spiracles are
guarded by
valves controlled by muscles that enables the grasshopper to open and close them
hairs that filter out dust as the air enters the spiracles

Figure 15.2.4.3 Fraenkel experiment

The experiment illustrated (first performed by the insect physiologist Gottfried Fraenkel) shows that there is a one-way flow of air
through the grasshopper. The liquid seals in the tubing move to the right as air enters the spiracles in the thorax and is discharged
through the spiracles in the abdomen. The rubber diaphragm seals the thorax from the abdomen. The one-way flow of air increases
the efficiency of gas exchange as CO2-enriched air can be expelled without mingling with the incoming flow of fresh air.

Gas Exchange in Aquatic Insects

Even aquatic insects use a tracheal system for gas exchange.
Some, like mosquito larvae ("wigglers"), get their air by poking a breathing tube — connected to their tracheal system —
through the water surface.
Some insects that can submerge for long periods carry a bubble of air with them from which they breathe.
Still others have spiracles mounted on the tips of spines. With these they pierce the leaves of underwater plants and obtain
oxygen from the bubbles formed (by photosynthesis) within the leaves.
Even in aquatic insects that have gills, after oxygen diffuses from the water into the gills, it then diffuses through a gas-filled
tracheal system for transport through the body.

Figure 15.2.4.4 Aquatic animal trachea

This page titled 15.2D: Tracheal Breathing is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.2D.1 https://bio.libretexts.org/@go/page/5388
 SECTION OVERVIEW
15.3: Circulatory Systems
Topic hierarchy

15.3A: Anatomy of Human Circulatory System

15.3B: How the Human Circulatory System Works

15.3C: The Heartbeat

15.3D: The Lymphatic System

15.3E: Blood

15.3F: Blood Groups

15.3G: The Transport of Heat

15.3H: Blood Clotting

15.3I: Sickle-Cell Disease

15.3J: Serine Proteases

15.3K: Animal Circulatory Systems

This page titled 15.3: Circulatory Systems is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.3.1 https://bio.libretexts.org/@go/page/5337
15.3A: Anatomy of Human Circulatory System
The circulatory system is an organ system that permits blood to circulate and transport nutrients (such as amino acids and
electrolytes), oxygen, carbon dioxide, hormones, and blood cells to and from the cells in the body to provide nourishment and help
in fighting diseases, stabilize temperature and pH, and maintain homeostasis.

Basilar artery
Internal carotid artery
External carotid artery
External jugular vein
Internal jugular vein
Subclavian artery Vertebral arteries
Common carotid arteries
Subclavian vein
Cephalic vein
Aorta Pulmonary arteries
Axillary vein Pulmonary veins
Axillary artery Heart
Superior vena cava
Inferior vena cava
Celiac trunk
Descending aorta
Hepatic veins
Brachial artery
Renal veins
Basilic vein
Renal artery
Median cubital vein
Gonadal vein
Cephalic vein
Gonadal artery
Common iliac vein
Radial artery
Common iliac artery
Ulnar artery
Internal iliac artery
Palmar digital veins Internal iliac vein
Digital artery External iliac vein
External iliac artery

Great saphenous vein

Femoral artery
Femoral vein

Popliteal artery
Popliteal vein
Small saphenous vein
Anterior tibial artery
Posterior tibial artery
Peroneal artery
Anterior/posterior tibial veins
Dorsal venous arch
Dorsal digital vein

Arcuate artery
Dorsal digital arteries

Simplified diagram of the human Circulatory system in anterior view. (Public Domain; LadyofHats)

Main Features of the Human Circulatory System

A liquid, blood, to transport nutrients, wastes, oxygen and carbon dioxide, and hormones.
Two pumps (in a single heart): one to pump deoxygenated blood to the lungs and the other to pump oxygenated blood to all
the other organs and tissues of the body
A system of blood vessels to distribute blood throughout the body
Specialized organs for exchange of materials between the blood and the external environment; for example organs like the
lungs and intestine that add materials to the blood and organs like the lungs and kidneys that remove materials from the blood
and deposit them back in the external environment

15.3A.1 https://bio.libretexts.org/@go/page/5393
The Heart and Pulmonary System
The heart is located roughly in the center of the chest cavity. It is covered by a protective membrane, the pericardium.
Deoxygenated blood from the body enters the right atrium.
It flows through the tricuspid valve into the right ventricle. The term tricuspid refers to the three flaps of tissue that make up
the valve.
Contraction of the ventricle then closes the tricuspid valve and forces open the pulmonary valve.
Blood flows into the pulmonary artery.
This branches immediately, carrying blood to the right and left lungs.
Here the blood gives up carbon dioxide and takes on a fresh supply of oxygen.
The capillary beds of the lungs are drained by venules that are the tributaries of the pulmonary veins.
Four pulmonary veins, two draining each lung, carry oxygenated blood to the left atrium of the heart.

Figure 15.3.1.1 Human heart

The above figure shows the human heart, with a schematic view of the pathway of blood through the lungs and internal organs.
Oxygenated blood is shown in red; deoxygenated blood in blue. Note that the blood draining the stomach, spleen, and intestines
passes through the liver before it is returned to the heart. Here surplus or harmful materials picked up from those organs can be
removed before the blood returns to the general circulation.

The Coronary System

From the left atrium,
Blood flows through the mitral valve (also known as the bicuspid valve) into the left ventricle.
Contraction of the ventricle closes the mitral valve and opens the aortic valve at the entrance to the aorta.
The first branches from the aorta occur just beyond the aortic valve still within the heart.
Two openings lead to the right and left coronary arteries, which supply blood to the heart itself. Although the coronary arteries
arise within the heart, they pass directly out to the surface of the heart and extend down across it. They supply blood to the
network of capillaries that penetrate every portion of the heart.
The capillaries drain into two coronary veins that empty into the right atrium.

 Diseases of the Coronary system: Arteriosclerosis and Atherosclerosis

The coronary arteries arise at the point of maximum blood pressure in the circulatory system. Over the course of time, the
arterial walls are apt to lose elasticity, which limits the amount of blood that can surge through them and hence limits the
supply of oxygen to the heart. This condition is known as arteriosclerosis.
Alternatively, fatty deposits, called plaque, may accumulate on the interior surface of the coronary arteries; this condition is
known as atherosclerosis. This is particularly common in people who have high levels of cholesterol in their blood. Plaque
deposits reduce the bore of the coronary arteries and thus the amount of blood they can carry. Atherosclerosis (usually along
with arteriosclerosis) may limit the blood supply to the heart that during times of stress the heart muscle is so deprived of
oxygen that the pain of angina is created. It triggers the formation of a clot causing a coronary thrombosis. This stops the
flow of blood through the vessel and the capillary network it supplies causing a heart attack. The portion of the heart muscle

15.3A.2 https://bio.libretexts.org/@go/page/5393
 deprived of oxygen dies quickly of oxygen starvation. If the area is not too large, the undamaged part of the heart can, in time,
compensate for the damage.
Coronary bypass surgery uses segments of leg veins to bypass the clogged portions of the coronary arteries.

The Systemic Circulation

The remainder of the system is known as the systemic circulation. The graphic shows the major arteries (in bright red) and veins
(dark red) of the system. Blood from the aorta passes into a branching system of arteries that lead to all parts of the body. It then
flows into a system of capillaries where its exchange functions take place.

Figure 15.3.1.2 Human circulation system

Blood from the capillaries flows into venules which are drained by veins.
Veins draining the upper portion of the body lead to the superior vena cava.
Veins draining the lower part of the body lead to the inferior vena cava.
Both empty into the right atrium.

This page titled 15.3A: Anatomy of Human Circulatory System is shared under a CC BY 3.0 license and was authored, remixed, and/or curated
by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available
upon request.

15.3A.3 https://bio.libretexts.org/@go/page/5393
15.3B: How the Human Circulatory System Works
All the functions of the circulatory system occur in the capillary beds. The rest of the system consists of two pumps (in the heart)
and associated plumbing:
arteries and their terminal branches, the arterioles
veins and their tributaries, the venules.

Blood Pressure
Blood moves through the arteries, arterioles, and capillaries because of the force created by the contraction of the ventricles.

Blood pressure in the arteries.

The surge of blood that occurs at each contraction is transmitted through the elastic walls of the entire arterial system where it can
be detected as the pulse. Even during the brief interval when the heart is relaxed — called diastole — there is still pressure in the
arteries. When the heart contracts — called systole — the pressure increases.
Blood pressure is expressed as two numbers, e.g., 120/80. The first is the pressure during systole. The unit of measure is the torr,
in this example, the pressure equivalent to that produced by a column of mercury 120 mm high. The second number is the pressure
at diastole.
Although blood pressure can vary greatly in an individual, continual high pressure — especially diastolic pressure — may be the
symptom or cause of a variety of ailments. The medical term for high blood pressure is hypertension.

Blood pressure in the capillaries

The pressure of arterial blood is largely dissipated when the blood enters the capillaries. Capillaries are tiny vessels with a diameter
just about that of a red blood cell (7.5 µm). Although the diameter of a single capillary is quite small, the number of capillaries
supplied by a single arteriole is so great that the total cross-sectional area available for the flow of blood is increased. Therefore, the
pressure of the blood as it enters the capillaries decreases.

Blood pressure in the veins

When blood leaves the capillaries and enters the venules and veins, little pressure remains to force it along. Blood in the veins
below the heart is helped back up to the heart by the muscle pump. This is simply the squeezing effect of contracting muscles on
the veins running through them. One-way flow to the heart is achieved by valves within the veins.

Exchanges Between Blood and Cells

Figure 15.3.2.1 Tissue space

With rare exceptions, our blood does not come into direct contact with the cells it nourishes. As blood enters the capillaries
surrounding a tissue space, a large fraction of it is filtered into the tissue space. It is this interstitial or extracellular fluid (ECF)
that brings to cells all of their requirements and takes away their products. The number and distribution of capillaries is such that
probably no cell is ever farther away than 50 µm from a capillary.
When blood enters the arteriole end of a capillary, it is still under pressure (about 35 torr) produced by the contraction of the
ventricle. As a result of this pressure, a substantial amount of water and some plasma proteins filter through the walls of the
capillaries into the tissue space. Thus fluid, called interstitial fluid, is simply blood plasma minus most of the proteins. It has the
same composition and is formed in the same way as the nephric filtrate in kidneys. Interstitial fluid bathes the cells in the tissue

15.3B.1 https://bio.libretexts.org/@go/page/5395
space and substances in it can enter the cells by diffusion or active transport. Substances, like carbon dioxide, can diffuse out of
cells and into the interstitial fluid.
Near the venous end of a capillary, the blood pressure is greatly reduced (to about 15 torr). Here another force comes into play.
Although the composition of interstitial fluid is similar to that of blood plasma, it contains a smaller concentration of proteins than
plasma and thus a somewhat greater concentration of water. This difference sets up an osmotic pressure. Although the osmotic
pressure is small (~ 25 torr), it is greater than the blood pressure at the venous end of the capillary. Consequently, the fluid reenters
the capillary here.
The first of the four graphs (a) shows this balanced relationship in the capillary bed; the others show what happens when the system
is altered.

Figure 15.3.2.2 Pressure relations in capillaries

Pressure relations in the capillaries.

PA = blood pressure at the arteriole end of the capillary.

PV = blood pressure at the venule end of the capillary.
The horizontal line represents the osmotic pressure of the blood.
When the blood pressure is greater than the osmotic pressure, filtration of interstitial fluid occurs (downward-pointing arrows).
When the blood pressure is less than the osmotic pressure, reabsorption of interstitial fluid occurs (up arrows).

(a) The normal situation. Filtration and absorption are balance.

(b) Result of dilating the arterioles. PA increases and the tissue space becomes engorged with interstitial fluid.

(c) Result of constricting the arterioles. PA decreases and interstitial fluid is withdrawn from the tissue space.

(d) Result of a lowered concentration of protein in the blood (such as occurs during prolonged malnutrition). Because of the
reduced osmotic pressure (lower horizontal line), fluid accumulates in the tissue spaces resulting in edema.

Control of the Capillary Beds

An adult human has been estimated to have some 60,000 miles (96,560 km) of capillaries with a total surface area of some 800–
1000 m2 (an area greater than three tennis courts). The total volume of this system is roughly 5 liters, the same as the total volume
of blood. However, if the heart and major vessels are to be kept filled, all the capillaries cannot be filled at once. So a continual
redirection of blood from organ to organ takes place in response to the changing needs of the body. During vigorous exercise, for
example, capillary beds in the skeletal muscles open at the expense of those in the viscera. The reverse occurs after a heavy meal.
The table shows the distribution of blood in the human body at rest and during vigorous exercise. Note the increase in blood supply
to the working organs (skeletal muscles and heart). The increased blood supply to the skin aids in the dissipation of the heat
produced by the muscles. Note also that the blood supply to the brain remains constant. The total blood flow during exercise
increases because of a more rapid heartbeat and also a greater volume of blood pumped at each beat.

15.3B.2 https://bio.libretexts.org/@go/page/5395
 Blood Flow ml/min

During Strenuous
At Rest
Exercise

Heart 250 750

Kidneys 1,200 600

Skeletal Muscles 1,000 12,5000

Skin 400 1,900

Viscera 1,400 600

Brain 750 750

Other 600 400

Total 5,600 17,500

The walls of arterioles are encased in smooth muscle. Constriction of arterioles decreases blood flow into the capillary beds they
supply while dilation has the opposite effect. In time of danger or other stress, for example, the arterioles supplying the skeletal
muscles will be dilated while the bore of those supplying the digestive organs will decrease. These actions are carried out by
the autonomic nervous system
local controls in the capillary beds

Local Control in the Capillary Beds

Nitric oxide (NO) is a potent dilator of arteries and arterioles.
When the endothelial cells that line these vessels are stimulated, they synthesize nitric oxide. It quickly diffuses into the
muscular walls of the vessels causing them to relax.
In addition, as the hemoglobin in red blood cells releases its O2 in actively-respiring tissues, the lowered pH causes it to also
release NO which helps dilate the vessels to meet the increased need of the tissue.
Nitroglycerine, which is often prescribed to reduce the pain of angina, does so by generating nitric oxide, which relaxes the
walls of the arteries and arterioles. The prescription drug sildenafil citrate ("Viagra") does the same for vessels supplying
blood to the penis. The effects of these two drugs are additive and using them together could precipitate a dangerous drop in
blood pressure.
Cells where infection or other damage is occurring release substances like histamine that dilate the arterioles and thus increase
blood flow in the area.
In most of the body, the flow of blood through a capillary is controlled by the arteriole supplying it. In the brain, however,
another mechanism participates. The degree of contraction of pericytes, cells that surround the capillary, also adjusts the flow
of blood through the capillary. The changes in brain activity seen by such imaging procedures as fMRI and PET scans are
probably influenced by pericyte activity.

Shock
Under some circumstances, capillary beds may open without others closing in compensation. Although the volume of blood
remains unchanged, blood pressure declines abruptly as blood pools in the capillary beds. If untreated shock is usually fatal.
Shock can also result from severe bleeding. The heart can only pump as much blood as it receives. If insufficient blood gets back to
the heart, its output — and hence blood pressure — drops. The tissues fail to receive enough oxygen. This is especially critical for
the brain and the heart itself. To cope with the problem, arterioles constrict and shut down the capillary beds — except those in the
brain and heart. This reduces the volume of the system and helps maintain normal blood pressure.
Air-breathing vertebrates that spend long periods under water (e.g., seals, penguins, turtles, and alligators) employ a similar
mechanism to ensure that the oxygen supply of the heart and brain is not seriously diminished. When the animal dives, the blood
supply to the rest of the body is sharply reduced so that what oxygen remains will be available for those organs needing it most: the
brain and heart.

15.3B.3 https://bio.libretexts.org/@go/page/5395
Regulation of Blood Pressure by Hormones

Figure 15.3.2.3 Human kidney

One of the functions of the kidney is to monitor blood pressure and take corrective action if it should drop. The kidney does this by
secreting the protease renin.
Renin acts on angiotensinogen, a plasma peptide, splitting off a fragment containing 10 amino acids called angiotensin I.
angiotensin I is cleaved by a peptidase secreted by blood vessels called angiotensin converting enzyme (ACE) producing
angiotensin II, which contains 8 amino acids.
angiotensin II
constricts the walls of arterioles closing down capillary beds
stimulates the proximal tubules in the kidney to reabsorb sodium ions
stimulates the adrenal cortex to release aldosterone. Aldosterone causes the kidneys to reclaim still more sodium and thus
water
increases the strength of the heartbeat
stimulates the pituitary to release the vasopressin
All of these actions, which are mediated by its binding to G-protein-coupled receptors on the target cells, lead to an increase in
blood pressure.

The Heart
A rise in blood pressure stretches the atria of the heart. This triggers the release of atrial natriuretic peptide (ANP). ANP is a
peptide of 28 amino acids. ANP lowers blood pressure by:
relaxing arterioles
inhibiting the secretion of renin and aldosterone
inhibiting the reabsorption of sodium ions in the collecting ducts of the kidneys
The effects on the kidney reduce the reabsorption of water by them thus increasing the flow of urine and the amount of sodium
excreted in it (These actions give ANP its name: natrium = sodium; uresis = urinate). The net effect of these actions is to reduce
blood pressure by reducing the volume of blood volume in the system.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 15.3B: How the Human Circulatory System Works is shared under a CC BY 3.0 license and was authored, remixed, and/or
curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is
available upon request.

15.3B.4 https://bio.libretexts.org/@go/page/5395
15.3C: The Heartbeat
During rest, the heart beats about 70 times a minute in the adult male, while pumping about 5 liters of blood.

Figure 15.3.3.1 Interior of human heart

The stimulus that maintains this rhythm is self-contained. Embedded in the wall of the right atrium is a mass of specialized heart
tissue called the sino-atrial (S-A) node. The S-A node is also called the pacemaker because it establishes the basic frequency at
which the heart beats.
The interior of the fibers of heart muscle, like all cells, is negatively charged with respect to the exterior. In the cells of the
pacemaker, this charge breaks down spontaneously about 70 times each minute. This, in turn, initiates a similar discharge of the
nearby muscle fibers of the atrium. A tiny wave of current sweeps over the atria, causing them to contract.
When this current reaches the region of insulating connective tissue between the atria and the ventricles, it is picked up by the A-V
node (atrio-ventricular node). This leads to a system of branching fibers that carries the current to all parts of the ventricles. The
contraction of the heart in response to this electrical activity creates systole. A period of recovery follows called diastole.
The heart muscle and S-A node become recharged.
The heart muscle relaxes.
The atria refill.

The Electrocardiogram
The electrical activity of the heart can be detected by electrodes placed at the surface of the body. Analysis of an electrocardiogram
(ECG or EKG) aids in determining, for example, the extent of damage following a heart attack. This is because death of a portion
of the heart muscle blocks electrical transmission through that area and alters the appearance of the ECG.

Ventricular Fibrillation
The ventricles can maintain a beat even without a functioning A-V node, although the beat is slower. There is, however, a danger
that impulses arising in the ventricles may become disorganized and random. If this happens, they begin to twitch spasmodically, a
condition called ventricular fibrillation. Blood flow ceases and unless the heart rhythm is restarted, death follows swiftly. In fact,
ventricular fibrillation is the immediate cause of as much as 25% of all deaths.
Hospital emergency rooms, ambulances, commercial air craft and many other public places are now equipped with defibrillators
which, by giving the heart a jolt of direct current, may restore its natural rhythm and save the victim's life.

Artificial Pacemakers
These are devices that generate rhythmic impulses that are transmitted to the heart by fine wires. Thanks to miniaturization and
long-lived batteries, pacemakers can be implanted just under the skin and reached through a small incision when maintenance is
needed.

Auxiliary Control of the Heart

Although the A-V node sets the basic rhythm of the heart, the rate and strength of its beating can be modified by two auxiliary
control centers located in the medulla oblongata of the brain.
One sends nerve impulses down accelerans nerves.
The other sends nerve impulses down a pair of vagus nerves

15.3C.1 https://bio.libretexts.org/@go/page/5397
The Accelerans Nerve
The accelerans nerve is part of the sympathetic branch of the autonomic nervous system, and like all post-ganglionic sympathetic
neurons releases noradrenaline at its endings on the heart. It increases the rate and strength of the heartbeat and thus increase the
flow of blood. Its activation usually arises from some stress such as fear or violent exertion. The heartbeat may increase to 180
beats per minute. The strength of contraction increases as well so the amount of blood pumped may increase to as much as 25–30
liters/minute.

 Note

The 24 Feb 2000 issue of the New England Journal of Medicine reports on a family some of whose members have inherited
a mutant gene for the transporter that is responsible for reuptake of noradrenaline back into the neuron that released it. Those
with the mutation are prone to bouts of rapid heartbeat and fainting when they suddenly stand up.

Vigorous exercise accelerates heartbeat in two ways:

As cellular respiration increases, so does the carbon dioxide level in the blood. This stimulates receptors in the carotid arteries
and aorta, and these transmit impulses to the medulla for relay by the accelerans nerve to the heart.
As muscular activity increases, the muscle pump drives more blood back to the right atrium. The atrium becomes distended
with blood, thus stimulating stretch receptors in its wall. These, too, send impulses to the medulla for relay to the heart.
Distention of the wall of the right atrium also triggers the release of atrial natriuretic peptide (ANP) which initiates a set of
responses leading to a lowering of blood pressure.

The Vagus Nerves

The vagus nerves are part of the parasympathetic branch of the autonomic nervous system. They, too, run from the medulla
oblongata to the heart. Their activity slows the heartbeat. Pressure receptors in the aorta and carotid arteries send impulses to the
medulla which relays these by way of the vagus nerves to the heart. Heartbeat and blood pressure diminish.

This page titled 15.3C: The Heartbeat is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.3C.2 https://bio.libretexts.org/@go/page/5397
15.3D: The Lymphatic System

Figure 15.3.4.1 Tissue Space

Most (~90%) of this interstitial fluid returns at the venule end of the capillary. The 10% that does not is picked up by tiny vessels
called lymph capillaries. The cells forming the walls of the lymph capillaries are loosely fitted together, thus making the wall very
porous. Any serum proteins that filtered through the capillary wall pass easily from the tissue space into the interior of the lymph
capillary. The lymph capillaries of the intestinal villi, called lacteals, also pick up fat droplets. White blood cells (leukocytes)
migrate from the tissue space into the lymph capillary squeezing between the cells that make up its wall.
The lymph capillaries drain into still larger collecting vessels. The flow through the collecting vessels is quite slow. Like blood in
the veins, contraction of skeletal muscles compresses the collecting vessels and squeezes the fluid — now called lymph — along.
Again, like the return of blood in the veins, the lymph can flow only in one direction because of valves in the vessels. All the lymph
collected from the entire left side of the body, the digestive tract and the right side of the lower part of the body flows into a single
major vessel, the thoracic duct.
The thoracic duct empties into the left subclavian vein. The lymph in the right side of the head, neck, and chest is collected by the
right lymph duct and empties into the right subclavian vein. Together they empty 1–2 liters of lymph into the blood each day.

Lymph Nodes
The collecting vessels of the lymphatic system are interrupted by lymph nodes. These are especially abundant in the groin, armpits,
abdomen and neck. These contain cavities called sinuses into which the lymph flows bringing various leukocytes (e.g.,
lymphocytes and dendritic cells) and out of which pass antibodies and lymphocytes which then enter the blood at the subclavian
veins.
The walls of the sinuses are lined with phagocytic cells, which engulf any foreign particles, e.g., bacteria, that might be present in
the lymph. Tests have demonstrated that over 99% of the bacteria carried into a node are screened out before the lymph leaves the
node on its return to the blood. This filtering mechanism is one of the most important body defenses against infectious disease.
When combating a heavy infection, the lymph nodes enlarge producing "swollen glands".

Edema
The production of lymph is increased by
increased blood pressure in the capillaries
increased capillary permeability such as occurs if the adherens junctions between the cells lining the capillaries are damaged
a decreased concentration of plasma proteins (such as occurs in prolonged malnutrition).
The lymphatic system may be unable to handle the increased volume of lymph, and it may accumulate in the tissues and distend
them. This condition is known as edema.

This page titled 15.3D: The Lymphatic System is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.3D.1 https://bio.libretexts.org/@go/page/5399
15.3E: Blood
Blood is a liquid tissue. Suspended in the watery plasma are seven types of cells and cell fragments.
1. red blood cells (RBCs) or erythrocytes
2. platelets or thrombocytes
3. five kinds of white blood cells (WBCs) or leukocytes
Three kinds of granulocytes
neutrophils
eosinophils
basophils
Two kinds of leukocytes without granules in their cytoplasm
lymphocytes
monocytes
If one takes a sample of blood, treats it with an agent to prevent clotting, and spins it in a centrifuge, the red cells settle to the
bottom and the white cells settle on top of them forming the "buffy coat". The fraction occupied by the red cells is called the
hematocrit. Normally it is approximately 45%. Values much lower than this are a sign of anemia

Figure 15.3.5.1 Hematocrit

Functions of the blood

Blood performs two major functions:
transport through the body of
oxygen and carbon dioxide
food molecules (glucose, lipids, amino acids)
ions (e.g., Na+, Ca2+, HCO3−)
wastes (e.g., urea)
hormones
heat
defense of the body against infections and other foreign materials. All the WBCs participate in these defenses.

The formation of blood cells

All the various types of blood cells are produced in the bone marrow (some 1011 of them each day in an adult human). They arise
from a single type of cell called a hematopoietic stem cell — an "adult" multipotent stem cell. These stem cells are very rare (only
about one in 10,000 bone marrow cells) and are attached (probably by adherens junctions) to osteoblasts lining the inner surface of
bone cavities. They also express a cell-surface protein designated CD34.

15.3E.1 https://bio.libretexts.org/@go/page/5401
 Figure 15.3E. 1: Types of blood cells
Hematopoietic stem cell produce, by mitosis, two kinds of progeny: (1) more stem cells (A mouse that has had all its blood stem
cells killed by a lethal dose of radiation can be saved by the injection of a single living stem cell) and (2) cells that begin to
differentiate along the paths leading to the various kinds of blood cells. Which path is taken is regulated by the need for more of
that type of blood cell which is, in turn, controlled by appropriate cytokines and/or hormones. For example, Interleukin-7 (IL-7) is
the major cytokine in stimulating bone marrow stem cells to start down the "lymphoid" path leading to the various lymphocytes
(mostly B cells and T cells).
Some of the cytokines that drive the differentiation of the "myeloid" leukocytes are
Erythropoietin (EPO), produced by the kidneys, enhances the production of red blood cells (RBCs).
Thrombopoietin (TPO), assisted by Interleukin-11 (IL-11), stimulates the production of megakaryocytes. Their fragmentation
produces platelets.
Granulocyte-macrophage colony-stimulating factor (GM-CSF), as its name suggests, sends cells down the path leading to
both those cell types. In due course, one path or the other is taken.
Under the influence of granulocyte colony-stimulating factor (G-CSF), they differentiate into neutrophils.
Further stimulated by interleukin-5 (IL-5) they develop into eosinophils.
Interleukin-3 (IL-3) participates in the differentiation of most of the white blood cells but plays a particularly prominent role
in the formation of basophils (responsible for some allergies).
Stimulated by macrophage colony-stimulating factor (M-CSF) the granulocyte/macrophage progenitor cells differentiate
into monocytes, macrophages, and dendritic cells (DCs).

Red Blood Cells (erythrocytes)

The most numerous type in the blood. They average 7 µm in diameter. Women average about 4.8 million of these cells per cubic
millimeter (mm3; which is the same as a microliter [µl]) of blood. Men average about 5.4 x 106 per µl. These values can vary over
quite a range depending on such factors as health and altitude. (Peruvians living at 18,000 feet may have as many as 8.3 x 106
RBCs per µl.)
RBC precursors mature in the bone marrow closely attached to a macrophage. They manufacture hemoglobin until it accounts for
some 90% of the dry weight of the cell. In mammals, the nucleus is squeezed out of the cell and is ingested by the macrophage. All
the mitochondria as well as the endoplasmic reticulum and Golgi apparatus are destroyed. No-longer-needed proteins are expelled
from the cell in vesicles called exosomes. Figure 15.3E. 2 shows a scanning electron micrograph that shows the characteristic
biconcave shape of red blood cells.

15.3E.2 https://bio.libretexts.org/@go/page/5401
 Figure 15.3E. 2: Red blood cells courtesy of Dr. Marion J. Barnhart
Thus RBCs are terminally differentiated; that is, they can never divide. They live about 120 days and then are ingested by
phagocytic cells in the liver and spleen. Most of the iron in their hemoglobin is reclaimed for reuse. The remainder of the heme
portion of the molecule is degraded into bile pigments and excreted by the liver. Some 3 million RBCs die and are scavenged by
the liver each second.
Red blood cells are responsible for the transport of oxygen and carbon dioxide.

Oxygen Transport
In adult humans the hemoglobin (Hb) molecule consists of four polypeptides:
two alpha (α) chains of 141 amino acids
two beta (β) chains of 146 amino acids

Figure 15.3E. 3: oxyhemoglobin

To each of these is attached the prosthetic group heme. There is one atom of iron at the center of each heme. One molecule of
oxygen can bind to each heme. The reaction is reversible. Under the conditions of lower temperature, higher pH, and increased
oxygen pressure in the capillaries of the lungs, the reaction proceeds to the right. The purple-red deoxygenated hemoglobin of the
venous blood becomes the bright-red oxyhemoglobin of the arterial blood. Under the conditions of higher temperature, lower pH,
and lower oxygen pressure in the tissues, the reverse reaction is promoted and oxyhemoglobin gives up its oxygen.

Figure 15.3E. 4: Oxygen pressure vs hemoglobin saturation

The pressure of oxygen in the lungs is 90–95 torr; in the interior tissues it is about 40 torr. Therefore, only a portion of the oxygen
carried by the red blood cells is normally unloaded in the tissues. However, vigorous activity can lower the oxygen pressure in
skeletal muscles below 40 torr, which causes a large increase in the amount of oxygen released. This effect is enhanced by the high

15.3E.3 https://bio.libretexts.org/@go/page/5401
concentration of carbon dioxide in the muscles and the resulting lower pH (7.2). The lower carbon dioxide concentration (and
hence higher pH) at the lungs promotes the binding of oxygen to hemoglobin and hence the uptake of oxygen.
Temperature changes also influence the binding of oxygen to hemoglobin. In the relative warmth of the interior organs, the curve is
shifted to the right (like the curve for pH 7.2), helping to unload oxygen. In the relative coolness of the lungs, the curve is shifted to
the left, aiding the uptake of oxygen.
Although the oxygen transported by RBCs make possible cellular respiration throughout the body, RBCs lack mitochondria and so
cannot perform cellular respiration themselves and must subsist on glycolysis.

Carbon Dioxide Transport

Carbon dioxide (CO2) combines with water forming carbonic acid, which dissociates into a hydrogen ion (H+) and a bicarbonate
ion:
+ −
CO +H O −
↽⇀
− H CO −
↽⇀
− H + HCO (15.3E.1)
2 2 2 3 3

95% of the CO2 generated in the tissues is carried in the red blood cells. It enters (and leaves) the cell by diffusion through the
plasma membrane. Once inside, about one-half of the CO2 is directly bound to hemoglobin (at a site different from the one that
binds oxygen). The rest is converted following the equation above by the enzyme carbonic anhydrase into bicarbonate ions that
diffuse back out into the plasma and hydrogen ions (H+) that bind to the protein portion of the hemoglobin (thus having no effect
on pH). The bicarbonate ions pass out of the red cell by facilitated diffusion through transmembrane channels in the plasma
membrane. Only about 5% of the CO2 generated in the tissues dissolves directly in the plasma. (A good thing, too: if all the CO2
we make were carried this way, the pH of the blood would drop from its normal 7.4 to an instantly-fatal 4.5) When the red cells
reach the lungs, these reactions are reversed and CO2 is released to the air of the alveoli.

Anemia
Anemia is a shortage of RBCs and/or the amount of hemoglobin in them. Anemia has many causes. One of the most common is an
inadequate intake of iron in the diet.

Blood Groups
Red blood cells have surface antigens that differ between people and that create the so-called blood groups such as the ABO system
and the Rh system.

White Blood Cells (leukocytes)

White blood cells are much less numerous than red (the ratio between the two is around 1:700) and have nuclei. They consist of
lymphocytes and monocytes with relatively clear cytoplasm, and three types of granulocytes, whose cytoplasm is filled with
granules. They participate in protecting the body from infection.

Lymphocytes
There are several kinds of lymphocytes (although they all look alike under the microscope), each with different functions to
perform . The most common types of lymphocytes are:
B lymphocytes ("B cells"). These are responsible for making antibodies.
T lymphocytes ("T cells"). There are several subsets of these:
inflammatory T cells that recruit macrophages and neutrophils to the site of infection or other tissue damage
cytotoxic T lymphocytes (CTLs) that kill virus-infected and, perhaps, tumor cells
helper T cells that enhance the production of antibodies by B cells

15.3E.4 https://bio.libretexts.org/@go/page/5401
 Figure 15.3.5.6 Lymphocytes surrounding a macrophage courtesy of Drs. Jan M. Orenstein and Emma Shelton
Although bone marrow is the ultimate source of lymphocytes, the lymphocytes that will become T cells migrate from the bone
marrow to the thymus where they mature. Both B cells and T cells also take up residence in lymph nodes, the spleen and other
tissues where they encounter antigens, continue to divide by mitosis, mature into fully functional cells.

Monocytes
Monocytes leave the blood and become macrophages and one type of dendritic cell. See Figure 15.3.5.6

Neutrophils

Figure 15.3.5.7 Neutorphils

The most abundant of the WBCs. This photomicrograph shows a single neutrophil surrounded by red blood cells. Neutrophils
squeeze through the capillary walls and into infected tissue where they kill the invaders (e.g., bacteria) and then engulf the
remnants by phagocytosis. This is a never-ending task, even in healthy people: Our throat, nasal passages, and colon harbor vast
numbers of bacteria. Most of these are commensals, and do us no harm. But that is because neutrophils keep them in check.
However heavy doses of radiation, chemotherapy and many other forms of stress can reduce the numbers of neutrophils so that
formerly harmless bacteria begin to proliferate. The resulting opportunistic infection can be life-threatening.

Eosinophils
The number of eosinophils in the blood is normally quite low (0–450/µl). However, their numbers increase sharply in certain
diseases, especially infections by parasitic worms. Eosinophils are cytotoxic, releasing the contents of their granules on the invader.

Basophils
Ordinarily representing less than 1% of the WBCs, their numbers also increase during infection. Basophils leave the blood and
accumulate at the site of infection or other inflammation. There they discharge the contents of their granules, releasing a variety of
mediators such as histamine, serotonin, prostaglandins and leukotrienes which increase the blood flow to the area and in other ways
add to the inflammatory process. The mediators released by basophils also play an important part in some allergic responses such
as hay fever and an anaphylactic response to insect stings.

Platelets
Platelets are cell fragments produced from megakaryocytes. These polyploid (128n) cells in the bone marrow send pseudopodia-
like projections into the lumen of adjacent blood vessels. Blood flowing through the vessel shears off the platelets. Blood normally
contains 150,000–400,000 per microliter (µl) or cubic millimeter (mm3). This number is normally maintained by a homeostatic

15.3E.5 https://bio.libretexts.org/@go/page/5401
(negative-feedback) mechanism. If this value should drop much below 20,000/µl, there is a danger of uncontrolled bleeding. Some
causes include certain drugs and herbal remedies as well as autoimmunity.
When blood vessels are cut or damaged, the loss of blood from the system must be stopped before shock and possible death occur.
This is accomplished by solidification of the blood, a process called coagulation or clotting. A blood clot consists of a plug of
platelets enmeshed in a network of insoluble fibrin molecules. Platelets also promote inflammation.

Plasma
Plasma is the straw-colored liquid in which the blood cells are suspended.
Composition of blood plasma
Component Percent

Water ~92

Proteins 6–8

Salts 0.8

Lipids 0.6

Glucose (blood sugar) 0.1

Plasma transports materials needed by cells and materials that must be removed from cells:
various ions (Na+, Ca2+, HCO3−, etc.)
glucose and traces of other sugars
amino acids
other organic acids
cholesterol and other lipids
hormones
urea and other wastes
Most of these materials are in transit from a place where they are added to the blood (a "source")
exchange organs like the intestine
depots of materials like the liver
to places ("sinks") where they will be removed from the blood.
every cell
exchange organs like the kidney, and skin.

Serum Proteins
Proteins make up 6–8% of the blood. They are about equally divided between serum albumin and a great variety of serum
globulins. After blood is withdrawn from a vein and allowed to clot, the clot slowly shrinks. As it does so, a clear fluid called
serum is squeezed out. Thus Serum is blood plasma without fibrinogen and other clotting factors. The serum proteins can be
separated by electrophoresis.

15.3E.6 https://bio.libretexts.org/@go/page/5401
 Figure 15.3.5.8 Electrophoresis
A drop of serum is applied in a band to a thin sheet of supporting material, like paper, that has been soaked in a slightly-alkaline
salt solution.
At pH 8.6, which is commonly used, all the proteins are negatively charged, but some more strongly than others.
A direct current can flow through the paper because of the conductivity of the buffer with which it is moistened.
As the current flows, the serum proteins move toward the positive electrode.
The stronger the negative charge on a protein, the faster it migrates.
After a time (typically 20 min), the current is turned off and the proteins stained to make them visible (most are otherwise
colorless).
The separated proteins appear as distinct bands.
The most prominent of these and the one that moves closest to the positive electrode is serum albumin.
Serum albumin
is made in the liver
binds many small molecules for transport through the blood
helps maintain the osmotic pressure of the blood
The other proteins are the various serum globulins.
They migrate in the order
alpha globulins (e.g., the proteins that transport thyroxine and retinol [vitamin A])
beta globulins (e.g., the iron-transporting protein transferrin)
gamma globulins.
Gamma globulins are the least negatively-charged serum proteins. (They are so weakly charged, in fact, that some are
swept in the flow of buffer back toward the negative electrode.)
Most antibodies are gamma globulins.
Therefore gamma globulins become more abundant following infections or immunizations.
Gamma globulins can be harvested from donated blood (usually pooled from several thousand donors) and injected into
persons exposed to certain diseases such as chicken pox and hepatitis. Because such preparations of immune globulin
contain antibodies against most common infectious diseases, the patient gains temporary protection against the disease.
If a precursor of an antibody-secreting cell becomes cancerous, it divides uncontrollably to generate a clone of plasma cells
secreting a single kind of antibody molecule.

15.3E.7 https://bio.libretexts.org/@go/page/5401
 Figure 15.3.5.8 Electrophoretic seperation courtesy Beckman Instruments, Inc.
The above image shows — from left to right — the electrophoretic separation of:
normal human serum with its diffuse band of gamma globulins
serum from a patient with multiple myeloma producing an IgG myeloma protein
serum from a patient with Waldenström's macroglobulinemia where the cancerous clone secretes an IgM antibody
serum with an IgA myeloma protein

Serum Lipids
Because of their relationship to cardiovascular disease, the analysis of serum lipids has become an important health measure. The
table shows the range of typical values as well as the values above (or below) which the subject may be at increased risk of
developing atherosclerosis.

LIPID Typical values (mg/dl) Desirable (mg/dl)

Cholesterol (total) 170–210 <200

LDL cholesterol 60–140 <100

HDL cholesterol 35–85 >40

Triglycerides 40–160 <160

Total cholesterol is the sum of HDL cholesterol, LDL cholesterol and 20% of the triglyceride value
Note that high LDL values are bad, but high HDL values are good.
Using the various values, one can calculate a
cardiac risk ratio = total cholesterol divided by HDL cholesterol
A cardiac risk ratio greater than 7 is considered a warning.

Blood Transfusions
In the United States, in 2001, some 15 million "units" (~475 ml) of blood were collected from blood donors.
Some of these units ("whole blood") were transfused directly into patients (e.g., to replace blood lost by trauma or during
surgery).
Most were further fractionated into components, including:
RBCs - When refrigerated these can be used for up to 42 days.
Platelets - These must be stored at room temperature and thus can be saved for only 5 days.
Plasma - This can be frozen and stored for up to a year.

Ensuring the safety of donated blood

A variety of infectious agents can be present in blood. Infections such as
viruses (e.g., HIV-1, hepatitis B and C, West Nile virus)
bacteria like the spirochete of syphilis
protozoans like the agents of malaria and babesiosis
prions (e.g., the agent of variant Crueutzfeldt-Jakob disease)
These could be transmitted to recipients. To minimize these risks donors are questioned about their possible exposure to these
agents. Each unit of blood is tested for a variety of infectious agents. Most of these tests are performed with enzyme immunoassays
(EIA) and detect antibodies against the agents. However, it takes a period of time for the immune system to produce antibodies
following infection, and during this period ("window"), infectious virus is present in the blood. For this reason, blood is now also

15.3E.8 https://bio.libretexts.org/@go/page/5401
checked for the presence of the RNA of these RNA viruses HIV-1, hepatitis C and West Nile virus by the nucleic acid-
amplification test (NAT).
Thanks to all these precautions, the risk of acquiring an infection from any of these agents is vanishingly small. Despite this, some
people — in anticipation of need — donate their own blood ("autologous blood donation") prior to surgery.

Blood Typing
Donated blood must also be tested for certain cell-surface antigens that might cause a dangerous transfusion reaction in an
improperly-matched recipient.

Blood Substitutes
Years of research have gone into trying to avoid the problems of blood perishability and safety by developing blood substitutes.
Most of these have focused on materials that will transport adequate amounts of oxygen to the tissues.
Some are totally synthetic substances.
Others are derivatives of hemoglobin.
Although some have reached clinical testing, none has as yet proved acceptable for routine use.

This page titled 15.3E: Blood is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.3E.9 https://bio.libretexts.org/@go/page/5401
15.3F: Blood Groups
Blood groups are created by molecules present on the surface of red blood cells (and often on other cells as well).

The ABO Blood Groups

The ABO blood groups were the first to be discovered (in 1900) and are the most important in assuring safe blood transfusions.
The table shows the four ABO phenotypes ("blood groups") present in the human population and the genotypes that give rise to
them.

Blood Group Antigens on RBCs Antibodies in Serum Genotypes

A A Anti-B AA or AO

B B Anti-A BB or BO

AB A and B Neither AB

O Neither Anti-A and Anti-B OO

When red blood cells carrying one or both antigens are exposed to the corresponding antibodies, they agglutinate; that is, clump
together. People usually have antibodies against those red cell antigens that they lack. The antigens in the ABO system are O-linked
glycoproteins with their sugar residues exposed at the cell surface. The terminal sugar determines whether the antigen is A or B.
The critical principle to be followed is that transfused blood must not contain red cells that the recipient's antibodies can clump.
Although theoretically it is possible to transfuse group O blood into any recipient, the antibodies in the donated plasma can damage
the recipient's red cells. Thus, when possible, transfusions should be done with exactly-matched blood.
In 2007, Danish and French investigators reported the properties of two bacterial glycosidases that specifically remove the sugars
responsible for the A and B antigens. This discovery raises the possibility of being able to treat A, B, or AB blood with these
enzymes and thus convert the blood to Group O, the "universal donor".
Why do we have antibodies against red cell antigens that we lack? Bacteria living in our intestine, and probably some foods,
express epitopes similar to those on A and B. We synthesize antibodies against these if we do not have the corresponding epitopes;
that is, if our immune system sees them as "foreign" rather than "self".

The Rh System
Rh antigens are transmembrane proteins with loops exposed at the surface of red blood cells. They appear to be used for the
transport of carbon dioxide and/or ammonia across the plasma membrane. They are named for the rhesus monkey in which they
were first discovered.
There are a number of Rh antigens. Red cells that are "Rh-positive" express the one designated D. About 15% of the population
have no RhD antigen and thus are "Rh-negative". The major importance of the Rh system for human health is to avoid the danger
of RhD incompatibility between mother and fetus.
During birth, there is often a leakage of the baby's red blood cells into the mother's circulation. If the baby is Rh-positive (having
inherited the trait from its father) and the mother Rh-negative, these red cells will cause her to develop antibodies against the RhD
antigen. The antibodies, usually of the IgG class, do not cause any problems for that child, but can cross the placenta and attack the
red cells of a subsequent Rh+ fetus. This destroys the red cells producing anemia and jaundice. The disease, called
erythroblastosis fetalis or hemolytic disease of the newborn, may be so severe as to kill the fetus or even the newborn infant. It
is an example of an antibody-mediated cytotoxicity disorder.
Although certain other red cell antigens (in addition to Rh) sometimes cause problems for a fetus, an ABO incompatibility does
not. Why is an Rh incompatibility so dangerous when ABO incompatibility is not?
It turns out that most anti-A or anti-B antibodies are of the IgM class and these do not cross the placenta. In fact, an Rh−/type O
mother carrying an Rh+/type A, B, or AB fetus is resistant to sensitization to the Rh antigen. Presumably her anti-A and anti-B
antibodies destroy any fetal cells that enter her blood before they can elicit anti-Rh antibodies in her. This phenomenon has led to
an extremely effective preventive measure to avoid Rh sensitization. Shortly after each birth of an Rh+ baby, the mother is given an

15.3F.1 https://bio.libretexts.org/@go/page/5403
injection of anti-Rh antibodies. The preparation is called Rh immune globulin (RhIG) or Rhogam. These passively acquired
antibodies destroy any fetal cells that got into her circulation before they can elicit an active immune response in her.
Rh immune globulin came into common use in the United States in 1968, and within a decade the incidence of Rh hemolytic
disease became very low.

Other blood groups

Several other blood group antigens have been identified in humans. Some examples: MN, Duffy, Lewis, Kell.
These groups also sometimes cause transfusion reactions and even hemolytic disease of the newborn in cases where there is no
ABO or Rh incompatibility. The Duffy red cell antigen also serves as the receptor for entry by the malaria parasite Plasmodium
vivax.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 15.3F: Blood Groups is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.3F.2 https://bio.libretexts.org/@go/page/5403
15.3G: The Transport of Heat
In addition to its role in the transport of materials, the circulatory system is responsible for the distribution of heat throughout the
body. This is true both of
endotherms, animals — birds and mammals — that generate internally the heat needed to maintain their body temperature.
Birds and mammals are "warm-blooded' or homeothermic, maintaining their body temperature within narrow limits, no matter
what the ambient temperature.
mesotherms, animals that generate heat internally but do not maintain a fixed body temperature. Tuna, some sharks, and the
echidna are mesotherms.
ectotherms, animals — the other vertebrates and the invertebrates — that secure their heat from their surroundings (e.g., by
basking in the sun). Ectotherms are "cold-blooded" or poikilothermic.
The major source of heat for endotherms is the metabolism of their internal organs. Over two-thirds of the heat generated in a
resting human is created by the organs of the thoracic and abdominal cavities and the brain (which contributes 16% of the total —
about the same as all our skeletal muscles when they are at rest). There are several measures that an endothermic animal can take if
it begins to lose heat to its surroundings faster than it can generate heat (i.e., it begins to grow cold). It can increase the metabolic
rate of its tissues. Many small mammals and human infants do this as their surroundings get colder, but it is still uncertain whether
adult humans can. The increase in metabolism, with the accompanying release of heat, occurs in brown adipose tissue. It can also
increase its physical activity. At rest, muscles make only a small contribution (about 16%) to body heat. During vigorous exercise,
this can increase greatly. In the absence of voluntary muscle action, the same effect is achieved by shivering. The greater the
surface-to-volume ratio of a part of the body, the faster is can transfer heat to its surroundings. This is why you first notice cold in
your hands and feet. The loss of heat from the extremities can be sharply reduced by diminishing their blood supply. In extreme
cold, for example, the blood supply to the fingers can drop to 1% or so of its normal value.

Countercurrent heat exchanger

Many animals (including humans) have another way to conserve heat. The arteries of our arms and legs run parallel to a set of deep
veins. As warm blood passes down the arteries, the blood gives up some of its heat to the colder blood returning from the
extremities in these veins. Such a mechanism is called a countercurrent heat exchanger. When heat loss is no problem, most of
the venous blood from the extremities returns through veins located near the surface.

Figure 15.3.7.1 Countercurrent heat exchanger

Countercurrent heat exchangers can operate with remarkable efficiency. A sea gull can maintain a normal temperature in its torso
while standing with its unprotected feet in freezing water. When you consider that the blood of fishes passes over the gills which
are bathed in the surrounding water, it is easy to see why fishes are "cold-blooded". Nonetheless, some marine fishes (e.g., the tuna)
are mesotherms — able to keep their most active swimming muscles warmer than the sea by using a countercurrent heat exchanger.

15.3G.1 https://bio.libretexts.org/@go/page/5405
 Figure 15.3.7.2 Skipjack courtesy of E. D. Stevens, Dept. of Zoology, University of Guelph, Ontario
The above photograph on the right shows a cross section through a skipjack tuna. The dark muscle on either side of the vertebral
column is maintained at a higher temperature than the rest of the fish thanks to its countercurrent heat exchanger. The cold, oxygen-
rich arterial blood passes into a series of fine arteries that take the blood into the active muscles. These fine arteries lie side by side
with veins draining those muscles. So as the cold blood passes into the muscles, it picks up the heat that had been generated by
these muscles and keeps it from being lost to the surroundings. Thanks to this countercurrent heat exchanger, a tuna swimming in
the winter can maintain its active swimming muscles 14°C warmer than the surrounding water. The photomicrograph on the left is
of a cross section through the heat exchanger. Note the close, parallel packing of the arteries (thick walls) and veins (thin walls).
Countercurrent exchangers also operate in the kidney and are built into the design of artificial kidneys.
The circulatory system is also responsible for cooling an animal. If the animal's "core" body temperature gets too high, the blood
supply to the surface and extremities is increased enabling heat to be released to the surroundings. If this is insufficient, the animal
can evaporate water from the blood — in the form of sweat for those animals with sweat glands. The evaporation of 1 gram of
water absorbs some 540 calories of heat.
Most endotherms cannot tolerate a rise in body temperature of more than 5°C or so. The brain is the organ most susceptible to
damage by a high temperature. Some mammals, dogs for example, have a countercurrent heat exchanger located between the
carotid arteries and the vessels that distribute blood to the brain. This heat exchanger transfers some of the heat of the arterial blood
to the relatively cool venous blood returning from the nose and mouth. This cools their arterial blood before it reaches the brain.
The shifting of blood flow as needed to maintain homeothermy is controlled by temperature receptors in the hypothalamus of the
brain. One set of receptors here responds to small (0.01°C) increases in the temperature of the blood. When triggered, all the
activities such as shunting blood vessels to the skin and extremities and sweating by which the body cools itself are brought into
play. It is this center that enables us to maintain a constant body temperature (homeothermy) during periods of extreme exertion or
in hot surroundings.
A second region of the hypothalamus triggers warming responses such as shunting blood away from the skin and extremities and
shivering when the body becomes chilled. It is the hypothalamus that executes the fever response. In effect, the hypothalamus is
the body's thermostat. The release of prostaglandins during inflammation increases the setting; that is, turns the thermostat "up". If
the body temperature is not yet there, the body begins shivering violently — causing "chills" — to generate the heat needed. The
result is fever when the new set point is reached.

This page titled 15.3G: The Transport of Heat is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.3G.2 https://bio.libretexts.org/@go/page/5405
15.3H: Blood Clotting
When blood vessels are cut or damaged, the loss of blood from the system must be stopped before shock and possible death occur.
This is accomplished by solidification of the blood, a process called coagulation or clotting. A blood clot consists of a plug of
platelets enmeshed in a network of insoluble fibrin molecules. Platelet aggregation and fibrin formation both require the proteolytic
enzyme thrombin. Clotting also requires calcium ions (Ca2+) (which is why blood banks use a chelating agent to bind the calcium
in donated blood so the blood will not clot in the bag) and about a dozen other protein clotting factors. Most of these circulate in the
blood as inactive precursors. They are activated by proteolytic cleavage becoming, in turn, active proteases for other factors in the
system. By tradition, these factors are designated by Roman numerals.

Figure 15.3.8.1: Clotting process. Blood coagulation pathways in vivo showing the central role played by thrombin. Image used
wtih permission (CC BY-SA 3.0; Dr Graham Beards).
There are two processes that can initiate clotting: A very rapid process the so-called extrinsic pathway or a slower but larger
intrinsic pathway.

The Extrinsic Pathway

Damaged cells display a surface protein called tissue factor (TF). Tissue factor then binds to activated Factor 7. The TF-7
heterodimer is a protease with two substrates: Factor 9 and Factor 10.

The Intrinsic Pathway

Factor 12 (also called the Hageman factor) circulates in the blood. If blood escapes into tissue spaces (e.g., as a result of an injury),
contact with collagens in the tissue space activates Factor 12. Activated Factor 12 is a serine protease that activates Factor 11 which
in turn activates Factor 9 which in turn activates Factor 10.

The Two Pathways Converge at Factor 10

Factor 10 - produced by either or, more likely, both pathways - binds and activates Factor 5. This heterodimer is called
prothrombinase because it is a protease that converts prothrombin (also known as Factor II) to thrombin. Thrombin has several
different activities. Two of them are:
proteolytic cleavage of fibrinogen (aka "Factor I") to form soluble molecules of fibrin and a collection of small and
fibrinopeptides.
activation of Factor 13 which forms covalent bonds between the soluble fibrin molecules converting them into an insoluble
meshwork — the clot.
Thrombin and activated Factors 10 ("Xa") and 11 ("XIa") are also serine proteases.

15.3H.1 https://bio.libretexts.org/@go/page/5407
Amplifying the Clotting Process
The clotting process also has several positive feedback loops which quickly magnify a tiny initial event into what may well be a
lifesaving plug to stop bleeding.
The TF-7 complex (which started the process) also activates Factor 9.
Factor 9 binds to Factor 8, a protein that circulates in the blood stabilized by another protein, von Willebrand Factor
(vWF).
This complex activates more Factor 10.
As thrombin is generated, it activates more
Factor 5
Factor 8
Factor 11 (all shown above with green arrows).
Factor 11 amplifies the production of activated Factor 9.
Thus what may have begun as a tiny, localized event rapidly expands into a cascade of activity.

Platelets
Platelets are cell fragments produced from megakaryocytes. Blood normally contains 150,000 to 400,000 per microliter (µl). If
this value should drop much below 20,000/µl, there is a danger of uncontrolled bleeding. This is because of the essential role of
platelets in maintaining the integrity of the adherens junctions that provide a tight seal between the endothelial cells that line the
blood vessels and in forming a clot where blood vessels have been broken.
When blood vessels are damaged, fibrils of collagen in the extracellular matrix (ECM) are exposed. Platelets then begin to adhere
to the collagen through the action of specific receptors for collagen present on their plasma membrane and von Willebrand factor
which links the platelets to the collagen. These actions cause a plug of platelets to form at the site.
The bound platelets release ADP and thromboxane A2, which recruit and activate still more platelets circulating in the blood.
(This role of thromboxane accounts for the beneficial effect of low doses of aspirin — a cyclooxygenase inhibitor — in avoiding
heart attacks.), tissue factor, and serotonin, which enhances their clumping and promotes constriction of the blood vessel.

 ReoPro
ReoPro s a monoclonal antibody directed against platelet receptors. It inhibits platelet aggregation and appears to reduce the
risk that "reamed out" coronary arteries (after coronary angioplasty) will plug up again.

Bleeding Disorders
A deficiency of a clotting factor can lead to uncontrolled bleeding. The deficiency may arise because not enough of the factor is
produced or a mutant version of the factor fails to perform properly.
Examples:
von Willebrand disease (the most common)
hemophilia A for factor 8 deficiency
hemophilia B for factor 9 deficiency.
hemophilia C for factor 11 deficiency
In some cases of von Willebrand disease, either a deficient level or a mutant version of the factor eliminates its protective effect
on factor 8. The resulting low level of factor 8 mimics hemophilia A.

Figure 15.3.8.2 Bleeding disorders

Why do all the human bleeding disorders involve factors in amplification pathways? Probably because they are the only
deficiencies that can be tolerated. Loss of the genes for tissue factor or factor 7 in knockout mice is lethal.

15.3H.2 https://bio.libretexts.org/@go/page/5407
Hemophilia A and B
The genes encoding factors 8 and 9 are on the X chromosome. Thus their inheritance is X-linked. Like other X-linked disorders,
hemophilia A and B are found almost exclusively in males because they inherit just a single X chromosome, and if the gene for
factor 8 (or 9) on it is defective, they will suffer from the disease.
Queen Victoria of the UK was a carrier of a mutant factor 9 gene and passed it on to several of her descendants.
There are many different mutant versions of the genes for factors 8 and 9. Although some produce only a minor effect on the
function of their protein, others fail to produce any functioning clotting factor.

Treating Hemophilia A and B

What can be done?
Factor 8 and 9 can be extracted from donated blood, usually pooled from several thousand donors, and purified. Injections of this
material can halt episodes of bleeding in hemophiliacs and have allowed countless young men to live relatively normal lives.
However, in the early 1980s, blood contaminated with the human immunodeficiency virus (HIV) was unknowingly used to
manufacture preparations of factors 8 and 9. In some areas, 90% or more of the hemophiliacs became infected by these
contaminated preparations. Many have since died of AIDS. The future now looks brighter because:
all donated blood is now tested to see if the donor has been infected with HIV (as well as hepatitis B and C)
plasma-derived preparations of factors 8 and 9 are now treated with heat and/or solvents to destroy any viruses that might be
present
recombinant factor 8 and recombinant factor 9 made by genetic engineering are now available
These recombinant factors are made by inserting the DNA encoding the human protein into mammalian cells grown in culture. E.
coli cannot be used because these factors are glycoproteins, and E. coli lacks the machinery to attach carbohydrate properly.
And the team that brought us Dolly reported in the 19 December 1997 issue of Science that they have succeeded in cloning female
sheep transgenic for the human factor 9 gene. The human gene is coupled to the promoter for the ovine (sheep) milk protein beta-
lactoglobulin. When the lambs mature, it is hoped that they will secrete large amounts of human factor 9 in their milk, which can
then be purified for human therapy.
Attempts to cure hemophilia by gene therapy also look promising. It is difficult to see how even the most worried critics of genetic
engineering can fail to approve its potential to save the lives of thousands of hemophiliacs in the years to come.

Liver Transplants
People with liver failure can be cured with a liver transplant. On the rare occasions when the patient has happened to be a
hemophiliac (A, B or C), the transplant cured not only the patient's liver disease but cured his hemophilia as well!

Controlling Clotting
While the ability to clot is essential to life, the process must be carefully regulated. Inappropriate clot formation, especially in the
brain or lungs, can be life-threatening.

Antithrombin III
As its name suggests, this plasma protein (a serpin) inhibits the formation of thrombin. It does so by binding to and thus
inactivating prothrombin, factor 9 and factor 10. Heparin is a mixture of polysaccharides that bind to antithrombin III, inducing an
allosteric change that greatly enhances its inhibition of thrombin synthesis. Some surgical patients, especially those receiving hip
or heart valve replacements, and people at risk of ischemic stroke (clots in the brain), are given heparin.

Protein C
With its many clot-promoting activities, it is probably no accident that thrombin sits at the center of the control mechanism.
Excess thrombin binds to cell-surface receptors called thrombomodulin.
The resulting complex activates a plasma protein called Protein C and its cofactor Protein S.
Together these inhibit further thrombin formation
directly — by inactivating Factor 5
indirectly — by inactivating Factor 8.

15.3H.3 https://bio.libretexts.org/@go/page/5407
Some inherited disorders that predispose to spontaneous clots, especially in the leg veins:
inherited deficiency of Protein C or Protein S
inherited mutation in the Factor 5 gene producing a protein that no longer responds to the inhibitory effect of Protein C
Recombinant Protein C is now available to treat people threatened with inappropriate clotting, e.g., as a result of widespread
infection (sepsis).

Vitamin K
Vitamin K is a cofactor needed for the synthesis (in the liver) of factors 2 (prothrombin), 7, 9, and 10 and proteins C and S. A
deficiency of Vitamin K predisposes to bleeding. Conversely, blocking the action of vitamin K helps to prevent inappropriate
clotting.
Warfarin (Coumadin®) is sometimes prescribed as a "blood thinner" because it is an effective vitamin K antagonist. (Warfarin is
also used as a rat poison because it can cause lethal internal bleeding.) Warfarin treatment is tricky because the therapeutic window
(neither too much nor too little) is very narrow, and there is substantial variability between people in their response. So treatment
requires regular monitoring of clotting time until the proper dosage is established. However, a number of new anti-clotting agents
— that work by inhibiting activated factor 10 (Factor Xa) — are being tested and may turn out to be safer and effective alternatives
to warfarin.

Dissolving clots
Plasma contains plasminogen, which binds to the fibrin molecules in a clot. Nearby healthy cells release tissue plasminogen
activator (TPA), which also binds to fibrin and, as its name suggests, activates plasminogen forming plasmin. Plasmin (another
serine protease) proceeds to digest fibrin, thus dissolving the clot.
Recombinant human TPA is now produced by recombinant DNA technology. Injected within the first hours after a heart attack, it
has saved many lives by dissolving the clot blocking the coronary artery and restoring blood flow before the heart muscle becomes
irreversibly damaged. It is also used for people who suffer an ischemic stroke; that is, a clot in the brain. (It must not, of course, be
used for hemorrhagic strokes, that is, a burst blood vessel)

Angiogenesis
Thrombin (as well as factors 7 and 10) promotes healing by stimulating the growth of new blood vessels at the site of damage.

This page titled 15.3H: Blood Clotting is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.3H.4 https://bio.libretexts.org/@go/page/5407
15.3I: Sickle-Cell Disease
The most common hemoglobin of adult humans is known as hemoglobin A (HbA). However, other variant forms of hemoglobin
are found in some humans. One of these is called hemoglobin S (HbS). Individuals who manufacture HbS exclusively suffer from
sickle-cell disease. Sickle-cell disease is quite common in malaria-ridden parts of Africa and Asia and also occurs in African-
Americans and others descended from inhabitants of those regions. The disease gets its name from the fact that the patient's red
cells become crescent or sickle-shaped while passing through the capillaries, especially in tissues that are metabolizing actively.
The distorted cells are very fragile and are apt to rupture long before their normal life span (about 120 days) is over. This causes a
severe anemia (giving rise to an alternate name for the disease: sickle-cell anemia).

Figure 15.3I. 1: Sickle-cell anemia. (CC BY-SA 4.0; BruceBlaus).

Causes of sickle-cell anemia

Individuals with sickle-cell disease have inherited from each parent a gene — βS — encoding the beta chain of hemoglobin.
Individuals who inherit only one βS gene along with the βA allele have both HbA and HbS in their red cells. In the malaria-free
United States, these heterozygotes are well. In regions where malaria is common, having one of each beta chain gene (βA and βS)
confers resistance to one of the most dangerous types of malaria (falciparum). This would explain why the HbS gene is so prevalent
in those regions.
The amino acid sequences of the beta chains of HbA and HbS have been determined. The beta chains are identical except for the
amino acid at position 6 (counting, as always, from the amino terminal). This position is occupied by glutamic acid in HbA chains,
but in HbS beta chains, valine is found there instead.

Figure 15.3I. 2: Sequence alignment between HbA and HbS

Why does this single amino acid change in a chain of 146 amino acids so drastically alter the properties of deoxygenated
hemoglobin? In switching from glutamic acid to valine, a strongly hydrophilic molecule has been replaced by a strongly
hydrophobic one. Position 6 is located at the surface of the beta chain, where it would normally be exposed to water. This switch
from a hydrophilic to a hydrophobic region on the surface reduces the solubility of the molecule and promotes the formation of
large insoluble aggregates.
The mutation that produces HbS is a single-base substitution in which the substitution of a T for an A at the 17th nucleotide of the
sense strand of the first exon of the beta chain gene converts a codon for glutamic acid (GAG) to a codon for valine (GTG).

15.3I.1 https://bio.libretexts.org/@go/page/5409
Although this change might at first appear trivial, the resulting substitution of valine for glutamic acid so alters the physical
properties of hemoglobin that a serious disease is produced in people carrying both genes for the trait.

This page titled 15.3I: Sickle-Cell Disease is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.3I.2 https://bio.libretexts.org/@go/page/5409
15.3J: Serine Proteases
The serine proteases are a family of enzymes that cut certain peptide bonds in other proteins. This activity depends on a set of
amino acid residues in the active site of the enzyme — one of which is always a serine (thus accounting for their name). In
mammals, serine proteases perform many important functions, especially in digestion, blood clotting, and the complement system.

Digestive Enzymes
Three protein-digesting enzymes secreted by the pancreas are serine proteases: chymotrypsin, trypsin and elastase. These three
share closely-similar structures (tertiary as well as primary). In fact, their active serine residue is at the same position (Ser-195) in
all three. Despite their similarities, they have different substrate specificities; that is, they cleave different peptide bonds during
protein digestion.

Clotting Factors
Several activated clotting factors are serine proteases, including Factors 10 (X), 11 (XI), and 12 (XII), Thrombin. and Plasmin.

Complement Factors
Several proteins involved in the complement cascade are serine proteases, including
C1r and C1s
the C3 convertases
C4b,2a
C3b,Bb

Serpins
Serpins are Serine Protease Inhibitors. Here is a list of a few important serine proteases and the serpins that control them.

Serine Protease Serpin

Chymotrypsin alpha-1-antichymotrypsin

Complement factors C1r and C1s C1 Inhibitor (C1INH)

Elastase (secreted by neutrophils) alpha-1-antitrypsin

Clotting factor 10 (X) antithrombin III

Thrombin antithrombin III

Plasmin alpha-2-antiplasmin

Trypsin pancreatic trypsin inhibitor

How Serpins Work

The serpins inhibit the action of their respective serine protease by mimicking the three-dimensional structure of the normal
substrate of the protease. The serine protease binds the serpin instead of its normal substrate. This alone would block any further
activity by the protease. But the serpin has another trick to play. The protease makes a cut in the serpin leading to the formation of a
covalent bond linking the two molecules, a massive allosteric change in the tertiary structure of the serpin, which moves the
attached protease to a site where it can be destroyed.

Importance of Serpins
Almost 20% of the proteins found in blood plasma are serpins. Their abundance reflects their importance: putting a stop to
proteolytic activity when the need for it is over. This is especially important for the clotting and complement systems where a tiny
initial activating event leads to a rapidly amplifying cascade of activity.

15.3J.1 https://bio.libretexts.org/@go/page/5411
  Serpin Deficiencies

A number of inherited human diseases are caused by a deficiency of a particular serpin. The deficiency usually results from a
mutation in the gene encoding the serpin.
Alpha-1-antitrypsin deficiency
Alpha-1-antitrypsin inactivates the elastase secreted by neutrophils. When the lungs become inflamed, neutrophils secrete
elastase as a defensive measure. However, it is important to inactivate this elastase as soon as its job is done. That is the
function of alpha-1-antitrypsin. Its name, alpha-1-antitrypsin, suggests that it attacks the digestive enzyme, trypsin. In vitro, it
does, but in the body, alpha-1-antitrypsin is found in the blood, not the intestine. Inactivation of trypsin in the intestine is the
function of another serpin, pancreatic trypsin inhibitor. People with an inherited deficiency of alpha-1-antitrypsin (they are
homozygous for a point mutation in its gene) are prone to emphysema. An effective treatment is on the horizon now that
genetic engineering has produced goats that secrete human alpha-1-antitrypsin in their milk.
Alpha-1-antitrypsin deficiency can also lead to liver damage. Alpha-1-antitrypsin is synthesized in the liver. However, some
mutant versions of the molecule form insoluble aggregates within the liver cells. This mechanism is similar to that of the prion
diseases where protein aggregates destroy neurons in the brain. A drug that enhances autophagy protects mice from the liver
damage caused by aggregates of mutant alpha-1-antitrypsin.
C1INH deficiency
A deficiency of C1INH produces hereditary angioedema (HAE). In addition to C1r and C1s, C1INH also inhibits several
other serine proteases including kallikrein, the enzyme responsible for forming the potent vasodilator bradykinin. Hence, a
deficiency of C1INH can trigger a dangerous swelling (edema) of the airways, as well as of the skin and intestine.
Antiplasmin deficiency
A deficiency in antiplasmin puts the person at risk of uncontrollable bleeding.
Antithrombin deficiency
A deficiency in antithrombin puts the person at risk of spontaneous blood clots, which can lead to a heart attack or stroke. In
January 2009, an advisory committee of the U.S. FDA decided that a recombinant human antithrombin (ATryn®) secreted into
the milk of transgenic goats was safe for use in therapy.

The Evolution of the Serine Proteases

The close sequence similarity of the various mammalian serine proteases suggests that each is the product of a gene descended by
repeated gene duplication from a single ancestral gene.

Other Serine Proteases

Serine proteases and molecules similar to them are found elsewhere in nature.
Subtilisin
Subtilisin is a serine protease secreted by the bacterium Bacillus subtilis. Although it has the same mechanism of action as the
serine proteases of mammals, its primary structure and tertiary structure are entirely different. An example at the molecular level of
convergent evolution: two molecules acquiring the same function (analogous) but having evolved from different genes.
Acetylcholinesterase
This enzyme is built like and acts like the other serine proteases, but its substrate is the neurotransmitter acetylcholine, not a
protein. It is found at several types of synapses as well as at the neuromuscular junction — the specialized synapse that triggers the
contraction of skeletal muscle. The organophosphate compounds used as insecticides (e.g., parathion) and nerve gases (e.g. Sarin)
bind to the serine at the active site of acetylcholinesterase blocking its action.

Serpinlike Molecules
Angiotensinogen
This peptide is the precursor of angiotensin II — a major factor in maintaining blood pressure.

15.3J.2 https://bio.libretexts.org/@go/page/5411
Chicken Ovalbumin
This is the major protein in the "white" of the egg (and a favorite antigen in immunological research).

This page titled 15.3J: Serine Proteases is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.3J.3 https://bio.libretexts.org/@go/page/5411
15.3K: Animal Circulatory Systems

An efficient circulatory system has:

a fluid, e.g., blood, to carry the materials to be transported
a system of vessels to distribute the blood
a pump to push the blood through the system
exchange organs to carry out exchanges between the blood and external environment, e.g.
lungs and intestine to add materials to the blood;
lungs and kidneys to remove materials from the blood.
The most crucial demand on the circulatory system is the transport of oxygen and carbon dioxide to and from a gas exchange
organ such as lungs or gills and the tissues.
All exchanges between blood and cells occur in the capillaries.
The force of the pump that pushes blood through the arteries is dissipated as the blood flows through capillaries. Although
capillaries are tiny, the total cross-sectional area of all the capillaries supplied by a single artery is much greater than that of the
artery itself. Like a rapid, narrowly-confined stream spreading out over a flat plain, the force and velocity of flow diminish
quickly.
This creates a problem:
If the pump is used to deliver blood with force to the gas exchange organ, little force remains to distribute the oxygenated blood
to the tissues.
If the pump is used to deliver blood with force to the tissues, little force remains to send the deoxygenated blood to the gas
exchange organ.

The Fish Heart

Figure 15.3.11.1 Fish heart

Most fishes have never solved this problem, which is probably why most of them are "cold-blooded".
Blood collected from throughout the fish's body enters a thin-walled receiving chamber, the atrium.
As the heart relaxes, the blood passes through a valve into the thick-walled, muscular ventricle.
Contraction of the ventricle forces the blood into the capillary networks of the gills where gas exchange occurs.
The blood then passes on to the capillary networks that supply the rest of the body where exchanges with the tissues occur.
Then the blood returns to the atrium.
While obviously adequate to the fish's needs, this is not a very efficient system. The pressure generated by contraction of the
ventricle is almost entirely dissipated when the blood enters the gills.

The Squid Hearts

15.3K.1 https://bio.libretexts.org/@go/page/5412
 Figure 15.3.11.2 Squid heart
This group of marine invertebrates has solved the problem by having separate pumps:
two gill hearts to force blood under pressure to the gills
a systemic heart to force blood under pressure to the rest of the body

The Frog and Lizard heart

Figure 15.3.11.3 Frog and lizard heart

The Frog Heart

The frog heart has 3 chambers: two atria and a single ventricle.
The atrium receives deoxygenated blood from the blood vessels (veins) that drain the various organs of the body.
The left atrium receives oxygenated blood from the lungs and skin (which also serves as a gas exchange organ in most
amphibians).
Both atria empty into the single ventricle.
While this might appear to waste the opportunity to keep oxygenated and deoxygenated bloods separate, the ventricle is divided
into narrow chambers that reduce the mixing of the two blood.
So when the ventricle contracts
oxygenated blood from the left atrium is sent, relatively pure, into the carotid arteries taking blood to the head (and brain)
deoxygenated blood from the right atrium is sent, relatively pure, to the pulmocutaneous arteries taking blood to the skin
and lungs where fresh oxygen can be picked up
Only the blood passing into the aortic arches has been thoroughly mixed, but even so it contains enough oxygen to supply
the needs of the rest of the body
Note that in contrast to the fish, both the gas exchange organs and the interior tissues of the body get their blood under full
pressure.

The Lizard Heart

Lizards have a muscular septum which partially divides the ventricle.
When the ventricle contracts, the opening in the septum closes and the ventricle is momentarily divided into two separate
chambers.
This prevents mixing of the two bloods.
The left half of the ventricle pumps oxygenated blood (received from the left atrium) to the body.
The right half pumps deoxygenated blood (received from the right atrium) to the lungs.

15.3K.2 https://bio.libretexts.org/@go/page/5412
Birds, Crocodiles, and Mammals
The septum is complete in the hearts of birds, crocodiles, and mammals providing two separate circulatory systems:
pulmonary for gas exchange with the environment
systemic for gas exchange (and all other exchange needs) of the rest of the body
The efficiency that results makes possible the high rate of metabolism on which the endothermy ("warm-bloodedness") of birds and
mammals depends.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 15.3K: Animal Circulatory Systems is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.3K.3 https://bio.libretexts.org/@go/page/5412
 SECTION OVERVIEW
15.4: Immune System
Topic hierarchy

15.4.1: 15.4T Allergies

15.4A: Clonal Selection and Immunological Memory

15.4B: Antibody-Antigen Binding

15.4C: B Cells and T Cells

15.4D: Antigen Receptors

15.4E: Histocompatibility Molecules

15.4F: Antigen Receptor Diversity

15.4G: Anatomy of the Immune System

15.4H: T Helper cells

15.4I: Cytotoxic T lymphocytes (CTL)

15.4J: Cell-Mediated Immunity

15.4K: Organ Transplants

15.4L: Bone Marrow Transplants

15.4M: Antigen Presentation

15.4N: The Immunological Synapse

15.4O: Dendritic Cells

15.4P: Passive Immunity

15.4Q: Innate Immunity

15.4R: The Complement System

15.4S: Inflammation

15.4U: Asthma

15.4V: AIDS

15.4.1 https://bio.libretexts.org/@go/page/5338
15.4W: Vaccines

This page titled 15.4: Immune System is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4.2 https://bio.libretexts.org/@go/page/5338
15.4.1: 15.4T Allergies
Immunologists, as well as the general public, use the term allergy in several different ways. An allergy is a harmful immune
response elicited by an antigen that is not itself intrinsically harmful. Examples:
The windblown pollen released by orchard grass has no effect on me but produces a violent attack of hay fever (known to
physicians as allergic rhinitis) in my wife.
She, on the other hand, can safely handle the leaves of poison ivy while if I do so, I break out in a massive skin rash a day or
two later.
Antigens that trigger allergies are often called allergens.

Four different immune mechanisms can result in allergic responses.

Immediate Hypersensitivities: These occur quickly after exposure to the allergen. They are usually mediated by antibodies of
the IgE class. Examples include hay fever, hives and asthma.
Antibody-Mediated Cytotoxicity: Cell damage caused by antibodies directed against cell surface antigens. Hence a form of
autoimmunity. Examples include Hemolytic disease of the newborn (Rh disease) and Myasthenia gravis (MG)
Immune Complex Disorders: Damage caused by the deposit in the tissues of complexes of antigen and their antibodies.
Examples include Serum sickness and Systemic lupus erythematosus (SLE)
Cell-Mediated Hypersensitivities: These reactions are mediated by CD4+ T cells. Examples:
The rash produced following exposure to poison ivy. Because it takes a day or two for the T cells to mobilize following exposure to
the antigen, these responses are called delayed-type hypersensitivities (DTH). Those, like poison ivy, that are caused by skin
contact with the antigen are also known as contact sensitivities or contact dermatitis.
certain autoimmune diseases, including
Type 1 diabetes mellitus
Multiple sclerosis (MS)
Rheumatoid arthritis (RA)

Immediate Hypersensitivities
Local Anaphylaxis

Figure 15.4.20.1 Mast cell

The constant region of IgE antibodies (shown in blue) has a binding site for a receptor present on the surface of basophils and their
tissue-equivalent the mast cell. These cell-bound antibodies have no effect until and unless they encounter allergens (shown in red)
with epitopes that can bind to their antigen-binding sites. When this occurs, the mast cells to which they are attached
explosively discharge their granules by exocytosis. The granules contain a variety of active agents including histamine;
synthesize and secrete other mediators including leukotrienes and prostaglandins.
Release of these substances into the surrounding tissue causes local anaphylaxis: swelling, redness, and itching. In effect, each
IgE-sensitized mast cell is a tiny bomb that can be exploded by a particular antigen. The most common types of local anaphylaxis
are:
allergic rhinitis (hay fever) in which airborne allergens react with IgE-sensitized mast cells in the nasal mucosa and the tissues
around the eyes;
bronchial asthma in which the allergen reaches the lungs either by inhalation or in the blood

15.4.1.1 https://bio.libretexts.org/@go/page/5456
 hives (physicians call it urticaria) where the allergen usually enters the body in food.
Leukotrienes are far more potent than histamine in mediating these reactions.

Figure 15.4.20.2 Arachidonic acid

Leukotrienes and prostaglandins are derivatives of arachidonic acid (AA) an unsaturated fatty acid produced from membrane
phospholipids. The principal pathways of arachidonic acid metabolism are
the 5-lipoxygenase pathway, which produces a collection of leukotrienes (LT) and
the cyclooxygenase pathway, which yields a number of prostaglandins (PG) and thromboxanes (Tx).
All three are synthesized by monocytes and macrophages. Mast cells and basophils generate a mixture of leukotrienes. The
products of both pathways act in concert to cause inflammation with prostaglandins producing fever and pain. Aspirin, ibuprofen,
and certain other nonsteroidal anti-inflammatory drugs (NSAIDs) achieve their effects (fever and pain reduction) by blocking the
activity of cyclooxygenase.
Some people respond to environmental antigens (e.g., pollen grains, mold spores) with an unusually vigorous production of IgE
antibodies. Why this is so is unclear; heredity certainly plays a role. In any case, the immune system of these people is tilted
toward the production of T helper cells of the Th2 subtype. These release interleukin 4 (IL-4) and interleukin 13 (IL-13) on the B
cells that they "help". These lymphokines promote class switching in the B cell causing it to synthesize IgE antibodies.
An inherited predisposition to making IgE antibodies is called atopy. Atopic people are apt to have higher levels of circulating IgE
(up to 12 µg/ml) than is found usually (about 0.3 µg/ml). Whereas only 20–50% of the receptors on mast cells are normally
occupied by IgE, all the receptors may be occupied in atopic individuals.

Skin Testing
When the problem allergen is not obvious, it can often be identified by skin testing. A panel of suspected allergens is injected into
separate sites in the skin and each site is observed for the development of a "wheal and flare" reaction. The wheal is a sharply
delineated soft swelling surrounded by the flare - a reddened area. Both are caused by the release of leukotrienes at the site, which
increase the flow of blood to the site making it swollen and red.
A positive skin test occurs within minutes or even seconds (in contrast to patch testing for DTH responses).

Systemic Anaphylaxis
Some allergens can precipitate such a massive IgE-mediated response that a life-threatening collapse of the circulatory and
respiratory systems may occur.
Frequent causes:
insect (e.g., bee) stings
many drugs (e.g., penicillin)
a wide variety of foods. Egg white, cow's milk, and nuts are common offenders in children; in fact, some school systems in the
US now ban peanuts and peanut-butter sandwiches when they have a student at risk of systemic anaphylaxis from exposure to
peanuts. Fish and shellfish are frequent causes of anaphylaxis in adults.
Treatment of systemic anaphylaxis centers on the quick administration of adrenaline, antihistamines, and if shock has occurred then
intravenous fluid replacement.
An example of systemic anaphylaxis

15.4.1.2 https://bio.libretexts.org/@go/page/5456
 Figure 15.4.20.3 Reaction to bee sting
The three graphs show the physiological responses of a physician (Dr. Vick) stung by a single bee while on a picnic with coworkers
(fortunately some with medical training!). Dr. Vick required cardiac massage and intravenous injections of adrenaline at the times
shown. He and his colleagues worked in a laboratory studying bee venom, but prior to this episode he had no idea that he had
developed such extreme susceptibility. [Courtesy of Dr. J. Vick from L. M. Lichtenstein, "Allergic Responses to Airborne Allergens
and Insect Venoms", Fed. Proc. 36:1727, 1977.]

Desensitization
So far, the most effective preventive for IgE-mediated allergies is to inject the patient with gradually-increasing doses of the
allergen itself. The goal is to shift the response of the immune system away from Th2 cells in favor of Th1 cells. Unfortunately, this
therapy takes a long time and the results are too often disappointing. Clinical trials are now underway to test the safety and efficacy
of a complex of ragweed pollen allergen with chemically-modified DNA. This complex binds to the immune receptor TLR-9
causing a shift of the immune response from Th2 to Th1 much more rapidly than desensitization by the allergen alone.

Anti-IgE Antibodies
IgE molecules bind to mast cells and basophils through their constant region. If you could block this region, you could interfere
with binding — hence sensitization of — these cells. Humanized monoclonal antibodies specific for the constant region of IgE are
in clinical trials. They have shown some promise against asthma and peanut allergy, but such treatment will probably have to be
continued indefinitely (and will be very expensive).

IgE-Independent Allergic Reactions

Figure 15.4.20.4 Mast cell

Mast cells have surface receptors in addition to IgE molecules. Binding of ligands to these other receptors can also trigger
degranulation and immediate anaphylactic responses. Some culprits are:
pathogen-associated molecular patterns (PAMPs)
substance P
some components of wasp venoms
some antibiotics

Antibody-Mediated Cytotoxicity
In these disorders, the person produces antibodies directed against antigens present on the surface of his or her own cells. Thus
these qualify as autoimmune disorders. Some examples:
hemolytic disease of the newborn (Rh disease)

15.4.1.3 https://bio.libretexts.org/@go/page/5456
 immune hemolytic anemia
immune thrombocytopenic purpura
myasthenia gravis (MG)
thyrotoxicosis (Graves' disease)
pemphigus and pemphigoid, in which the antibodies are directed against the proteins in desmosomes (pemphigus) or
hemidesmosomes (pemphigoid).
Goodpasture's Syndrome
Binding of antibodies to the surface of the cell can result in:
phagocytosis of the cell
lysis of the cell
damage to molecules on the cell surface (e.g., myasthenia gravis)
activation of cell-surface receptors (e.g., thyrotoxicosis)

Hemolytic Disease of the Newborn (Rh Disease)

Rh antigens are expressed at the surface of red blood cells. During pregnancy, there is often a tiny leakage of the baby's red blood
cells into the mother's circulation. If the baby is Rh-positive (having inherited the trait from its father) and the mother Rh-negative,
these red cells will cause her to develop antibodies against the Rh antigen. The antibodies, usually of the IgG class, may not
develop fast enough to cause problems for that child, but can cross the placenta and attack the red cells of a subsequent Rh+ fetus.
This destroys the red cells producing anemia and jaundice. The disease may be so severe as to kill the fetus or even the newborn
infant.
Although certain other red cell antigens (in addition to Rh) sometimes cause problems for a fetus, an ABO incompatibility does
not. Why is an Rh incompatibility so dangerous when ABO incompatibility is not? It turns out that most anti-A or anti-B antibodies
are of the IgM class and these do not cross the placenta. In fact, an Rh-/type O mother carrying an Rh+/type A, B, or AB fetus is
resistant to sensitization to the Rh antigen. Presumably her anti-A and anti-B antibodies destroy any fetal cells that enter her blood
before they can elicit anti-Rh antibodies in her.
This phenomenon has led to an extremely effective preventive measure to avoid Rh sensitization. Shortly after each birth of an Rh+
baby, the mother is given an injection of anti-Rh antibodies. The preparation is called Rh immune globulin (RhIG) or Rhogam.
These passively acquired antibodies destroy any fetal cells that got into her circulation before they can elicit an active immune
response in her.
Rh immune globulin came into common use in the United States in 1968, and within a decade the incidence of Rh hemolytic
disease became very low.

Immune Hemolytic Anemia

Some people synthesize antibodies against their own red blood cells, and these may lyze the cells producing anemia. Infections,
cancer, or an autoimmune disease like systemic lupus erythematosus (SLE) are often involved. Many drugs (e.g. penicillin,
quinidine) can also trigger the disorder. In these cases, stopping the drug usually brings about a quick cure.

Immune Thrombocytopenic Purpura

This is an autoimmune disorder in which the patient develops antibodies against his or her own platelets (thrombocytes). The life
span of the platelets may be reduced from the normal of 8 days to as little as 1 hour, and platelet counts may drop from a normal of
140,000–440,000/µl to 20,000/µl or less. This greatly interferes with normal clotting, causing
external bleeding (e.g., from the nose)
internal bleeding into the skin causing purple patches (called purpura)

15.4.1.4 https://bio.libretexts.org/@go/page/5456
 Figure 15.4.20.4 Platelet count graph
The fact that antibodies are the culprit was dramatically demonstrated by using a patient's serum to passively — but only
temporarily —transfer the disorder to a normal recipient. The graph shows the decline and recovery in the platelet count of a
normal human subject receiving two transfusions of serum from a patient with thrombocytopenic purpura. [From W. J. Harrington
et al., J. Lab. Clin. Med. 38:1, 1951.]
Often no cause of the disorder can be found (the physicians call it "idiopathic"). Some cases are triggered by drugs like quinine,
aspirin, digitoxin, and sulfa drugs. These cases can be cured by stopping the drug. The idiopathic cases can sometimes be helped by
giving corticosteroids and/or removing the patient's spleen. Rituximab, a monoclonal antibody directed against B cells is also used.
If these treatments are inadequate, attempts can be made to increase the platelet count by giving synthetic agonists (e.g.,
Romiplastin [Nplate®]) that stimulate the production of thrombopoietin.

Myasthenia Gravis (MG)

The hallmark of this autoimmune disorder is weakness of the skeletal muscles, especially those in the upper part of the body. It is
caused by antibodies that attack the acetylcholine (ACh) receptors at the subsynaptic membrane of neuromuscular junctions. As
the number of receptors declines, the ACh released with the arrival of a volley of nerve impulses is inadequate to generate end-
plate potentials (EPPs) of the normal size. After repeated stimulation, the EPPs fail to reach the threshold needed to generate an
action potential and the muscle stops responding.
The signs and symptoms of myasthenia gravis can be quickly but only temporarily relieved by injecting a drug that inhibits the
action of cholinesterase. This prolongs the action of ACh at the neuromuscular junction. The immunosuppressant action of
corticosteroids, like prednisone, can provide long-term improvement for patients. The exclusive role of antibodies (of the IgG
class) in this disorder is demonstrated by the presence of the disease in the newborn babies of mothers with the disorder. As these
antibodies, which the fetus had received from the mother's circulation, disappear (in 1–2 weeks), so do all signs of the disease.

Thyrotoxicosis (Graves' disease))

In this disorder, the patient has antibodies that bind to the TSH receptors on the thyroxine-secreting cells of the thyroid. These
antibodies mimic the action of TSH itself (thus they behave as a TSH agonist) and trigger secretion of thyroxine (T4) and T3 by the
thyroid gland. The role of antibodies (of the IgG class) in this disorder is demonstrated by the presence of the disease in the
newborn babies of mothers with the disorder. As these antibodies, which the fetus had received from the mother's circulation,
disappear (in 1–2 weeks), so do all signs of the disease.

Immune Complex Disorders

While binding of antibody to antigen is often a helpful — even life-saving — response, in some circumstances it causes
pathological changes.

Serum Sickness

15.4.1.5 https://bio.libretexts.org/@go/page/5456
 Figure 15.4.20.5 Irregular, lumpy deposits of immune complexes in a glomerulus courtesy of Dr. Frank J. Dixon
In passive immunization, an antiserum containing needed antibodies is injected into the patient. At one time, these antisera were
prepared by immunizing horses or sheep. While they did their intended work (usually to provide immediate protection to a person
exposed to diphtheria or tetanus), they also often later lead to a syndrome called serum sickness. The patient developed fever,
hives, arthritis and protein in the urine. After a week or two, the symptoms would disappear spontaneously.
Serum sickness is caused by the many extraneous proteins present in the antiserum. Being foreign to the recipient, an active
immunity develops against these proteins. The resulting antibodies bind to them forming immune complexes. These are carried
by the blood and deposited in the walls of blood vessels as well as in the glomeruli of the kidneys (see figure).
Antigen-antibody complexes
bind to Hageman factor — one (XII) of the blood clotting factors. This activates inflammatory kinins.
bind to a system of serum proteins collectively known as complement. This generates
complement factor C3a, an anaphylatoxin which activates basophils and mast cells and causes them to release their
histamine and leukotrienes producing inflammation.
complement factor C5a, another anaphylatoxin which also attracts neutrophils to the site.
Thanks to nearly universal active immunization against both tetanus and diphtheria, serum sickness is now quite rare. However,
kidney damage (called glomerulonephritis) produced by deposits of immune complexes is found in some persistent infections.
Examples:
the protozoans that cause malaria
the flatworms that cause schistosomiasis and the filarial worms that cause elephantiasis and other diseases in humans.
the virus that causes hepatitis B.
In these cases, the continued presence of the pathogen provides a renewable source of antigen to combine with antibodies
synthesized by the host resulting in deposits of immune complexes.

Systemic Lupus Erythematosus (SLE)

Humans with SLE develop (for unknown reasons) antibodies against a wide variety of self components:
their own double-stranded DNA
nucleosomes
red blood cells
platelets
NMDA receptors in the brain
even their own IgG molecules. (These "anti-antibodies" are called rheumatoid factors. They are also found in people with
rheumatoid arthritis (hence the name) and, for a time, in people with mononucleosis.)
In all these cases of autoimmunity, immune complexes form and are deposited in the skin, joints, and kidneys where they initiate
inflammation.

15.4.1.6 https://bio.libretexts.org/@go/page/5456
Farmer's Lung
Repeated exposure to airborne organic particles, like mold spores, can elicit formation of antibodies. When these interact with
inhaled antigen, inflammation of the alveoli occurs. The sufferer develops a cough, fever, and difficulty in breathing. Once
removed from the source of antigen, the attack subsides within a few days.
Farmers exposed to moldy hay often develop this problem (technically known as extrinsic allergic alveolitis). Sugarcane workers,
cheese makers, mushroom growers, pigeon fanciers, and a number of other occupational or hobby groups are apt to develop
allergic alveolitis from exposure to the spores and dusts associated with their activities.

Cell-Mediated Hypersensitivities
Cell-mediated hypersensitivities can occur with extrinsic antigens or with internal ("self") antigens.

Extrinsic Antigens
The most common example of cell-mediated hypersensitivity to external antigens is the contact dermatitis caused in some people
when their skin is exposed to a chemical to which they are allergic. Some examples:
the catechols found in poison ivy, poison oak, and poison sumac
nickel (often used in jewelry)
some dyes
certain organic chemicals used in industry
In every case, these simple chemicals probably form covalent bonds with proteins in the skin, forming the antigen that initiates the
immune response. Dendritic cells in the skin take up the complex, process it, and "present" it to CD4+ T cells in nearby lymph
nodes. Because it takes a day or two for the CD4+ T cells to mobilize to the affected area of skin, these cases are examples of
delayed-type hypersensitivity (DTH).
When a patient is unsure of what chemical is causing the dermatitis, the physician can try a patch test. Pieces of gauze
impregnated with suspected allergens are placed on the skin. After 48 hours, they are removed and each site is examined for a
positive response (a reddened, itching, swollen area).

Intrinsic ("self") Antigens

Cell-mediated hypersensitivities to "self" cause autoimmune diseases. Examples:
Type 1 diabetes mellitus
Multiple sclerosis (MS)
Rheumatoid arthritis (RA)
Type 1 diabetes mellitus
In this disease, T cells initiate the destruction of the insulin-producing beta cells of the islets of Langerhans in the pancreas. The
chief culprits are CD8+ cytotoxic T lymphocytes (CTL) aided and abetted by CD4+ helper T cells of the Th1 subset. Although
antibodies against beta cell antigens are also found, these appear to be a secondary effect. Evidence: a diabetic boy with X-linked
agammaglobulinemia so unable to make any antibodies at all.
Multiple Sclerosis (MS)

In this case, T cells — again mostly Th1 cells — initiate an attack that destroys the myelin sheath of neurons. As the disease
progresses, other cells (e.g. macrophages) as well as antibodies participate in causing the damage.
Rheumatoid Arthritis (RA)
In this disorder, antibodies and T cells — again probably Th1 cells — react to antigens in the joints and release tumor necrosis
factor-alpha (TNF-α) with resulting inflammation and damage to the joints.
A genetically engineered fusion protein consisting of the TNF receptor fused to the constant region of human IgG1 has shown
promise as a treatment for RA. Given by injection, the fusion protein binds TNF-α and interferes with its action.

Autoimmune disorders are more common in females than in males

Graves' disease, systemic lupus erythematosus (SLE), multiple sclerosis, and rheumatoid arthritis are all more common in women
than in men. The sex bias ranges from 9:1 for SLE to >2:1 for multiple sclerosis and rheumatoid arthritis. Why?

15.4.1.7 https://bio.libretexts.org/@go/page/5456
The answer is unclear, but hormones are probably involved.
A few clues:
In mice susceptible to Type 1 diabetes, testosterone seems to play a key role.
Castration causes male mice to become as susceptible as females.
Giving androgens like testosterone to females protects them.
High levels of estrogen and progesterone suppress Th1 responses (cell-mediated immunity).
Pregnant women — with extra-high levels of these hormones — produce large numbers of immunosuppressive regulatory T
cells. Together these two responses may account for the improvement that often occurs in multiple sclerosis and rheumatoid
arthritis during pregnancy (an improvement that ends after birth).
High levels of these hormones promote Th2 responses (antibody-mediated immunity). SLE results from antigen-antibody
complexes and so it is not surprising that pregnancy does not help — and in some women actually exacerbates — this
autoimmune disorder.

The Hygiene Hypothesis

Allergies, like asthma and hay fever, and some autoimmune diseases are more common in regions with good sanitation.
For example,
Crohn's disease, an inflammation of the small intestine and
ulcerative colitis, an inflammation of the large intestine
are rare in developing countries with poor sanitation but have become more common in developed regions with good sanitation.
Why?
No one knows for certain, but one intriguing possibility, called the hygiene hypothesis, is that infection by parasitic worms
(helminths) shifts the balance of the immune response:
promoting regulatory T cells (Treg) with their anti-inflammatory cytokines IL-10 and TGF-β and
inhibiting pro-inflammatory effector T cells, e.g., Th17 cells.
Small clinical trials of feeding whipworm (a nematode) eggs to patients with Crohn's disease or ulcerative colitis have begun. After
the eggs develop into mature worms in their intestine, most patients showed marked improvement of their symptoms.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 15.4.1: 15.4T Allergies is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4.1.8 https://bio.libretexts.org/@go/page/5456
15.4A: Clonal Selection and Immunological Memory

The ability of the immune system to respond to an antigen exists before it ever encounters that antigen. The immune system relies
on the prior formation of an incredibly diverse population of:
B cells (B lymphocytes) each with its surface covered with thousands of identical copies of a receptor for antigen (the B-cell
receptor for antigen = BCR)
T cells (T lymphocytes) each with its surface covered with thousands of identical copies of a T-cell receptor for antigen (TCR)

Figure 15.4.1.1 Clonal selection

The above figure illustrates the activation of the one B cell in a pool of B cells whose BCR is specific for an epitope (small dark
spheres) on the antigen. This phenomenon is called clonal selection because it is antigen that selects particular lymphocytes for
clonal expansion. Clonal selection leads to the eventual production of:
A pool of antibody-secreting plasma cells. Plasma cells are B-cells that have tooled up (e.g., forming a large endoplasmic
reticulum) for massive synthesis and secretion of an antibody. The antibody is the secreted version of the BCR. (For clarity,
each BCR is shown with a single binding site for the epitope; actually, the BCRs are IgM and each has 10 identical binding
sites.
A pool of "memory" cells. These are B lymphocytes with receptors of the same specificity as those on the original activated B
cell.

How B cells and T cells meet antigens

Fig.15.4.1.2 Postcapillary venule

What is the probability that those few lymphocytes able to bind to a particular epitope will actually encounter the antigen carrying
that epitope?
Surprisingly, it is quite high because both B cells and T cells migrate in and out of lymph nodes and the spleen. Lymph nodes serve
as lymph filters, trapping foreign matter that gains access to the tissues. It has been shown that as much as 99% of the bacteria

15.4A.1 https://bio.libretexts.org/@go/page/5428
entering a node are removed by it. Similarly, the spleen traps antigens that gain access to the blood. Even if an invader fails to enter
either lymphatic or blood vessels, its antigens can still reach lymph nodes and spleen carried there by dendritic cells that
engulf the antigen in the tissues
migrate in the lymphatic vessels to nearby lymph nodes or spleen
process the antigen and "present" it to T cells and also B cells

Figure 15.4.1.4 Graft rejection in a mouse

Graft rejection is a form of cell-mediated immunity. If a piece of skin from a mouse of one strain (B) is grafted onto the flank of a
mouse of a second strain (A), the graft does well at first. Blood vessels from the host grow into it, and it functions normally. After
some 10–14 days, however, the blood supply to the graft breaks down and the graft degenerates. Finally it is sloughed off like an
old scab. This is called a first-set rejection. That the graft rejection is an immune response is demonstrated by now grafting the
mouse with two pieces of skin a repeat of skin from strain B and skin from another strain (C)
The results are quite different.
The B skin may not even survive long enough to acquire a blood supply. It is rejected in a much shorter period (less than a
week). This "second-set" phenomenon is the T-cell equivalent of the secondary "memory" response of B cells. Its specificity
and memory is shown by the fact that
The graft of C skin is rejected in the normal "first-set" period.

This page titled 15.4A: Clonal Selection and Immunological Memory is shared under a CC BY 3.0 license and was authored, remixed, and/or
curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is
available upon request.

15.4A.2 https://bio.libretexts.org/@go/page/5428
15.4B: Antibody-Antigen Binding
Antibodies are proteins synthesized and secreted by B cells that bind to antigens. Most antigens are macromolecules: proteins,
polysaccharides, even DNA and RNA. The interaction occurs by noncovalent forces (like that between enzymes and their
substrate) between the antigen-combining site on the antibody and a portion of the antigen called the antigenic determinant or
epitope.

Figure 15.4.2.1 Precipitation between antibodies and antigen

These photos show one type of interaction — precipitation — between antibodies and antigen.
a. The tube contains antibodies to the Type III pneumococcal polysaccharide isolated from the capsule surrounding the
bacteria.
b. A solution of the polysaccharide is added.
c. The formation of insoluble antigen-antibody complexes is revealed by the almost instantaneous appearance of turbidity.
d. After an hour, the complexes settle out as a precipitate. If the proportion of antigen to antibody in the mixture is selected
properly, the fluid above the precipitate will be devoid of both.
In the human body, this binding can literally be life-saving. The capsule that surrounds pneumococci protects them from
phagocytosis. Pneumococci that fail to make a capsule — "R" forms — do not cause disease. If the appropriate antibodies are
present in the body, they combine with the capsule. Coated with protein instead of polysaccharide, the pneumococci are now easy
to ingest.

Figure 15.4.2.2 Phagocytosis of antibody-coated pneumococci courtesy W. B. Wood, M. R. Smith, and B. Watson, Journal of
Experimental Medicine 84:387, 1946
These photomicrographs show phagocytosis of antibody-coated pneumococci.
Left: A neutrophil extends a pseudopod toward two pneumococci.
Center: these bacteria have been engulfed (arrows), and the neutrophil is beginning to engulf four more pneumococci at the
upper right.
Right: Two pneumococci have escaped.
In the days before antibiotics, the start of antibody production by the immune system of the patient marked the turning point in the
progression of the disease.

The Antigen-Combining Site

15.4B.1 https://bio.libretexts.org/@go/page/5430
 Figure 15.4.2.3 IgG antibody
The fig. 15.4.2.3 shows the primary structure of an IgG antibody. Different IgG antibodies differ most markedly at the so-called
hypervariable regions (shown in red):
three in the heavy chain
three in the light chain
In the three-dimensional (tertiary) structure of the molecule, the 6 hypervariable regions are brought close together and make up the
antigen-combining site. For this reason, the hypervariable regions are also called complementarity determining regions (CDRs).

Figure 15.4.2.5 Space-filling model of the same antibody courtesy of A. G. Amit

The fig. 15.4.2.4 shows the tertiary structure of one arm of an antibody specific for the lysozyme found in hen's egg white (upper
right) bound to lysozyme (lower left).
The following are indicated on the diagram:
constant region of the light chain (CL) and the first constant region of the heavy chain (CH)
variable regions of the heavy (VH) and light chains (VL)
the third hypervariable region of the heavy (Hv3H) and light (Hv3L) chains. The importance of the pair of third hypervariable
or complementarity determining regions in binding the epitope is typical of both antibodies and of T cell receptors for antigen.

15.4B.2 https://bio.libretexts.org/@go/page/5430
 This makes good sense as the opportunities for genetic diversity at those sites is far greater than for the first and second CDRs.
Gln121 is a glutamine that is a dominant feature of the epitope on lysozyme
The fig. 15.4.2.5 is a space-filling model of the same antibody with the light chain in yellow, the heavy chain in blue. The view is
looking down on the epitope-binding surface (left) and the epitope on lysozyme (right). In the antigen-antibody complex, the two
surfaces fit snugly together. The 17 amino acid residues that contact lysozyme in the antigen-antibody complex are numbered (1–7
on the L chain, 8–17 on the H chain. The 16 amino acid residues of lysozyme that contact the antibody; that is, that make up its
epitope are also numbered. Number 14 is Gln-121. The complementarity of the antigen-binding site and the epitope, their
respective shapes and the opportunities for multiple noncovalent interactions determine how strongly the two bind together. The
strength of the binding of an antibody to its antigen is called its affinity.

This page titled 15.4B: Antibody-Antigen Binding is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4B.3 https://bio.libretexts.org/@go/page/5430
15.4C: B Cells and T Cells
Lymphocytes are one of the five kinds of white blood cells (leukocytes) that circulate in the blood. Although mature lymphocytes
all look pretty much alike, they are extraordinarily diverse in their functions. The most abundant lymphocytes are B lymphocytes
(B cells) and T lymphocytes (T cells). B cells are produced in the bone marrow. The precursors of T cells are also produced in the
bone marrow but leave the bone marrow and mature in the thymus (which accounts for their designation). Each B cell and T cell is
specific for a particular antigen. What this means is that each is able to bind to a particular molecular structure. The specificity of
binding resides in a receptor for antigen: the B cell receptor (BCR) for antigen and the T cell receptor (TCR) respectively.
Both BCRs and TCRs share these properties:
They are integral membrane proteins.
They are present in thousands of identical copies exposed at the cell surface.
They are made before the cell ever encounters an antigen.
They are encoded by genes assembled by the recombination of segments of DNA.
They have a unique binding site.
This site binds to a portion of the antigen called an antigenic determinant or epitope.
The binding, like that between an enzyme and its substrate depends on complementarity of the surface of the receptor and the
surface of the epitope.
The binding occurs by non-covalent forces (again, like an enzyme binding to its substrate).
Successful binding of the antigen receptor to the epitope, if accompanied by additional signals, results in:
stimulation of the cell to leave G0 and enter the cell cycle.
Repeated mitosis leads to the development of a clone of cells bearing the same antigen receptor; that is, a clone of cells of
the identical specificity.
BCRs and TCRs differ in their structure, the genes that encode them and the type of epitope to which they bind.

B Cells

Fig.15.4.3.1 B cell and lymphokines

BCRs bind intact antigens (like diphtheria toxoid, the protein introduced into your body in the DTP vaccine). These may be
soluble molecules present in the extracellular fluid
intact molecules that the B cell plucks from the surface of antigen-presenting cells like macrophages and dendritic cells
The bound antigen molecules are engulfed into the B cell by receptor-mediated endocytosis.
The antigen is digested into fragments which are then displayed at the cell surface nestled inside a class II histocompatibility
molecule.
Helper T cells specific for this structure (i.e., with complementary TCRs) bind the B cell and secrete lymphokines that:
stimulate the B cell to enter the cell cycle and develop, by repeated mitosis, into a clone of cells with identical BCRs
switch from synthesizing their BCRs as integral membrane proteins to a soluble version
differentiate into plasma cells that secrete these soluble BCRs, which we now call antibodies

15.4C.1 https://bio.libretexts.org/@go/page/5432
T Cells
The surface of each T cell also displays thousands of identical T cell receptors (TCRs). There are two types of T cells that differ in
their TCR:
alpha/beta (αβ) T cells. Their TCR is a heterodimer of an alpha chain with a beta chain. Each chain has a variable (V) region
and a constant (C) region. The V regions each contain 3 hypervariable regions that make up the antigen-binding site.
gamma/delta (γδ) T cells. Their TCR is also a heterodimer of a gamma chain paired with a delta chain.
The discussion that follows now concerns alpha/beta T cells. Gamma/delta T cells, which are less well understood, are discussed at
the end.
The TCR (of alpha/beta T cells) binds a bimolecular complex displayed at the surface of some other cell called an antigen-
presenting cell (APC). This complex consists of a fragment of an antigen lying within the groove of a histocompatibility molecule.
The complex has been compared to a "hot dog in a bun".

Figure 15.4.3.2 T cell structure

Most of the T cells in the body belong to one of two subsets. These are distinguished by the presence on their surface of one or the
other of two glycoproteins designated:
CD4
CD8
Which of these molecules is present determines what types of cells the T cell can bind to.
CD8+ T cells bind epitopes that are part of class I histocompatibility molecules. Almost all the cells of the body express class I
molecules.
CD4+ T cells bind epitopes that are part of class II histocompatibility molecules. Only specialized antigen-presenting cells
express class II molecules. These include dendritic cells, phagocytic cells like macrophages and B cells.

CD8 + T cells
The best understood CD8+ T cells are cytotoxic T lymphocytes (CTLs). They secrete molecules that destroy the cell to which they
have bound.

Figure 15.4.3.3 cytotoxic T lymphocytes

15.4C.2 https://bio.libretexts.org/@go/page/5432
This is a very useful function if the target cell is infected with a virus because the cell is usually destroyed before it can release a
fresh crop of viruses able to infect other cells. An example will show the beauty and biological efficiency of this mechanism.

 Example

Every time you get a virus infection, say influenza (flu), the virus invades certain cells of your body (in this case cells of the
respiratory passages). Once inside, the virus subverts the metabolism of the cell to make more virus. This involves synthesizing
a number of different macromolecules encoded by the viral genome. In due course, these are assembled into a fresh crop of
virus particles that leave the cell (often killing it in the process) and spread to new target cells. Except while in transit from
their old homes to their new, the viruses work inside of your cells safe from any antibodies that might be present in blood,
lymph, and secretions. But early in the process, infected cells display fragments of the viral proteins in their surface class I
molecules. CTLs specific for that antigen will be able to bind to the infected cell and often will be able to destroy it before it
can release a fresh crop of viruses.

In general, the role of the CD8+ T cells is to monitor all the cells of the body, ready to destroy any that express foreign antigen
fragments in their class I molecules.

CD4 + T cells
CD4+ T cells bind an epitope consisting of an antigen fragment lying in the groove of a class II histocompatibility molecule. CD4+
T cells are essential for both the cell-mediated and antibody-mediated branches of the immune system:
cell-mediated immunity: These CD4+ cells bind to antigen presented by antigen-presenting cells (APCs) like phagocytic
macrophages and dendritic cells. The T cells then release lymphokines that attract other cells to the area. The result is
inflammation: the accumulation of cells and molecules that attempt to wall off and destroy the antigenic material (an abscess is
one example, the rash following exposure to poison ivy is another).
antibody-mediated immunity: These CD4+ cells, called helper T cells, bind to antigen presented by B cells. The result is the
development of clones of plasma cells secreting antibodies against the antigenic material.

 T cells

AIDS provides a vivid illustration of the importance of CD4+ T cells in immunity. The human immunodeficiency virus (HIV)
binds to CD4 molecules and thus is able to invade and infect CD4+ T cells. As the disease progresses, the number of CD4+ T
cells declines below its normal level of about 1000 per microliter (µl). A partial explanation for this may be the unceasing
efforts of the patient's CD8+ T cells to destroy the infected CD4+ cells. However, it turns out that only a small fraction of the
patients CD4+ T cells are infected at any given time. How uninfected CD4+ cells may be induced to commit suicide is
discussed in the page on apoptosis.
When the number of CD4+ T cells drops below 400 per microliter, the ability of the patient to mount an immune response
declines dangerously. Not only does the patient become hypersusceptible to pathogens that give all of us grief but also to
microorganisms, especially viruses and fungi, that normally inhabit our tissues without harming us. These opportunistic
infections can be fatal.

Building the T-cell Repertoire

T cells have receptors (TCRs) that bind to antigen fragments nestled in MHC molecules. But all cells express class I MHC
molecules containing fragments derived from self proteins. Many cells express class II MHC molecules that also contain self
peptides. This presents a risk to the animal of the T cells recognizing these self-peptide/self-MHC complexes and mounting an
autoimmune attack against them. Fortunately, this is usually avoided by a process of selection that goes on in the thymus (where all
T cells develop).
The process works like this:
The precursors of T cells like all blood cells are formed in the bone marrow.
These cells then migrate to the cortex of the thymus. At this time they have neither a complete TCR nor either CD4 or CD8
(thus are called "double-negative" or DN cells).

15.4C.3 https://bio.libretexts.org/@go/page/5432
 In the cortex of the thymus they begin to form a TCR and synthesize both CD4 and CD8 (so now they are "double-positive" or
DP cells). The cortical cells of the thymus express a wide variety of small molecules, usually a peptide of 6–8 amino acids
derived from body proteins; that is, "self" proteins such as proteins within the cytosol and serum proteins - proteins circulating
in the blood and lymph nestled in a histocompatibility molecule (encoded by the MHC).
Most of the cells (~97%) will produce a TCR that does not bind to any of the peptide-MHC molecules present on the surface
of the cortical cells. Unless they can try again with a new TCR, these cells die by "neglect" (by apoptosis, actually).
Those remaining cells whose TCR has bound a peptide antigen presented in class II MHC molecule stop expressing CD8
and become CD4+ T cells. It is these cells that will go on to become
Th1 cells in cell-mediated immune responses
Th1 helper cells for cytotoxic T lymphocytes (CTLs)
Th2 helper cells for B cells
Those remaining cells whose TCR has bound a peptide antigen presented in class I MHC molecule stop expressing CD4 and
become CD8+ T cells.
Both sets of cells are said to have undergone positive selection.
After positive selection, these cells migrate to the medulla of the thymus.
There those cells whose TCR binds very strongly to complexes of self-peptide and self-MHC are destroyed (again by
apoptosis).
This process of negative selection is important as it eliminates cells that might otherwise mount an autoimmune attack. It is one
of the ways in which tolerance to self antigens is achieved. [Link to discussion of T-cell tolerance.]
The cells whose TCRs bind antigen at an affinity below the threshold that triggers apoptosis are free to leave the thymus and
migrate throughout the immune system (lymph nodes, spleen, etc.)
It is this population that we depend on to mount immune responses against foreign antigens. A TCR that binds self-peptide/self-
MHC with low affinity may well bind a foreign-peptide in self MHC with high affinity.

Gamma/Delta (γδ) T Cells

Gamma/delta T cells differ from their alpha/beta cousins in several ways:
Their TCR is encoded by different gene segments.
Their TCR binds to
antigens that can be intact proteins (just as antibodies do) as well as a variety of other types of organic molecules (often
containing phosphorus atoms).
antigens that are not "presented" within class I or class II histocompatibility molecules;
antigens that are not presented by "professional" antigen-presenting cells (APCs) like dendritic cells.
Most of these T cells have neither CD8 nor CD4 on their surface. This makes sense because they have no need to recognize
class I and class II histocompatibility molecules.
Gamma/Delta T cells, like alpha/beta T cells, develop in the thymus. However, they migrate from there into body tissues,
especially epithelia (e.g., intestine, skin, lining of the vagina), and don't recirculate between blood and lymph nodes (they
represent no more than 5% of the T cells in the blood and are even rarer in lymph nodes). They encounter antigens on the
surface of the epithelial cells that surround them rather than relying on the APCs found in lymph nodes.

What is the Function of γδ T cells?

That is still something of a mystery. Situated as they are at the interfaces between the external and internal worlds, they may
represent a first line of defense against invading pathogens. Their response does seem to be quicker than that of αβ T cells.
Curiously, many of the antigens to which γδ T cells respond are found not only on certain types of invaders (e.g., Mycobacterium
tuberculosis, the agent of tuberculosis) but also on host cells that are under attack by pathogens.
Knockout mice that cannot make γδ T cells are slower to heal injuries to their skin. They are also much more susceptible to skin
cancers than normal mice. Perhaps immune surveillance is one of the functions of γδ T cells.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

15.4C.4 https://bio.libretexts.org/@go/page/5432
This page titled 15.4C: B Cells and T Cells is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4C.5 https://bio.libretexts.org/@go/page/5432
15.4D: Antigen Receptors

Both B cells and T cells have surface receptors for antigen. Each cell has thousands of receptors of a single specificity; that is, with
a binding site for a particular epitope. T-cell receptors (TCRs) enable the cell to bind to and, if additional signals are present, to be
activated by and respond to an epitope presented by another cell called the antigen-presenting cell or APC. B-cell receptors
(BCRs) enable the cell to bind to and, if additional signals are present, to be activated by and respond to an epitope on molecules of
a soluble antigen. The response ends with descendants of the B cell secreting vast numbers of a soluble form of its receptors.
These are antibodies.

Antibodies
Antibodies are glycoproteins. They are built of subunits containing two identical light chains (L chains), each containing about
200 amino acids and two identical heavy chains (H chains), which are at least twice as long as light chains. The first 100 or so
amino acids at the N-terminal of both H and L chains vary greatly from antibody to antibody. T These are the variable (V) regions.
Unless members of the same clone (and often not even then), no two B cells are likely to secrete antibodies with the same variable
region. The amino acid sequence variability in the V regions is especially pronounced in 3 hypervariable regions. The tertiary
structure of antibodies brings the 3 hypervariable regions of both the L and the H chains together. Together they construct the
antigen binding site against which the epitope fits. For this reason, the hypervariable regions are also called complementarity
determining regions (CDRs). Only a few different amino acid sequences are found in the C-terminals of H and L chains. These
are the constant (C) regions.
Humans make two different kinds of C regions for their L chains producing kappa (κ) L chains and lambda (λ) L chains. They
also make five different kinds of C regions for their H chains producing:
mu (µ) chains (the H chain of IgM antibodies)
gamma (γ) chains (IgG)
alpha (α) chains (IgA)
delta (δ) chains (IgD)
epsilon (ε) chains (IgE)

Figure 15.4.4.2 Tertiary structure of L chain courtesy of Dr. D. R. Davies

The images above() represent the folded (tertiary) structure of an entire L chain (right side with thin connecting lines) and the V
region plus the first third of the C region of a heavy chain (left side; darker lines). Each circle represents the location in 3D space
of an alpha carbon. The filled circles at the top are amino acids in the hypervariable or complementary determining regions
(CDRs); they form the site that binds the antigen.
Antibody molecules have two functions to perform:
recognize and bind to an epitope on an antigen
trigger a useful response to the antigen
The division of labor is:
V regions are responsible for epitope recognition.
C regions are responsible for triggering a useful response

15.4D.1 https://bio.libretexts.org/@go/page/5434
So, V regions finger the culprit; the C regions take action.
If an antibody's H chains (see IgG above), are cut at its hinge region on the N-terminal side of the disulfide bonds holding the H
chains together, 3 fragments are produced:
2 Fab fragments ("fragment antigen-binding") and
1 Fc fragment ("fragment crystalline" — because the uniformity of this region allows crystals to form while the great diversity
of V regions prevents them from forming).
Why 5 kinds of heavy chains? To provide for different effector functions.
The 5 classes of antibodies
Class H chain L chain Subunits mg/ml Notes

transferred across
placenta; four
IgG gamma kappa or lambda H2L2 6–13
subclasses: IgG1-4 in
humans
first antibodies to
IgM mu kappa or lambda (H2L2)5 0.5–3 appear after
immunization
much higher
concentrations in
IgA alpha kappa or lambda (H2L2)2 0.6–3
secretions; two
subclasses

IgD delta kappa or lambda H2L2 <0.14 function uncertain

binds to basophils and

mast cells sensitizing
IgE epsilon kappa or lambda H2L2 <0.0004
them for certain
allergic reactions

"mg/ml" gives the concentration normally found in human serum. The subclasses of IgG and IgA are encoded by different C-
region gene segments.
If an antibody-secreting cell becomes cancerous, it will grow into a clone secreting its single class of molecule. The disease is
called multiple myeloma.

This page titled 15.4D: Antigen Receptors is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4D.2 https://bio.libretexts.org/@go/page/5434
15.4E: Histocompatibility Molecules
Histocompatibility molecules are glycoproteins expressed at the surface of almost all vertebrate cells. They get their name because
they are responsible for the compatibility — or rather the lack of it — of the tissues of genetically different individuals.
Monozygotic ("identical") human twins have the same histocompatibility molecules on their cells, and they can accept transplants
of tissue from each other. The rest of us have a set of histocompatibility molecules that is probably unique to us. A graft of our
tissue into another human will provoke an immune response which, if left unchecked, will end in the rejection of the transplant. So
the histocompatibility molecules of one individual act as antigens when introduced into a different individual. In fact, the
histocompatibility molecules are often called histocompatibility antigens or transplantation antigens.
The most rapid and severe rejection of foreign tissue occurs when there is a failure to properly match the donor and recipient for
the major histocompatibility molecules. There are two categories: class I and class II.

Class I Histocompatibility Molecules

Class I molecules consist of two polypeptide chains, a long one (on the left) of 346 amino acids — it is called the heavy chain —
and a short one (on the right) of 99 amino acids. The heavy chain consists of 5 main regions or domains:
three extracellular domains, designated here as N (includes the N terminal), C1, and C2
a transmembrane domain where the polypeptide chain passes through the plasma membrane of the cell
a cytoplasmic domain (with the C terminal) within the cytoplasm of the cell

Figure 1: Schematic representation of MHC class I (CC BY 2.5; atropos235).

he above figure shows a protein molecule called beta-2 microglobulin ("β2M"). It is not attached to the heavy chain by any
covalent bonds, but rather by a number of noncovalent interactions. The dark bars represent disulfide (S-S) bridges linking portions
of each domain (except the N domain). However, the bonds in S-S bridges are no longer than any other covalent bond, so if this
molecule could be viewed in its actual tertiary (3D) configuration, we would find that the portions of the polypeptide chains
containing the linked Cys are actually close together. The outermost domains ("N" and "C1") contain two segments of alpha helix
that form two ridges with a groove between them. A small molecule (e.g., a short peptide) is attached noncovalently in the groove
between the two alpha helices, rather like a hot dog in a bun(See fig. 15.4.5.2)
The two objects on the left of the image that look like candelabra represent the short, branched chains of sugars in this
glycoprotein. The regions marked "Papain" represent the places on the heavy chain that are attacked by the proteinase papain (and
made it possible to release the extracellular domains from the plasma membrane for easier analysis). The image represents the
structure of a class I histocompatibility molecule, called H-2K. Almost all the cells of an animal's body (in this case, a mouse) have
thousands of these molecules present in their plasma membrane. These molecules provide tissue identity and serve as major targets
in the rejection of transplanted tissue and organs. But tissue rejection is not their natural function. Class I molecules serve to
display antigens on the surface of the cell so that they can be "recognized" by T cells.
Humans synthesize three different types of class I molecules designated HLA-A, HLA-B, and HLA-C. (HLA stands for human
leukocyte antigen; because the molecules were first studied on leukocytes). These differ only in their heavy chain, all sharing the
same type of beta-2 microglobulin. The genes encoding the different heavy chains are clustered on chromosome 6 in the major

15.4E.1 https://bio.libretexts.org/@go/page/5436
histocompatibility complex (MHC). We inherit a gene for each of the three types of heavy chain from each parent so it is
possible, in fact common, to express two allelic versions of each type. Thus a person heterozygous for HLA-A, HLA-B, and HLA-
C expresses six different class I proteins. These are synthesized and displayed by most of the cells of the body (except those of the
central nervous system).

Histocompatibility molecules present antigens to T cells

Although histocompatibility molecules were discovered because of the crucial role they play in graft rejection, clearly evolution did
not give vertebrates these molecules for that function. So what is their normal function? The answer: to display antigens so that
they can be "seen" by T lymphocytes. The antigen receptor on T lymphocytes (or T cells, as they are commonly called) "sees" an
epitope that is a mosaic of the small molecule in the groove and portions of the alpha helices flanking it.

Figure 15.4.5.2 Histocompatibility molecule

The small molecules ("hot dogs") are enormously diverse. They probably represent fragments derived from all the proteins present
within the cell. These would include fragments of normal cell constituents, fragments of proteins encoded by intracellular parasites
(like viruses), and fragments of proteins encoded by mutated genes in cancer cells.

Class II Histocompatibility Molecules

Human class II molecules are designated HLA-D, and the genes encoding them are also located in the major histocompatibility
complex (MHC). Class II molecules consist of two transmembrane polypeptides. These interact to form a groove at their outer end
which, like class I molecules, always contains a fragment of antigen. But the fragments bound to class II molecules are derived
from antigens that the cell has taken in from its surroundings. Extracellular molecules are engulfed by endocytosis. The
endosomes fuse with lysosomes and their contents are partially digested. The resulting fragments are placed in class II molecules
and returned to the cell surface.
Class II molecules, in contrast to class I, are normally expressed on only certain types of cells. These are cells like macrophages
and B lymphocytes that specialize in processing and presenting extracellular antigens to T lymphocytes. Thus antigen presentation
by class II molecules differs from that by class I in two important ways:
All cells can present antigens with class I molecules, whereas only certain cells can do so with class II.
The antigen fragments (hot dogs) displayed in class I molecules are generated from macromolecules synthesized within the cell,
whereas those displayed in class II molecules have been acquired from outside the cell.

Class I and Class II molecules present antigen fragments to different subsets of T cells
Most of the T cells of the body belong to one of two distinct subsets: CD4+ or CD8+. CD4 and CD8 are surface glycoproteins.
Both CD4+ and CD8+ T cells have an antigen receptor (TCR) that "sees" a complex hot-dog-in-bun epitope. The CD8 molecules
on CD8+ T cells bind to a site found only on class I histocompatibility molecules (shown here as a gray hemisphere). The CD4
molecules on CD4+ T cells bind to a site found only on class II histocompatibility molecules (shown below as a yellow triangle).
However, neither type can be activated by simply binding its complementary epitope. Additional molecular interactions must take
place.

The CD8 + T Cell/Class I Interaction

Because of the need for CD8 to bind to a receptor site found only on class I histocompatibility molecules, CD8+ T cells are only
able to respond to antigens presented by class I molecules. Most CD8+ T cells are cytotoxic T cells (CTLs). They contain the
machinery for destroying cells whose class I epitope they recognize.

15.4E.2 https://bio.libretexts.org/@go/page/5436
 Figure 15.4.5.3 Class I CD8

 Example

Every time you get a viral infection, say influenza (flu), the virus invades certain cells of your body. Once inside, the virus
subverts the metabolism of the cell to make more virus. This involves synthesizing molecules encoded by the viral genome. In
due course, these are assembled into a fresh crop of virus particles that leave the cell (often killing it in the process) and spread
to new cells. Except while in transit from their old home to their new, the virus works inside cells safe from any antibodies. But
early in their intracellular life, infected cells display fragments of the viral proteins being synthesized in the cytoplasm in their
surface class I molecules. Any cytotoxic T cells specific for that antigen will bind to the infected cell and often will be able to
destroy it before it can release a fresh crop of virus.

The bottom line: the function of the body's CD8+ T cells is to monitor all the cells of the body ready to destroy any that express
foreign antigen fragments in their class I molecules.

The CD4 + T Cell/Class II Interaction

The CD4 molecules expressed on the surface of CD4+ T cells enable them to bind to cells presenting antigen fragments in class II
molecules but not in class I. Only certain types of cells, those specialized for taking up antigen from extracellular fluids, express
class II molecules. Among the most important of these are dendritic cells, macrophages (phagocytic cells that develop from
monocytes that have migrated from the blood to the tissues), and B lymphocytes ("B cells") that take up exogenous antigen by
receptor-mediated endocytosis.

Figure 15.4.5.4 Class II CD4

So CD4+ T cells see antigen derived from extracellular fluids and processed by specialized antigen-presenting cells. To respond to
an antigen, a CD4+ T cell must have a T cell receptor (TCR) able to recognize (bind to) a complex epitope comprising an
antigenic fragment displayed by a class II molecule, bind a site on the class II molecule (shown above as a yellow triangle) with its
CD4, and bind to costimulatory molecules on the antigen-presenting cell. If these conditions are met, the T cell becomes activated.
Activated T cells enter the cell cycle leading to the growth of a clone of identical T cells and begin to secrete lymphokines.
Lymphokines activate and recruit other cells (e.g., mast cells) to the region producing inflammation (e.g., to cope with a bacterial
infection). They also activate B cells enabling them to develop into a clone of antibody-secreting cells. The CD4+ T cells that
activate B cells are called Helper T cells.

15.4E.3 https://bio.libretexts.org/@go/page/5436
Contributors and Attributions
John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and made
possible by funding from The Saylor Foundation.

This page titled 15.4E: Histocompatibility Molecules is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4E.4 https://bio.libretexts.org/@go/page/5436
15.4F: Antigen Receptor Diversity
The human genome is presently estimated to contain 20–25 thousand genes. The number of T-cell receptors for antigen (TCRs)
that we make is estimated at 2.5 x 107; the number of different kinds of antibody molecules (BCRs) is probably about the same.
How could 2.5 x 104 genes encode 2.5 x 107 different TCRs and the same number of different BCRs?
The answer: each receptor chain
heavy (H) plus kappa (κ) or lambda (λ) chains for BCRs;
alpha (α) and beta (β) or gamma (γ) and delta (δ) chains for TCRs)
is encoded by several different gene segments. The genome contains a pool of gene segments for each type of chain. Random
assortment of these segments makes the largest contribution to receptor diversity.

B cells
Gene segment usage for BCRs
For the heavy (H) chains of BCRs (antibodies), the gene segments are:
51 VH segments. Each of these encodes most of the N-terminal of the antibody, including the first two (but not the third)
hypervariable or complementarity determining region (CDR).
27 DH (="diversity") gene segments. These encode part of the third CDR ("CDR3").
6 JH (="joining") gene segments. These encode the remainder of the V region of the BCR (including the remainder of CDR3).
9 CH gene segments. These encode the C region of the BCR (and the antibody derived from it). The C gene segments are
1 mu (µ); encodes the C region of IgM
1 delta (δ) for IgD
4 gamma (γ) gene segments for the four types of IgG
1 epsilon (ε) for IgE
2 alpha (α) gene segments for the two types of IgA

Figure 15.4.6.1 VH Locus

All of these gene segments are clustered in a complex locus on chromosome 14. During the differentiation of the B cell (and long
before any encounter with an antigen), the DNA in this locus is cut and recombined to make an intact gene for the heavy chain.
This gene can then be transcribed into pre-mRNA, which is then processed to form the mRNA that will be translated into the
heavy (H) polypeptide chain.

V(D)J Joining

15.4F.1 https://bio.libretexts.org/@go/page/5438
 Figure 15.4.6.2 V-D-J segment
Each gene segment (V, D, and J) has an adjacent Recombination Signal Sequence (RSS)
at the 3' end of each V segment
at both ends of each D segment
at the 3' end of each J segment
These are recognized by two proteins encoded by two Recombination Activating Genes
RAG-1
RAG-2
The RAG-1 and RAG-2 proteins cut through both strands of DNA at the RSS forming double-stranded breaks (DSBs).
Then the regular machinery for repairing DSBs (by nonhomologous end-joining) swings into action.
The cut ends are stitched together (ligated) to form:
a coding joint (D-J or V-DJ for heavy chains; V-J for light chains)
a signal joint (usually a loop of DNA deleting all the intervening DNA initially present between the 2 gene segments
chosen).
D-J joining occurs first; then the combined DJ segment (still attached to the cluster of constant region gene segments) is joined
to a V segment (as shown in the figure).
The V gene segment chosen may be thousands of base pairs away from the D-J segment so the chromosome must be drawn into
a loop to bring the two together. The loop is stabilized by
a protein designated CTCF ("CCCTC binding factor"; named for the nucleotide sequence to which it binds). The CTCF at
the D-J site on the DNA forms a dimer with the CTCF at the V site on the DNA binding the two regions together.
cohesin — the same protein complex that holds sister chromatids together during mitosis and meiosis.
In the process, the cluster of gene segments moves from the periphery of the nucleus (a region of inactive genes) to the center of
the nucleus (a region of active gene transcription).

 SCID
Some cases of severe combined immunodeficiency in humans (SCID) are caused by defects in V(D)J joining.
One version is caused by mutations in both copies of either RAG1 or RAG2.
Another is caused by mutations in a gene needed for nonhomologous end-joining. (No coding joint is formed even though a
signal joint forms normally.)

If the 51 VH, 27 DH, and 6 JH gene segments were assembled randomly (they probably are not), that would provide a minimum
of 8.3 x 103 different possible combinations. But the possibilities of antibody V region diversity turn out to be greater than that.
The recombination process is not precise.
The exact points of splicing between VH and DH and between DH and JHcan vary over several nucleotides
Extra nucleotides, called N regions, can also be inserted at these joints.
All of these add greatly to the diversity of CDR3.

Light chains
Once the H chain gene is assembled, transcribed, and translated, the resulting H chain can pair with an L chain that is itself the
product of a similar recombination process occurring

15.4F.2 https://bio.libretexts.org/@go/page/5438
 on chromosome 2 for kappa gene segments
on chromosome 22 for lambda gene segments

Antibodies (BCRs) Gene Segments Combinations

Vκ 40

Jκ 5 200 κ chains

Vλ 31

Jλ 4 124 λ chains

VH 51

DH 25

JH 6 7,650 H chains

Any H chain with any L chain (324) 2.5 x 106

As the table shows, this lays the foundation for a potential B-cell repertoire of 2.5 x 106 different antibody V regions. But the true
number is probably virtually limitless because of variation in the exact splice point and the introduction of N nucleotides both of
which increase the diversity of CDR3.

Diversity comes at a price

The combining of V, D, and J gene segments coupled with the random incorporation of extra nucleotides (N regions) at the joints,
creates enormous coding variability. It also creates a high risk (two times out of three) of introducing a frameshift so that the
codons for the rest of the V region encode nonsense. Although many B cells are wasted, the odds are not quite as bad as they seem.
If the B cell fails to make a functional product from the cluster of gene segments on one of its chromosomes, it can turn to the gene
segments on its homolog and try again. If it fails both times to make a functional kappa L chains, it still has two tries at making a
functional lambda L chain.

Somatic Hypermutation (SHM) and Antibody Diversity

The diversifying mechanisms described above take place before the B cell encounters antigen. After a B cell encounters antigen, it
may begin mitosis, growing into a clone of cells synthesizing the same BCR (and, eventually, secreting antibodies with the same
binding site). Point mutations can occur while this is going on. Some of these may generate a binding site with increased affinity
for its epitope. These are favorable mutations, and the "subclone" in which they occur tends to be favored and may replace the
ancestral clone. The result is affinity maturation — the production of antibodies of ever-increasing affinity for the antigen.

Class Switch Recombination (CSR)

Figure 15.4.6.3 Class switch

As B cells grow into a clone in response to antigen, they may rearrange their DNA once again. For example, a B cell that has
assembled a complete gene for the H chain of IgM (µ), may cut the gene on the 3´ side of the assembled V-region segments and
move the assembly to the 5´ side of another of its CH gene segments. Now the cell begins to make a different class of antibody,
such as IgG or IgA. But the antigen specificity of the antibody remains the same because the N-terminal of the H chain remains
unchanged (as does the entire L chain).
Class switch recombination enables the body to produce antibodies with different effector functions; that is, different means of
dealing with the same antigen. The ability of a B cell to switch CH gene segments depends on its receiving help from helper T
cells.

15.4F.3 https://bio.libretexts.org/@go/page/5438
T Cells

Alpha/beta (αβ) T cells

The most abundant T cells in the blood express a receptor for antigen (TCR) that is a heterodimer of two chains designated alpha
(α) and beta (β). Each of these is encoded by a gene assembled from V, D, J, and C gene segments. Like BCRs, there are multiple
variants of these gene segments arranged in clusters:
alpha chain gene segments on chromosome 14
beta chain gene segments on chromosome 7

T cell receptors (TCRs) Gene segments Combinations

Vα 50

Jα 50 2.5 x 103 alpha chains

Vβ 20

Jβ 13

Dβ 2 520 beta chains

Any alpha with any beta chain 1.3 x 106

And like B cells, the greatest diversity in the receptors of αβ T cells occurs in the third complementarity determining region
(CDR3) of the alpha and beta chains because of the junctional diversity between the V, J, and D segments and the addition of N
region nucleotides. However, T cells do not seem to use somatic mutation to increase receptor diversity. Actual measurements of
the repertoire in humans reveals a figure of about 2.5 x 107.

Gamma/delta (γδ) T cells

The TCR repertoire of γδ T cells seems much smaller than that of their αβ cousins. The gamma chain gene segments are clustered
on chromosome 7. The delta chain gene segments are clustered on chromosome 14 (within the alpha chain cluster).

This page titled 15.4F: Antigen Receptor Diversity is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4F.4 https://bio.libretexts.org/@go/page/5438
15.4G: Anatomy of the Immune System

Figure 15.4.7.1 Immune system

This page titled 15.4G: Anatomy of the Immune System is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

15.4G.1 https://bio.libretexts.org/@go/page/5440
15.4H: T Helper cells
T cells are T lymphocytes that belong to the CD4+ subset. These cells have a number of direct functions, but they get their name
from the help they provide to other types of effector cells, such as B cells and cytotoxic T lymphocytes (CTLs). The help consists
of secreted cytokines that stimulate the helped cells.

Types of Helper T Cells

Four kinds have been identified:

Th1
These participate in both cell-mediated immunity and antibody-mediated immunity. They are essential for controlling such
intracellular pathogens as viruses and certain bacteria, e.g., Listeria and Mycobacterium tuberculosis (the bacillus that
causes TB). They provide cytokine-mediated "help" to cytotoxic T lymphocytes — perhaps the body's most potent weapon
against intracellular pathogens.
Th2
These provide help for B cells and are essential for the production of IgE antibodies and assist in the production of some
subclasses of IgG as well. Antibodies are needed to control extracellular pathogens (which unlike intracellular parasites are
exposed to antibodies in blood and other body fluids).
Tfh
These also provide help to B cells enabling them to develop into antibody-secreting plasma cells. This occurs in nests of
lymphoid cells called follicles — in the lymph nodes. The most abundant helper T cells there are B-cell helpers called
follicular helper T (Tfh) cells.
Th17
These protect surfaces (e.g., skin, lining of the intestine) against extracellular bacteria.
In addition, there is another related subset that dampens rather than promotes immune responses. These cells, designated Treg, are
discussed on another page. Link to it.

Origin of Helper T Cells

Like all T cells, Th cells arise in the thymus.
When they acquire CD4, they are called pre-Th cells.
When they are presented with both an antigen and appropriate cytokines,they begin to proliferate and become activated.
It is the nature of the stimulation — the type of antigen-presenting cell and cytokine(s) — that determines which path they
enter.

Th1 Cells

15.4H.1 https://bio.libretexts.org/@go/page/5442
 Figure 15.4.8.1 Th1 and Th2 cells
Th1 cells are produced when dendritic cells and pre-Th cells form an immunological synapse in which the dendritic cell presents
antigen to the T cell's receptor for antigen (TCR), and secretes interleukin 12 (IL-12) as well as IFN-γ. The paracrine stimulation
by these cytokines causes the Th1 cells to secrete their own lymphokines:
interferon-gamma (IFN-γ)
tumor-necrosis factor-beta (TNF-β) (also known as lymphotoxin)
These stimulate macrophages to kill the bacteria they have engulfed, recruit other leukocytes to the site producing inflammation,
act on B cells to promote antibody class switching, and help cytotoxic T cells (CTL) do their work and probably help convert some
of them to memory cells.

Th2 Cells
Th2 cells are produced when antigen-presenting cells (APCs) present antigen (e.g., on parasitic helminth worms or certain
allergens) to the T cell's receptor for antigen (TCR) along with
the costimulatory molecule B7 (CD80 & 86)
the paracrine stimulants interleukin 4 (IL-4) and interleukin 2 (IL-2).
The identity of the APCs for Th2 responses is still uncertain. Some research indicates that basophils are the APCs, but other
research questions this role.
The major lymphokines secreted by Th2 cells are
interleukin 4 (IL-4). This
stimulates class-switching in B cells and promotes their synthesis of IgE antibodies.
acts as a positive-feedback device promoting more pre-Th cells to enter the Th2 pathway.
blocks the IFN-γ receptors from entering the immunological synapse on pre-Th cells thus inhibiting them from entering the
Th1 path (shown in red).
Interleukin 13 (IL-13). This also promotes the synthesis of IgE antibodies as well as recruiting and activating basophils.
Interleukin 5 (IL-5). Attracts and activates eosinophils.
Two transcription factors have been found that play a critical role in the choice between becoming a Th1 or a Th2 cell.
T-bet for Th1 cells
GATA3 for Th2 cells
T-bet produces Th1 cells by
turning on the genes needed for Th1 function (e.g., for IFN-γ)
blocking the activity of GATA3.
Mice whose genes for T-bet have been "knocked-out" lack Th1 cells and have elevated numbers of Th2 cells (making them
susceptible to such Th2-mediated disorders as asthma).

15.4H.2 https://bio.libretexts.org/@go/page/5442
GATA3 produces Th2 cells by
turning on the genes needed for Th2 function (e.g., for IL-5)
blocking the activity of T-bet

Reciprocal inhibition of Th1 and Th2 cells.

The antigenic stimulus that sends pre-Th cells down one path or the other also sets the stage for reinforcing the response.
A Th1 response inhibits the Th2 path in two ways:
IFN-γ (shown above in red) and IL-12 inhibit the formation of Th2 cells
IFN-γ also inhibits class-switching in B cells
A Th2 response inhibits the Th1 path:
IL-4 suppresses Th1 formation (shown above in red)
significance for public health: infection by helminths — common in the tropics — increases one's risk of viral and bacterial
diseases, and in laboratory mice has been shown to enhance viral infections

Negative feedback of Th1 and Th2 cell formation

There is also evidence that late in the immune response, negative feedback mechanisms come into play to dampen the response.
IL-4 kills (by apoptosis) the precursors of the dendritic cells that induce the Th2 path and thus further production of IL-4.
IFN-γ may eventually turn off the Th1 response that produced it.

Th1 and Th2 cells have different chemokine receptors.

Chemokines are cytokines that are chemotactic for (attract) leukocytes. The members of one group, who share a pair of adjacent
cysteine (C) residues near their N-terminal, are designated CC chemokines. Chemokines bind to receptors on the responding
leukocyte. The receptors are transmembrane proteins with the chemokine binding site exposed at the surface of the plasma
membrane. CC chemokine receptors are designated CCR.
With their different functions, we might expect that Th1 cells and Th2 cells would respond differently to chemokines. And so they
do.
Th1 cells express the chemokine receptor CCR5 (but not CCR3).
Th2 cells express the chemokine receptor CCR3 (but not CCR5).

CCR3
One chemokine that binds to CCR3 is called eotaxin. It is secreted by epithelial cells and phagocytic cells in regions where allergic
reactions are occurring.
CCR3 is found on all cells implicated in allergic responses (e.g., asthma). They are:
Th2 cells
eosinophils
basophils

CCR5
CCR5 is found on
Th1 cells, especially those in the lymphoid tissue of the intestine
macrophages
CCR5 also acts — along with the CD4 molecule — as a coreceptor for HIV-1, the retrovirus that causes AIDS. This fact may
explain
why destruction of the lymphoid tissue of the intestine occurs soon after HIV infection;
why certain HIV-infected men
with inherited mutations preventing the expression of CCR5 or

15.4H.3 https://bio.libretexts.org/@go/page/5442
 who produce high levels of the natural ligand for CCR5 (a chemokine designated CCL3L1, which presumably competes
with HIV for access to CCR5)
can tolerate their infection for long periods without progressing to a full-blown case of AIDS;
the collapse of cell-mediated immunity in the late stages of AIDS

 Example

One striking illustration: an AIDS patient with leukemia was given a bone marrow transplant from a donor whose cells
expressed a nonfunctional version of CCR5. Two years later, the patient was not only cured of his leukemia but of AIDS as
well.
Another: Gene therapy in which samples of a patient's CD4+ T cells were treated in vitro so that their CCR5 gene became
nonfunctiona. Expanded in culture and then returned to the donor, five (of six) patients had their CD4+ T cell counts rebound.

Tfh Cells

Figure 15.4.8.2 Lymph node

Follicular helper T cells (Tfh) are CD4+ helper T cells found in nests of B cells called follicles — in the lymph nodes. When
exposed (in the paracortical area of the lymph node) to cells presenting antigen to them, e.g., dendritic cells and a cocktail of
cytokines they migrate into the follicles. The combined stimuli of antigen binding to their TCR and exposure to cytokines activate a
transcription factor called Bcl-6 (first identified in a B-cell lymphoma). Bcl-6 turns on a collection of genes which, among other
things, cause the Tfh cells to form an immunological synapse with those B cells expressing the antigen fragments in class II
histocompatibility molecules that match their TCR.
Several other pairs of ligands and their receptors stabilize the synapse, including the interaction between CD28 on the Tfh cell and
its ligand, B7, on the B cell. These binding interactions stimulate the B cell to
undergo class switching with the synthesis of other antibody classes (except IgE)
undergo affinity maturation
form antibody-secreting plasma cells and memory B cells
This intense activity within the follicle forms a germinal center. It is not yet certain whether Tfh cells represent a distinct class of
Th cells or are simply a further stage in the maturation of Th1, or Th2, or Th17 cells.

Th17 Cells
Th17 cells are a recently-identified subset of CD4+ T helper cells. They are found at the interfaces between the external
environment and the internal environment, e.g., skin and lining of the GI tract. They probably start out like other "naive" Th cells,
but when exposed to
cells presenting antigen to them, e.g., dendritic cells
several cytokines notably transforming growth factor-beta TGF-β and IL-6
they enter a pathway distinct from that of Th1, Th2, and Tfh cells. The combined stimuli of antigen binding to the TCR and
exposure to the cytokinesactivate a nuclear retinoid receptor designated RORγt. This is a transcription factor that turns on a
collection of genes which, among other things, leads to
the synthesis and secretion of IL-17 (giving the cells their name)

15.4H.4 https://bio.libretexts.org/@go/page/5442
 increased synthesis of the plasma membrane receptor for the interleukin IL-23. Interaction of IL-23 (perhaps secreted from
nearby dendritic cells) with the receptor drives the rapid proliferation of the Th17 cells
Situated in the skin and the lining of the GI tract, Th17 cells are positioned to attack fungi and bacteria at those locations. They do
this by secreting defensins and recruiting scavenging cells, especially neutrophils, to the site. The result: clearing away of the
invaders with accompanying inflammation.
But inflammation is a double-edged sword. So it is not surprising that Th17 cells have been implicated as potent effectors of such
damaging inflammatory disorders as
Crohn's disease (an inflammation of the small intestine)
Ulcerative colitis (inflammation of the large intestine)
Psoriasis (inflammation of the skin)
An animal model (in mice) of multiple sclerosis
Rheumatoid arthritis
Summary Table
Master
Effector Effector Pathological
Type Cytokine Stimulus Transcription Main Target Cells
Cytokine(s) Targets/Functions Effects
Factor

Autoimmunity;
Macrophages, Intracellular
Th1 T-bet IFN-γ & TNF-β cell-mediated
dendritic cells pathogens
allergies

Eosinophils, Asthma and IgE-

Th2 IL-4 GATA3 Various helminths
basophils, B cells mediated allergies

Class Switch
Recombination
Autoimmune
Tfh Bcl-6 B cells and Affinity
diseases?
Maturation of
antibodies

Extracellular
TGF-β plus IL-6
bacteria and fungi Autoimmune
Th17 Inhibited by RORγt Neutrophils
mediates diseases
retinoic acid
inflammation

TGF-β minus IL-

6 Immunosuppressi
all the other types
pTreg Stimulated by Foxp3 on; anti- None?
of T cells
retinoic acid and inflammatory
IL-2

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 15.4H: T Helper cells is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4H.5 https://bio.libretexts.org/@go/page/5442
15.4I: Cytotoxic T lymphocytes (CTL)

Cytotoxic T lymphocytes are lymphocytes that kill other ("target") cells.

Targets may include:
virus-infected cells (e.g., HIV-infected CD4+ T cells)
cells infected with intracellular bacterial or protozoal parasites
allografts such as transplanted kidney, heart, lungs, etc.
cancer cells. (The tumor-infiltrating lymphocytes, TIL, that have shown some promise in cancer therapy contain CTLs.)
There is also evidence that CTL are active in some autoimmune disorders, e.g. help destroy the beta cells of the islets of
Langerhans, leading to Type I diabetes mellitus.

Properties of CTLs
Most of them
belong to the CD8+ subset of T cells;
use the αβ T-cell receptor for antigen (TCR)
thus recognize antigens nestled in the groove of class I histocompatibility (MHC) molecules.
If they encounter (on a dendritic cell) the antigen/MHC for which their TCR is specific, they
enter the cell cycle and go through several rounds of mitosis ("clonal expansion") followed by
differentiation into effector ("killer") cells. Their differentiation includes forming a large number of modified lysosomes
stuffed with proteins: perforin and several types of granzyme. They are helped in these activities by helper T cells that
secrete stimulatory cytokines like IL-21.
Most of these CTLs will die (of apoptosis) when they have done their job, but some (especially those that have received
"help" from helper T cells) will become memory cells — long-lived cells poised to respond to the antigen if it should
reappear.
An example will show the beauty and biological efficiency of CTLs.
Every time you get a virus infection, say influenza (flu), the virus invades certain cells of your body (in this case cells of the
respiratory passages). Once inside, the virus subverts the metabolism of the cell to make more virus. This involves synthesizing a
number of different macromolecules encoded by the viral genome. In due course, these are assembled into a fresh crop of virus
particles that leave the cell (often killing it in the process) and spread to new target cells. Except while in transit from their old
homes to their new, the viruses work inside of your cells safe from any antibodies that might be present in blood, lymph, and
secretions. But early in the process, infected cells display fragments of the viral proteins in their surface class I molecules. CTLs
specific for that antigen will be able to bind to the infected cell and often will be able to destroy it before it can release a fresh crop
of viruses.
In general, the role of the CD8+ T cells is to monitor all the cells of the body, ready to destroy any that express foreign antigen
fragments in their class I molecules. Some CD4+ T cells can develop into CTLs, but they can attack only those cell types (e.g. B
cells, macrophages, dendritic cells) that express class II MHC molecules. Virtually every cell in the body expresses class I MHC
molecules, so CD8+ CTLs are not limited in the targets they can attack.

Mechanisms of Killing
There are two different types of mechanisms.

Perforin/Granzyme Killing
CTLs have cytoplasmic granules that contain the proteins perforin and granzymes. When the CTL binds to its target, the contents
of the granules are discharged by exocytosis. A dozen or more perforin molecules insert themselves into the plasma membrane of
target cells forming a pore that enables granzymes to enter the cell. Granzymes are serine proteases. The two most abundant ones
are
Granzyme A. Once inside the cell, it enters the mitochondria and cleaves a subunit of complex I (the NADH dehydrogenase) of
the electron transport chain producing reactive oxygen species (ROS) that kill the cell.

15.4I.1 https://bio.libretexts.org/@go/page/5444
 Granzyme B. Once inside the cell, it proceeds to cleave the precursors of caspases thus activating them to cause the cell to self-
destruct by apoptosis.
Both in structure and function, the interaction of CTL and its target resembles the synapses of the nervous system. The two cells are
attached tightly at a small patch of plasma membrane. Special adhesion molecules hold them together. The granules are discharged
only at that small portion of the plasma membrane (like the neurotransmitters released at a synapse).

This page titled 15.4I: Cytotoxic T lymphocytes (CTL) is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

15.4I.2 https://bio.libretexts.org/@go/page/5444
15.4J: Cell-Mediated Immunity

The human body can respond to antigen in many different ways. These fall into two major categories:
antibody-mediated immunity. Antibodies — dissolved in blood, lymph, and other body fluids — bind the antigen and trigger
a response to it. (This form of immunity is also called humoral immunity.)
cell-mediated immunity (CMI). T cells (lymphocytes) bind to the surface of other cells that display the antigen and trigger a
response. The response may involve
other lymphocytes
any of the other white blood cells (leukocytes)

Examples of Cell-Mediated Immunity

Delayed-Type Hypersensitivity (DTH): the tuberculin test
Many states in the United States require that professors and teachers (among others) be checked periodically for tuberculosis. This
chronic disease, caused by Mycobacterium tuberculosis, evokes an immune response that, unfortunately, does not cure the
patient, but does provide an inexpensive test for the disease called the tuberculin test (or Mantoux test). A tiny amount of protein,
extracted from the bacteria, is injected into the skin. If the subject is currently infected, or has ever been infected, with the
bacteria, a positive test results. In 24 hours or so, a hard, red nodule develops at the site of the injection. This nodule is densely
packed with lymphocytes and macrophages.
In Europe, most people produce a positive tuberculin reaction, not because they have had the infection, but because earlier they had
been vaccinated against tuberculosis with a preparation of a related (but harmless) bacterium called BCG.
The response to tuberculin is called "delayed" because of the time it takes to occur (in contrast to the "immediate" responses
characteristic of many antibody-mediated sensitivities like an allergic response to a bee sting).
DTH is a cell-mediated response (in fact, anti-tuberculin antibodies are rarely found in tuberculin-positive people). The T cells
responsible for DTH are members of the CD4+ subset.

Contact Sensitivity
Many people develop rashes on their skin following contact with certain chemicals. Nickel, certain dyes, and the active ingredient
of the poison ivy plant are common examples. The response takes some 24 hours to occur, and like DTH, is triggered by CD4+ T
cells. The actual antigen is probably created by the binding of the chemical to proteins in the skin. After the antigen is engulfed by
dendritic cells in the skin, they migrate to nearby lymph nodes where they present fragments of the antigen to CD4+ T cells. The
activated T cells migrate from the lymph nodes to the skin to elicit the inflammatory response.

Killing intracellular parasites

Some human pathogens avoid exposure to antibodies by taking up residence within cells. These include all viruses (discussed in the
next section), and some bacteria such as
the bacterium that causes Legionnaires's disease
Listeria monocytogenes, that humans sometimes acquire from contaminated food and even some protozoans.
These microorganisms are engulfed by phagocytic cells, like macrophages, but evade the normal intracellular mechanisms that
should destroy them. However, the macrophages can present fragments of antigens derived from these parasites. These are
displayed in the class II histocompatibility molecules of the macrophages. CD4+ T cells responding to these epitopes release
lymphokines that stimulate the macrophages sufficiently that they can now begin to destroy the organisms.

This page titled 15.4J: Cell-Mediated Immunity is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4J.1 https://bio.libretexts.org/@go/page/5446
15.4K: Organ Transplants
New parts for old
Many organs and tissues are now routinely transplanted from one human to another. Except for the rare cases where the donor and
recipient are monozygotic ("identical") twins, such grafts are called allografts.
kidney
Living donors can be used because they have two kidneys and can get along with only one.
heart
For patients with failing hearts (often because of inherited defects). Only cadavers can be used as donors.
lungs
Usually transplanted along with a heart. Some attempts have been made with portions of lungs from living donors.
pancreas
For people with Type 1 diabetes mellitus.
liver
For irreversible liver failure (e.g., from toxins, hepatitis B infection).
skin
For burns; usually taken from elsewhere on the patient's own body.
cornea
To restore sight; taken from cadavers.
blood
To temporarily restore blood volume.
bone marrow
As a source of blood ("hematopoietic") stem cells to repopulate the patient's own marrow that is
congenitally deficient in its ability to make one or more kinds of blood cells — Example: severe combined
immunodeficiency (SCID)
has been destroyed by cancer therapy.
cord blood
Blood drained (through the umbilical cord) from the placenta of newborn infants. A convenient source of blood stem cells.
ovary
Has restored fertility and produced healthy babies but so far only when donor and recipient were monozygotic (identical)
twins.

The Problems
Graft rejection
The patient's immune system "sees" an allograft as foreign (antigenic) and mounts an immune response against it.
Graft-versus-host disease (GVHD)
T cells in the graft "see" the tissues of the recipient as foreign antigens and mount an immune attack against them. This a
particularly serious problem with grafts of bone marrow because of the many T cells in it.
Infections
Attempts to suppress the immune response to avoid graft rejection and GVHD weaken the ability of the body to combat
infectious agents (bacteria, viruses, fungi).
More rarely, the donated organ may be infected and transmit the agent to the recipient. Tuberculosis, rabies, syphilis,
hepatitis B, HIV-1, and several other diseases have been transmitted in this way. Potential organ donors are now routinely
tested for evidence of infection by HIV-1 and -2, HTLV-1 and -2, hepatitis B and C (HBV, HCV), human cytomegalovirus
(HCMV) and Epstein-Barr virus (EBV) as well as by Treponema pallidum (syphilis).
Cancer

15.4K.1 https://bio.libretexts.org/@go/page/5447
 Suppressing the host's immune responses also increases the risk of cancer.

Coping with the Immunological Problems

Use the patient's own tissue when possible (skin, bone marrow, blood vessels).
Use tissue from an "identical" (monozygotic) twin in the very rare cases that one is available. Being genetically identical, the
recipient sees the transplant as "self", not as foreign, and does not mount an attack against it. The first successful kidney
transplants (done in the mid 1950s) were between identical twins, and both donors and recipients went on to lead normal lives.
Use an "immunologically privileged" site. These are parts of the body where the immune system is prevented from mounting an
attack. They include the eye, testes, and brain, but only the eye's privileged status has so far been exploited (for corneal grafts).
Use a relative, preferably a sibling, as the donor. While never identical, they may have inherited some of the same
histocompatibility antigens so the recipient's immune response may not be as strong as it otherwise would be.
Tissue-typing. Determine the histocompatibility antigens of both recipient and potential donor and use the organ with the
fewest mismatches.
Immunosuppression. Use immunosuppressive agents to blunt the recipient's immune response. Invariably required for all
allografts.

Tissue Typing
The strongest antigens expressed by tissues are the class I and class II histocompatibility molecules. These are encoded by an array
of genes on chromosome 6 called the major histocompatibility complex (MHC).

Figure 15.4.11.1 HLA

Class I molecules consist of a transmembrane protein to which are attached (noncovalently), a molecule of beta-2 microglobulin,
and a short peptide. The class I transmembrane proteins are encoded by three loci: HLA-A, HLA-B, and HLA-C. Class I
molecules are expressed at the surface of almost all the cells of the body (except for red blood cells and the cells of the central
nervous system).
Class II molecules consist of two transmembrane polypeptides: an alpha (α) chain and beta (β) chain between which is nestled
(noncovalently) a short peptide. The alpha and beta chains are encoded by clusters of loci in the region of chromosome 6
designated HLA-D. Unlike class I molecules, class II molecules are expressed on only a few types of cells, chiefly antigen-
presenting cells (APCs) such as dendritic cells and macrophages, as well as other cells where inflammation is occurring.

Why so many MHC alleles

The genes of the MHC are the most polymorphic known. The graphic above shows the latest counts of alleles found at each locus
in the human population. Of course, any one human can inherit a maximum of two alleles at each locus. The diversity of alleles in
the population makes possible thousands of different combinations. In a study of 1000 blood and organ donors in San Francisco
that were typed for HLA-A and HLA-B,
Over half the group had a combination that was unique.
Another 111 donors had a set of these molecules that they shared with only one other person in the group.
The most frequent phenotype (HLA-A1, HLA-A3, HLA-B7, and HLA-B8) was found in 11 donors.
The extreme polymorphism of the MHC did not evolve to frustrate transplant surgeons and their patients.
Why, then?

15.4K.2 https://bio.libretexts.org/@go/page/5447
The function of class I and class II molecules is to "present" antigenic peptides to the T cells of the immune system. The peptides
— usually about 9 amino acids long — are bound by noncovalent forces in a groove at the surface of the MHC molecule. These
peptides can include fragments of protein antigens derived from intracellular pathogens (e.g. viruses). Different pathogens generate
different antigenic fragments. Different MHC molecules differ in the efficiency with which they bind particular sequences of amino
acids in these fragments. Therefore, we might expect that some MHC products would be better than others at presenting pathogen
antigens to the immune system.
One piece of evidence: People infected with the human immunodeficiency virus (HIV-1) who have one particular HLA-B molecule
are more resistant to developing a full-blown case of AIDS than those with other HLA-B molecules (even though some of these
differ by only a single amino acid).
Another piece of evidence: Wegner and colleagues reported in the 5 September 2003 issue of Science the results of a direct test of
this hypothesis. They exposed groups of sticklebacks — differing in the number of their class II alleles — to three types of parasite
(all at once). They used two species of parasitic nematode and one species of trematode). Those fish with 5–6 different alleles
resisted infection better than those with fewer (or more).
So it may well be that the great diversity of class I and class II alleles in the human population has helped ensure that no single
pathogen can wipe out the entire population.

Techniques of tissue typing

Most tissue typing is done using serological methods: antibodies specific for those HLA antigens that have been identified in the
human population. A reaction between cells of the subject and, for example, anti-HLA-A28 antibodies and HLA-A9 antibodies —
but no other antibodies — establishes the phenotype. At the present time, routine typing is limited to establishing the phenotype at
HLA-A, HLA-B, and HLA-DR.
Coming into wider use is DNA typing, especially for HLA-D antigens. It promises to improve the sensitivity and specificity of
tissue typing. The totals of numbers of alleles at each HLA locus given in the graphic above are based on DNA typing.

How useful is tissue typing?

Figure 15.4.11.2 Possible combinations

So what hope do these data hold for the dialysis patient awaiting a kidney transplant? If the patient has a large family of willing
donors, the odds for a good match are not bad because of the tight linkage of the HLA loci.
Assuming that no crossing over occurs within the HLA region of either the mother's or the father's two number 6 chromosomes,
there are four possible combinations in which they may transmit their alleles to their children. So even if the parents carry different
alleles at each locus (which is often the case), there is a 1:4 probability that any one of their children will be an exact match with
any other. (Only the HLA-A and HLA-B antigens are shown here, but the tight linkage of the entire HLA region makes it likely
that all the loci on each chromosome will be passed on as a block.)
But most organs are transplanted from cadavers to complete strangers. In the United States, the program is monitored by the
United Network for Organ Sharing (UNOS). Tissue typing is usually limited to looking for 6 HLA antigens: the two each at
HLA-A, HLA-B, and HLA-DR. If only one antigen is found at a locus, it means that either the tissue is homozygous for that allele
or no reagent exists yet to detect the second allele. This table shows the results of one study of several thousand kidney recipients.

Number of HLA % kidneys surviving

mismatches after 5 years

0 68

1 61

15.4K.3 https://bio.libretexts.org/@go/page/5447
 2 61

3 58

4 58

5 57

6 56

The results tell us that:

Having no mismatches provides a clear, but modest, advantage over mismatched kidneys. (This advantage is cumulative: at 17
years, 50% of the kidneys with no mismatches are still functioning while 50% of those with one or more mismatches have been
lost after 8 years.)
However, the incremental disadvantage of additional mismatches is small. In fact, the procedures to prevent rejection are now
sufficiently good that ~90% of all kidneys — even those with all loci mismatched — can be expected to be functioning at the
end of the first year.

Minor histocompatibility antigens

Even if it were possible to match donor and recipient at every locus of the MHC, some tissue incompatibility would still remain
(except between identical twins). Few of the antigens responsible have been identified, but they include:
H-Y, an antigen encoded on the Y chromosome and thus present in male, but not female, tissue
HA-2, an antigen derived from the contractile protein myosin.
The number and variety of histocompatibility antigens tell us that probably no two humans (again, except for identical twins) exist
on earth with perfectly compatible tissues. Therefore successful transplantation of allografts requires some degree of
immunosuppression to avoid graft rejection.

Graft-versus-host disease (GVHD)

Allografts that contain T cells of the donor can cause graft-versus-host disease (GVHD). The T cells in the transplant see the host
as "foreign" and proceed to mount a widespread attack against the tissues of the host. GVHD is an especially serious problem with
grafts of bone marrow (the source of all blood cells) and cord blood. Even when the donor and recipient have identical HLA
alleles, grafts of bone marrow often cause GVHD because of differences in their minor histocompatibility antigens.
Some cancer patients are now deliberately treated so vigorously with radiation and chemotherapy that their bone marrow is
destroyed along with their cancer cells. In order to survive, these patients must be given stem cells to repopulate their marrow after
their therapy. In some cases, their own bone marrow is used. Some of it is removed prior to the onset of treatment of the patient
and is itself treated to remove any cancer cells that may be lurking in it. If allografted bone marrow is required, there is a strong
danger of GVHD. If the GVHD can be controlled, the stem cells should eventually establish themselves in the bone marrow of
their new host and in due course generate some or even all of the patient's blood cells. Cord blood — another source of stem cells
— presents less of a risk of serious GVHD even from a donor with HLA molecules not present in the recipient. This is because
cord blood does not contain any mature T cells.
In mice, GVHD can be minimized by injecting large numbers of regulatory T cells, but for humans, control of GVHD — like
control of graft rejection — still depends on the use of immunosuppression.

Immunosuppression
Immunosuppression is the treatment of the patient with agents that inhibit the immune response. The following is the list of
immunosuppressants currently used.
Purine analogs
These are relatives of the purines used in DNA synthesis. Because they interfere with DNA synthesis, they interfere with the rapid
cell proliferation needed for immune responses. Azathioprine (trade name = Imuran) is a widely-used purine analog.
Unfortunately, these drugs also interfere with the many other tissues that depend on rapid cell division (e.g., lining of the intestine,
hair follicles) so they have many unpleasant side effects. Therefore, the search for agents that specifically target immune cells goes
on.

15.4K.4 https://bio.libretexts.org/@go/page/5447
Corticosteroids

These relatives of cortisol interfere with a transcription factor needed to turn on the genes for T cells to become activated.
Prednisone and prednisolone are most commonly used.
Tacrolimus (Prograf®) and cyclosporine (Neoral®)
These are natural products isolated from microbial cultures. They inhibit the signaling pathway used by T cells to turn on their
genes for activation, e.g., for IL-2 secretion.
Rapamycin
This is a macrolide antibiotic produced by an actinomycete found on Easter Island (which the inhabitants call Rapa Nui — hence
the name). Rapamycin inhibits T cell proliferation, and shows great promise in reducing the problems of transplant rejection.
Rapamycin is also known as sirolimus and is sold under the trade name Rapamune.
Mycophenolate mofetil
This small molecule inhibits an enzyme needed by B and T cells for purine synthesis. Other types of cells are not dependent on the
enzyme so side effects are mild. The trade name is CellCept.
Antithymocyte globulin (ATG)
This preparation contain antibodies — raised in horses or rabbits — directed against T cells.
Monoclonal antibodies
Several preparations are now used:
Muromonab-CD3 (OKT3) and two humanized anti-CD3 monoclonals. They bind to the CD3 molecule on the surface of T
cells.
Daclizumab and basiliximab. Target the IL-2 receptor and thus inhibit only activated T cells.
Alemtuzumab (Campath-1H®). Binds to CD52, a molecule found on lymphocytes and depletes both T cells and B cells.
Belatacept
This is a protein, produced by recombinant DNA technology, that combines
the extracellular portion of CTLA-4 ("cytotoxic T-lymphocyte-associated antigen 4", one of the ligands for B7) with
the Fc region (the C-terminal two-thirds of the constant region) of a human IgG1 antibody.
It blocks the "Signal Two" needed to activate T cells.

Side effects of immunosuppression

They are serious.
Infections
The immune system is vital to protect us against infectious agents (bacteria, viruses, fungi). So infection is a frequent side effect of
immunosuppression in transplant recipients. Fortunately, the infections can usually be controlled by the appropriate antibiotic,
antiviral drug, etc.
Cancer

5% or more of transplant recipients will develop cancer within a few years of receiving their allograft. This may not seem to
represent a great risk, but it does represent a 100-fold increase in risk compared to the general population. Allograft recipients are
particularly prone to developing skin cancers and lymphomas. Curiously, transplant recipients do not seem to be at any greater risk
for developing the most common types of cancer in the rest of the population: cancers of the lung, breast, colon, and prostate. One
exception: recipients of allografted bone marrow run a slightly, but significantly, higher (2–3 fold) risk of developing these types
of tumors. In most cases, these cancers arise from a cell of the host. But in some cases of melanoma and Kaposi's sarcoma the
cancer cells were present in the graft and proliferated in the immunosuppressed host.
Things that can be done to help in such cases include stopping the immunosuppression. The chief culprit seems to be the
immunosuppression that these patients have been receiving. In most cases,this leads to regression of the cancer, but often rejection
of the transplant as well. The choice is usually clear for patients with allografted kidneys; they can go back on dialysis and
anticipate receiving another kidney at a future date. But what of the cancer patient with a heart transplant?

15.4K.5 https://bio.libretexts.org/@go/page/5447
Future prospects for transplantation
Although organ transplants have helped thousands of people, much remains to be done. In particular, ways need to be found to
increase the number of available organs (the need now far exceeds the supply)
find more precise methods of immunosuppression in order to prevent rejection without the dangerous side effects of infection
and cancer.
Both these problems may be helped by xenotransplantation.
Xenotransplantation
Xenotransplantation is the use of organs from other animals. A number of attempts have been made to use hearts, livers, and
kidneys from such primates as chimpanzees and baboons — so far with limited success. One reason is that xenotransplants usually
are attacked immediately by antibodies of the host resulting in hyperacute rejection. But perhaps the use of pigs as organ donors
will be feasible.
Their organs are about the right size for use in humans.
They can be made transgenic for molecules that may circumvent
hyperacute rejection (by knocking out the genes responsible for cell-surface antigens that humans have preformed
antibodies against);
the chronic, T-cell-mediated, rejection that plagues all allografts.
They can be produced in the numbers needed.
However, pigs contain retroviruses (called PERV = porcine endogenous retrovirus), and there is fear that these might infect the
human recipient.
Only a few transplants of pig tissue into humans have been done to date: skin grafts and grafts of pancreatic islets. A larger number
of people have been temporarily hooked up to pig organs or "bioreactors" containing pig cells to provide support for their failing
spleen, liver, or kidneys. Most of these recipients have been monitored for signs of infection by PERV and — even though PERV
can infect human cells growing in culture — there is no evidence that any of these people exposed to pig tissue have become
infected.
Is xenotransplantation safe?
Pigs are not the only animals that contain latent viruses in their cells. Could the viruses in the cells of other kinds of animal donors
infect the transplant recipient? start an epidemic? The danger seems greater for xenotransplants from other primates. (HIV, the
retrovirus that causes AIDS appears to have entered humans from a primate host)
For these reasons, many biologists are urging that transplant surgeons proceed cautiously with xenotransplants.
Immune Privilege
It has long been know that certain sites in the body, for example,
the anterior chamber of the eye
the testes
the brain
are "privileged". They are protected from attack by the immune system.
This can cause problems. Several cases have emerged of survivors of Ebola who no longer have Ebola virus in their blood and are
symptom-free but still retain live virus in such privileged sites as brain, testis, and aqueous humor of the eye where the virus has
escaped attack by the immune system.
Many factors are involved in immune privilege, such as
tight junctions between the cells of the tissue
little expression of class I histocompatibility molecules
expression of the Fas ligand, FasL.
The presence of FasL on their surface protects cells in privileged locations from immune attack because when threatened by a
cytotoxic T cell, they force the T cell to commit suicide by apoptosis. Activated cytotoxic T cells express Fas on their surface.
When they engage (with their T cell receptor) a privileged cell expressing FasL, instead of killing the target, the target kills them!

15.4K.6 https://bio.libretexts.org/@go/page/5447
So if the organs of transgenic pigs can be made to expresses human FasL, perhaps they will be resistant to T-cell mediated
rejection.
The human placenta also enjoys immune privilege. It is almost as foreign to the mother as a kidney transplant from her husband
would be, but unlike the kidney, she will not reject it (at least not for 9 months). In lab rats, the embryos (and the mother's
endometrium) secrete corticotropin-releasing hormone (CRH). This hormone induces the expression of Fas ligand (FasL) on the
cells of the placenta. Activated T cells express Fas, so any threatening T cells would commit suicide by apoptosis when they
encounter FasL on their target.

This page titled 15.4K: Organ Transplants is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4K.7 https://bio.libretexts.org/@go/page/5447
15.4L: Bone Marrow Transplants
Transplants of Hematopoietic Stem Cells

Figure 15.4.12.1 Bone marrow transplant

These can be:
autologous — from hematopoietic stem cells that were
removed from the patient before cancer therapy began,
stored alive,
and, if there were cancer cells in the bone marrow (the case with multiple myeloma and leukemias), treated to "purge" them.
Most failures of autologous stem cell transplants occur because of failure to get all the cancer cells out of the harvested cells
rather than failure to eliminate them from the patient.
allogeneic — hematopoietic stem cells removed from someone else, often a close relative. Another source of hematopoietic
stem cells is cord blood — blood drained (through the umbilical cord) from the placenta of newborn infants.
Allogeneic stem cells
avoid the problem of lurking residual cancer cells but
should be closely matched to the major histocompatibility loci (MHC) of the patient. If not, the donor cells will attack the
recipient causing often-fatal graft-versus-host disease (GVHD). Even with an exact match at the MHC, some GVHD is
likely.
In one remarkable case, an AIDS patient with leukemia was given a bone marrow transplant from a donor whose cells did not
express a functional version of CCR5 — a coreceptor needed by HIV to infect T cells. Two years later, the patient was not only
cured of his leukemia but of AIDS as well. Autologous hematopoietic stem cell transplants also show promise of being an effective
treatment for the autoimmune disorder systemic lupus erythematosus (SLE). If the patient's own marrow was not completely
destroyed, the donor lymphocytes and the patient's lymphocytes can exist together. Then a later infusion of the donor's T cells may
be able to kill off all the patient's remaining malignant cells leaving the patient with a bone marrow that produces donor-type cells
exclusively. So hematopoietic stem cell transplants (HSCT) can be life-saving but create their own problems. (Another example: an
"immediate"-type allergy like hay fever or asthma of the donor can create the same allergy in the recipient.)

This page titled 15.4L: Bone Marrow Transplants is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4L.1 https://bio.libretexts.org/@go/page/5448
15.4M: Antigen Presentation
Antigens are macromolecules that elicit an immune response in the body. Antigens can be proteins, polysaccharides, conjugates of
lipids with proteins (lipoproteins) and polysaccharides (glycolipids). Most of this page will describe how protein antigens are
presented to the immune system. The presentation of lipid and polysaccharide antigens will be mentioned at the end. It will be
helpful to distinguish between two limiting cases.
Antigens that enter the body from the environment; these would include inhaled macromolecules (e.g., proteins on cat hairs that
can trigger an attack of asthma in susceptible people), ingested macromolecules (e.g., shellfish proteins that trigger an allergic
response in susceptible people), and molecules that are introduced beneath the skin (e.g., on a splinter or in an injected vaccine).
Alternatively, antigens can be generated within the cells of the body; these would include proteins encoded by the genes of viruses
that have infected a cell and aberrant proteins that are encoded by mutant genes; such as mutated genes in cancer cells. In all cases,
however, the initial immune response to any antigen absolutely requires that the antigen be recognized by a T lymphocyte ("T
cell"). The truth of this rule is clearly demonstrated in AIDS: the infections (viral or fungal or bacterial) that so often claim the life
of AIDS patients do so when the patient has lost virtually all of his or her CD4+ T cells. The two categories of antigens are
processed and presented to T cells by quite different mechanisms.

Exogenous Antigens
Exogenous antigens (inhaled, ingested, or injected) are taken up by antigen-presenting cells (APCs). These include phagocytic cells
like dendritic cells and macrophages and B lymphocytes ("B cells") which are responsible for producing antibodies against the
antigen. Antigen-presenting cells
engulf the antigen by endocytosis
endosome fuses with a lysosome where the antigen is degraded into fragments (e.g. short peptides)
these antigenic peptides are then displayed at the surface of the cell nestled within a class II histocompatibility molecule.
they may be recognized by CD4+T cells

Figure 15.4.13.2 Class I histocompatibility molecule

The Class I Pathway

Class I histocompatibility molecules are transmembrane proteins expressed at the cell surface. Like all transmembrane proteins,
they are synthesized by ribosomes on the rough endoplasmic reticulum (RER) and assembled within its lumen. There are three
subunits in each class I histocompatibility molecule:
the transmembrane polypeptide (called the "heavy chain")
the antigenic peptide
beta-2 microglobulin
All of these must be present within the lumen of the endoplasmic reticulum if they are to assemble correctly and move through the
Golgi apparatus to the cell surface. The Problem: proteins encoded by the genes of an infecting virus are synthesized in the cytosol.

15.4M.1 https://bio.libretexts.org/@go/page/5449
How to get them into the endoplasmic reticulum?
The Solution: TAP (= transporter associated with antigen processing).
Viral proteins in the cytosol are degraded by proteasomes into viral peptides.
The peptides are picked up by TAP proteins embedded in the membrane of the endoplasmic reticulum.
Using the energy of ATP, the peptides are pumped into the lumen of the endoplasmic reticulum where they assemble with the
transmembrane polypeptide and beta-2 microglobulin.
This trimolecular complex then moves through the Golgi apparatus and is inserted in the plasma membrane.
The complex can be bound by a T cell with a receptor (TCR) able to bind the peptide and flanking portions of the
histocompatibility molecule (the hot dog in the bun) and CD8 molecules that bind the CD8 receptor (shown above as a gray
hemisphere) on the histocompatibility molecule.

The Class II Pathway

Class II histocompatibility molecules consist of two transmembrane polypeptides and a third molecule nestled in the groove they
form. All three components of this complex must be present in the endoplasmic reticulum for proper assembly. But antigenic
peptides are not transported to the endoplasmic reticulum, so a protein called the invariant chain ("Ii") temporarily occupies the
groove.
The steps:
The two chains of the class II molecule are inserted into the membrane of the endoplasmic reticulum.
They bind (in their groove) one molecule of invariant chain.
This trimolecular complex is transported through the Golgi apparatus and into vesicles called lysosomes.
Meanwhile foreign antigenic material is engulfed by endocytosis forming endosomes. These also fuse with lysosomes. Then,
The antigen is digested into fragments.
The invariant (Ii) chain is digested.
This frees the groove for occupancy by the antigenic fragment.
The vesicles move to the plasma membrane and the complex is displayed at the cell surface.
The complex can be bound by a T cell with
a receptor (TCR) able to bind the peptide and flanking portions of the histocompatibility molecule (the hot dog in the bun)
and
CD4 molecules that bind the CD4 receptor (shown above as a yellow triangle) found on all class II histocompatibility
molecules.

Interconnections Between the Class I and Class II Pathways

Cross-Presentation: Transferring Exogenous Antigens to the Class I Pathway
Cross-presentation is the transferring of extracellular antigens like bacteria, some tumor antigens, and antigens in cells infected by
viruses into the class I pathway for stimulation of CD8+ cytotoxic T cells (CTL). Only certain "professional" antigen-presenting
cells (APCs) like dendritic cells can do this - use the class I as well as the class II pathways of antigen presentation.
Cross-presentation following infection by viruses is important because:
Most viruses infect cells other than APCs (e.g., liver cells, epithelial cells of the lung) (and, of course, are intracellular in these).
While viral antigens displayed on the surface of any infected cell can serve as targets for cytotoxic T cells (CTLs),
the lack of any costimulatory molecules on the cell surface makes them poor stimulants for the development of clones of CTLs
in the first place.
However, when an infected cell dies, it can be engulfed by a professional APC, and the antigens within it can enter the class I
pathway. One mechanism:
The dead cell is engulfed by endocytosis.
The endosome that forms fuses with a lysosome and degradation of the dead cell begins.
Antigens pass into the cytosol and are degraded in proteasomes.
The peptides formed are then are picked up by TAP and inserted into class I MHC molecules and displayed at the cell surface
— along with the costimulatory molecules needed to start a vigorous clonal expansion of CD8+ cytotoxic T cells.

15.4M.2 https://bio.libretexts.org/@go/page/5449
Diverting Antigens from the Class I to the Class II Pathway
Autophagy provides a mechanism by which cells can transfer endogenous (intracellular) antigens into the class II pathway, for
example
self-proteins so as to be able to delete CD4+ T cells with receptors capable of attacking them and thus potentially capable of
causing autoimmunity
proteins synthesized by an infecting virus. In this way viral infection can generate CD4+ T cells as well as cytotoxic T cells
(CD8+)

B Lymphocytes: A Special Case

Figure 15.4.13.3 B-cell

B lymphocytes are both antigen-receiving and antigen-presenting cells. They bind intact antigens (e.g., virus particles, proteins)
with their B cell receptor (BCR). They can come in contact with these antigens by encountering them in the surrounding lymph or
by being presented them by macrophages or dendritic cells. B lymphocytes process antigen by the class II pathway for presentation
to T cells.
The process:
B cells engulf antigen by receptor-mediated endocytosis
The B cell receptors for antigen (BCRs) are antibodies anchored in the plasma membrane.
The affinity of these for an epitope on an antigen may be so high that the B cell can bind and internalize the antigen when it is
present in body fluids in concentrations thousands of times smaller than a macrophage would need.
The remaining steps of antigen processing occur by the same class II pathway described above for macrophages producing
fragments of antigen displayed at the cell surface nestled in the groove of class II histocompatibility molecules.
A CD4+ T cell that recognizes the displayed antigen is stimulated to release lymphokines.
These, in turn, stimulate the B cell to enter the cell cycle.
Because of the part they play in stimulating B cells, these CD4+ T cells are called Helper T cells ("Th").
The B cell grows into a clone of cells (called plasma cells)
These synthesize receptors (BCRs) with the identical binding site for the epitope but without the transmembrane tail.
These antibodies are secreted into the surroundings.

Lipid and Polysaccharide Antigens

Lipid Antigens
Lipid antigens are presented to T cells by cell-surface molecules designated CD1 ("cluster of differentiation" 1).
Antigen-presenting cells express several different forms of CD1 at their surface. Each is probably specialized to bind a
particular type of lipid antigen (e.g. lipopeptide vs glycolipid).
The exposed surface of CD1 molecules forms an antigen-binding groove much like that of MHC molecules except that

15.4M.3 https://bio.libretexts.org/@go/page/5449
 the amino acids in the groove are more hydrophobic than those in MHC molecules.
Like protein antigens, lipid antigens are also presented as fragments, i.e., as a "hot dog in a bun".

Polysaccharide Antigens
Some bacterial polysaccharides ingested by APCs
can be degraded in their lysosomes
and presented to T cells by MHC class II molecules.

Figure 15.4.13.4 Co-stimulation

The binding of a T cell to an antigen-presenting cell (APC) is by itself not enough to activate the T cell and turn it into an effector
cell: one able to, for examples,
kill the APC (CD8+ cytotoxic T lymphocytes [CTLs])
carry out cell-mediated immune reactions (CD4+ Th1 cells)
provide help to B cells (CD4+ Th2 cells)
In order to become activated, the T cell must not only bind to the epitope (MHC-peptide) with its TCR but also receive a second
signal from the APC. The receipt of this second signal is called costimulation. Among the most important of these costimulators
are molecules on the APC designated B7 and their ligand on the T cell designated CD28. The binding of CD28 to B7 provides the
second signal needed to activate the T cell.
Although T cells may encounter self antigens in body tissues, they will not respond unless they receive a second signal. In fact,
binding of their TCR ("signal one") without "signal two" causes them to self-destruct by apoptosis. Most of the time, the cells
presenting the body's own antigens either
fail to provide signal two or
transmit an as-yet-unidentified second signal that turns the T cell into a regulatory T cell (Treg) that suppresses immune
responses.
In either case, self-tolerance results.

This page titled 15.4M: Antigen Presentation is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4M.4 https://bio.libretexts.org/@go/page/5449
15.4N: The Immunological Synapse

Immunological responses, both antibody-mediated and cell-mediated involve close contact between a T cell and an antigen-
presenting cell (APC).
Examples:
Helper T cells (Th1) with "professional" antigen-presenting cells like dendritic cells and some macrophages
Helper T cells (Th2) with B cells
Cytotoxic T lymphocytes (CTLs) with their targets
NK cells with their targets

Figure 15.4.14.2 Pairs of molecules in immunosynapse

TCR/MHC-peptide pair
On the T cell, the T-cell receptor for antigen (TCR) bound to
a major histocompatibility complex (MHC) molecule on the antigen-presenting cell (APC).
For CD4+ T cells, the MHC molecules are class II, and the binding is aided by CD4.
For CD8+ T cells (e.g., CTLs), the MHC molecules are class I, and the binding is aided by CD8.
In both cases, the MHC molecule has an antigenic peptide nestled in an exterior groove (MHC-peptide).
The TCR molecules are tethered by actin filaments in the cytoplasm.
Several hundred TCR/MHC-peptide pairs are needed to stimulate a naive T cell to begin mitosis, but only 50 or so are needed
to activate a "memory" T cell to do its work; that is, to become an effector T cell.

Costimulatory pairs
The costimulatory molecule CD28 on the T cell bound to its ligand, B7, on the APC.

General adhesion molecules

Leukocyte Function-associated Antigen-1 (LFA-1), an integrin on the T cell, bound to
InterCellular Adehesion Molecule-1 (ICAM-1) on the APC.

Cytokine receptors
Cytokine receptors also cluster in the synapse (not shown in the diagram) where they are exposed to cytokines secreted into the
synapse.
Formation of an immunological synapse causes the T cell to
become activated with various signal pathways turning on new gene transcription
release, by exocytosis, the contents of its vesicles:
Type 1 helper T cells (Th1): lymphokines like IFN-γ and TNF-β
Type 2 helper T cells (Th2): lymphokines like IL-4, IL-5, IL-10, and IL-13 that stimulate B cells
Cytotoxic T Lymphocytes (CTLs): cytotoxic molecules like perforin and granzymes that kill the target

15.4N.1 https://bio.libretexts.org/@go/page/5450
This page titled 15.4N: The Immunological Synapse is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4N.2 https://bio.libretexts.org/@go/page/5450
15.4O: Dendritic Cells
Dendritic cells (DCs) get their name from their surface projections (that resemble the dendrites of neurons). They are found in most
tissues of the body and are particularly abundant in those that are interfaces between the external and internal environments (e.g.,
skin, lungs, and the lining of the gastrointestinal tract) where they are ideally placed to encounter extrinsic antigens, including those
expressed by invading pathogens.
Although there are several distinct subtypes of DCs, they all share these features:
They are actively motile.
They continuously sample their surroundings — ingesting antigens by endocytosis (using phagocytosis, receptor-mediated
endocytosis, and pinocytosis).
Many of these antigens are "self" antigens, e.g., dead cells, proteins in the extracellular fluid.
But the antigens can also be foreign antigens, for example, bacteria that are resident in the body (e.g., in the colon) or that
invade the body.
In either case, the ingested antigens are degraded in lysosomes into peptide fragments that are then displayed at the cell-surface
nestled in class II MHC molecules.
Having ingested antigen in the tissue, they migrate to lymph nodes and spleen where they can meet up with T cells bearing the
appropriate T-cell receptor for antigen (TCR).
What happens next depends on the nature of the antigen.
Self antigens are presented to T cells without any costimulatory molecules. This interaction causes the T cells to divide for a
brief time, but then they commit suicide by apoptosis and so cannot attack tissues of the body. The animal becomes tolerant to
that antigen.
Foreign antigens produce a different outcome. The dendritic cells becomes "activated' and begin to display not only
the MHC-peptide complex for the TCR of the T cells but also
costimulatory molecules, e.g. B7 which binds to CD28 on the T cell
The importance of dendritic cells in developing immunity to pathogens is dramatically shown in those rare infants who lack a
functioning gene needed for the formation of dendritic cells. They are so severely immunodeficient that they are at risk of life-
threatening infections.
What accounts for the activation of dendritic cells by foreign antigens but not by self antigens? Pathogens, especially bacteria, have
molecular structures that
are not shared with their host
are shared by many related pathogens
are relatively invariant; that is, do not evolve rapidly (in contrast, for example, to such pathogen molecules as the hemagglutinin
and neuraminidase of influenza viruses).
These are called Pathogen-Associated Molecular Patterns (PAMPs)
Examples:
the flagellin of bacterial flagella
the peptidoglycan of Gram-positive bacteria
the lipopolysaccharide (LPS, also called endotoxin) of Gram-negative bacteria
double-stranded RNA. (Some viruses of both plants and animals have a genome of dsRNA. And many other viruses of both
plants and animals have an RNA genome that in the host cell is briefly converted into dsRNA).
unmethylated DNA (eukaryotes have many times more cytosines, in the dinucleotide CpG, with methyl groups attached).
Dendritic cells have a set of transmembrane receptors that recognize different types of PAMPs. These are called Toll-like receptors
(TLRs) because of their homology to receptors first discovered and named in Drosophila.
TLRs identify the nature of the pathogen and turn on an effector response appropriate for dealing with it. These signaling cascades
lead to the expression of various cytokine genes.

15.4O.1 https://bio.libretexts.org/@go/page/5451
 Interleukin 12 (IL-12) drives the nearby T cells to become Th1 cells, which will provide help for cell-mediated immunity
including attack against intracellular pathogens.
IL-23, which promotes differentiation of the T cells into Th17 helper cells, which can deal with extracellular bacteria.
IL-4, which promotes differentiation of the T cells into Th2 cells which provide help for antibody production by B cells.
Under other circumstances, activated dendritic cells may secrete TGF-β and IL-10, leading to the formation of regulatory T cells
(Treg) that dampen immune responses.

Dendritic Cell Subsets

While all DCs share certain features, they actually represent a variety of cell types with different differentiation histories,
phenotypic traits and, as outlined above, different effector functions.
Examples:

Myeloid Dendritic Cells

As their name implies, these cells ("mDCs") are derived from the same myeloid progenitors in the bone marrow that give rise to
granulocytes and monocytes. They present antigen to T cells and activate the T cells by secreting large amounts of IL-12.

Plasmacytoid Dendritic Cells

These cells ("pDCs") get their name from their extensive endoplasmic reticulum which resembles that of plasma cells. However,
unlike plasma cells that are machines for pumping out antibodies, pDCs secrete huge amounts of interferon-alpha especially in
response to viral infections.
Plasmacytoid DCs have internal toll-like receptors:
TLR-7 and TLR-8, which bind to the single-stranded RNA (ssRNA) genomes of such viruses as influenza, measles, and
mumps.
TLR-9, which binds to the unmethylated cytosines in the dinucleotide CpG in the DNA of the pathogen. (The cytosines in the
host's CpG dinucleotides often have methyl groups attached.)

CD8+ vs. CD8− Dendritic Cells

These subsets are found in the mouse spleen.
The CD8− subset presents antigen engulfed from the surroundings — using the class II pathway — to CD4+ helper T cells.
The CD8+ subset can present extracellular antigens using the class I pathway as well. The peptide/MHC class I molecules are
presented to CD8+ T cells which go on to become cytotoxic T lymphocytes (CTL). This phenomenon is called cross-
presentation.
Dendritic cells can also present undegraded antigen to B cells; that is, antigen that has not been processed into peptide/MHC
complexes.

Monocyte-derived Dendritic Cells (Mo-DCs)

Humans (and mice) have another population of dendritic cells that develop from blood-borne monocytes that have been exposed to
Gram-negative bacteria (or their LPS). The LPS is detected by their TLR4 molecules. Mo-DCs can present antigen to both CD4+
T cells and CD8+ T cells (cross-presentation).

Ralph Steinman
Ralph Steinman, the pioneer in the study of dendritic cells, has provided striking visual evidence of the cellular interactions
between antigen-presenting dendritic cells, T cells, and B cells. When spleen cells are cultured with antigen, tight clusters of cells
form (see figure). The clustering occurs in two phases:
an early phase (days 0–2) during which only the dendritic cells and T cells need to be present to form clusters
a later phase (days 2–5) when antigen-primed B cells enter the cluster and differentiate into antibody-secreting cells

15.4O.2 https://bio.libretexts.org/@go/page/5451
 Figure 15.4.15.2 spleen cells after 2 days in culture. Four dendritic cells (arrows)
Pictures Courtesy of Ralph Steinman from K. Inaba et al., J. Exp. Med. 160:858,
1984

Homing
Some dendritic cells not only activate T cells to respond to a particular antigen but tell them where to go to deal with that antigen.
Two examples:

Antigens in the skin

Dendritic cells engulf antigens in (or even on!*) the skin and, while doing so, convert calciferol (vitamin D3) present in the skin
into calcitriol (1,25[OH]2 Vitamin D3).
When they activate the appropriate T cells in a nearby lymph node, the calcitriol induces those T cells to express a surface
receptor designated CCR10 (a member of the CC chemokine receptor family).
CCR10 binds the chemokine CCL27 — which is present in the skin.
So when these T cells reajavascript:void('Remove Anchor')ch the skin, they stop their travels and go to work there.

Antigens in the GI tract

Dendritic cells in the lining of the intestine are always busy engulfing the many antigens present there.
While doing so, they convert the abundant amount of retinol (vitamin A) there into retinoic acid.
When they activate the appropriate T cells in a nearby lymph node, the retinoic acid induces those T cells to express another CC
chemokine receptor designated CCR9.
CCR9 binds the chemokine CCL25 present in the intestine.
So when these T cells reach the intestine, they stop their travels and go to work. (CCL25 also attracts IgA-secreting B cells.)

Switching Homing Directions

Most vaccines are given by injection into muscle or skin. This works very well for inducing systemic immunity; that is, IgG
antibodies in the blood able to attack pathogens (e.g., tetanus) that are present in the blood.
Injected vaccines do not work as well for illnesses caused by intestinal pathogens such as
typhoid fever (caused by Salmonella typhi)
cholera (caused by Vibrio cholerae)
However, a group of German immunologists reported in July 2011 that:
whereas dendritic cells receiving antigens from injections under the skin influence T cells to migrate back to the skin (as we
saw above),

15.4O.3 https://bio.libretexts.org/@go/page/5451
 if these subcutaneous injections are accompanied by injections of retinoic acid, the T cells migrate to the intestine instead.
CCR9+ plasma cells secreting antigen-specific IgA antibodies also appeared in the intestine.
Using this technique, these workers were able to protect their mice from mouse typhoid (Salmonella typhimurium) and cholera
toxin.

This page titled 15.4O: Dendritic Cells is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4O.4 https://bio.libretexts.org/@go/page/5451
15.4P: Passive Immunity

Figure 15.4.16.1: Milking a snake for the production of antivenom. from Wikipedia (CC-BY-2.0; Barry Rogge).

Immune Globulin (IG)

Horse and sheep proteins are foreign to the human patient and will, in due course, elicit an active immune response. This may lead
to an allergic reaction such as systemic anaphylaxis or serum sickness. To avoid such problems, humans are often used as the
source of passive antibodies.
IG is also used to provide protection to boys with X-linked agammaglobulinemia, who are unable to manufacture antibodies
because of a mutation in their single (because on their X chromosome) gene for Bruton's tyrosine kinase.
hepatitis A ("infectious" hepatitis), measles, and rubella. Some immune globulin (IG) is prepared from the gamma globulin
fraction of pooled plasma from the outdated blood of several thousand blood donors on the assumption that this large pool will
contain good levels of antibodies against many common diseases such as
Some preparations of immune globulin are harvested from selected individual donors who have either recently recovered from
the disease or who have been deliberately and intensively immunized against it. These are used to provide immediate protection
against such diseases as rabies, tetanus, varicella (chicken pox), and complications arising from giving the smallpox vaccine
(vaccinia immune globulin or VIG).
The recent need for an effective treatment for people with inhalational anthrax has led to the use of plasma donated by
military personnel previously actively immunized with anthrax vaccine. Soon it should be possible to prepare a purified
immune globulin from this plasma. Further down the road will be the use of antianthrax monoclonal antibodies.
Rh immune globulin (RhIg) or Rhogam is used to prevent Rh-negative mothers from becoming sensitized to the Rh antigen of
their newborn child.

Advantages of human immune globulin

The preparation contains fewer irrelevant serum proteins and of those that remain, being human proteins, they are far less
immunogenic and are catabolized more slowly than horse proteins. However, care must be (and is) taken to ensure that the
preparations are not contaminated with human pathogens such as the AIDS virus (HIV) or hepatitis viruses.

Non-antigen-specific effects of human immune globulin

Intravenous injections of IG have helped patients with such autoimmune disorders as
immune hemolytic anemia
immune thrombocytopenic purpura
myasthenia gravis
The therapeutic effect seems to have nothing to do with the antigen specificities (e.g., antitetanus) of the antibodies in the
preparation. Instead it is the C-region portion of the antibody molecules that provides the protection. Animal studies suggest that it
does so by binding to a class of receptors on macrophages, which inhibits them from phagocytosing antibody-coated cells, e.g.,
antibody-coated red cells in immune hemolytic anemia
antibody-coated platelets in idiopathic thrombocytopenic purpura
The spleen is packed with macrophages and is where most of red blood cell and platelet destruction occurs in these diseases (and
explains why removal of the spleen so often helps the patient).

15.4P.1 https://bio.libretexts.org/@go/page/5452
This page titled 15.4P: Passive Immunity is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4P.2 https://bio.libretexts.org/@go/page/5452
15.4Q: Innate Immunity
The ability of a multicellular organism to defend itself against invasion by pathogens (bacteria, fungi, viruses, etc.) depends on its
ability to mount immune responses. All metazoans (probably) have inborn defense mechanisms that constitute innate immunity.
Vertebrates have not only innate immunity but also are able to mount defense mechanisms that constitute adaptive immunity. This
table gives some of the distinguishing features of each type of immunity.

Innate Immunity Adaptive Immunity

Pathogen recognized by receptors encoded in the germline Pathogen recognized by receptors generated randomly

Receptors have broad specificity, i.e., recognize many related molecular Receptors have very narrow specificity; i.e., recognize a particular
structures called PAMPs (pathogen-associated molecular patterns) epitope

PAMPs are essential polysaccharides and polynucleotides that differ Most epitopes are derived from polypeptides (proteins) and reflect the
little from one pathogen to another but are not found in the host. individuality of the pathogen.

In jawed vertebrates, the receptors are B-cell (BCR) and T-cell (TCR)
Receptors are PRRs (pattern recognition receptors)
receptors for antigen
Slow (3–5 days) response (because of the need for clones of responding
Immediate response
cells to develop)

Little or no memory of prior exposure Memory of prior exposure

Occurs in all metazoans Occurs in vertebrates only

The Cells of the Innate Immune System

A variety of different types of cells participate in innate immunity. What they all have in common is that the receptors by which
they recognize pathogens are limited in their specificity. This is in contrast to the B cells and T cells of the adaptive immune system
that generate receptors — BCRs and TCRs respectively — that are exquisitely specific for the pathogen. The players:
The several granulocytes of the blood and tissues
neutrophils
eosinophils
basophils and mast cells
monocytes and macrophages
dendritic cells
Innate Lymphoid Cells (ILCs). These are cells that look like lymphocytes but do not have the antigen receptors found on B
lymphocytes (BCRs) and T lymphocytes (TCRs). They include cytotoxic Natural Killer (NK) cells and several subsets of non-
cytotoxic cells (ILC1, ILC2, ILC3, etc.) each with it own pattern of cytokine secretion and favored targets.

Pathogen-Associated Molecular Patterns (PAMPs)

Pathogens, especially bacteria, have molecular structures that are not shared with their host and are shared by many related
pathogens. They are relatively invariant; that is, do not evolve rapidly (in contrast, for example, to such pathogen molecules as the
hemagglutinin and neuraminidase of influenza viruses).
Examples:
the flagellin of bacterial flagella
the peptidoglycan of Gram-positive bacteria
the lipopolysaccharide (LPS, also called endotoxin) of Gram-negative bacteria
double-stranded RNA. (Some viruses of both plants and animals have a genome of dsRNA. And many other viruses of both
plants and animals have an RNA genome that in the host cell is briefly converted into dsRNA).
unmethylated DNA (eukaryotes have many times more cytosines, in the dinucleotide CpG, with methyl groups attached).

Pattern Recognition Receptors (PRRs)

There are three groups:

15.4Q.1 https://bio.libretexts.org/@go/page/5453
 1. secreted molecules that circulate in blood and lymph;
2. surface receptors on phagocytic cells like macrophages that bind the pathogen for engulfment;
3. cell-surface receptors that bind the pathogen initiating a signal leading to the release of effector molecules (cytokines).

Secreted PRRs
Example: Circulating proteins (e.g., C-reactive protein) that bind to PAMPs on the surface of many pathogens. This interaction
triggers the complement cascade leading to the opsonization of the pathogen and its speedy phagocytosis.

Phagocytosis Receptors
Macrophages have cell-surface receptors that recognize certain PAMPs, e.g., those containing mannose. When a pathogen covered
with polysaccharide with mannose at its tips binds to these, it is engulfed into a phagosome.

Toll-Like Receptors (TLRs)

Macrophages, dendritic cells, and epithelial cells have a set of transmembrane receptors that recognize different types of PAMPs.
These are called Toll-like receptors (TLRs) because of their homology to receptors first discovered and named in Drosophila.
Mammals have 12 different TLRs each of which specializes — often with the aid of accessory molecules — in a subset of PAMPs.
In this way, the TLRs identify the nature of the pathogen and turn on an effector response appropriate for dealing with it. These
signaling cascades lead to the expression of various cytokine genes. Examples:
TLR-1: Forms a heterodimer with TLR-2 at the cell surface which binds to the peptidoglycan of Gram-positive bacteria like
Streptococci and Staphylococci.
TLR-2: With TLR-1, binds cell-wall components of Gram-positive bacteria.
TLR-3: Binds to the double-stranded RNA of viruses engulfed in endosomes.
TLR-4: Activated by the lipopolysaccharide (endotoxin) in the outer membrane of Gram-negative bacteria like Salmonella and
E. coli O157:H7
TLR-5: Binds to the flagellin of motile bacteria like Listeria.
TLR-6: Forms a heterodimer with TLR-2 and responds to peptidoglycan and certain lipoproteins.
TLR-7 and TLR-8: Form a heterodimer that binds to the single-stranded RNA (ssRNA) genomes of such viruses as influenza,
measles, and mumps that have been engulfed in endosomes.
TLR-9: Binds to the unmethylated CpG of the DNA of bacteria that have been engulfed in endosomes. (The cytosines in the
host's CpG dinucleotides often have methyl groups attached.)
TLR-11:In mice, it binds proteins expressed by several infectious protozoans (Apicomplexa) as well as, like TLR-5, to
flagellin. Humans do not have TLR-11.
In all these cases, binding of the pathogen to the TLR initiates a signaling pathway leading to the activation of NF-κB. This
transcription factor turns on many cytokine genes such as those for tumor necrosis factor-alpha (TNF-α), interleukin-1 (IL-1), and
chemokines, which attract white blood cells to the site. All of these effector molecules lead to inflammation at the site. And even
before these late events occur, the binding of Gram-positive bacteria to TLR-2 and Gram-negative bacteria to TLR-4 enhances
phagocytosis and the fusion of the phagosomes with lysosomes.

Innate Immunity can trigger Adaptive Immunity

This can occur in several ways:
Macrophages and dendritic cells are phagocytes and are also responsible for "presenting" antigens to T cells to initiate both cell-
mediated and antibody-mediated adaptive immune responses.
Digested fragments of the engulfed pathogen are returned to the cell surface nestled in the cavity of class II histocompatibility
molecules.
Gene transcription turned on by the interaction of PAMPs and TLRs causes transmembrane molecules called B7 to appear at the
cell surface.
T cells have a receptor for B7 called CD28.
Simultaneous binding of
CD28 to B7 and
the antigen/class II complex to TCRs specific for it

15.4Q.2 https://bio.libretexts.org/@go/page/5453
 activates the T cell.
This leads to repeated mitotic divisions producing clones of CD4+ T cells that can carry out cell-mediated immune responses
and/or stimulate B cells to secrete antibodies of the appropriate specificity
Dendritic cells also engulf self-antigens, e.g., body cells that have died by apoptosis, but because these have no PAMPs associated
with them, there is no second signal to activate the T cells.
The interaction of PAMPs and TLRs on dendritic cells causes them to secrete cytokines, including
interleukin 12 (IL-12) which stimulates the production of Th1 cells
interleukin 23 (IL-23) which stimulates the production of Th17 cells
interleukin 6 (IL-6), which interferes with the ability of regulatory T cells to suppress the responses of effector T cells to
antigen. A double-negative is a positive.
B cells are also antigen-presenting cells. They bind antigen with their BCRs and engulf it into lysosomes. They then transport the
digested fragments to the cell surface incorporated in class II histocompatibility molecules just as macrophages and dendritic cells
do. B cells also have TLRs. When a PAMP such as LPS binds the TLR, it enhances the response of the B cell to the antigen.
It has been known for many years that for vaccines to be effective, the preparation must contain not only the antigen but also
materials called adjuvants. Several adjuvants contain PAMPs, and their stimulus to the innate immune system enhances the
response of the adaptive immune system to the antigen in the vaccine. Pathogens coated with fragments of the complement protein
C3 are not only opsonized for phagocytosis but also bind more strongly to B cells that have bound the pathogen through their BCR.
This synergistic effect enables antibody production to occur at doses of antigen far lower than would otherwise be needed. Some
workers feel that, in fact, adaptive immunity is not possible without the assistance of the mechanisms of innate immunity.

Antimicrobial Peptides
In addition to their innate pathogen-recognition systems, vertebrates (including ourselves), invertebrates (e.g., Drosophila), even
plants and fungi secrete antimicrobial peptides that protect them from invasion by bacteria and other pathogens. In fact, probably
all multicellular organisms benefit from this form of innate immunity. For humans, the best-studied antimicrobial peptides are the
defensins, hepcidin and the cathelicidins

Defensins
All our epithelial surfaces
skin
lining of the GI tract
lining of the genitourinary tracts
lining of the nasal passages and lungs
are protected by defensins.
Some defensins are secreted by the epithelial cells themselves; others by Th17 cells and neutrophils.
Some are secreted all the time; others only in response to attack by pathogens. (In some cases their genes are turned on by
activated TLRs.)
They are synthesized from larger gene-encoded precursors which are
cut to produce the active peptide.
These range in length from 25 to 45 amino acids.
In humans, they contain 6 invariant cysteines that form 3 disulfide bonds that assist in producing a secondary structure that
consists of 3 strands of anti-parallel beta sheet.
They attack the outer surface of the cell membrane surrounding the pathogen eventually punching lethal holes in it. (Unlike
eukaryotes, the phospholipids in the outer membrane of bacteria carry a surplus of negative charges, and the positive charges on
the defensins probably enable them to penetrate the bacterial membranes while sparing host membranes.)
Curiously, some defensins (β-defensin) also affect coat color (in dogs and mice) and in other ways mimic the effects of melanocyte-
stimulating hormone (MSH).

15.4Q.3 https://bio.libretexts.org/@go/page/5453
Hepcidin
Hepcidin is a peptide of 25 amino acids with a secondary structure (beta sheet) like that of the defensins. It is secreted by the liver
and controls the level of iron in the blood and ECF by regulating its release from intracellular stores. Hepcidin secretion is
increased in response to invasion by pathogens (fungi and bacteria). Many of these require iron for their virulence and by blocking
the release of iron into the blood, hepcidin starves them of this essential factor.

Cathelicidins
The best known human cathelicidin is LL37, a peptide of 37 amino acids synthesized by macrophages, neutrophils, adipocytes, and
epithelial cells (providing antimicrobial protection to our skin and the lining of our urinary tract). Unlike the defensins, its
secondary structure is alpha helix.
Like defensins, the gene for LL37 can be turned on by activated TLRs. In macrophages, for example, cathelicidin synthesis within
the cell promotes killing of engulfed bacteria like M. tuberculosis, the agent of TB. Activation of the cathelicidin gene requires the
presence of the active form of vitamin D (1,25 [OH]2 vitamin D3). This may explain:
why people with a deficiency of vitamin D are more susceptible to tuberculosis;
the physiological basis for the practice of exposing patients to sunlight in TB sanitariums (before the days of antibiotics).

Antimicrobial Peptides and the GI Tract

The contents of the GI tract (especially the colon) are loaded with bacteria. But most of these cause no trouble thanks to a variety of
defenses. Among these is the barrier of antimicrobial peptides that exists from mouth to anus.
The epithelium of the mouth and tongue is protected by a layer of antimicrobial peptides as well as those secreted in the saliva.
The stomach is also protected by antimicrobial peptides (cut by pepsin from a larger precursor) as well as by the low pH of
gastric juice.
The liquefied contents that leave the stomach are quickly neutralized by the bicarbonate ions in the pancreatic fluid. However,
any bacteria that survived the trip through the stomach (e.g., E. coli has a proton pump that enables it to survive the strong acid
of the gastric juice) are kept in check by the antimicrobial peptides secreted by the Paneth cells of the small intestine. So, the
contents of the small intestine normally contain only a small population of microbes.
Not so for the large intestine (colon). The colon supports an enormous population (>1013) of microorganisms, but these seldom
invade its lining thanks to
a protective barrier of antimicrobial peptides as well as
the protective actions of continuous stimulation of
TLR-2s by Gram-positive commensals and
TLR-4s by Gram-negative commensals
The rectum is also protected by an epithelial barrier of antimicrobial peptides.

This page titled 15.4Q: Innate Immunity is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4Q.4 https://bio.libretexts.org/@go/page/5453
15.4R: The Complement System
Sometimes the interaction of antibodies with antigen is useful by itself. For example,
coating a virus or bacterium thus preventing it from binding to — and invading — a host cell (e.g., antipolio antibodies)
binding to a toxin molecule (e.g., diphtheria or tetanus toxin) thus keeping the toxin from entering a cell where it does its dirty
work
But most of the time, the binding of antibodies to antigen performs no useful function until and unless it can activate an effector
mechanism. The complement system serves several effector roles. The complement system provides the actual protection from the
response while the interaction of antibodies and antigen provides the specificity of the response. Put another way, antibodies
"finger" the target, complement destroys it.
Features of the system
The complement system consists of some 30 proteins circulating in blood plasma.
Most of these are inactive until they are cleaved by a protease which, in turn, converts them into a protease.
Thus many components of the system serve as the substrate of a prior component and then as an enzyme to activate a
subsequent component.
This pattern of sequential activation produces an expanding cascade of activity (reminiscent of the operation of the blood
clotting system).

The Classical Pathway

The binding of antibody to its antigen often triggers the complement system through the so-called classical pathway. It can occur in
solution or — as shown here — when the antibodies have bound to antigens on a cell surface.
The proteins of the classical pathway

Figure 15.4.18.1 Classical pathway

C1
C1 exists in blood serum as a molecular complex containing:
6 molecules of C1q
2 molecules of C1r
2 molecules of C1s
The constant regions of mu chains (IgM) and some gamma chains (IgG) contain a binding site for C1q. A single molecule of IgM
is enough to initiate the pathway. IgG is far less efficient, requiring several molecules to do so (6 is the optimum — the same as the
number of C1q molecules in C1).
Binding of C1q activates C1s and C1r.

15.4R.1 https://bio.libretexts.org/@go/page/5454
 Activated C1s (a serine protease) cleaves two serum proteins:
C4 is cleaved into a large fragment
C4b, which binds covalently to sugar residues on cell-surface glycoproteins, and a smaller, inactive, fragment of
C4a which diffuses away.
C2 is cleaved into
C2b, which binds noncovalently to a site on C4b, leaving a smaller, inactive, fragment of
C2a which diffuses away.
The complex of C4b•2b is called "C3 convertase" because it catalyzes the cleavage of C3. (C4b•2b is also a serine
protease.)

C3
C3 is the most abundant protein of the complement system (~1.3 mg/ml). Because of its abundance and its ability to activate
itself, it greatly magnifies the response.
C4b•2b cuts C3 into two major fragments:
C3b, which binds covalently to glycoproteins scattered across the cell surface. Macrophages and neutrophils have receptors
for C3b and can bind the C3b-coated cell or particle preparatory to phagocytosis. This effect qualifies C3b as an opsonin.
C3a This small fragment is released into the surrounding fluids. It can bind to receptors on basophils and mast cells
triggering them to release their vasoactive contents (e.g., histamine). Because of the role of these materials in anaphylaxis,
C3a is called an anaphylatoxin.
Some of the C3b binds to molecules of C5 creating an allosteric change that exposes them to cleavage by C4b•2b (which is thus
a "C3/C5 convertase".)

C5
Cleavage of C5 by the C3/C5 convertase initiates the assembly of a set of complement proteins that make up the membrane attack
complex. (The membrane attack complex can also be formed by another C5 convertase produce by the "alternative pathway".)

The Membrane Attack Complex

Cleavage of C5 by the C3/C5 convertase, produces:
C5a, which is released into the fluid surroundings where it
is a potent anaphylatoxin (like C3a)
is a chemotactic attractant for neutrophils
C5b, which serves as the anchor for the assembly of a single molecule each of C6, C7 and C8.
The resulting complex C5b•6•7•8 guides the polymerization of as many as 18 molecules of C9 into a tube inserted into the lipid
bilayer of the plasma membrane. This tube forms a channel allowing the passage of ions and small molecules. Water enters the
cell by osmosis and the cell lyses.

Figure 15.4.18.2 Holes punched in a membrane by complement system

The electron micrograph (courtesy of Drs. J. H. Humphrey and R. Dourmashkin) shows holes punched through the cell wall of the
Gram-negative bacterium Shigella dysenteriae by the terminal components of the complement system. (Some of the holes are
larger than expected for C9 channels and probably were enlarged later by the action of lysozyme.)

15.4R.2 https://bio.libretexts.org/@go/page/5454
Effector Functions of Complement
Cell lysis is only one function (and probably not the most important one) of the complement system. The complement system acts
in several ways to mobilize defense mechanisms.
Opsonization by C3b targets foreign particles for phagocytosis.
Chemotaxis by C5a attracts phagocytic cells to the site of damage.
This is aided by the increased permeability of the capillary beds mediated by C3a and C5a.
The early complement components are also important for solubilizing antigen-antibody complexes assisting in their catabolism
and elimination from the body. Failure of this function can lead to immune complex disorders.
Lysis of antibody-coated cells. (In some cases, this causes more harm than good; complement-mediated lysis can cause such
serious disorders as
Rh disease
immune hemolytic anemia
immune thrombocytopenic purpura
Promoting antibody formation. Breakdown of C3b generates a fragment (C3d) that binds to antigens enhancing their uptake by
dendritic cells and B cells.
(The C3d.antigen complex binds to the same receptor on B cells that the Epstein-Barr virus (EBV) uses to gain entry into B
cells — where it may cause mononucleosis and, sometimes, Burkitt's lymphoma.)

The Alternative Pathway

The complement system can also be triggered without antigen-antibody complexes. Even in their absence, there is a spontaneous
conversion of C3 to C3b. Ordinarily the C3b is quickly inactivated: the C3b binds to inhibitory proteins and sialic acid present on
the surface of the body's own cells, and the process is aborted. However, bacteria and other foreign materials that may get into the
body lack these proteins and have little or no sialic acid.

Figure 15.4.18.3 C3b

So the C3b
binds a protein called Factor B forming a complex of C3b•Bb.
C3b•Bb is also a C3 convertase acting on more C3 to form:
C3b•Bb•C3b, which is a C5 convertase and can start the assembly of the membrane attack complex.
more C3b! This second function (shown here) creates a positive feedback loop, amplifying what might have started as a
small reaction (the formation of C3b by either or both the classical and alternative pathways) into a massive production of
C3b.

Regulation of Complement Activity

The explosive potential of the complement system requires that it be kept under tight control. At least 12 proteins are known that
do this. Three examples:
Factor H removes Bb from the alternative pathway C3 convertase breaking the positive feedback loop.
Factor I inactivates C3b.
C1 inhibitor (C1INH) binds to sites on activated C1r and C1s shutting down their proteolytic activity. So when C1 is activated
by antigen-antibody complexes, there is only a brief interval during which it can cleave C4 and C2 before it is deactivated by
C1INH.

Disorders of the Complement System

With so many proteins involved, it is not surprising that inherited deficiencies of one or another are sometimes encountered in
humans. Four examples:
C3. An inherited deficiency of C3 predisposes the person to frequent bouts of bacterial infections.

15.4R.3 https://bio.libretexts.org/@go/page/5454
 C2. Curiously, immune complex disorders, not bacterial infections, are the main problem with a deficiency of C2 (or of one of
the other "early" components like C1q, C1r, C1s, or C4). This emphasizes the important role of the complement system in
clearing away antigen-antibody complexes. A deficiency of C2 (or one of the other early components) is frequently found in
patients with the autoimmune disorder systemic lupus erythematosus (SLE).
C9. Another curiosity: most people who cannot make C9 have no more of a problem with bacterial infections than those who
can. Laboratory studies suggest that the C5b•6•7•8 complex by itself is able to lyze bacteria although not as efficiently as C9.
And, in fact, a deficiency of C8 is associated with a sharply-increased risk of bacterial meningitis.
C1INH. A deficiency of C1INH produces hereditary angioedema (HAE).

This page titled 15.4R: The Complement System is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4R.4 https://bio.libretexts.org/@go/page/5454
15.4S: Inflammation
Inflammation is a response of a tissue to injury, often injury caused by invading pathogens. It is characterized by increased blood
flow to the tissue causing increased temperature, redness, swelling, and pain.
A bacterial infection initiates inflammation through several interconnecting mechanisms:
The "nonself" surface of bacteria allows the complement system to be activated through the "alternative pathway".
Certain surface molecules of the bacteria, called Pathogen-Associated Molecular Patterns (PAMPs), bind to Toll-like receptors
(TLRs) on or in a variety of leukocytes.

Mast Cells

Figure 15.4.19.1 Mast cell

Mast cells are found in the tissues. Their cytoplasm is loaded with granules containing mediators of inflammation. Their surface is
coated with a variety of receptors which, when engaged by the appropriate ligand, trigger exocytosis of the granules. Mast cells
appear to be key players in the initiation of inflammation.
Their Toll-like receptors trigger exocytosis when they interact with PAMPs like
the lipopolysaccharide (LPS or "endotoxin") of Gram-negative bacteria (TLR-4)
the peptidoglycan of Gram-positive bacteria (bind TLR-2)
Their receptors for complement fragments trigger exocytosis when they bind C3a and C5a bacteria coated with C3b
Activated mast cells release literally dozens of potent mediators. Some immediately as they discharge their granules, some later as
they synthesize them by new gene transcription. These mediators are active in either (or, in some cases, both)
recruiting all the types of white blood cell to the site
monocytes that become macrophages when they leave the blood and enter the tissue
neutrophils
antigen-presenting dendritic cells
all kinds of lymphocytes:
B cells and T cells, leading to an adaptive immune response;
NK cells (an effector cell in innate immunity).
eosinophils
activating many of these recruited cells to produce their own mediators of inflammation.

Tumor Necrosis Factor-alpha (TNF-α)

Large amounts of TNF-α are quickly released by stimulated mast cells. All the cells involved in inflammation have receptors for
TNF-α and are activated by it to synthesize more on their own. This positive feedback quickly amplifies the response.

Tryptase
Tryptase is the most abundant protein released by mast cells. It is a serine protease. Like the mammalian enzyme trypsin, tryptase
cleaves peptide bonds on the C-terminal side of arginines and lysines. It activates C3 of the complement system and probably
supports inflammation in other ways as well.

15.4S.1 https://bio.libretexts.org/@go/page/5455
Chemokines
These are chemotactic cytokines; that is, secreted proteins that attract other leukocytes into the area. Several have been identified.

Reactive Oxygen Species (ROS)

These are produced by activated phagocytes: macrophages and neutrophils. They are toxic for microorganisms but can also lead to
tissue injury. ROS are described in detail on another page. Link to it.

Histamine
The granules of mast cells are loaded with histamine and their exocytosis releases this potent mediator. Histamine increases the
blood flow to the area and the leakage of fluid and proteins from the blood into the tissue space. Thus the quick release of
histamine produces the redness and swelling associated with inflammation.

Interleukin-1 (IL-1)
Macrophages, monocytes, and activated platelets are sources of this cytokine. IL-1 has both
paracrine effects on cells in the vicinity
causing them to produce tissue factor and thus triggering the blood clotting cascade
stimulating the synthesis and secretion of a variety of other interleukins
helping to activate T cells and thus initiate an adaptive immune response
endocrine (hormonal) effects as it is carried in the blood throughout the body
decreasing blood pressure
inducing fever.
IL-1 causes fever by stimulating the release of prostaglandins, which act on the temperature control center of the hypothalamus.

Inflammasomes
IL-1 is synthesized from a larger precursor that is cleaved by a caspase (caspase-1). Caspase-1 is part of a multi-protein complex in
the cytosol of macrophages and neutrophils called an inflammasome. Inflammasomes are activated by several different products
produced by invading bacteria. Some of these are first "seen" by toll-like receptors (TLRs) thus providing a link between the innate
immune system and inflammation.

Bradykinin
Bradykinin is a nonapeptide (9 amino acids). It is synthesized by proteolytic cleavage of an inactive precursor (a kininogen) that is
produced by the liver and circulates at all times in the blood (one of the alpha-globulins).
Bradykinin relaxes the smooth muscle walls of the arterioles lowering blood pressure and increasing blood flow to the tissue and
makes the capillaries leakier, allowing blood components to enter the tissue space. These effects (like those of histamine) produce
the redness, warmth, and swelling of inflammation.
The process:
Hageman factor (also known as clotting factor XII [12]) normally circulates in the blood as inactive precursor.
When tissue damage allows blood to escape into the tissue space, Hageman factor comes in contact with the collagens in the
tissue space and becomes activated.
Activated Hageman factor is a serine protease that cleaves an inactive precursor called prekallikrein into another serine protease
— kallikrein.
Kallikrein then cleaves kininogen forming bradykinin.
Bradykinin also
stimulates the release of nitric oxide
stimulates phospholipase to increase the production of prostaglandins
mediates the closing of the ductus arteriosus when a baby is born
plays a major role in the dangerous swelling associated with hereditary angioedema (HAE)

15.4S.2 https://bio.libretexts.org/@go/page/5455
Prostaglandins and Leukotrienes

Figure 15.4.19.2 Prostaglandins

These potent mediators of inflammation are derivatives of arachidonic acid (AA) a 20-carbon unsaturated fatty acid produced
from membrane phospholipids. The principal pathways of arachidonic acid metabolism are
the cyclooxygenase (COX) pathway, which produces prostaglandin H2 (PGH2). PGH2 serves as the substrate for two
enzymatic pathways - one leading to the production of several prostaglandins (PG); the other leading to the production of
thromboxane (Tx).
the 5-lipoxygenase pathway, which produces a collection of leukotrienes (LT)

Acute Inflammation: The Good Side of Inflammation

The acute inflammatory response to tissue damage is of great value. By
isolating the damaged area
mobilizing effector cells and molecules to the site
in the late stages - promoting healing,
inflammation protects the body. Its importance is demonstrated by the problems people with inherited defects in components of the
process have with infections.
Some examples:
a failure to produce reactive oxygen species (ROS) leads to chronic granulomatous disease (CGD)
inherited defects in the ability to produce the later complement components (C5, C6, C7, C8, C9) increase the risk of certain
infections.

Chronic Inflammation: The Bad Side of Inflammation

In chronic inflammation, the inflammatory response is out of proportion to the threat it is faced with or is directed against
inappropriate targets. In the first case, the result can be more damage to the body than the agent itself would have produced.

Allergies and Autoimmune Diseases

All the many types of allergies and many of the autoimmune diseases are examples of inflammation in response to what should
have been a harmless agent.
Some examples:
Asthma
Rheumatoid Arthritis (RA)
Multiple Sclerosis (MS)
Systemic Lupus Erythematosus (SLE)
In many of these cases, the problem is made worse by the formation of antibodies against self antigens or persistent antigens from
smoldering infections. The antibodies complex with the antigens triggering the complement system with all its mediators of
inflammation. The result: immune complex disorders.

15.4S.3 https://bio.libretexts.org/@go/page/5455
Treating Inflammation
Inappropriate inflammation can be treated with
steroids like the glucocorticoid cortisol
nonsteroidal anti-inflammatory drugs (NSAIDs) like aspirin and ibuprofen (e.g., Motrin®, Advil®).
a number of therapeutic proteins produced by recombinant DNA technology.

NonSteroidal Anti-Inflammatory Drugs (NSAIDs)

The NSAIDs achieve their effects by blocking the activity of cyclooxygenases. The body produces two different forms of
cyclooxygenase:
COX-1, which is involved in pain, promoting clotting, and protecting the stomach
COX-2, which is involved in the pain produced by inflammation.
In addition to reducing the fever and pain of inflammation, NSAIDs also inhibit clotting. They do this by interfering with the
synthesis of thromboxane A2 in platelets. This is the reason that aspirin is given to patients undergoing angioplasty. Many people
take a baby aspirin a day in the hope of avoiding heart attacks. But regular use of NSAIDs has a downside: a tendency to develop
ulcers in the stomach and duodenum. Most of the NSAIDs inhibit both COX-1 and COX-2. However, some newer drugs, the so-
called COX-2 inhibitors, such as rofecoxib (Vioxx®) and celecoxib (Celebrex®) are much more active against COX-2 than COX-
1.
COX-2 inhibitors are effective against inflammation and avoid damage to the GI tract. But, unfortunately, they increase the risk of
blood clots — which can cause heart attacks and strokes — because they do not block the synthesis of thromboxane A2 by platelets
(which contain only COX-1). So people depending on NSAIDs for their heart protective effects must monitor any use of COX-2
inhibitors carefully.
In fact, because of the increased risk of heart attacks and strokes, the manufacturer of Vioxx® removed it from the market on 30
September 2004.

Therapeutic Proteins
Recombinant DNA and monoclonal antibody technology have produced some new therapies that are being enlisted in the battle
against damaging inflammation.
an IL-1 antagonist that binds and inactivates the IL-1 receptor.
etanercept (Embrel®). A soluble version of the TNF-α receptor. It binds TNF-α preventing it from carrying out its many
inflammatory actions. Potent but carries a severe risk of allowing infections to develop.
recombinant protein C. To help the body dissolve the tiny clots that are triggered during inflammation.
Infliximab (Remicade®). Binds to tumor necrosis factor-alpha (TNF-α). Shows promise against some inflammatory diseases
such as rheumatoid arthritis (by blunting the activity of Th1 cells). Side-effects: can convert a latent case of tuberculosis into
active disease; can induce the formation of autoantibodies (by promoting the development of Th2 cells).
In fact, all the more powerful anti-inflammatory agents (e.g., glucocorticoids) increase the risk of infection.

Sepsis and Septic Shock

On occasions, for reasons that are not entirely clear, the inflammatory response — usually to an infection by lipopolysaccharide
(LPS)-bearing Gram-negative bacteria — spirals out of control progressing until it involves the entire body. This life-threatening
development is called sepsis.
The circulatory system loses its integrity:
There is a breakdown of the adherens junctions between the cells lining the capillaries allowing fluid to leak into the tissue
spaces — edema.
There is a breakdown in the control of blood clotting. What should have been a mechanism to help wall off an infected area and
promote healing leads instead to a dangerous deposition of fibrin in small blood vessels throughout the body.
If these responses are massive, they can lead to septic shock
a failure of many organs: lungs, kidneys, etc.

15.4S.4 https://bio.libretexts.org/@go/page/5455
 a sharp drop in blood pressure
death

Toxic Shock Syndrome

Some Gram-positive cocci can produce a similar condition, but here the eliciting agent is not LPS but a toxin liberated by the
bacteria. In theory, anti-inflammatory agents should be useful in combating sepsis. But so far, only recombinant protein C has
shown any promise (by inhibiting the formation of thrombin), and severe bleeding is a dangerous side-effect.

Inflammation and Cancer

Chronic inflammation is also a frequent cause of cancer. Liver cancer is often the sequel to years of inflammation caused by
infection by hepatitis B and/or C viruses. Lung cancer often is the end stage of years of chronic inflammation caused by inhaled
irritants, of which tobacco smoke is the most reliable. Cervical cancer can follow chronic infection and inflammation caused by
papilloma viruses and chlamydiae. Chronic infection with the liver fluke Opisthorchis viverrini is responsible for many cases of
bile duct cancer in Thailand and Laos. Bladder, colon, pancreas, stomach, and other cancers may similarly be the final stage of
years of inflammation.
The strong link between chronic inflammation and cancer should not be surprising when you consider that the reactive oxygen
species (ROS) liberated during inflammation are powerful DNA-damaging agents. There is increased mitosis in response to
inflammation puts more cells at risk of mutations as they replicate their DNA during S phase. Apoptosis, the programmed death of
damaged cells, is suppressed in inflamed tissue. So cells with precancerous genetic mutations, which should have committed
suicide, live on to grow into a full-blown cancer.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 15.4S: Inflammation is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4S.5 https://bio.libretexts.org/@go/page/5455
15.4U: Asthma
The incidence of asthma in the United States (as well as in many other developed countries) has reached epidemic proportions. In
the last two decades, the number of sufferers in the U. S. has doubled to more than 14 million people. In an attack of asthma, the
bronchi become constricted, making it difficult to breathe in and — especially — out. The sufferer wheezes and coughs. Severe
attacks can be life-threatening.

The Mechanism
An attack of asthma begins when an allergen is inhaled. The allergen binds to IgE antibodies — those that have binding sites for
the allergen — on mast cells in the lungs. Binding triggers exocytosis of the mast cells with the release of histamine and
leukotrienes. These substances cause the smooth muscle cells of the bronchi to contract narrowing the lumen of the bronchi. This
is the early phase. They attract an accumulation of inflammatory cells — especially eosinophils — and the production of mucus.
This is the late phase. With repeated attacks, the lining of the bronchi becomes damaged. Although asthma begins as an allergic
response, in time attacks can be triggered by nonspecific factors like cold air, exercise, and tobacco smoke.

Figure 15.4.21.1: Mast cell

Some people are predispositioned to develop asthma

For reasons that are not yet understood, some people have a predisposition to respond to antigens by making antibodies of the IgE
class. The trait tends to run in families suggesting a genetic component. These people are said to suffer from atopy. The T helper
cells of atopic people are largely of the Th2 type rather that Th1. And mice whose genes for a transcription factor (called "T-bet")
used to make Th1 cells have been knocked out make fewer Th1 and more Th2 cells and suffer the lung changes typical of human
asthma even though not exposed to any known allergen. Th2 helper cells help B cells make IgE antibodies by synthesizing
interleukin 4 (IL-4) and interleukin 13 (IL-13), which promote class switching. They also release interleukin 5 (IL-5) which
attracts eosinophils and other inflammatory cells to the site, producing the late phase of the response.

Asthma - a disease of developed countries

No one knows for certain. It is certainly not a matter of air pollution. Air pollution can trigger attacks of asthma, but some regions
with heavily-polluted air have a much lower incidence of asthma than regions with relatively clean air. One intriguing possibility:
sanitation and widespread childhood immunization may enable children to avoid the infections — especially viral — that stimulate
the immune system to respond with Th1 helper cells rather than Th2 cells. Children in Europe that give positive DTH responses to
tuberculin (a response mediated by Th1 cells) have lower rates of asthma than children who are negative in the tuberculin test.
European children growing up on farms where they are exposed to high levels of bacteria and fungi associated with farm animals
have a lower incidence of asthma and atopy than their suburban peers. But children in tropical, undeveloped countries, who are
often infected with parasitic worms, have high levels of Th2 cells and IgE but a very low incidence of asthma. Perhaps, then, a
variety of chronic infections in childhood activate mechanisms (e.g., production of regulatory T cells) that suppress all
inflammatory immune responses both Th1- and Th2-mediated.

Treatments
Beta-adrenergic agonists
These drugs (albuterol is a popular example) mimic the action of adrenaline.
They relax the smooth muscle of the bronchi.
They may be inhaled or given by mouth.

15.4U.1 https://bio.libretexts.org/@go/page/5457
 While useful in the early phase of an attack, they provide no protection against the longterm damage produced during the late
phase.

Corticosteroids
These drugs reduce the inflammation of the late phase of the response.
They may be given in an inhaler (e.g., beclomethasone) or by mouth (e.g., prednisone)

Cromolyn sodium
Cromolyn sodium (disodium cromoglycate)
inhibits exocytosis of mast cells thus blocking the release of histamine and leukotrienes
is used mainly to prevent attacks (e.g., triggered by exercise) and is of no use in the early phase of an ongoing attack

Leukotriene inhibitors
Two types of leukotriene inhibitors received FDA approval in 1996.
Zileuton (Zyflo®) blocks leukotriene synthesis by inhibiting the action of 5-lipoxygenase.
Montelukast (Singulair®) blocks the leukotriene receptors on the surface of
smooth muscle cells
eosinophils

Possible future treatments still under investigation

Anti-IgE antibodies. These interfere with the binding of IgE to mast cells. Omalizumab (Xolair®), a humanized monoclonal
antibody produced by recombinant DNA technology, has been approved for use against allergic asthma (but carrying a "black-
box" warning of the slight risk of its precipitating an anaphylactic reaction).
Drugs that bind to IL-13 keeping it from promoting IgE synthesis.
Treatments that stimulate the production of Th1 cells by the immune system. Injections of a harmless mycobacterium (a
relative of the TB bacillus) might do the trick. Th1 cells secrete interferon-gamma which is a powerful inhibitor of Th2 cells.
Some of these treatments are already in clinical trials.

This page titled 15.4U: Asthma is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4U.2 https://bio.libretexts.org/@go/page/5457
15.4V: AIDS
AIDS stands for Acquired Immune Deficiency Syndrome. It represents the late stages of infection by a retrovirus called Human
Immunodeficiency Virus (HIV). The immune deficiency is caused by the loss of the CD4+ T cells that are essential for both cell-
mediated immunity and antibody-mediated immunity.

HIV - Human Immunodeficiency Viruses

They are retroviruses. There are two of them:
HIV-1 — the major cause of AIDS throughout the world;
HIV-2 — mostly found in West Africa.

Infection
HIV can only enter cells that express
the transmembrane protein CD4 found on helper T cells
a second G protein-coupled "coreceptor" (GPCR) on these cells:
Strains of HIV (designated "R5") bind the coreceptor CCR5. These are the strains that are most infectious.
Strains of HIV (designated "X4") bind the coreceptor CXCR4.
Both strains usually coexist in an ongoing infection with X4 tending to dominate in the final stages of AIDS.

Figure 15.4.22.2 Endocytic vesicle

The virion binds to both CD4 and either coreceptor by means of molecules on its surface called glycoprotein 120 (gp120). The
virion then is swept into the cell by receptor-mediated endocytosis. Fusion of the lipid membranes of the virion and the endosome -
Endocytic vesicle, releases the contents of the virion into the cytosol. The fusion is mediated by gp41. When HIV infects a cell its
molecules of reverse transcriptase and integrase are carried into the cell attached to the viral RNA molecules. The reverse
transcriptase synthesizes DNA copies of the RNA. These enter the nucleus where the integrase catalyzes their insertion into the
DNA of the host's chromosomes. The HIV DNA is transcribed into fresh RNA molecules which reenter the cytosol where some
are translated by host ribosomes. The env RNA is translated into molecules of the envelope protein (gp160). These pass through
the endoplasmic reticulum and then the Golgi apparatus where they become glycosylated by enzymes of the host cell.
Proteases of the host cell then cut gp160 into
gp120 which sits on the surface of the virions (and is the target of most of the vaccines currently being tested).
gp41, a transmembrane protein associated with gp120.
the gag and pol genes are translated into a single protein molecule which is cleaved by the viral protease into
6 different capsid proteins
the protease
reverse transcriptase
the integrase
other RNA molecules become incorporated into fresh virus particles

15.4V.1 https://bio.libretexts.org/@go/page/5458
Disease Transmission
HIV is present in body fluids especially blood and semen, especially in the early and late phases of the disease. Breaks or abrasions
in mucous membranes and skin allow the virus in.
In North America, transmission occurs primarily
between men when one ejaculates into the rectum (or mouth — the adenoids and tonsils are filled with dendritic cells) of the
other
among intravenous drug users who share needles
in women who are the sexual partners of bisexual men or i.v. drug users
in the newborn babies of these women
in recipients of infected blood or blood products. This last category accounted for a devastating epidemic among hemophiliacs
in the 1980s who unknowingly used HIV-contaminated preparations of factor 8 (VIII). In some areas, 90% or more of the
hemophiliacs developed AIDS. That risk, and the risk from blood transfusions, is now virtually zero because
all donated blood is now tested to see if the donor has been infected with HIV (as well as some other viruses)
plasma-derived preparations of factors 8 (VIII) and 9 (IX) are now treated with heat and/or solvents to destroy any viruses
that might be present;
recombinant factor 8 (VIII) and recombinant factor 9 (IX) made by genetic engineering are now available.

Disease Progression
Infection by HIV produces three phases of disease:
an early phase that
lasts about 2 weeks
is accompanied by fever, aches, and other flu-like symptoms
is accompanied by high levels of virus in the blood.
a middle phase with these features:
lasts for months or even years
produces few, if any, symptoms
patient's blood contains few viruses, but contains antibodies to the virus which are the basis of the most common test for
HIV infection
continuous infection, death, and replacement of CD4+ T cells
It is the late phase that is called AIDS. It has these features:
A rapid decline in the number of CD4+ T cells. When these drop below about 350 per µl (normal is >1000), the patient's
immunity is sufficiently weakened that opportunistic infections begin. These are infections caused by organisms that
ordinarily do not cause disease symptoms in immunocompetent people. They include:
viruses, e.g., herpes simplex, herpes varicella-zoster, Epstein-Barr virus (EBV)
bacteria, e.g., Mycobacterium tuberculosis
fungi, e.g. Candida albicans (the cause of "thrush"), Pneumocystis jirovecii (causes pneumonia)
protozoans, e.g., Microsporidia
When the CD4+ count drops below 200 per µl (mm3), opportunistic infections become more severe and cancer (e.g.,
lymphoma, Kaposi's sarcoma) may develop. Untreated, these usually kill the patient within a year or so.

Treatment
In affluent countries, the progression of HIV disease has been markedly slowed by the use of HAART (= Highly Active
AntiRetroviral Therapy). This refers to combined therapy with three or more drugs, e.g., two that target the reverse transcriptase
and one that targets the viral protease.

Reverse Transcriptase Inhibitors

Nucleoside analogs. Examples:
zidovudine (AZT)(Retrovir®)
lamivudine (Epivir®)

15.4V.2 https://bio.libretexts.org/@go/page/5458
 didanosine (Videx®)
Each of these drugs "fools" the reverse transcriptase into incorporating it into the growing DNA strand which then halts further
DNA synthesis.
Other Reverse Transcriptase Inhibitors
These drugs, e.g., efavirenz (Sustiva®) inhibit the enzyme by other mechanisms.

Protease Inhibitors
These block the viral protease so that the proteins needed for assembly of new viruses cannot be cleaved from the large protein
precursor. Examples:
indinavir (Crixivan®)
saquinavir (Invirase®)
ritonavir (Norvir®)

Fusion Inhibitors
Fusion of the virion membrane with the endosome membrane involves noncovalent binding between two segments of the gp41
molecule designated HR1 and HR2. Enfuvirtide (Fuzeon®), a synthetic polypeptide containing 36 of the amino acids present in
the HR2 segment, interferes with this process. It probably acts as a kind of competitive inhibitor, binding to HR1 thus preventing
HR2 from binding HR1.

Integrase Inhibitors
Raltegravir (Isentress®), a drug that inhibits the HIV-1 integrase, has slowed disease progression in patients for whom other drugs
were losing their effectiveness.

Inhibiting Coreceptor Binding

Several drugs — as well as some monoclonal antibodies — that block the binding of HIV to the coreceptors CCR5 and CXCR4 are
being tested for safety and efficacy. Maraviroc®, a drug that binds to CCR5, has performed so well that it received FDA approval
in 2007. People who have a mutation in their CCR5 gene are resistant to infection. Early clinical trials of gene therapy in which a
patient's normal CCR5 gene is deliberately disrupted have shown promise.

Problems with drug treatment

Despite the great advances in slowing the progression of the disease, reversing at least for a time the symptoms of the late stages of
the disease and preventing the infection of babies born to infected mothers drug therapy has many drawbacks.
The drugs are so expensive ($7,000 to $10,000 per year) that they not only drain resources in affluent countries but are simply
unavailable in the many poor countries where the epidemic rages.
They have many unpleasant side-effects (e.g., nausea, diarrhea, liver damage).
They demand a very complicated dosing regimen: over a dozen pills a day (not counting those needed to cope with the
accompanying opportunistic infections).
They have to be continued even after active virus disappears because HIV-1 can integrate into the DNA of resting memory
CD4+ T cells as a provirus and emerge as active virus later.
They often lose effectiveness as they select for the emergence of drug-resistant virions in the patient. This latter problem is
particularly serious because of the speed at which mutations occur in HIV (as we shall now see).

Genetic Variability of HIV

Reverse transcription (RNA → DNA) lacks the proofreading capabilities of DNA replication or of normal transcription (DNA →
RNA). Therefore errors, i.e., mutations, are frequent. Because of these,
The population of viruses in a single patient becomes genetically more diverse as time goes by. This can lead to:
appearance of strains that invade other types of cells such as X4 strains that target T cells and strains that target cells of the
brain, etc.
Development of resistance to the anti-viral drugs being used.
New strains and subtypes of HIV-1 and HIV-2 arise in the human population.

15.4V.3 https://bio.libretexts.org/@go/page/5458
 These complicate the efforts to develop a vaccine against HIV
But as we shall now see that these have helped to unravel the origins of the disease.

Origin of HIV
Genome sequencing of different isolates of HIV-1 and HIV-2 shows that each is related to retroviruses that occur in primates in
Africa. These are designated simian immunodeficiency viruses (SIV) although they do not cause immune deficiency (or any
disease) in their natural host. However, on those occasions when a SIV accidentally infects a primate of a different species, it does
cause disease in the new host. The human epidemic is one example.
HIV-1 is most closely related to a SIV found in chimpanzees (Pan troglodytes troglodytes)
HIV-2 is most closely related to a SIV that occurs in the sooty mangabey (Cercocebus atys).
Genome analysis also permits the construction of phylogenetic trees which reveal different clades of HIV just as such analysis
reveals evolutionary relationship between species. The picture so far:
HIV-1 appears to have infected humans on at least 4 different occasions giving rise to 4 clades: M, N, O, and P. Groups M and
N appear to have jumped at separate times from chimpanzees to humans while O may have jumped from gorillas to humans.
Except in parts of West Africa, most human cases are caused by members of Group M.
HIV-2 appears to have jumped from sooty mangabeys to humans on at least 4 different occasions (there are 4 clades).
How? These (and other) primates are often slaughtered for food and exposure to their blood and tissues is probably the route of
transmission. In fact the chimpanzee SIV that gave rise to HIV-1 appears to be itself the product of recombination between two
monkey SIVs that infected chimpanzees. (Chimps often eat monkeys.)
Just as with other evolutionary trees, one can also estimate from genome sequences the time of divergence of two branches. This
evidence indicates that the Group M clade of HIV-1 invaded humans sometime very early in the 20th century.
But the worldwide epidemic of AIDS did not get its start until the 1980s. What took so long? An answer to that requires an
appreciation of the way in which contagious diseases spread. Their rate of spread depends on:
The ease of transmission. The transmissibility of HIV is very low. HIV is not like influenza or measles which spread like
wildfire.
The length of time the host remains contagious. Again, HIV is not like influenza or measles where the period of
contagiousness is just a few days. For HIV, it can be years.
The number of susceptible contacts; that is, the proximity of potential new hosts. For sexually-transmitted diseases (STDs),
that means the number of sexual contacts.
So diseases like HIV only smolder in isolated populations because they lack the density of susceptible contacts. In crowded
populations, the equation changes. There has been a dramatic population shift from rural to urban areas in sub-Saharan Africa since
1950. In the case of STDs, the availability of multiple sexual contacts — perhaps accompanied by changing sexual mores — tips
the scales. In any case, the major factor today in the spread of HIV is promiscuity, whether homosexual or heterosexual.

Prevention of AIDS
Vaccines
Many once-feared infectious diseases have been reduced or eliminated by the development of a vaccine to prevent the disease.
Over two dozen experimental anti-HIV vaccines have been developed and clinical trials of some of these have been and are
presently being undertaken. So far, the results have been disappointing. There are probably several reasons. Some of the vaccines
attempt to induce antibodies, e.g., against the outer portion of the envelope protein (called gp120). But antibody-mediated
immunity may not give adequate protection. The gene (env) encoding the envelope protein mutates too rapidly. The virus may be
able to stay within cells out of the reach of circulating antibodies. High levels of antibodies (the basis of the most common test of
infection) persist even while the disease pursues its inexorable course.
So other vaccines have been designed to favor the development of cell-mediated immunity; e.g., cytotoxic T cells.
Many of these are DNA vaccines, for example,
a live virus such as canarypox (a harmless relative of smallpox) or an adenovirus which serves as a vector for introducing HIV
genes (DNA)
a mixture of plasmids encoding several HIV genes (e.g., gag, pol, and env of several HIV strains).

15.4V.4 https://bio.libretexts.org/@go/page/5458
It is hoped that expression of these genes within the cells (e.g., muscle) of the subject will induce a protective immune response,
but to date there has been no success.

Behavior
Because HIV transmission is so difficult, changing behavior could go a long way toward stopping the epidemic.
Reducing the number of sexual partners.
If injecting drugs cannot be stopped, then using sterile needles (thus not sharing them) would prevent infection.
Using condoms and/or other (e.g., chemical) barriers to prevent contact with infectious semen.
In the words of Anthony S. Fauci, Director of the National Institute of Allergy and Infectious Diseases, "Unlike microbial scourges,
such as malaria and tuberculosis (among many others), for which there is very little that people can do to prevent infection, HIV
infection in adults is entirely preventable by behavior modification".

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 15.4V: AIDS is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4V.5 https://bio.libretexts.org/@go/page/5458
15.4W: Vaccines
Active Immunization or Vaccination
The terms vaccination and vaccine derive from the work of Edward Jenner who, over 200 years ago, showed that inoculating
people with material from skin lesions caused by cowpox (L. vaccinus, of cows) protected them from the highly contagious and
frequently fatal disease smallpox. Since Jenner's time, the term has been retained for any preparation of dead or weakened
pathogens, or their products, that when introduced into the body, stimulates the production of protective antibodies or T cells
without causing the disease. In molecular terms, the goal is to introduce harmless antigen(s) with epitopes that are also found on the
pathogen.
Vaccination is also called active immunization because the immune system is stimulated to develop its own immunity against the
pathogen. Passive immunity, in contrast, results from the injection of antibodies formed by another animal (e.g., horse, human)
which provide immediate, but temporary, protection for the recipient.

Kinds of Vaccines
Killed whole organisms
In this relatively crude approach, the vaccine is made from the entire organism, killed to make it harmless. The typhoid and cholera
vaccines are examples.

Attenuated organisms
Here, the organism has been cultured so as to reduce its pathogenicity, but still retain some of the antigens of the virulent form. The
Bacillus Calmette-Guérin (BCG) is a weakened version of the bacterium that causes tuberculosis in cows. BCG is used as a vaccine
against tuberculosis in many European countries but is rarely used in the U.S.

Toxoids
In some diseases, diphtheria and tetanus are notorious examples, it is not the growth of the bacterium that is dangerous, but the
protein toxin that is liberated by it. Treating the toxin with, for example, formaldehyde, denatures the protein so that it is no longer
dangerous, but retains some epitopes on the molecule that will elicit protective antibodies.

Surface molecules
Antibodies are most likely to be protective if they bind to the surface of the invading pathogen triggering its destruction. Several
vaccines employ purified surface molecules:
Influenza vaccine contains purified hemagglutinins from the viruses currently in circulation around the world.
The gene encoding a protein expressed on the surface of the hepatitis B virus, called hepatitis B surface antigen or HBsAg, can
now be expressed in E. coli cells and provides the material for an effective vaccine. Hepatitis B infection is strongly associated
with the development of liver cancer. Here then is a vaccine against a cancer.
The genes encoding the capsid proteins of 9 strains of human papilloma virus (HPV) can be expressed in yeast and the resulting
recombinant proteins are incorporated in a vaccine (Gardasil 9®). Because infection with some of these strains of HPV can lead
to cervical cancer, here is another vaccine against cancer.
Some 80 different strains of Streptococcus pneumoniae cause pneumonia in humans. They differ in the chemistry of the
polysaccharide capsule that surrounds them and makes it difficult for phagocytes to engulf them by endocytosis. One current
vaccine consists of tiny amounts of the purified capsular polysaccharides of the 23 most common and/or dangerous strains.

Inactivated virus
Like killed bacterial vaccines, these vaccines contain whole virus particles that have been treated (again, often with formaldehyde)
so that they cannot infect the host's cells but still retain some unaltered epitopes. The Salk vaccine for polio (IPV) is an example.

Attenuated virus
In these vaccines, the virus can still infect but has been so weakened that it is no longer dangerous. The measles, mumps, and
rubella ("German measles") vaccines are examples. The Sabin oral polio vaccine (OPV) is another example. It has advantages over
the Salk vaccine in that

15.4W.1 https://bio.libretexts.org/@go/page/5459
 it is given by mouth rather than by injection;
the viruses it contains can spread to the other members of the vaccinee's family thus immunizing them as well.
It has the disadvantage that on rare occasions one of the strains in the vaccine regains full virulence and causes the disease. For this
reason, the Salk vaccine has once again become the preferred vaccine worldwide.

 Example: A new method of attenuation

The various attenuated-virus vaccines in current use were developed by rather hit-or-miss methods. However, scientists have
been working on a technology exploiting the phenomenon of codon bias - that may make possible the rational development of
safer vaccines.
One group, at Stony Brook University (see J.R. Coleman et al., Science, 27 June 2008), has engineered polio virus with
hundreds of mutations in the genes encoding its capsid protein. However, every one of these is a "silent" mutation; that is, it
simply changes the codon for the amino acid to a different codon for the same amino acid. When they created polio viruses in
which pairs of new codons were ones that the wild polio virus avoids using (because its human host does), they found that the
new viruses were far less infectious that the original. But note, that this procedure did not introduce any change in the amino
acid sequence of the capsid protein. So one would expect that all the epitopes recognized by the immune system would be
unchanged. And, indeed, they went on to show that mice immunized with the synthetic virus were protected from disease
caused by the wild virus.
As mentioned above, one of problems associated with the attenuated live virus polio vaccine (Sabin) is the rare back mutation
to full virulence. Such back mutation in these engineered viruses would be extremely unlikely considering the hundreds of
silent mutations that would have to be reversed.

Summary Table: Here is a table describing some of the most widely-used vaccines used in humans.
Disease Agent Preparation Notes

Diphtheria Toxoid Often given in a single preparation

DTaP (Daptacel®) for infants and young
Tetanus Toxoid children; Tdap for teenagers and adults (the
lower case letters signify the smaller amounts
Killed bacteria ("P") or their purified of the diphtheria and pertussis antigens in
Pertussis
components (acellular pertussis = "aP") Tdap).

Inactivated virus Inactivated polio vaccine: IPV (Salk)

Polio Oral polio vaccine; OPV (Sabin)
Attenuated virus
Both vaccines trivalent (types 1, 2, and 3)
HAVRIX® and VAQTA®; also available in
Hepatitis A Inactivated virus
single shot with HBsAg (Twinrix®)

Hepatitis B Protein (HBsAg) from the surface of the virus Made by recombinant DNA technology

Attenuated virus (Rotarix®) or 5 strains of the to prevent this serious diarrheal disease in
Rotavirus
virus (RotaTeq®) infants

Gardasil 9®; made by recombinant DNA

Human Papilloma Virus (HPV) Protein from the capsid of 9 strains of the virus
technology

Diphtheria, tetanus, pertussis, polio, and Pediarix®; combination vaccine given in 3

Uses acellular pertussis and IPV (Salk)
hepatitis B doses to infants

Diphtheria, tetanus, pertussis, polio, and Pentacel®; combination vaccine given in 4

Uses acellular pertussis and IPV (Salk)
Hemophilus influenzae type b (Hib) doses to infants

Measles Attenuated virus Often given as a mixture (MMR)

Do not increase the risk of autism. (Nor do any
Mumps Attenuated virus
vaccines containing thimerosal as a
Rubella Attenuated virus preservative.)

Also available combined with MMR

Chickenpox (Varicella) Attenuated varicella-zoster virus (VZV)
("MMRV" or ProQuad®)

15.4W.2 https://bio.libretexts.org/@go/page/5459
 Disease Agent Preparation Notes

Cholera Killed bacteria Three oral vaccines available

Contains hemagglutinins from the type A

Hemagglutinins
and type B viruses recently in circulation
Influenza FluMist® — contains weakened viruses of the
Attenuated virus type B
and two type A strains recently in circulation
A mixture of the capsular polysaccharides of
Capsular polysaccharides
23 common types. Works poorly in infants.
Pneumococcal infections
13 capsular polysaccharides conjugated to
Mobilizes helper T cells; works well in infants.
protein ("PCV13")

To prevent outbreaks among new groups of

Meningococcal disease 4 polysaccharides conjugated to protein young adults, e.g., college freshmen, military
recruits

Hemophilus influenzae, type b (Hib) Capsular polysaccharide conjugated to protein Prevents meningitis in children

Vaccine prepared from human diploid cell

Rabies Inactivated virus cultures (HDCV)
or chick embryo cells (PCECV)
Despite the global eradication of smallpox, is
Smallpox Vaccinia virus used to protect against a possible bioterrorist
attack
Primarily for veterinarians and military
Anthrax Extract of attenuated bacteria
personnel

Three types are available:

1. killed bacteria
Typhoid
2. live, attenuated bacteria (oral)
3. polysaccharide conjugated to protein

Yellow fever Attenuated virus

Tuberculosis Attenuated bacteria (BCG) Rarely used in the U.S.

Some of the Triumphs of Vaccination

The greatest triumph is the eradication of smallpox from the planet, with no naturally-occurring cases having been found since
1977. "Naturally-occurring" because one case (fatal) occurred later following the accidental release of the virus in a laboratory. As
far as the public knows, smallpox virus now exists only in laboratories in the U.S. and Russia. There is currently a vigorous debate
as to whether these should be destroyed. If smallpox ever should get back out into the environment, the results could be devastating
because smallpox vaccination is no longer given and so the population fully susceptible to the disease grows year by year.
A program to try to eliminate polio from the world is now underway. Except for cases caused by OPV, the disease has now been
eliminated from the Western hemisphere. Outbreaks of polio still occur in Africa, the Indian subcontinent, and parts of the Near
East. Table 1 compares the number of cases of illness in the U.S. in a representative year (either before a vaccine was available or
before it came into widespread use) with the number of cases reported in 1994.
Table 1
Disease Total cases Year Cases in 1994 % Change

Diphtheria 206,939 1921 2 -99.9%

Measles 894,134 1941 963 -99.9%

Mumps 152,209 1968 1537 -99.9%

Pertussis 265,269 1934 4617 -99.9%

Poliomyelitis* 21,269 1952 0 -100%

15.4W.3 https://bio.libretexts.org/@go/page/5459
 Disease Total cases Year Cases in 1994 % Change

Rubella 57,686 1969 227 -99.9%

Tetanus 1,560 1923 51 -99.9%

*Since 1979, an average of 8 cases of poliomyelitis have occurred in the U.S. each year that are acquired from the vaccine (OPV,
the Sabin vaccine) itself. For this reason, the "killed" virus vaccine (IPV, the Salk vaccine) is being reintroduced. As of June 17,
1999, it is recommended that in the future all children receive 4 doses of the Salk vaccine and — except in special circumstances
— none of the Sabin vaccine.

Problems of Vaccine Development

With so many triumphs, why haven't vaccines eliminated other common diseases such as malaria and HIV-1 infection?
One problem is that experimental vaccines often elicit an immune response that does not actually protect against the disease. Most
vaccines preferentially induce the formation of antibodies rather than cell-mediated immunity. This is fine for those diseases
caused by
toxins (diphtheria, tetanus)
extracellular bacteria (pneumococci)
even viruses that must pass through the blood to reach the tissues where they do their damage (polio, rabies)
But viruses are intracellular parasites, out of the reach of antibodies while they reside within their target cells. They must be
attacked by the cell-mediated branch of the immune system, such as by cytotoxic T lymphocytes (CTLs). Most vaccines do a poor
job of eliciting cell-mediated immunity (CMI).
Example:
Much of the early and so far unsuccessful work on anti-HIV-1 vaccines has focused on the antibody response of the test animal.
Antibodies may have a role in preventing infection or minimizing its spread, but cell-mediated responses will probably turn out to
be far more important. Certainly there are thousands of patients dying of AIDS despite their high levels of anti-HIV-1 antibodies.
The most widespread test for HIV-1 infection does not detect the presence of the virus but the presence of antibodies against the
virus.

DNA Vaccines
With DNA vaccines, the subject is not injected with the antigen but with DNA encoding the antigen.
The DNA is incorporated in a plasmid containing
DNA sequences encoding one or more protein antigens or, often, simply epitopes of the complete antigen(s);
DNA sequences incorporating a promoter that will enable the DNA to be efficiently transcribed in the human cells.
Sometimes DNA sequences encoding costimulatory molecules and sequences that target the expressed protein to specific
intracellular locations (e.g., endoplasmic reticulum) are included as well.
The DNA vaccine can be injected into a muscle just as conventional vaccines are. In contrast to conventional vaccines, DNA
vaccines elicit cell-mediated as well as antibody- mediated immune responses.

The cell-mediated response

The plasmid is taken up by an antigen-presenting cell (APC) like a dendritic cell.
The gene(s) encoding the various components are transcribed and translated.
The protein products are degraded into peptides.
These are exposed at the cell surface nestled in class I histocompatibility molecules where
they serve as a powerful stimulant for the development of cell-mediated immunity.

The antibody-mediated response

If the plasmid is taken up by other cells (e.g. muscle cells), the proteins synthesized are released and can be engulfed by
antigen-presenting cells (including B cells).
In this case, the proteins are degraded in the class II pathway and presented to helper T cells.
These secrete lymphokines that aid B cells to produce antibodies.

15.4W.4 https://bio.libretexts.org/@go/page/5459
So far, most of the work on DNA vaccines has been done in mice where they have proved able to protect them against
tuberculosis, SARS, smallpox, and other intracellular pathogens. In addition, more than a dozen different DNA vaccines against
HIV-1 the cause of AIDS are in clinical trials.

This page titled 15.4W: Vaccines is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.4W.5 https://bio.libretexts.org/@go/page/5459
 SECTION OVERVIEW
15.5: Excretion
Topic hierarchy

15.5A: Human Kidneys

15.5B: Vertebrate Kidneys

15.5C: Urea Cycle

This page titled 15.5: Excretion is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.5.1 https://bio.libretexts.org/@go/page/5364
15.5A: Human Kidneys
The human kidneys are two bean-shaped organs, one on each side of the backbone. They represent about 0.5% of the total weight
of the body, but receive 20–25% of the total arterial blood pumped by the heart. Each contains from one to two million nephrons.

Figure 15.5.1.1 Human kidneys

The Nephron

Figure 15.5.1.2 Nephrons

The nephron is a tube closed at one end and open at the other. It consists of:
Bowman's capsule. Located at the closed end, the wall of the nephron is pushed in forming a double-walled chamber.
Glomerulus. A capillary network within the Bowman's capsule. Blood leaving the glomerulus passes into a second capillary
network surrounding the proximal tubule.
Proximal convoluted tubule. Coiled and lined with cells carpeted with microvilli and stuffed with mitochondria.
Loop of Henle. It makes a hairpin turn and returns to the distal convoluted tubule.
Distal convoluted tubule, which is also highly coiled and surrounded by capillaries.
Collecting duct. It leads to a calyx, one of many small chambers from which urine drains into the pelvis of the kidney from
where it flows through a ureter to the bladder and, periodically, on to the outside world.
The Bowman's capsules are packed in the cortex of the kidney, the tubules and collecting ducts descend into the medulla.

15.5A.1 https://bio.libretexts.org/@go/page/5460
 Figure 15.5.1.3 Cortex of a mouse kidney courtesy of Keith R. Porter
The image above shows a cut section of the cortex of a mouse kidney as seen under the scanning electron microscope. Near the top
(center) can be seen a Bowman's capsule with its glomerulus. Directly beneath is another Bowman's capsule with its glomerulus
removed. The remainder of the field shows the lumens of both proximal and distal tubules as they have been cut at various angles.

Formation of Urine
The nephron makes urine by filtering the blood of its small molecules and ions and then reclaiming the needed amounts of useful
materials. Surplus or waste molecules and ions are left to flow out as urine. In 24 hours the kidneys reclaim: ~1,300 g of NaCl,
~400 g NaHCO3, ~180 g glucose and almost all of the 180 liters of water that entered the tubules. Blood enters the glomerulus
under pressure. This causes water, small molecules (but not macromolecules like proteins) and ions to filter through the capillary
walls into the Bowman's capsule. This fluid is called nephric filtrate. As the table shows, it is simply blood plasma minus almost
all of the plasma proteins. Essentially it is no different from interstitial fluid.
Table 1: Composition of plasma, nephric filtrate, and urine (each in g/100 ml of fluid). These are representative values. The values for salts
are especially variable, depending on salt and water intake.
Component Plasma Nephric Filtrate Urine Concentration % Reclaimed

Urea 0.03 0.03 1.8 60X 50%

Uric acid 0.004 0.004 0.05 12X 91%

Glucose 0.10 0.10 None - 100%

Amino acids 0.05 0.05 None - 100%

Total inorganic salts 0.9 0.9 <0.9–3.6 <1–4X 99.5%

Proteins and other

8.0 None None - -
macromolecules

Figure 15.5.1.4 Urine formation process

Nephric filtrate collects within the Bowman's capsule and then flows into the proximal tubule.
Here all of the glucose and amino acids, >90% of the uric acid, and ~60% of inorganic salts are reabsorbed by active transport.
The active transport of Na+ out of the proximal tubule is controlled by angiotensin II.
The active transport of phosphate (PO43-) back into the blood is regulated (suppressed) by both the parathyroid hormone
and fibroblast growth factor 23 (FGF-23).
As these solutes are removed from the nephric filtrate, a large volume of the water follows them by osmosis (80–85% of the
180 liters deposited in the Bowman's capsules in 24 hours).
As the fluid flows into the descending segment of the loop of Henle, water continues to leave by osmosis because the
interstitial fluid is very hypertonic. This is caused by the active transport of Na+ out of the tubular fluid as it moves up the
ascending segment of the loop of Henle.
In the distal tubules, more sodium is reclaimed by active transport, and still more water follows by osmosis.
Final adjustment of the sodium and water content of the body occurs in the collecting ducts.

15.5A.2 https://bio.libretexts.org/@go/page/5460
Sodium
Although 97% of the sodium has already been removed, it is the last 3% that determines the final balance of sodium and hence
water content and blood pressure in the body. The reabsorption of sodium in the distal tubule and the collecting ducts is closely
regulated by the synergistic action of the hormones vasopressin and aldosterone.

Water
The hypertonic interstitial fluid surrounding the collecting ducts provides a high osmotic pressure for the removal of water.
Transmembrane channels made of proteins called aquaporins are inserted in the plasma membrane greatly increasing its
permeability to water. When open, an aquaporin channel allows 3 billion molecules of water to pass through each second.
Insertion of aquaporin-2 channels requires signaling by vasopressin (also known as arginine vasopressin [AVP] or the
antidiuretic hormone [ADH]).
Vasopressin binds to receptors (called V2 receptors) on the basolateral surface of the cells of the collecting ducts.
Binding of the hormone triggers a rising level of cAMP within the cell.
This "second messenger" initiates a chain of events culminating in the insertion of aquaporin-2 channels in the apical
surface of the cell.
The release of vasopressin (from the posterior lobe of the pituitary gland) is regulated by the osmotic pressure of the blood.
Anything that dehydrates the body, such as perspiring heavily,
increases the osmotic pressure of the blood
turns on the vasopressin → V2 receptors → aquaporin-2 pathway.
The result:
As little as 0.5 liter/day of urine may remain of the original 180 liters/day of nephric filtrate.
The concentration of salts in the urine can be as much as four times that of the blood. (But not high enough to enable
humans to benefit from drinking sea water, which is saltier still.)
If the blood should become too dilute (as would occur after drinking a large amount of water),
Vasopressin secretion is inhibited.
The aquaporin-2 channels are taken back into the cell by endocytosis.
The result: a large volume of watery urine is formed (with a salt concentration as little as one-fourth of that of the blood).

Diabetes insipidus
This disorder is characterized by excretion of large amounts of a watery urine (as much as 30 liters - about 8 gallons each day and
unremitting thirst.
It can have several causes:
Insufficient secretion of vasopressin.
Inheritance of two mutant genes for the vasopressin receptor (V2) [in females; because the gene is X-linked, only one does it
for males].
Inheritance of one (for dominant mutations) or two (for recessive versions) mutant genes for aquaporin-2.

Liddle's Syndrome
The most obvious effect of this rare inherited disorder is extremely high blood pressure (hypertension). It is caused by a single
mutant allele (therefore the syndrome is inherited as a dominant trait) encoding the aldosterone-activated sodium channel in the
collecting ducts. The defective channel is always "on" so too much Na+ is reabsorbed and too little is excreted. The resulting
elevated osmotic pressure of the blood produces hypertension.

Tubular Secretion
Although urine formation occurs primarily by the filtration-reabsorption mechanism described above, an auxiliary mechanism,
called tubular secretion, is also involved. The cells of the tubules remove certain molecules and ions from the blood and deposit
these into the fluid within the tubules.
Example: Excess hydrogen ions (H+) are combined with ammonia (NH3) to form ammonium ions (NH4+) and transported to the
cells of the collecting ducts. Here the NH4+ dissociates back into ammonia and H+. Both are then secreted into the fluid within the

15.5A.3 https://bio.libretexts.org/@go/page/5460
collecting ducts (the protons by active transport).
Tubular secretion of H+ is important in maintaining control of the pH of the blood. When the pH of the blood starts to drop, more
hydrogen ions are secreted. If the blood should become too alkaline, secretion of H+ is reduced. In maintaining the pH of the blood
within its normal limits of 7.3–7.4, the kidney can produce a urine with a pH as low as 4.5 or as high as 8.5. Excess potassium ions
(K+) are also disposed of by tubular secretion.

The Kidney and Homeostasis

While we think of the kidney as an organ of excretion, it is more than that. It does remove wastes, but it also removes normal
components of the blood that are present in greater-than-normal concentrations. When excess water, sodium ions, calcium ions,
potassium ions, and so on are present, the excess quickly passes out in the urine. On the other hand, the kidneys step up their
reclamation of these same substances when they are present in the blood in less-than-normal amounts. Thus the kidney
continuously regulates the chemical composition of the blood within narrow limits. The kidney is one of the major homeostatic
devices of the body.

Hormones of the Kidneys

The human kidney is also an endocrine gland secreting two hormones:
Erythropoietin (EPO)
Calcitriol (1,25[OH]2 Vitamin D3), the active form of vitamin D
as well as the enzyme renin.

The Artificial Kidney

The artificial kidney uses the principle of dialysis to purify the blood of patients whose own kidneys have failed.

Figure 15.5.1.5 Artificial kidney

The left portion of the figure ("Dialysis unit") shows the mechanism used today in artificial kidneys. Small molecules like urea are
removed from the blood because they are free to diffuse between the blood and the bath fluid, whereas large molecules (e.g.,
plasma proteins) and cells remain confined to the blood. The bath fluid must already have had essential salts added to it to prevent
the dangerous loss of these ions from the blood. Note that blood and bath fluid flow in opposite directions across the dialysis
membrane. This "counter-current" exchange maintains a diffusion gradient through the entire length of the system. An
anticoagulant is added to the blood so it will not clot while passing through the machine. The anticoagulant is neutralized as the
blood is returned to the patient.
Artificial kidneys have proved of great benefit in helping patients of acute kidney malfunction survive the crisis until their own
kidneys resume operation. They have also enabled people suffering from chronic kidney failure to remain alive, though at an
enormous expense of time (often three sessions of 6 or more hours per week), money, and psychological well-being. Furthermore,
although dialysis does a good job at removing wastes, it cannot perform the other functions of the kidney:
providing precise homeostatic control over the concentration of such vital ingredients as glucose and Na+
secreting its hormones

An Artificial Kidney of the Future?

In an attempt to solve these problems, a research team at the University of Michigan is experimenting with adding a "Bioreactor
unit" (above) to the dialysis unit. The bioreactor consists of many hollow, porous tubes on the inner wall of which is attached a
monolayer of proximal tubule cells (derived from pigs). The dialysis bath fluid passes through the lumen of the tubes where
molecules and ions can be picked up by the apical surface of the cells. Discharge of essential molecules and ions (as well as
hormones) at the basolateral surface of the cells places these materials back in the blood (just as the proximal tubule cells in the
nephron normally do). So far, all the testing has been done using dogs, but the results seem promising.

15.5A.4 https://bio.libretexts.org/@go/page/5460
Kidney Transplants

Figure 15.5.1.6 Kidney transplant

The ideal alternative to long-term dialysis is transplantation of a new kidney. The operation is technically quite easy. The recipient's
diseased kidneys are usually left in place, but the renal arteries and veins are tied off except for the branches supplying the adrenal
glands. The major problems is the shortage of donors suitably matched for histocompatibility molecules so as to avoid the problem
of graft rejection by the recipient's immune system - that unless the donor and recipient are identical twins - "sees" the kidney as
"foreign".

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 15.5A: Human Kidneys is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.5A.5 https://bio.libretexts.org/@go/page/5460
15.5B: Vertebrate Kidneys
All vertebrates have kidneys. Like the human kidney, they are made up of many nephrons. However, there are differences in the
structure and functioning of various vertebrate kidneys that adapt them to the environment in which the animals live.

Freshwater Vertebrates
All animals that live in fresh water must cope with a continual inflow of water from their hypotonic environment. In order to
maintain homeostasis of its extracellular fluid (ECF), the freshwater fish must excrete this excess water. Contraction of its heart
(powered by ATP) provides the pressure to force the water, small molecules, and ions into the glomerulus as nephric filtrate. The
essential ingredients are then reclaimed by the tubules, returning to the blood in the capillaries surrounding the tubules. The blood
in these capillaries comes from the glomerulus (as in humans) and also from the renal portal veins which drain the posterior part
of the fish's body.

Figure 15.5.2.1 Freshwater kidneys

After solute reabsorption is complete, the urine is little more than water. Most of the nitrogenous wastes (including large amounts
of ammonia, NH3) leave by diffusion out of the gills. So, the kidney is mostly a device for maintaining water balance in the animal,
rather than an organ of excretion.

Amphibians
The amphibian kidney also functions chiefly as a device for excreting excess water. The permeable skin of the frog provides an
easy route for the fresh water of its pond to enter by osmosis. But, as their name suggests, amphibians also spend time on land.
Then the problem is to conserve water, not eliminate it.
The frog adjusts to the varying water content of its surroundings by adjusting the rate of filtration at the glomerulus. When blood
flow through the glomerulus is restricted, a renal portal system is present to carry away materials reabsorbed through the tubules.
The frog is also able to use its urinary bladder to aid water conservation. When in water, the frog's bladder quickly fills up with a
hypotonic urine. On land, this water is reabsorbed into the blood helping to replace water lost through evaporation through the skin.
The reabsorption is controlled by a hormone similar to mammalian ADH.

Lizards and Snakes

Many reptiles live in dry environments (e.g., rattlesnakes in the desert). Among the many adaptations to such environments is their
ability to convert waste nitrogen compounds into uric acid. Uric acid is quite insoluble and so can be excreted using only a small
amount of water. Thus we find that reptile glomeruli are quite small and, in fact, some reptiles have no glomeruli at all. Those with
glomeruli filter just enough fluid to wash the uric acid, which is secreted by the tubules, into the cloaca. Most of this moisture is
reabsorbed in the cloaca. Emptying the cloaca deposits feces (brown) and uric acid (a white paste). The cloaca is a chamber
through which the feces and the gametes, as well as urine, pass on the way to the outside. The name comes from the Latin word for
sewer. These water conservation mechanisms can allow the reptile to forgo drinking water. The water content of its food plus the
water produced by cellular respiration is usually sufficient.

Figure 15.5.2.2 Reptile kidneys

15.5B.1 https://bio.libretexts.org/@go/page/5461
Birds
Bird kidneys function like those of reptiles (from which they are descended). Uric acid is also their chief nitrogenous waste. Most
birds have a limited intake of fresh water. However, they need filter only enough to wash a slurry of uric acid into the cloaca where
enough additional water is reclaimed to convert the uric acid into a semisolid paste. It is the whitish material that pigeons leave on
statues.

Mammals
All mammals share our use of urea as their chief nitrogenous waste. Urea requires much more water to be excreted than does uric
acid. Mammals produce large amounts of nephric filtrate but are able to reabsorb most of this in the tubules. But even so, humans
lose several hundred ml each day in flushing urea out of the body. Some mammals have more efficient kidneys than ours. The
kangaroo rat of the desert can produce a urine 17 times more concentrated that its blood. (The best we can do is 3-4 times as
concentrated.) The efficiency of the kangaroo rat kidney enables it to survive without drinking water — simply depending on the
water content of its food and that produced by cellular respiration.
We like to think of ourselves as highly advanced. Why don't we have kidneys as efficient as those of the reptiles and birds? It is the
luck of our inheritance. The line of vertebrate evolution that produced the mammals split off before the evolution of the diapsids
whose ability to convert nitrogenous wastes into uric acid was passed on to all their descendants, including the lizards, snakes, and
birds.

Marine Fishes
Marine fishes face just the opposite problem from that of freshwater fishes. The salt content of sea water (~3%) is so hypertonic to
that of their extracellular fluid that they are in continual danger of dehydration. The two major groups of marine fishes have solved
this dilemma differently.

Figure 15.5.2.3 Marine kidneys

Cartilaginous Fishes (Chondrichthyes)

The cartilaginous fishes such as sharks, skates, and rays have developed high levels of urea in their blood. Shark's blood may
contain 2.5% urea in contrast to the 0.01-0.03% in other vertebrates. This high level makes sharks blood isotonic to sea water, so
the shark lives in osmotic balance with its environment and has a kidney that functions like ours with the exception that far more
urea is reabsorbed in the shark's tubules than in ours.

Bony Fishes (Osteichthyes)

Marine bony fishes have solved the problem differently. They do lose water continuously but replace it by drinking sea water and
then desalting it. The salt is returned to the sea by active transport at the gills. Living in constant danger of dehydration by the
hypertonic sea, there is no reason to pump out large amounts of nephric filtrate at the glomerulus. The less water placed in the
tubules, the less that has to be reabsorbed. So it is not surprising that many bony fishes have small glomeruli and some have no
glomeruli at all. With a reduction in the filtration-reabsorption mechanism, the marine bony fishes rely more on tubular secretion
for eliminating excess or waste solutes. Tubular secretion requires a good blood supply to the tubules. Lacking efficient glomeruli,
the renal portal system must carry most of the burden.

This page titled 15.5B: Vertebrate Kidneys is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.5B.2 https://bio.libretexts.org/@go/page/5461
15.5C: Urea Cycle
Urea is the chief nitrogenous waste of mammals. Most of our nitrogenous waste comes from the breakdown of amino acids. This
occurs by deamination.

Figure 15.5.3.1 Deamination

Deamination of amino acids results in the production of ammonia (NH3). Ammonia is an extremely toxic base and its
accumulation in the body would quickly be fatal. However, the liver contains a system of carrier molecules and enzymes which
quickly converts the ammonia (and carbon dioxide) into urea. This is called the urea cycle.

The Urea Cycle

Figure 15.5.3.2 The Urea cycle

One turn of the cycle:
consumes 2 molecules of ammonia
consumes 1 molecule of carbon dioxide
creates 1 molecule of urea ((NH2)2CO
regenerates a molecule of ornithine for another turn.
Although our bodies cannot tolerate high concentrations of urea, it is much less poisonous than ammonia. Urea is removed
efficiently by the kidneys.

15.5C.1 https://bio.libretexts.org/@go/page/5462
Problems in Urea Cycle
There are several inherited diseases of the urea cycle caused by mutations in genes encoding one or another of the necessary
enzymes. The most common of these is an inherited deficiency of ornithine transcarbamylase, an enzyme needed for the
conversion of ornithine to citrulline. It results in elevated levels of ammonia that may be so high as to be life-threatening. It is an X-
linked disorder; therefore most commonly seen in males. It can be cured by a liver transplant. It can also be caused by a liver
transplant! In 1998, an Austrian woman was given a new liver from a male cadaver who - unknown to the surgeons - had a
mutation in his single ornithine transcarbamylase gene. The woman's blood level of ammonia shot up, and she died a few days
later.

Uric acid
Humans also excrete a second nitrogenous waste, uric acid. It is the product of nucleic acid, not protein, metabolism. It is
produced within peroxisomes. Uric acid is only slightly soluble in water and easily precipitates out of solution forming needlelike
crystals of sodium urate. These contribute to the formation of kidney stones and produce the excruciating pain of gout when
deposited in the joints.
Curiously, our kidneys reclaim most of the uric acid filtered at the glomeruli. Why, if it can cause problems?
Uric acid is a potent antioxidant and thus can protect cells from damage by reactive oxygen species (ROS).
The concentration of uric acid is 100-times greater in the cytosol than in the extracellular fluid. So when lethally-damaged cells
release their contents, crystals of uric acid form in the vicinity. These enhance the ability of nearby dendritic cells to "present"
any antigens released at the same time to T cells leading to a stronger immune response.
So the risk of kidney stones and gout may be the price we pay for these protections.
Most mammals have an enzyme - uricas - for breaking uric acid down into a soluble product. However, during the evolution of
great apes and humans, the gene encoding uricase became inactive. A predisposition to gout is our legacy.
Uric acid is the chief nitrogenous waste of insects, lizards and snakes and birds. It is the whitish material that birds leave on statues.
These animals convert the waste products of protein metabolism as well as nucleic acid metabolism into uric acid. Because of its
low solubility in water, these animals are able to eliminate waste nitrogen with little loss of water.

This page titled 15.5C: Urea Cycle is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.5C.2 https://bio.libretexts.org/@go/page/5462
 SECTION OVERVIEW
15.6: Hormones
Topic hierarchy

15.6.1: Human Hormones

15.6.1.1: Thyroid and Parathyroids
15.6.1.2: Hormones of the Gut
15.6.1.3: Hormones of the Pancreas
15.6.1.4: Hormones of the Pituitary
15.6.1.5: Hormones of the Hypothalamus
15.6.1.6: Adrenal Glands
15.6.1.7: Sex Hormones
15.6.1.8: Progesterone
15.6.1.9: Melatonin and the Pineal Gland
15.6.1.10: Hormones of Kidney, Skin and Heart
15.6.1.11: Leptin - the Fat Hormone
15.6.1.12: Hormones of the Liver
15.6.1.13: Melanocyte Stimulating Hormone (MSH)

15.6.2: Insect Hormones

This page titled 15.6: Hormones is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.6.1 https://bio.libretexts.org/@go/page/5366
15.6.1: Human Hormones
The essence of multicellularity is the coordinated interaction of the various kinds of cells that make up the body. Cells
communicate with each other by chemical signals. Three kinds of chemical signaling can be distinguished:
autocrine: the cell signals itself through a chemical that it synthesizes and then responds to. Autocrine signaling can occur
solely within the cytoplasm of the cell or by a secreted chemical interacting with receptors on the surface of the same cell
paracrine: chemical signals that diffuse into the area and interact with receptors on nearby cells. Examples include the release
of cytokines that cause an inflammatory response in the area and the release of neurotransmitters at synapses in the nervous
system.
endocrine: the chemicals are secreted into the blood and carried by blood and tissue fluids to the cells they act upon.
This page will examine the properties of endocrine signaling.

Kinds of Hormones
There are two major classes of hormone: (1) proteins, peptides, and modified amino acids and (2) steroids.

Proteins, peptides and modified amino acids

These hydrophilic (and mostly large) hormone molecules bind to receptors on the surface of "target" cells; that is, cells able to
respond to the presence of the hormone. These receptors are transmembrane proteins. Binding of the hormone to its receptor
initiates a sequence of intracellular signals that may alter the behavior of the cell (such as by opening or closing membrane
channels) or stimulate (or repress) gene expression in the nucleus by turning on (or off) the promoters and enhancers of the genes

Figure 15.6.1.1 : Protein hormone

This is the sequence of events:
The hormone binds to a site on the extracellular portion of the receptor.
The receptors are transmembrane proteins that pass through the plasma membrane 7 times, with their N-terminal exposed at
the exterior of the cell and their C-terminal projecting into the cytoplasm.
Binding of the hormone to the receptor
activates a G protein associated with the cytoplasmic C-terminal
This initiates the production of a "second messenger". The most common of these are
cyclic AMP, (cAMP) which is produced by adenylyl cyclase from ATP
inositol 1,4,5-trisphosphate (IP3)
The second messenger, in turn, initiates a series of intracellular events (shown here as short arrows) such as
phosphorylation and activation of enzymes
release of Ca2+ into the cytosol from stores within the endoplasmic reticulum
In the case of cAMP, these enzymatic changes activate the transcription factor CREB (cAMP response element binding
protein).
Once bound to its response element 5' TGACGTCA 3' in the promoters of genes that are able to respond to the hormone,
activated CREB turns on gene transcription.
The cell begins to produce the appropriate gene products in response to the hormonal signal it had received at its surface.

15.6.1.1 https://bio.libretexts.org/@go/page/5463
Steroid Hormones
Steroid hormones, being hydrophobic molecules, diffuse freely into all cells. However, their "target" cells contain cytoplasmic
and/or nuclear proteins that serve as receptors of the hormone. The hormone binds to the receptor and the complex binds to
hormone response elements — stretches of DNA within the promoters of genes responsive to the hormone. The hormone/receptor
complex acts as a transcription factor turning target genes "on" (or "off").

Figure 15.6.1.2 Steroid receptors

Hormone Regulation
The levels of hormones circulating in the blood are tightly controlled by three homeostatic mechanisms:
1. When one hormone stimulates the production of a second, the second suppresses the production of the first. Example: The
follicle stimulating hormone (FSH) stimulates the release of estrogens from the ovarian follicle. A high level of estrogen, in
turn, suppresses the further production of FSH.
2. Antagonistic pairs of hormones. Example: Insulin causes the level of blood sugar (glucose) to drop when it has risen. Glucagon
causes it to rise when it has fallen.
3. Hormone secretion is increased (or decreased) by the same substance whose level is decreased (or increased) by the hormone.
Example: a rising level of Ca2+ in the blood suppresses the production of the parathyroid hormone (PTH). A low level of Ca2+
stimulates it.

Hormone Transport
Although a few hormones circulate simply dissolved in the blood, most are carried in the blood bound to plasma proteins. For
example, all the steroid hormones, being highly hydrophobic, are transported bound to plasma proteins.
Summary Table of Human Hormaones
Hormone Structure (1) Principal Source

Thyroid-stimulating hormone (TSH) protein (201)

Follicle-stimulating hormone (FSH) protein (204)

Luteinizing hormone (LH) protein (204)

Anterior lobe of pituitary
Prolactin (PRL) protein (198)

Growth hormone (GH) protein (191)

Adrenocorticotropic hormone (ACTH) peptide (39)

Vasopressin peptide (9)

Posterior lobe of pituitary
Oxytocin peptide (9)

Thyrotropin-releasing hormone (TRH) peptide (3)

Gonadotropin-releasing hormone (GnRH) peptide (10)

Growth hormone-releasing hormone (GHRH) peptides (40, 44)

Hypothalamus
Corticotropin-releasing hormone (CRH) peptide (41)

Somatostatin peptides (14, 28)

Dopamine tyrosine derivative

15.6.1.2 https://bio.libretexts.org/@go/page/5463
 Hormone Structure (1) Principal Source

Melatonin tryptophan derivative Pineal gland

Thyroxine (T4) tyrosine derivative

Thyroid Gland
Calcitonin peptide (32)

Parathyroid hormone (PTH) protein (84) Parathyroid glands

protein (251)

Osteocalcin peptide (49) Bone

Erythropoietin (EPO) protein (166)

Glucocorticoids (e.g., cortisol) steroids

Mineralocorticoids (e.g., aldosterone) steroids Adrenal cortex

Androgens (e.g., testosterone) steroids

Adrenaline (epinephrine) tyrosine derivative

Adrenal medulla
Noradrenaline (norepinephrine) tyrosine derivative

Estrogens (e.g., estradiol) steroid Ovarian follicle

Progesterone steroid Corpus luteum and placenta

Human chorionic gonadotropin (HCG) protein (237) Trophoblast and placenta

Androgens (e.g., testosterone) steroid Testes

Insulin protein (51)

Glucagon peptide (29)

Pancreas (Islets of Langerhans)
Somatostatin peptides (14, 28)

Amylin peptide (37)

Erythropoietin (EPO) protein (166)

Kidney
Calcitriol steroid derivative

Calciferol (vitamin D3) steroid derivative Skin

Atrial-natriuretic peptide (ANP) peptides (28, 32) Heart

Gastrin peptides (e.g., 14)

Secretin peptide (27)

Cholecystokinin (CCK) peptides (e.g., 8)

Fibroblast Growth Factor 19 (FGF19) protein (216)

Incretins peptides (e.g., 31, 42) Stomach and intestine

Somatostatin peptides (14, 28)

Neuropeptide Y peptide (36)

Ghrelin peptide (28)

PYY3-36 peptide (34)

Serotonin tryptophan derivative

protein (70) Liver

Angiotensinogen protein (485)

Thrombopoietin protein (332)

Hepcidin peptide (25)

15.6.1.3 https://bio.libretexts.org/@go/page/5463
 Hormone Structure (1) Principal Source

Betatrophin protein (193)

Leptin protein (167)

Retinol Binding Protein 4 protein (~180)

Fat cells (adipocytes)
Adiponectin protein (117)

Asprosin protein (140)

Note: Numbers within parentheses indicate the number of amino acids in the protein or peptide(s).

This page titled 15.6.1: Human Hormones is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.6.1.4 https://bio.libretexts.org/@go/page/5463
15.6.1.1: Thyroid and Parathyroids
The Thyroid Gland
The thyroid gland is a double-lobed structure located in the neck. Embedded in its rear surface are the four parathyroid glands. The
thyroid gland synthesizes and secretes: thyroxine (T4), and triiodothyronine (T3) and calcitonin.

T 4 and T3
Both hormones are derivatives of the amino acid tyrosine with four atoms of iodine in T4 , three in T3. The thyroid secretes mainly
(80%) T4 , but when T4 enters target cells, one atom of iodine is removed from it converting it into T3. T3 is the more potent of the
two hormones. It has many effects. Among the most prominent of these are:
an increase in metabolic rate (seen by a rise in body temperature and the uptake of oxygen)
an increase in the rate and strength of the heart beat
The thyroid cells responsible for the synthesis of T4 and T3 take up circulating iodine from the blood and attach them to tyrosine
residues in the protein thyroglobulin. This action, as well as the synthesis of the hormones, is stimulated by the binding of thyroid
stimulating hormone (TSH; also known as thyrotropin) to transmembrane receptors at the cell surface.

3
Cretinism: hypothyroidism in infancy and childhood leads to stunted growth and intelligence. Can be corrected by giving
thyroxine if started early enough.
Myxedema: hypothyroidism in adults leads to lowered metabolic rate and vigor. Corrected by giving thyroxine.
Goiter: enlargement of the thyroid gland. Can be caused by:
inadequate iodine in the diet with resulting low levels of T4 and T3
an autoimmune attack against the thyroglobulin in the thyroid gland (called Hashimoto's thyroiditis)
Why should a hypothyroid disease produce an enlarged gland? The activity of the thyroid is under negative feedback
control:
The synthesis and release of thyrotropin releasing hormone (TRH) and TSH is normally inhibited as the levels of T4
and T3 rise in the blood.
When the iodine supply is inadequate, T4 and T3 levels fall.
This stimulates the hypothalamus and pituitary to increased TRH and TSH activity respectively. This stimulates the
thyroid gland to enlarge.
The symptoms of hypothyroidism can also result from inherited mutations in the genes encoding:
the receptor for TSH (present on the surface of thyroid cells)
the receptor for T3 (present in the nucleus of almost all cells)
The T3 receptor is a nuclear protein bound to the thyroid response element in the promoters of the many genes whose
expression is influenced by thyroid hormones. When its ligand, T3, binds to it, it becomes a transcription factor turning on
the transcription of many genes.

Graves´ disease: Autoantibodies against the TSH receptor bind to the receptor mimicking the effect of TSH binding.
Result: excessive production of thyroid hormones. Graves´ disease is an example of an autoimmune disease.
Osteoporosis: High levels of thyroid hormones suppress the production of TSH through the negative-feedback mechanism
mentioned above. The resulting low level of TSH causes an increase in the numbers of bone-reabsorbing osteoclasts
resulting in osteoporosis.

Calcitonin
Calcitonin is a polypeptide of 32 amino acids. The thyroid cells in which it is synthesized have receptors that bind calcium ions
(Ca2+) circulating in the blood. A rise in its level, such as would occur with the absorption of calcium from a meal, stimulates the cells to release calcitonin. Calcitonin prevents a sharp rise in blood calcium by
inhibiting the uptake of Ca2+ from the small intestine and inhibiting the Ca2+-releasing activity of osteoclasts.

Because it slows the loss of Ca2+ from bones, calcitonin has been examined as a possible treatment for osteoporosis, a weakening
of the bones that is a leading cause of hip and other bone fractures in the elderly. Being a polypeptide, calcitonin cannot be given by

15.6.1.1.1 https://bio.libretexts.org/@go/page/5465
mouth (it would be digested), and giving by injection is not appealing. However, inhaling calcitonin appears to be an effective way
to get therapeutic levels of the hormone into the blood. A synthetic version of calcitonin (trade name = Miacalcin) is now available
as a nasal spray.

The Parathyroid Glands

The parathyroid glands are 4 tiny structures embedded in the rear surface of the thyroid gland. They secrete parathyroid hormone
(PTH) a polypeptide of 84 amino acids. PTH increases the concentration of Ca2+ in the blood in three ways. PTH promotes
release of Ca2+ from the huge reservoir in the bones. (99% of the calcium in the body is incorporated in our bones.)
reabsorption of Ca2+ from the fluid in the tubules in the kidneys
absorption of Ca2+ from the contents of the intestine (this action is mediated by calcitriol, the active form of vitamin D.)
PTH also regulates the level of phosphate in the blood. Secretion of PTH reduces the efficiency with which phosphate is reclaimed
in the proximal tubules of the kidney causing a drop in the phosphate concentration of the blood.

Control of the Parathyroids

The cells of the parathyroid glands have surface G-protein-coupled receptors that bind Ca2+ (the same type of receptor is found on
the calcitonin-secreting cells of the thyroid and on the calcium absorbing cells of the kidneys). Binding of Ca2+ to this receptor
depresses the secretion of PTH and thus leads to a lowering of the concentration of Ca2+ in the blood. Two classes of inherited
disorders involving mutant genes encoding the Ca2+ receptor occur:
loss-of-function mutations with the mutant receptor always "off". Patients with these mutations have high levels of Ca2+ in
their blood and excrete small amounts of Ca2+ in their urine. These mutations cause hyperparathyroidism.
gain-of-function mutations with the mutant receptor always "on" (as though it had bound Ca2+). People with these mutations
have low levels of Ca2+ in their blood and excrete large amounts of Ca2+ in their urine. These mutations cause
hypoparathyroidism.
Rare autoimmune disorders can mimic one or the other of these inherited disorders. In each case, autoantibodies bind to the
receptors.
If these inhibit the receptors, they cause hyperparathyroidism.
If they activate the receptors (like those in Graves' disease), they cause hypoparathyroidism.

 Diseases of the thyroid: Hyperparathyroidism

Tumors in the parathyroids elevate the level of PTH causing a rise in the level of blood Ca2+ at the expense of calcium stores in
the bones. So much calcium may be withdrawn from the bones that they become brittle and break.
Until recently, treatment has been the removal of most — but not all — of the parathyroid tissue (i.e. the goal is the removal of
3 1/2 glands). Now clinical trials have begun on a drug (designated R-568) that mimics the action of calcium on the
parathyroids, resulting in a drop in PTH and blood Ca2+ and sparing the calcium stores in the bone.

Diseases of the thyroid: Hypoparathyroidism

Causes:
accidental removal of or damage to the parathyroids during neck surgery
inherited mutations in the PTH gene
inherited predisposition to an autoimmune attack against the parathyroids (and other glands)
inherited defect in the embryonic development of the parathyroids (DiGeorge syndrome)
Treatment:
give calcium supplements
give calcitriol (1,25[OH]2 vitamin D3)
give teriparatide (Forteo®), a synthetic (by recombinant DNA) version of PTH (containing only the 34 amino acids at the
N-terminal).
For reasons that are not yet clear, this drug when given in daily injections (because it would be digested if taken by mouth),
promotes strong bones and thus has been approved as a treatment for osteoporosis. While continuous high levels of PTH

15.6.1.1.2 https://bio.libretexts.org/@go/page/5465
 weaken bones by removing calcium from them, periodic injections of this drug strengthen bone by increasing the number and
activity of osteoblasts.

This page titled 15.6.1.1: Thyroid and Parathyroids is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.6.1.1.3 https://bio.libretexts.org/@go/page/5465
15.6.1.2: Hormones of the Gut
Over two dozen hormones have been identified in various parts of the gastrointestinal system. Most of them are peptides and many
of them are also found in other tissues, especially the brain. Many act in a paracrine manner as well as being carried in the blood as
true hormones. Their importance to health is uncertain as no known deficiency disorders have been found for any of them. We shall
look at 8 of them here:
1. gastrin
2. somatostatin
3. secretin
4. cholecystokinin (CCK)
5. fibroblast growth factor 19 (FGF19)
6. incretins
7. ghrelin
8. neuropeptide Y (NPY)
9. peptide YY3-36 (PYY3-36)
The endocrine cells of the small intestine also secrete serotonin and substance P.

Gastrin
Gastrin is a mixture of several peptides, of which the most active contains 14 amino acids. It is secreted by cells in the stomach and
duodenum. It stimulates the exocrine cells of the stomach to secrete gastric juice, a mixture of hydrochloric acid and the
proteolytic enzyme pepsin.

Somatostatin
This mixture of peptides is secreted by cells in the gastric glands of the stomach and acts on the stomach (thus a paracrine effect)
where it inhibits the release of gastrin and hydrochloric acid, the duodenum where it inhibits the release of secretin and
cholecystokinin and the pancreas where it inhibits the release of glucagon. Taken together, all of these actions lead to a reduction in
the rate at which nutrients are absorbed from the contents of the intestine. Somatostatin is also secreted by the hypothalamus and
the pancreas.

Secretin
It is a polypeptide of 27 amino acids and is secreted by cells in the duodenum when they are exposed to the acidic contents of the
emptying stomach. It stimulates the exocrine portion of the pancreas to secrete bicarbonate into the pancreatic fluid (thus
neutralizing the acidity of the intestinal contents).

Cholecystokinin (CCK)
A mixture of peptides, of which an octapeptide (8 amino acids) is the most active. It is secreted by cells in the duodenum and
jejunum when they are exposed to food. It acts on the gall bladder stimulating it to contract and force its contents of bile into the
intestine and on the pancreas stimulating the release of pancreatic digestive enzymes into the pancreatic fluid. CCK also acts on
vagal neurons leading back to the medulla oblongata which give a satiety signal (i.e., "that's enough food for now").

Fibroblast Growth Factor 19 (FGF19)

A protein of 216 amino acids and is secreted by cells in the lower portion of the small intestine (the ileum). Travels in the hepatic
portal system to the liver where is stimulates the the synthesis of bile acids, uptake of glucose and its conversion into glycogen. It
also travels to the gall bladder where it relaxes its smooth muscle wall allowing filling (in contrast to CCK which contracts the gall
bladder).

Incretins
The release of insulin from the pancreas is much greater when glucose is ingested with food rather than injected intravenously. It is
due to the fact that the arrival of food in the duodenum stimulates the release of polypeptides called incretins. The two most
important are:

15.6.1.2.1 https://bio.libretexts.org/@go/page/5467
 glucagon-like peptide-1 (GLP-1) the most active version of which has 29 amino acids
glucose-dependent insulinotropic polypeptide (GIP) of 42 amino acids.
Their effects:
enhancing the ability of glucose to stimulate insulin secretion by the pancreas
stimulating the ability of the tissues (e.g., liver and muscle) to take up glucose from the blood
slowing the emptying of the stomach
suppressing glucagon secretion
suppressing appetite thus reducing food intake.
All the actions prevent a sharp rise in blood glucose when consuming a sugar-rich meal. Exenatide (Byetta®) and liraglutide
(Victoza®) are synthetic peptides that mimic the action of GLP-1 but the effects are longer-lasting. They are being used to treat
patients with type 2 diabetes.

Ghrelin
Ghrelin is a lipopeptide consisting of 28 amino acids with a covalently attached 8-carbon fatty acid. Ghrelin is secreted by
endocrine cells in the stomach, especially when one is hungry and acts on the hypothalamus to stimulate feeding. This action
counteracts the inhibition of feeding by leptin and PYY3-36. Ghrelin increases the deposition of adipose tissue in mice and rats and
does not seem to increase their appetite (ghrelin knockout animals don't eat any more food than normal animals).

Neuropeptide Y (NPY)
Neuropeptide Y contains 36 amino acids. It is a potent feeding stimulant and causes increased storage of ingested food as fat.
Neuropeptide Y is also secreted by neurons in the hypothalamus where it blocks the transmission of pain signals to the brain and
induces a calming effect in laboratory animals exposed to stressful situations. Velneperit is a drug that blocks the action of
neuropeptide Y on its receptors. It is in clinical trials for the treatment of obesity.

PYY 3-36
Peptide YY3-36 contains 34 amino acids, many of them in the same positions as those in neuropeptide Y. But the action of PYY3-
36 is just the reverse of that of NPY, being a potent feeding inhibitor. It is released by cells in the intestine after meals. The amount
secreted increases with the number of calories ingested and especially when these are derived from proteins rather than
carbohydrates or fats. (This may explain the efficacy of the protein-rich, carbohydrate-poor Atkins diet.) PYY3-36 acts on the
hypothalamus to suppress appetite, the pancreas to increase its exocrine secretion of digestive juices, and the gall bladder to
stimulate the release of bile.
The appetite suppression mediated by PYY3-36 works more slowly than that of cholecystokinin and more rapidly than that of
leptin. In a recent human study, volunteers given PYY3-36 were less hungry and ate less food over the next 12 hours than those
who received saline. Neither group knew what they were getting, but one of the side-effects of injected PYY3-36 is a feeling of
nausea and a bad taste to food which might account for these results!

This page titled 15.6.1.2: Hormones of the Gut is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.6.1.2.2 https://bio.libretexts.org/@go/page/5467
15.6.1.3: Hormones of the Pancreas
The bulk of the pancreas is an exocrine gland secreting pancreatic fluid into the duodenum after a meal. However, scattered
through the pancreas are several hundred thousand clusters of cells called islets of Langerhans. The islets are endocrine tissue
containing four types of cells. In order of abundance, they are the:
beta cells, which secrete insulin and amylin
alpha cells, which secrete glucagon
delta cells, which secrete somatostatin
gamma cells, which secrete pancreatic polypeptide

Beta Cells
Insulin is a small protein consisting of an alpha chain of 21 amino acids linked by two disulfide (S—S) bridges to a beta chain of
30 amino acids. Beta cells have channels in their plasma membrane that serve as glucose detectors. Beta cells secrete insulin in
response to a rising level of circulating glucose ("blood sugar"). Insulin affects many organs. It stimulates skeletal muscle fibers
totake up glucose and convert it into glycogen. Insulin also take up amino acids from the blood and convert them into protein. It
acts on liver cells
stimulating them to take up glucose from the blood and convert it into glycogen while
inhibiting production of the enzymes involved in breaking glycogen back down ("glycogenolysis") and
inhibiting "gluconeogenesis"; that is, the conversion of fats and proteins into glucose.
acts on fat (adipose) cells to stimulate the uptake of glucose and the synthesis of fat
acts on cells in the hypothalamus to reduce appetite
In each case, insulin triggers these effects by binding to the insulin receptor - a transmembrane protein embedded in the plasma
membrane of the responding cells. Taken together, all of these actions result in:
the storage of the soluble nutrients absorbed from the intestine into insoluble, energy-rich products (glycogen, protein, fat)
a drop in the level of blood sugar

 Diabetes Mellitus

Diabetes mellitus is an endocrine disorder characterized by many signs and symptoms. Primary among these are a failure of the
kidney to efficiently reclaim glucose so that glucose spills over into the urine and a resulting increase in the volume of urine
because of the osmotic effect of this glucose (it reduces the return of water to the blood).
Diabetes mellitus is a disorder quite distinct from the similarly-named diabetes insipidus. They both result in the production of
large amounts of urine (diabetes), but in one the urine is sweet while in the other (caused by ADH deficiency) it is not. Before
the days of laboratory tests, a simple taste test ("mellitus" or "insipidus") enabled the doctor to make the correct diagnosis.
There are three categories of diabetes mellitus:
Type 1
Type 2
Inherited Forms of Diabetes Mellitus

Type 1 Diabetes Mellitus

(also known as Insulin-Dependent Diabetes Mellitus or IDDM)
is characterized by little (hypo) or no circulating insulin
most commonly appears in childhood
it results from destruction of the beta cells of the islets
the destruction results from a cell-mediated autoimmune attack against the beta cells
What triggers this attack is still a mystery. One possibility: peptides derived from insulin may bond to unrelated peptides to
form a "neoantigen"; that is, an antigen that was not present when tolerance to self-antigens was being established.
Type 1 diabetes is controlled by carefully-regulated injections of insulin. Insulin cannot be taken by mouth because, being a
protein, it would be digested. However, the U.S. FDA has approved [in January 2006] an insulin inhaler that delivers insulin

15.6.1.3.1 https://bio.libretexts.org/@go/page/5469
through the lungs and may reduce the number of daily injected doses needed.
Injections of insulin must be done carefully. Injections after vigorous exercise or long after a meal may drive the blood sugar
level down to a dangerously low value causing an insulin reaction. The patient becomes irritable, fatigued, and may lose
consciousness. If the patient is still conscious, giving a source of sugar (e.g., candy) by mouth usually solves the problem
quickly. Injections of glucagon are sometimes used.

Type 2 Diabetes Mellitus

Type 2 is also known as Non Insulin-Dependent Diabetes Mellitus (NIDDM) and adult-onset diabetes. However, this type
eventually leads to insulin dependence and also is now appearing in many children so those terms are no longer appropriate.
Many people develop Type 2 diabetes mellitus without an accompanying drop in insulin levels (at least at first). In many cases,
the problem appears to be a failure to express a sufficient number of glucose transporters in the plasma membrane (and T-
system) of their skeletal muscles.
Normally when insulin binds to its receptor on the cell surface, it initiates a chain of events that leads to the insertion in the
plasma membrane of increased numbers of a transmembrane glucose transporter (called GLUT4). This transporter forms a
channel that permits the facilitated diffusion of glucose into the cell.
Skeletal muscle is the major "sink" for removing excess glucose from the blood (and converting it into glycogen). In type 2
diabetes, the patient's ability to remove glucose from the blood and convert it into glycogen may be only 20% of normal. This
is called insulin resistance. Curiously, vigorous exercise seems to increase the expression of the glucose transporter on skeletal
muscle and this may explain why type 2 diabetes is more common in people who live sedentary lives.
Type 2 diabetes mellitus usually strikes in adults and, particularly often, in overweight people. However, over the last few
years in the U. S., the incidence of type 2 diabetes in children has grown to the point where they now account for 20% of all
newly-diagnosed cases (and, like their adult counterparts, are usually overweight). Several drugs, all of which can be taken by
mouth, are useful in restoring better control over blood sugar in patients with type 2 diabetes. However, late in the course of
disease, patients may have to begin to take insulin. It is as though after years of pumping out insulin in an effort to overcome
the patient's insulin resistance, the beta cells become exhausted.

Inherited Forms of Diabetes Mellitus

Some cases of diabetes result from mutant genes inherited from one or both parents. Examples:
mutant genes for one or another of the transcription factors needed for transcription of the insulin gene (5 mutant versions
have been identified).
mutations in one or both copies of the gene encoding the insulin receptor. These patients usually have extra-high levels of
circulating insulin but defective receptors. The mutant receptors
may fail to be expressed properly at the cell surface
may fail to transmit an effective signal to the interior of the cell.
a mutant version of the gene encoding glucokinase, the enzyme that phosphorylates glucose in the first step of glycolysis.
mutations in the gene encoding part of potassium channels in the plasma membrane of the beta cell. The channels fail to
close properly causing the cell to become hyperpolarized and blocking insulin secretion.
mutations in several mitochondrial genes which reduce insulin secretion by beta cells. These diseases are inherited from the
mother as only her mitochondria survive in the fertilized egg.
While symptoms usually appear in childhood or adolescence, patients with inherited diabetes differ from most children with
type 2 diabetes in having a history of diabetes in the family and not being obese.

 insulin
For many years, insulin extracted from the glands of cows and pigs was used. However, pig insulin differs from human insulin
by one amino acid; beef insulin by three. Although both work in humans to lower blood sugar, they are seen by the immune
system as "foreign" and induce an antibody response in the patient that blunts their effect and requires higher doses. Two
approaches have been taken to solve this problem:
Convert pig insulin into human insulin by removing the one amino acid that distinguishes them and replacing it with the
human version. This approach is expensive, so now the favored approach is to

15.6.1.3.2 https://bio.libretexts.org/@go/page/5469
 Insert the human gene for insulin into E. coli and grow recombinant human insulin in culture tanks. Insulin is not a
glycoprotein so E. coli is able to manufacture a fully-functional molecule (trade name = Humulin). Yeast is also used (trade
name = Novolin).
Recombinant DNA technology has also made it possible to manufacture slightly-modified forms of human insulin that work
faster (Humalog® and NovoLog®) or slower (Lantus®) than regular human insulin.

Amylin
Amylin is a peptide of 37 amino acids, which is also secreted by the beta cells of the pancreas. Some of its actions include inhibits
the secretion of glucagon, slows the emptying of the stomach, sends a satiety signal to the brain. All of its actions tend to
supplement those of insulin, reducing the level of glucose in the blood. A synthetic, modified, form of amylin (pramlintide or
Symlin®) is used in the treatment of type 2 diabetes.

Alpha Cells
The alpha cells of the islets secrete glucagon, a polypeptide of 29 amino acids. Glucagon acts principally on the liver where it
stimulates the conversion of glycogen into glucose ("glycogenolysis") and fat and protein into intermediate metabolites that are
ultimately converted into glucose ("gluconeogenesis"). In both cases, the glucose is deposited in the blood.

X-Ray Crystal Structure of Glucagon based on PDB 1GCN. (CC BY-SA 3.0; Truthortruth).
Glucagon secretion is
stimulated by low levels of glucose in the blood;
inhibited by high levels, and
inhibited by amylin.
The physiological significance of this is that glucagon functions to maintain a steady level of blood sugar level between meals.
Injections of glucagon (which is readily available thanks to recombinant DNA technology) are sometimes given to diabetics
suffering from an insulin reaction in order to speed the return of normal levels of blood sugar.

Delta Cells
The delta cells secrete somatostatin, which consists of two polypeptides, one of 14 amino acids and one of 28. Somatostatin has a
variety of functions. Taken together, they work to reduce the rate at which food is absorbed from the contents of the intestine.
Somatostatin is also secreted by the hypothalamus and by the intestine.

Gamma Cells
The gamma cells of the islets secrete a 36-amino-acid pancreatic polypeptide, which reduces appetite.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and made
possible by funding from The Saylor Foundation.

This page titled 15.6.1.3: Hormones of the Pancreas is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.6.1.3.3 https://bio.libretexts.org/@go/page/5469
15.6.1.4: Hormones of the Pituitary
The pituitary gland is pea-sized structure located at the base of the brain. In humans, it consists of two lobes: the Anterior Lobe and
the Posterior Lobe.

Hormones of the Anterior Lobe

The anterior lobe contains six types of secretory cells, all but one of which are specialized to secrete only one of the anterior lobe
hormones. All of them secrete their hormone in response to hormones reaching them from the hypothalamus of the brain.

Thyroid Stimulating Hormone (TSH)

TSH (also known as thyrotropin) is a glycoprotein consisting of a beta chain of 118 amino acids and an alpha chain of 92 amino
acids. The alpha chain is identical to that found in two other pituitary hormones, FSH and LH as well as in the hormone chorionic
gonadotropin. Thus it is its beta chain that gives TSH its unique properties. The secretion of TSH is stimulated by the arrival of
thyrotropin releasing hormone (TRH) from the hypothalamus and is inhibited by the arrival of somatostatin from the
hypothalamus.
As its name suggests, TSH stimulates the thyroid gland to secrete its hormone thyroxine (T4). It does this by binding to
transmembrane G-protein-coupled receptors (GPCRs) on the surface of the cells of the thyroid. Some people develop antibodies
against their own TSH receptors. When these bind the receptors, they "fool" the cell into making more T4 causing hyperthyroidism.
The condition is called thyrotoxicosis or Graves' disease.

 Hormone deficiencies
A deficiency of TSH causes hypothyroidism: inadequate levels of T4 (and thus of T3). Physicians occasionally encounter
patients who are homozygous for mutant TSH receptors or mutant TRH receptors. In either case, they suffer from
hypothyroidism. A deficiency of TSH, or mutant TSH receptors, have also been implicated as a cause of osteoporosis. Mice,
whose TSH receptors have been knocked out, develop increased numbers of bone-reabsorbing osteoclasts.

Follicle-Stimulating Hormone (FSH)

FSH is a heterodimeric glycoprotein consisting of the same alpha chain found in TSH (and LH) and a beta chain of 118 amino
acids, which gives it its unique properties. Synthesis and release of FSH is triggered by the arrival from the hypothalamus of
gonadotropin-releasing hormone (GnRH). The effect of FSH depends on one's sex. In sexually-mature females, FSH (assisted by
LH) acts on the follicle to stimulate it to release estrogens. FSH produced by recombinant DNA technology (Gonal-f®) is available
to promote ovulation in women planning to undergo in vitro fertilization (IVF) and other forms of assisted reproductive technology.
In sexually-mature males, FSH acts on spermatogonia stimulating (with the aid of testosterone) the production of sperm.

Luteinizing Hormone (LH)

LH is synthesized within the same pituitary cells as FSH and under the same stimulus (GnRH). It is also a heterodimeric
glycoprotein consisting of the same 92-amino acid alpha subunit found in FSH and TSH (as well as in chorionic gonadotropin) and
a beta chain of 121 amino acids that is responsible for its properties.
The effects of LH also depend on sex. In sexually-mature females, a surge of LH triggers the completion of meiosis I of the egg
and its release (ovulation) in the middle of the menstrual cycle; LH also stimulates the now-empty follicle to develop into the
corpus luteum, which secretes progesterone during the latter half of the menstrual cycle. Women with a severe LH deficiency can
now be treated with human LH (Luveris®) produced by recombinant DNA technology. LH in males acts on the interstitial cells
(also known as Leydig cells) of the testes stimulating them to synthesize and secrete the male sex hormone, testosterone. LH in
males is also known as interstitial cell stimulating hormone (ICSH).

Prolactin (PRL)
Prolactin is a protein of 198 amino acids. During pregnancy it helps in the preparation of the breasts for future milk production.
After birth, prolactin promotes the synthesis of milk. Prolactin secretion is stimulated by TRH and repressed by estrogens and
dopamine. In pregnant mice, prolactin stimulates the growth of new neurons in the olfactory center of the brain.

15.6.1.4.1 https://bio.libretexts.org/@go/page/5471
Growth Hormone (GH)
Human growth hormone (HGH; also called somatotropin) is a protein of 191 amino acids. The GH-secreting cells are stimulated to
synthesize and release GH by the intermittent arrival of growth hormone releasing hormone (GHRH) from the hypothalamus. GH
promotes body growth by:
binding to receptors on the surface of liver cells.
This stimulates them to release insulin-like growth factor-1 (IGF-1; also known as somatomedin)
IGF-1 acts directly on the ends of the long bones promoting their growth
Things that can go wrong:
In childhood,
hyposecretion of GH produces a short but normally-proportioned body.
Growth retardation can also result from an inability to respond to GH. This can be caused by inheriting two mutant genes
encoding the receptors for
GHRH or
GH (causing Laron syndrome, a form of dwarfism) or
homozygosity for a disabling mutation in STAT5b, which is part of the "downstream" signaling process after GH binds
its receptor.
hypersecretion leads to gigantism
In adults, a hypersecretion of GH or GHRH leads to acromegaly.

 Hormone-replacement therapy

GH from domestic mammals like cows and pigs does not work in humans. So for many years, the only source of GH for
therapy was that extracted from the glands of human cadavers. But this supply was shut off when several patients died from a
rare neurological disease attributed to contaminated glands. Now, thanks to recombinant DNA technology, recombinant human
GH (rHGH) is available. While a benefit to patients suffering from GH deficiency or the short stature associated with Turner
syndrome, there has also been pressure to use it to stimulate growth in youngsters who have no deficiency but whose parents
want them to grow up tall. So, in the summer of 2003, the U.S. FDA approved the use of human growth hormone (HGH) for
boys predicted to grow no taller than 5′3″ and for girls, 4′11″ even though otherwise perfectly healthy.

ACTH — the adrenocorticotropic hormone

ACTH is a peptide of 39 amino acids. It is cut from a larger precursor proopiomelanocortin (POMC). ACTH acts on the cells of the
adrenal cortex, stimulating them to produce
glucocorticoids, like cortisol
mineralocorticoids, like aldosterone
androgens (male sex hormones, like testosterone)
In the fetus, ACTH stimulates the adrenal cortex to synthesize a precursor of estrogen called dehydroepiandrosterone sulfate
(DHEA-S) which helps prepare the mother for giving birth.
Production of ACTH depends on the intermittent arrival of corticotropin-releasing hormone (CRH) from the hypothalamus.
Hypersecretion of ACTH is a frequent cause of Cushing's syndrome.

Alpha Melanocyte-Stimulating Hormone (α-MSH )

Alpha MSH is also a cleavage product of proopiomelanocortin (POMC). In fact, α-MSH is identical to the first 13 amino acids at
the amino terminal of ACTH. MSH is discussed in a separate page.

Hormones of the Posterior Lobe

The posterior lobe of the pituitary releases two hormones — both synthesized in the hypothalamus — vasopressin and oxytocin into
the circulation.

15.6.1.4.2 https://bio.libretexts.org/@go/page/5471
Vasopressin
Vasopressin is a peptide of 9 amino acids (Cys-Tyr-Phe-Gln-Asn-Cys-Pro-Arg-Gly). It is also known as arginine vasopressin (AVP)
and the antidiuretic hormone (ADH). Vasopressin acts on the collecting ducts of the kidney to facilitate the reabsorption of water
into the blood. Thus it acts to reduce the volume of urine formed (giving it its name of antidiuretic hormone). A deficiency of
vasopressin or inheritance of mutant genes for its receptor (called V2) leads to excessive loss of urine, a condition known as
diabetes insipidus. The most severely-afflicted patients may urinate as much as 30 liters (almost 8 gallons!) of urine each day. The
disease is accompanied by terrible thirst, and patients must continually drink water to avoid dangerous dehydration.
Another type of receptor for vasopressin (designated V1a) is found in the brain, e.g., in voles and mice (rodents) and in primates
like monkeys and humans.
Male prairie voles (Microtus pinetorum) and marmoset monkeys have high levels of the V1a receptor in their brains, tend to be
monogamous, and help with care of their young.
Male meadow voles (Microtus montanus) and rhesus monkeys have lower levels of the V1a receptor in their brains, are
promiscuous, and give little or no help with the care of their young.
Meadow voles whose brains have been injected with a vector causing increased expression of the V1a receptor become more like
prairie voles in their behavior. (See Lim, M. M. et al., Nature, 17 June 2004.)
The level of expression of the V1a receptor gene is controlled by a "microsatellite" region upstream (5') of the ORF. This region
contains from 178 to 190 copies of a repeated tetranucleotide (e.g., CAGA). Prairie voles have more copies of the repeat than
meadow voles, and they express higher levels of the receptor in the parts of the brain associated with these behaviors. A similar
microsatellite region is present in the pygmy chimpanzee or bonobo (Pan paniscus) but is much shorter in the less-affectionate
common chimpanzee (Pan troglodytes).

 Vasopressin and the Circadian Clock

Mice are nocturnal and become active at the start of the night. This is a circadian rhythm that persists for a time even after the
lights in the lab are turned off each day 8 hours sooner (like arriving in London after a flight from Los Angeles, California).
Only after 8–10 days do the mice overcome their "jet lag", adjusting to the new dark-light schedule. (It also takes us about one
day to reset our circadian rhythms for each hour that our day-night schedule is shifted.)
It turns out that arginine vasopressin, acting on the suprachiasmatic nucleus (SCN), plays a role in this resistance to resetting
their circadian clock. Mice with their genes for the V1a and V1b receptors knocked out adjust much more quickly (2–4 days)
to the change. What evolutionary advantage this resistance to resetting the circadian clock confers is not clear, but
understanding the mechanism raises the possibility of using drugs to speed getting over jet lag and also to help those whose
work shifts are periodically altered. (Read about this work in Yamaguchi, Y., et al. in the 4 October 2013 issue of Science.).

Oxytocin
Oxytocin is a peptide of 9 amino acids (Cys-Tyr-Ile-Gln-Asn-Cys-Pro-Leu-Gly). It acts on certain smooth muscles by stimulating
contractions of the uterus at the time of birth and stimulating release of milk when the baby begins to suckle. Oxytocin is often
given to prospective mothers to hasten birth.
In rodents, oxytocin also acts on the nucleus accumbens and amygdala in the brain where it enhances bonding between males and
females after they have mated and bonding between a mother and her newborn. In mice, oxytocin acts on striated muscle stem cells
to promote repair after they have been injured. In humans, oxytocin increases the level of one's trust in other people.

This page titled 15.6.1.4: Hormones of the Pituitary is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.6.1.4.3 https://bio.libretexts.org/@go/page/5471
15.6.1.5: Hormones of the Hypothalamus
The hypothalamus is a region of the brain. It contains several types of neurons responsible for secreting different hormones.
Thyrotropin-releasing hormone (TRH)
Gonadotropin-releasing hormone (GnRH)
Growth hormone-releasing hormone (GHRH)
Corticotropin-releasing hormone (CRH)
Somatostatin
Dopamine
All of these are released into the blood in the capillaries and travel immediately – in portal veins – to a second capillary bed in the
anterior lobe of the pituitary, where they exert their effects. All of them are released in periodic spurts. In fact, replacement
hormone therapy with these hormones does not work unless the replacements are also given in spurts. Two other hypothalamic
hormones vasopressin and oxytocin travel in the neurons themselves to the posterior lobe of the pituitary where they are released
into the circulation.

Thyrotropin-releasing hormone (TRH)

TRH is a tripeptide (GluHisPro). When it reaches the anterior lobe of the pituitary it stimulates the release there of thyroid-
stimulating hormone (TSH) and prolactin (PRL)

Gonadotropin-releasing hormone (GnRH)

GnRH is a peptide of 10 amino acids. Its secretion at the onset of puberty triggers sexual development, and from then on it is
essential for normal sexual physiology in both males and females. In both sexes, its secretion occurs in periodic pulses usually
occurring every 1–2 hours.

Space-filling model of gonadotropin-releasing hormone. (public domain, Fvasconcellos).

Primary Effects Secondary Effects

estrogen and progesterone Up (in females)

FSH and LH Up
testosterone Up (in males)

After puberty, a hyposecretion of GnRH may result from intense physical training or anorexia nervosa. Synthetic agonists of GnRH
are used to treat inherited or acquired deficiencies of GnRH secretion and prostate cancer. In this case, continuous high levels of the
GnRH agonist
reduces the number of GnRH receptors in the pituitary, which
reduces its secretion of FSH and LH, which
reduces the secretion of testosterone, which
reduces the stimulation of the cells of the prostate.

15.6.1.5.1 https://bio.libretexts.org/@go/page/5473
Growth hormone-releasing hormone (GHRH): GHRH is a mixture of two peptides, one containing 40 amino acids, the other 44.
As its name indicates, GHRH stimulates cells in the anterior lobe of the pituitary to secrete growth hormone (GH).
Corticotropin-releasing hormone (CRH): CRH is a peptide of 41 amino acids. As its name indicates, its acts on cells in the
anterior lobe of the pituitary to release adrenocorticotropic hormone (ACTH). CRH is also synthesized by the placenta and seems
to determine the duration of pregnancy. It may also play a role in keeping the T cells of the mother from mounting an immune
attack against the fetus.
Somatostatin: Somatostatin is a mixture of two peptides, one of 14 amino acids, the other of 28. Somatostatin acts on the anterior
lobe of the pituitary to inhibit the release of growth hormone (GH) and inhibit the release of thyroid-stimulating hormone (TSH).
Somatostatin is also secreted by cells in the pancreas and in the intestine where it inhibits the secretion of a variety of other
hormones.

Dopamine
Dopamine is a derivative of the amino acid tyrosine. It mediates several functions in the brain, including inhibiting the release of
prolactin (PRL) from the anterior lobe of the pituitary, modulating motor-control centers (a loss of dopamine-secreting cells
produces Parkinson's disease), and activating the reward centers of the brain. Dopamine-secreting cells are also found in other parts
of the body where most of its actions are paracrine; that is, acting on nearby cells.

Vasopressin and Oxytocin

These peptides are released from the posterior lobe of the pituitary and are described in the page devoted to the pituitary.

This page titled 15.6.1.5: Hormones of the Hypothalamus is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

15.6.1.5.2 https://bio.libretexts.org/@go/page/5473
15.6.1.6: Adrenal Glands

The adrenal glands are two small structures situated one atop each kidney. Both in anatomy and in function, they consist of two
distinct regions an outer layer, the drenal ortex, which surrounds the adrenal medulla.

The Adrenal Cortex

Using cholesterol as the starting material, the cells of the adrenal cortex secrete a variety of steroid hormones. These fall into three
classes:
glucocorticoids (e.g., cortisol)
mineralocorticoids (e.g., aldosterone)
androgens (e.g., testosterone)
Production of all three classes is triggered by the secretion of ACTH from the anterior lobe of the pituitary.
These hormones achieve their effects by:
Travelling through the body in the blood. Because they are so hydrophobic, they must be carried bound to a serum globulin.
Entering from the blood into all cells.
Binding to their recepto - a protein present in the cytoplasm and/or nucleus of "target" cells.
The hormone-receptor complex binds to a second to form a homodimer.
The homodimer migrates into the nucleus (if it did not form there) where it binds to specific hormone response elements in
DNA.
These are specific DNA sequences in the promoter of genes that will be turned on (or off) by the interaction.
Other transcription factors are recruited to the promoter and gene transcription begins at some genes and is inhibited at others.

Glucocorticoids
The glucocorticoids get their name from their effect of raising the level of blood sugar (glucose). One way
they do this is by stimulating gluconeogenesis in the liver: the conversion of fat and protein into
intermediate metabolites that are ultimately converted into glucose.
The most abundant glucocorticoid is cortisol (also called hydrocortisone). Cortisol and the other
glucocorticoids also have a potent anti-inflammatory effect on the body. They depress the immune
response, especially cell-mediated immune responses.
For this reason glucocorticoids are widely used in therapy:
to reduce the inflammatory destruction of rheumatoid arthritis and other autoimmune diseases
to prevent the rejection of transplanted organs
to control asthma

Mineralocorticoids
The mineralocorticoids get their name from their effect on mineral metabolism. The most important of
them is the steroid aldosterone. Aldosterone acts on the kidney promoting the reabsorption of sodium ions
(Na+) into the blood. Water follows the salt and this helps maintain normal blood pressure.
Aldosterone also
acts on sweat glands to reduce the loss of sodium in perspiration
acts on taste cells to increase the sensitivity of the taste buds to sources of sodium.
The secretion of aldosterone is stimulated by:
a drop in the level of sodium ions in the blood
a rise in the level of potassium ions in the blood
angiotensin II
ACTH (as is that of cortisol)

15.6.1.6.1 https://bio.libretexts.org/@go/page/5475
Androgens
The adrenal cortex secretes precursors to androgens such as testosterone.
In sexually-mature males, this source is so much lower than that of the testes that it is probably of little
physiological significance. However, excessive production of adrenal androgens can cause premature
puberty in young boys.
In females, the adrenal cortex is a major source of androgens. Their hypersecretion may produce a
masculine pattern of body hair and cessation of menstruation.

Addison's Disease: Hyposecretion of the adrenal cortices

Addison's disease has many causes, such as
destruction of the adrenal glands by infection
their destruction by an autoimmune attack
an inherited mutation in the ACTH receptor on adrenal cells
The essential role of the adrenal hormones means that a deficiency can be life-threatening. Fortunately, replacement therapy with
glucocorticoids and mineralocorticoids can permit a normal life.

Cushing's Syndrome: Excessive levels of glucocorticoids

In Cushing's syndrome, the level of glucocorticoids, especially cortisol, is too high.
It can be caused by:
excessive production of ACTH by the anterior lobe of the pituitary
excessive production by the adrenals themselves (e.g., because of a tumor), or (quite commonly)
as a result of glucocorticoid therapy for some other disorder such as rheumatoid arthritis or preventing the rejection of an
organ transplant

The Adrenal Medulla

The adrenal medulla consists of masses of neurons that are part of the sympathetic branch of the autonomic nervous system.
Instead of releasing their neurotransmitters at a synapse, these neurons release them into the blood. Thus, although part of the
nervous system, the adrenal medulla functions as an endocrine gland.
The adrenal medulla releases adrenaline (also called epinephrine) and noradrenaline (also called norepinephrine). Both are
derived from the amino acid tyrosine. Release of adrenaline and noradrenaline is triggered by nervous stimulation in response to
physical or mental stress. The hormones bind to adrenergic receptors — transmembrane proteins in the plasma membrane of
many cell types.
Some of the effects are:
increase in the rate and strength of the heartbeat resulting in increased blood pressure
blood shunted from the skin and viscera to the skeletal muscles, coronary arteries, liver, and brain
rise in blood sugar
increased metabolic rate
bronchi dilate
pupils dilate
hair stands on end ("gooseflesh" in humans)
clotting time of the blood is reduced
increased ACTH secretion from the anterior lobe of the pituitary
All of these effects prepare the body to take immediate and vigorous action.

This page titled 15.6.1.6: Adrenal Glands is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.6.1.6.2 https://bio.libretexts.org/@go/page/5475
15.6.1.7: Sex Hormones
The ovaries of sexually-mature females secrete both a mixture of estrogens (of which 17 β-estradiol is the most abundant and most
potent) and progesterone.

Estrogens
Estrogens are steroids and are primarily responsible for the conversion of girls into sexually-mature women including:
development of breasts
further development of the uterus and vagina
broadening of the pelvis
growth of pubic and axillary hair
increase in adipose (fat) tissue
participate in the monthly preparation of the body for a possible pregnancy
participate in pregnancy if it occurs
Estrogens also have non-reproductive effects. For example, they antagonize the effects of the parathyroid hormone, minimizing the
loss of calcium from bones and thus helping to keep bones strong. They also promote blood clotting.

Progesterone
Progesterone is also a steroid. It has many effects in the body, some having nothing to do with sex and reproduction. Here we shall
focus on the role of progesterone in the menstrual cycle and pregnancy.

How estrogens and progesterone achieve their effects

Steroids like estrogens and progesterone are small, hydrophobic molecules that are transported in the blood bound to a serum
globulin.
In "target" cells, i.e., cells that change their gene expression in response to the hormone, they bind to receptor proteins located
in the cytoplasm and/or nucleus.
The hormone-receptor complex enters the nucleus (if it formed in the cytoplasm) and binds to specific sequences of DNA,
called the estrogen (or progesterone) response elements.
Response elements are located in the promoters of genes.
The hormone-receptor complex acts as a transcription factor (often recruiting other transcription factors to help) which turns on
(sometimes off) transcription of those genes.
Gene expression in the cell produces the response.
Some "target" cells also have other types of estrogen and progesterone receptors that are embedded in a membrane (endoplasmic
reticulum and plasma membrane respectively). Binding of the hormone to them produces more rapid effects than those of the
nuclear receptors. For example, human sperm have receptors that within a second of being exposed to progesterone activate the
sperm to increased motility.

Regulation of Estrogen and Progesterone

The synthesis and secretion of estrogens is stimulated by follicle-stimulating hormone (FSH), which is, in turn, controlled by the
hypothalamic gonadotropin releasing hormone (GnRH).

Hypothala
→ GnRH → Pituitary → FSH → Follicle → Estrogens
mus

15.6.1.7.1 https://bio.libretexts.org/@go/page/5477
 Figure 15.6.1.7.1 Hypothalamic feedback
High levels of estrogens suppress the release of GnRH (bar) providing a negative-feedback control of hormone levels.
It works like this: Secretion of GnRH depends on certain neurons in the hypothalamus which express a gene (KISS-1) encoding a
protein of 145 amino acids. From this are cut several short peptides collectively called kisspeptin. These are secreted and bind to
G-protein-coupled receptors on the surface of the GnRH neurons stimulating them to release GnRH. However, high levels of
estrogen (or progesterone or testosterone) inhibit the secretion of kisspeptin and suppress further production of those hormones.
Progesterone production is stimulated by luteinizing hormone (LH), which is also stimulated by GnRH.

Hypothala Corpus Progestero

→ GnRH → Pituitary → LH → →
mus luteum ne

Elevated levels of progesterone control themselves by the same negative feedback loop used by estrogen (and testosterone).

The Menstrual Cycle

Figure 15.6.1.7.2 Menstrual cycle

About every 28 days, some blood and other products of the disintegration of the inner lining of the uterus (the endometrium) are
discharged from the uterus, a process called menstruation. During this time a new follicle begins to develop in one of the ovaries.
After menstruation ceases, the follicle continues to develop, secreting an increasing amount of estrogen as it does so.
The rising level of estrogen causes the endometrium to become thicker and more richly supplied with blood vessels and glands.
A rising level of LH causes the developing egg within the follicle to complete the first meiotic division (meiosis I), forming a
secondary oocyte.
After about two weeks, there is a sudden surge in the production of LH.
This surge in LH triggers ovulation: the release of the secondary oocyte into the fallopian tube.
Under the continued influence of LH, the now-empty follicle develops into a corpus luteum (hence the name luteinizing
hormone for LH).
Stimulated by LH, the corpus luteum secretes progesterone which
continues the preparation of the endometrium for a possible pregnancy
inhibits the contraction of the uterus
inhibits the development of a new follicle
If fertilization does not occur (which is usually the case)
the rising level of progesterone inhibits the release of GnRH which, in turn, inhibits further production of progesterone
As the progesterone level drops
the corpus luteum begins to degenerate
the endometrium begins to break down, its cells committing programmed cell death
the inhibition of uterine contraction is lifted

15.6.1.7.2 https://bio.libretexts.org/@go/page/5477
 the bleeding and cramps of menstruation begin.

Fertilization
Fertilization of the egg is also influenced by progesterone. Sperm swim towards the egg by chemotaxis following a gradient of
progesterone secreted by cells surrounding the egg. Progesterone opens CatSper ("cation sperm") channels in the plasma membrane
surrounding the anterior portion of the sperm tail. This allows an influx of Ca2+ ions which causes the flagellum to beat more
rapidly and vigorously.

Pregnancy
As the fertilized egg passes down the fallopian tube, it undergoes its first mitotic divisions. By the end of the week, the developing
embryo has become a hollow ball of cells called a blastocyst. At this time, the blastocyst reaches the uterus and embeds itself in
the endometrium, a process called implantation. With implantation, pregnancy is established.
The blastocyst has two parts:
the inner cell mass, which will become the baby
the trophoblast, which will
develop into the placenta and umbilical cord
begin to secrete human chorionic gonadotropin (HCG).
HCG is a glycoprotein. It is a heterodimer of the same alpha subunit (of 92 amino acids) used by TSH, FSH, and LH and a unique
beta subunit (of 145 amino acids). HCG behaves much like FSH and LH with one crucial exception: it is NOT inhibited by a rising
level of progesterone. Thus HCG prevents the deterioration of the corpus luteum at the end of the fourth week and enables
pregnancy to continue beyond the end of the normal menstrual cycle. Because only the implanted trophoblast makes HCG, its early
appearance in the urine of pregnant women provides the basis for the most widely used test for pregnancy (which can provide a
positive signal even before menstruation would have otherwise begun). As pregnancy continues, the placenta becomes a major
source of progesterone, and its presence is essential to maintain pregnancy. Mothers at risk of giving birth too soon can be given a
synthetic progestin to help them retain the fetus until it is full-term.

Birth
Toward the end of pregnancy,
The placenta releases large amounts of CRH which stimulates the pituitary glands of both mother and her fetus to secrete.
ACTH, which acts on their adrenal glands causing them to release the estrogen precursor dehydroepiandrosterone sulfate
(DHEAS).
This is converted into estrogen by the placenta.
The rising level of estrogen causes the smooth muscle cells of the uterus to
synthesize connexins and form gap junctions. Gap junctions connect the cells electrically so that they contract together as
labor begins.
express receptors for oxytocin.
Oxytocin is secreted by the posterior lobe of the pituitary as well as by the uterus.
Prostaglandins are synthesized in the placenta and uterus.
The normal inhibition of uterine contraction by progesterone is turned off by several mechanisms while
both oxytocin and prostaglandins cause the uterus to contract and labor begins.
Three or four days after the baby is born, the breasts begin to secrete milk. Milk synthesis is stimulated by the pituitary hormone
prolactin (PRL), and its release from the breasts is stimulated by oxytocin. Milk contains an inhibitory peptide. If the breasts are
not fully emptied, the peptide accumulates and inhibits milk production. This autocrine action thus matches supply with demand.

Other Hormones
Relaxin
As the time of birth approaches in some animals (e.g., pigs, rats), this polypeptide has been found to:
relax the pubic ligaments
soften and enlarge the opening to the cervix

15.6.1.7.3 https://bio.libretexts.org/@go/page/5477
 Relaxin is found in pregnant humans but at higher levels early in pregnancy than close to the time of birth. Relaxin promotes
angiogenesis, and in humans it probably plays a more important role in the development of the interface between the uterus and
the placenta that it does in the birth process.
Activins, Inhibins, Follistatin.
These proteins are synthesized within the follicle. Activins and inhibins bind to follistatin. Activins increase the action of FSH;
inhibins, as their name suggests, inhibit it. How important they are in humans remains to be seen. However the important role
that activin and follistatin play in the embryonic development of vertebrates justifies mentioning them here.

Oral contraceptives - the "pill"

The feedback inhibition of GnRH secretion by estrogens and progesterone provides the basis for the most widely-used form of
contraception. Dozens of different formulations of synthetic estrogens or progestins (progesterone relatives or both are available.
Their inhibition of GnRH prevents the mid-cycle surge of LH and ovulation. Hence there is no egg to be fertilized. Usually the
preparation is taken for about three weeks and then stopped long enough for normal menstruation to occur. The main side-effects of
the pill stem from an increased tendency for blood clots to form (estrogen enhances clotting of the blood).

RU-486
RU-486 (also known as mifepristone) is a synthetic steroid related to progesterone. Unlike the synthetic progestins used in oral
contraceptives that mimic the actions of progesterone, RU-486 is a progesterone antagonist; that is, it blocks the action of
progesterone. It does this by binding more tightly to the progesterone receptor than progesterone itself but without the normal
biological effects:
The RU-486/receptor complex is not active as a transcription factor.
Thus genes that are turned on by progesterone are turned off by RU-486.
The proteins needed to establish and maintain pregnancy are no longer synthesized.
The endometrium breaks down.
The embryo detaches from it and can no longer make chorionic gonadotropin (HCG).
Consequently the corpus luteum ceases its production of progesterone.
The inhibition on uterine contraction is lifted.
Soon the embryo and the breakdown products of the endometrium are expelled.
These properties of RU-486 have caused it to be used to induce abortion of an unwanted fetus. In practice, the physician assists
the process by giving a synthetic prostaglandin (e.g., misoprostol [Cytotec®]) 36–48 hours after giving the dose of RU-486. Use of
RU-486 is generally limited to the first seven weeks of pregnancy. RU-486 has been used for many years in some countries.
However, the controversies surrounding abortion in the United States kept it from being authorized for use here until September
2000.

Menopause
The menstrual cycle continues for many years. But eventually, usually between 42 and 52 years of age, the follicles become less
responsive to FSH and LH. They begin to secrete less estrogen. Ovulation and menstruation become irregular and finally cease.
This cessation is called menopause.
With levels of estrogen now running one-tenth or less of what they had been, the hypothalamus is released from their inhibitory
influence (bar). As a result it now stimulates the pituitary to increased activity. The concentrations of FSH and LH in the blood rise
to ten or more times their former values. These elevated levels may cause a variety of unpleasant physical and emotional
symptoms.

Hormone Replacement Therapy (HRT)

Many menopausal women elect to take a combination of estrogen and progesterone after they cease to make their own. The
benefits are (1) reduction in the unpleasant symptoms of the menopause and (2) a reduction in the loss of calcium from bones and
thus a reduction in osteoporosis and the fractures that accompany it. It was also believed that HRT reduced the risk of
cardiovascular disease. However, a recent study of 16,000 menopausal women was stopped 3 years early when it was found that, in
fact, HRT increased (albeit only slightly) not decreased the incidence of cardiovascular disease. Perhaps synthetic selective
estrogen response modulators or SERMs (raloxifene is an example) will provide the protective effects without the harmful ones.

15.6.1.7.4 https://bio.libretexts.org/@go/page/5477
Environmental estrogens
Some substances that find their way into the environment, such as
DDE, a breakdown product of the once widely-used insecticide DDT
DDT itself — still used in some countries (e.g., Mexico)
PCBs, chemicals once used in a wide variety of industrial applications
can bind to the estrogen (and androgen) receptors and mimic (weakly) the effects of the hormone. This has created anxiety that they
may be responsible for harmful effects such as cancer and low sperm counts.
However, there is as yet little evidence to support these worries. No epidemiological relationship has been found between the
incidence of breast cancer and the levels of these compounds in the body. As for laboratory studies that found a synergistic effect of
two of these substances on receptor binding (findings that created the great alarm), these have not been replicated in other
laboratories, and the authors of the original report have since withdrawn it as invalid.

Males
The principal androgen (male sex hormone) is testosterone. This steroid is manufactured by the interstitial (Leydig) cells of the
testes. Secretion of testosterone increases sharply at puberty and is responsible for the development of the so-called secondary
sexual characteristics (e.g., beard) of men.

Testosterone is also essential for the production of sperm. Production of testosterone is controlled by the release of luteinizing
hormone (LH) from the anterior lobe of the pituitary gland, which is in turn controlled by the release of GnRH from the
hypothalamus. LH is also called interstitial cell stimulating hormone (ICSH).

Hypothala Testosteron
→ GnRH → Pituitary → LH → Testes →
mus e

The level of testosterone is under negative-feedback control: a rising level of testosterone suppresses the release of GnRH from the
hypothalamus. This is exactly parallel to the control of estrogen secretion in females.
In mice, osteocalcin, a hormone secreted by osteoblasts of the bone, stimulates the synthesis of testosterone by Leydig cells even
more powerfully than LH. Whether this effect occurs in humans remains to be seen.

 Males need estrogen, too!

In 1994, a man was described who was homozygous for a mutation in the gene encoding the estrogen receptor. A single
nonsense mutation had converted a codon (CGA) for arginine early in the protein into a STOP codon (TGA). Thus no complete
estrogen receptor could be synthesized.
This man was extra tall, had osteoporosis and "knock-knees", but was otherwise well. His genetic defect confirms the
important role that estrogen has in both sexes for normal bone development. It is not known whether this man was fertile or
not. However, mutations in their estrogen receptor gene have been found in other men who are sterile, and male mice whose
estrogen receptor gene has been "knocked out" are sterile.
Another function of estrogen in males. The accumulation of fat in the abdomen, so characteristic of aging males (including
yours truly), is caused by declining levels of estrogen.

Anabolic steroids
A number of synthetic androgens are used for therapeutic purposes. These drugs promote an increase in muscle size with resulting
increases in strength and speed. This has made them popular with some athletes, e.g., weight lifters, cyclists, runners, swimmers,
professional football players. Usually these athletes (females as well as males) take doses far greater than those used in standard

15.6.1.7.5 https://bio.libretexts.org/@go/page/5477
therapy. Such illicit use carries dangers (besides being banned from an event because of a positive drug test): acne, a decrease in
libido, and — in males — testicle size and sperm counts to name a few.

Genetic abnormalities of gonadal function

Many things can go wrong with sexual development in both males and females, fortunately rarely. Let's look at a few that clearly
result from the inheritance of single-gene mutations.
Inherited mutations in both copies of the gene encoding the GnRH receptor result in failure to develop at puberty.
Mutations in the gene encoding the LH receptor prevent normal sexual development in both sexes.
Mutations in the gene encoding the FSH receptor block development of the gonads in both males and females.
Mutations in any of the genes encoding the enzymes for synthesis and metabolism of testosterone interfere with normal sexual
function in males.
A similar spectrum of disorders in males can be caused by mutations in the genes encoding the androgen receptor.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 15.6.1.7: Sex Hormones is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.6.1.7.6 https://bio.libretexts.org/@go/page/5477
15.6.1.8: Progesterone
Progesterone is one of the steroid hormones. It is secreted by the corpus luteum and by the placenta and is responsible for preparing
the body for pregnancy and, if pregnancy occurs, maintaining it until birth.
Corpus luteum: Progesterone secretion by the corpus luteum occurs after ovulation and continues the preparation of the
endometrium for a possible pregnancy. It also inhibits contraction of the uterus and inhibits development of a new follicle. If
pregnancy does not occur, secretion wanes toward the end of the menstrual cycle, and menstruation begins.
Placenta: If pregnancy does occur, the placenta begins to secrete progesterone which supplements that of the corpus luteum. In
fact, by the fifth month of pregnancy, the placenta secretes sufficient progesterone by itself that the corpus luteum is no longer
essential to maintain pregnancy.
Progesterone, like all steroids, is a small hydrophobic molecule. Thus it diffuses freely through the plasma membrane of all cells.
However, in target cells, like those of the endometrium it becomes tightly bound to a cytoplasmic protein the progesterone receptor.
The complex of receptor and its hormone moves into the nucleus. There it binds to a progesterone response element, which is a
specific sequence of DNA in the promoters of certain genes that is needed to turn those genes on (or off). Thus the complex of
progesterone with its receptor forms a transcription factor.

Progestins
Progestins are synthetic modifications of the progesterone molecule. Several different ones are prescribed
for birth control pills
for hormone replacement therapy (HRT) to reduce the unpleasant symptoms of the menopause
to treat young women who cease to menstruate normally
to prevent premature birth
Some examples:
norgestrel (Trade name = Orvette®) - used as an oral contraceptive
levonorgestrel
the ingredient in "Plan B", an oral contraceptive taken after unprotected intercourse.
released from Mirena®, an intrauterine device (IUD).
norethindrone (Trade name = Aygestin®; used in HRT (hormone replacement therapy)

Figure 1: Norethisterone is one of the most widely used progestins. (Public Domain; Fvasconcellos).

RU-486
RU-486 (also known as mifepristone) is a synthetic steroid related to progesterone. Unlike the progestins discussed above, that
mimic the action of progesterone, RU-486 blocks the action of progesterone. Synthetic molecules that mimic the action of a natural
molecule are called agonists; those that oppose it are antagonists. RU-486 is a progesterone antagonist. It binds to the progesterone
receptor, and in so doing prevents progesterone itself from occupying its receptor. Thus the gene transcription normally turned on
by progesterone is blocked, and the proteins necessary to begin and maintain pregnancy are not synthesized. If RU-486 is taken
shortly after intercourse, it prevents pregnancy. If taken early in pregnancy, it causes the embryo to be aborted. This result has
caused RU-486 to be widely used in Europe to terminate early pregnancy. It has not found widespread acceptance in the U.S.

This page titled 15.6.1.8: Progesterone is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.6.1.8.1 https://bio.libretexts.org/@go/page/5479
15.6.1.9: Melatonin and the Pineal Gland

The pineal gland is a tiny structure located at the base of the brain. Its principal hormone is melatonin, a derivative of the amino
acid tryptophan.
Synthesis and release of melatonin is
stimulated by darkness
inhibited by light.
But even without visual cues, the level of melatonin in the blood rises and falls on a daily (circadian) cycle with peak levels
occurring in the wee hours of the morning. However, this cycle tends to drift in people who are totally blind — often making them
sleepy during the day and wide awake at night. Giving melatonin at bedtime has proved helpful in a number of cases
Melatonin is readily available in drug stores and health food stores, and it has become quite popular. Ingesting even modest doses
of melatonin raises the melatonin level in the blood to as much as 100 times greater than normal. These levels appear:
to promote going to sleep and thus help insomnia
to hasten recovery from jet lag
not to have dangerous side effects

This page titled 15.6.1.9: Melatonin and the Pineal Gland is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

15.6.1.9.1 https://bio.libretexts.org/@go/page/5481
15.6.1.10: Hormones of Kidney, Skin and Heart
Kidney
The human kidney secretes two hormones:
Erythropoietin (EPO)
Calcitriol (1,25[OH]2 Vitamin D3)
as well as the enzyme renin.

Erythropoietin (EPO)
Erythropoietin is a glycoprotein that acts on the bone marrow to increase the production of red blood cells. Stimuli such as bleeding
or moving to high altitudes (where oxygen is scarcer) trigger the release of EPO. People with failing kidneys can be kept alive by
dialysis, which only cleanses the blood of wastes. Without a source of EPO, these patients suffer from anemia. Now, thanks to
recombinant DNA technology, recombinant human EPO is available to treat these patients.
Some other uses for recombinant EPO:
Some of the drugs used to treat AIDS, zidovudine (AZT) for example, cause anemia as a side effect. Recombinant EPO helps
AIDS patients cope with this one of the many problems that the disease creates.
Recombinant EPO improves the anemia that is such a frequent side effect of cancer chemotherapy.
Severe blood loss in Jehovah's Witnesses, whose religion forbids them to receive blood transfusions, can also be helped with
recombinant EPO.
Because EPO increases the hematocrit, it enables more oxygen to flow to the skeletal muscles. Some cyclists (and distance runners)
have used recombinant EPO to enhance their performance. Although recombinant EPO has exactly the same sequence of amino
acids as the natural hormone, the sugars attached by the cells used in the pharmaceutical industry differ from those attached by the
cells of the human kidney. This difference can be detected by a test of the athlete's urine.
Another problem: since recombinant EPO became available, over two dozen young competitive cyclists have died unexpectedly
(usually during the night). Perhaps an EPO-induced increase in their hematocrit — leading to a reduction in heart rate — is
responsible. Prolonged exposure to reduced oxygen levels (e.g., living at high altitude) leads to increased synthesis of EPO. In
mice, and perhaps in humans, this effect is mediated by the skin. Mouse skin cells can detect low levels of oxygen ("hypoxia") and
if this persists, blood flow to the kidneys diminishes leading to increased synthesis of EPO by them.
EPO is also synthesized by osteoblasts in mice that have been made anemic and in the brain when oxygen becomes scarce there
(e.g., following a stroke), and helps protect neurons from damage. Perhaps recombinant human EPO will turn out to be useful for
stroke victims as well.

Calcitriol
Calcitriol is 1,25[OH]2 Vitamin D3, the active form of vitamin D. It is derived from
calciferol (vitamin D3) which is synthesized in skin exposed to the ultraviolet rays of the sun
precursors ("vitamin D") ingested in the diet.
Calciferol in the blood is converted into the active vitamin in two steps:
calciferol is converted in the liver into 25[OH] vitamin D3
this is carried to the kidneys (bound to a serum globulin) where it is converted into calcitriol. This final step is promoted by the
parathyroid hormone (PTH).
Calcitriol Action
Calcitriol acts on
the cells of the intestine to promote the absorption of calcium and phosphate from food
bone to mobilize calcium from the bone to the blood
Calcitriol enters cells and, if they contain receptors for it (intestine cells do), it binds to them. The calcitriol receptors are zinc-
finger transcription factors. The receptor-ligand complex bind to its response element, the DNA sequence:

15.6.1.10.1 https://bio.libretexts.org/@go/page/5484
5' AGGTCAnnnAGGTCA 3'
This sequence of nucleotides (n can be any nucleotide) is found in the promoters of genes that are turned on by calcitriol. Once the
hormone-receptor complex is bound to its response element, other transcription factors are recruited to the promoter and
transcription of the gene(s) begins.
Deficiency disorders
Insufficient calcitriol prevents normal deposition of calcium in bone.
In childhood, this produces the deformed bones characteristic of rickets.
In adults, it produces weakened bones causing osteomalacia.

Figure 15.6.1.10.1 Angiotensin

Angiotensin II modulates all of the below actions to increase in blood pressure:
constricts the walls of arterioles closing down capillary beds
stimulates the proximal tubules in the kidney to reabsorb sodium ions
stimulates the adrenal cortex to release aldosterone. Aldosterone causes the kidneys to reclaim still more sodium and thus
water.
increases the strength of the heartbeat
stimulates the pituitary to release the vasopressin

Skin
When ultraviolet radiation strikes the skin, it triggers the conversion of dehydrocholesterol (a cholesterol derivative) into calciferol
(vitamin D3). Calciferol travels in the blood to the liver where it is converted into 25[OH] vitamin D3. This compound travels to
the kidneys where it is converted into calcitriol (1,25 [OH]2 vitamin D3). This final step is promoted by the parathyroid hormone
(PTH). Although called a vitamin, calciferol and its products fully qualify as hormones because they are
made in certain cells
carried in the blood
affect gene transcription in target cells

Heart
Natriuretic Peptides
In response to a rise in blood pressure, the heart releases two peptides:
A-type Natriuretic Peptide (ANP)
This hormone of 28 amino acids is released from stretched atria (hence the "A").
B-type Natriuretic Peptide (BNP)
This hormone (29 amino acids) is released from the ventricles. (It was first discovered in brain tissue; hence the "B".)
Both hormones lower blood pressure by
relaxing arterioles
inhibiting the secretion of renin and aldosterone
inhibiting the reabsorption of sodium ions by the kidneys.
The latter two effects reduce the reabsorption of water by the kidneys. So the volume of urine increases as does the amount of
sodium excreted in it. The net effect of these actions is to reduce blood pressure by reducing the volume of blood in the circulatory

15.6.1.10.2 https://bio.libretexts.org/@go/page/5484
system. These effects give ANP and BNP their name (natrium = sodium; uresis = urinate).

This page titled 15.6.1.10: Hormones of Kidney, Skin and Heart is shared under a CC BY 3.0 license and was authored, remixed, and/or curated
by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available
upon request.

15.6.1.10.3 https://bio.libretexts.org/@go/page/5484
15.6.1.11: Leptin - the Fat Hormone

Leptin
Several strains of laboratory mice are homozygous for single-gene mutations that causes them to become grossly obese.
These fall into two classes:
When ob/ob mice are treated with injections of leptin they lose their excess fat and return to normal body weight.
db/db = mutations in the gene that encodes the receptor for leptin
Study of these animals has led to an understanding of the action of leptin in humans.
Human leptin is a protein of 167 amino acids. It is manufactured in the adipocytes (fat cells) of white adipose tissue, and the level
of circulating leptin is directly proportional to the total amount of fat in the body.
Leptin acts on receptors in the hypothalamus of the brain where it:
counteracts the effects of neuropeptide Y (a potent feeding stimulant secreted by cells in the gut and in the hypothalamus)
counteracts the effects of anandamide (another potent feeding stimulant that binds to the same receptors as THC, the active
ingredient of marijuana)
promotes the synthesis of α-MSH, an appetite suppressant
the result is the inhibition of food intake
This inhibition is long-term, in contrast to
the rapid inhibition of eating by cholecystokinin (CCK)
the slower suppression of hunger between meals mediated by PPY3-36
The absence of a functional hormone (or its receptor) leads to uncontrolled food intake and resulting obesity.
Leptin also acts on hypothalamic neurons responsible for
the conversion of white adipose tissue (WAT) into "beige" adipose tissue. "Beige" cells metabolize food into heat rather than
storing it as fat. In mice, leptin promotes weight loss even with normal food intake.
the secretion of gonadotropin-releasing hormone (GnRH). Women who are very thin from limited food intake or intense
physical training may cease to menstruate because of their lack of leptin-secreting fat cells. Treating them with recombinant
human leptin can sometimes restore normal menstruation.
stimulating the sympathetic nervous system to trigger the breakdown of fat in adipose tissue.
In addition to its effect on the hypothalamus, leptin acts directly on the cells of the liver and skeletal muscle where it stimulates the
oxidation of fatty acids in the mitochondria. This reduces the storage of fat in those tissues. T cells where it enhances the
production of Th1 cells promoting inflammation. Mice without leptin are protected from autoimmune disease (which may account
for the reports that restricting food intake helps humans with rheumatoid arthritis).
Mutations in the gene for leptin, or in its receptor, are rarely found in obese people.
The rare cases:
Extreme obesity in five members of two families that are homozygous for mutations (frameshift in one family, missense in the
other) in their leptin gene; i.e., they are like ob/ob mice.
Extreme obesity among three members of a family that are homozygous for mutations in their leptin receptor gene; i.e., they
are like db/db mice.
Only moderate obesity in people who are heterozygous (one mutant and one normal) for their leptin genes.
Recombinant human leptin is now available, but trials to see if it can reduce obesity in humans as it does in ob/ob mice have been
disappointing.
However, the 16 September 1999 issue of The New England Journal of Medicine reported the results of a year-long trial of
recombinant human leptin in a 9-year-old girl who is homozygous for a frameshift mutation in her leptin genes. The findings:
She began the trial weighing 208 pounds (94.4 kg), of which 123 lbs (55.9 kg) was fat (adipose tissue).

15.6.1.11.1 https://bio.libretexts.org/@go/page/5485
 She was given daily injections of recombinant leptin for one year.
At the end of that time,
she had lost 36 lbs (16.4 kg), most of it fat.
Her appetite and thus food intake had decreased.
Her immune system made antileptin antibodies but these did not seem to interfere with the action of the hormone.
But trials of recombinant leptin in obese humans who do not have mutations in both their leptin genes have not shown any great
benefit in weight reduction.

This page titled 15.6.1.11: Leptin - the Fat Hormone is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.6.1.11.2 https://bio.libretexts.org/@go/page/5485
15.6.1.12: Hormones of the Liver

The liver synthesizes and secretes at least four important hormones:

Insulin-like Growth Factor-1 (IGF-1)
Angiotensinogen
Thrombopoietin
Hepcidin
Betatrophin

Insulin-like Growth Factor-1

This protein of 70 amino acids was once called somatomedin because it is not growth hormone but is the immediate stimulus for
growth of the body. Growth hormone released from the anterior lobe of the pituitary binds to receptors on the surface of liver cells
which stimulates the synthesis and release of IGF-1 from them. Many cells have receptors for IGF-1, especially cells in the bone
marrow and in the cartilaginous growing regions of the long bones.
Binding of IGF-1 to cells with receptors for it stimulates them to move from G1 of the cell cycle to S phase and on to mitosis.
Mice with one of their Igf-1receptor genes "knocked out" live 25% longer than normal mice. This may result from an increase in
their resistance to the damaging effects of reactive oxygen species (ROS) or to an increased efficiency at clearing away clumped
proteins in their cells (or both). These heterozygous mice appear to be normal in every other respect.
The levels of IGF-1 in the blood are highest during the years of puberty which is, of course, a time of rapid growth. Occasionally
children are found that have stunted growth because they have inherited mutant genes for the growth hormone (GH) receptor.
Recombinant human IGF-1 has been successfully used to treat them.

Angiotensinogen
This protein is released into the blood where it serves as the precursor for angiotensin. How angiotensin is manufactured, and the
role it plays in maintaining blood pressure, is described in the discussion of renin.

Thrombopoietin (TPO)
Thrombopoietin is a protein of 332 amino acids. It stimulates precursor cells in the bone marrow to differentiate into
megakaryocytes. Megakaryocytes generate platelets, essential to blood clotting.
The production of megakaryocytes — and thus platelets — is under homeostatic control. It works like this:
Circulating platelets are covered with receptors for TPO.
So are megakaryocytes and their precursors, but there are fewer of them.
When platelet counts are high, most of the circulating TPO is bound to the platelets and less is left to stimulate megakaryocytes.
When platelet counts drop, more TPO becomes available to stimulate megakaryocytes to replenish the platelet supply.
Humans manufacture about 1011 platelets each day under normal conditions.

This page titled 15.6.1.12: Hormones of the Liver is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.6.1.12.1 https://bio.libretexts.org/@go/page/5486
15.6.1.13: Melanocyte Stimulating Hormone (MSH)
Melanocyte-stimulating hormone gets its name because of its effect on melanocytes: skin cells that contain the black pigment,
melanin. In humans, melanocytes are responsible for moles, freckles, and suntan (and, if they turn cancerous, melanoma). In most
vertebrates, MSH is produced by an intermediate lobe of the pituitary gland. Its secretion causes a dramatic darkening of the skin
of fishes, amphibians, and reptiles. The darkening occurs as granules of melanin spread through the branches of specialized
melanocytes called melanophores.

Figure 15.6.1.13.1 Melanocytes

The photomicrograph on the right shows melanophores in the skin of a frog with the melanin dispersed throughout the branches of
the cells. This effect is produced by MSH. When the pigment retreats to the center of the cells, the skin lightens.
The granules are carried outward along microtubules using kinesin as the motor.
They assemble at the actin-rich periphery of the cell carried by a myosin.
The granules are carried back to the center of the cell along microtubules using dynein as the motor.

Figure 15.6.1.13.2 Frog with MSH

The above photo was taken a few moments after the frog on the right was injected with a small dose of MSH. The response to
MSH does not occur during mitosis; presumably the microtubules with their dyneins and kinesins are needed for operation of the
mitotic spindle.

Tanning
Proopiomelanocortin (POMC), the same precursor molecule from which the adrenocorticotropic hormone (ACTH) is
synthesized, also produces two forms of MSH. One of them, α-MSH, is identical to the first 13 amino acids at the amino terminal
of ACTH. α-MSH is responsible for tanning in humans.
When ultraviolet light strikes skin cells (keratinocytes), it activates the transcription factor p53.
p53 turns on transcription of the gene encoding POMC.
Cleavage of the POMC protein produces
α-MSH. This is secreted from the cells and stimulates nearby melanocytes (thus a paracrine effect) to synthesize melanin in
packets called melanosomes. The melanosomes are transferred to the skin cells where they form a protective cap over the
nucleus. This cap helps protect the DNA within the nucleus from the damaging effects of ultraviolet radiation.
ACTH. This is secreted into the blood and may help reduce skin inflammation by stimulating the release of glucocorticoids
from the adrenal cortex.

15.6.1.13.1 https://bio.libretexts.org/@go/page/5487
 β-endorphin. This may help suppress the pain of sunburn. In mice (and perhaps humans) the rise in the level of β-
endorphin upon exposure to uv light activates mu (µ) receptors — the same ones that opiates bind to. This leads to similar
addictive behavior - the mice seek uv exposure and show signs of withdrawal when β-endorphin binding is blocked (by
naloxone).
Injections of a synthetic version of α-MSH called Melanotan I also darkens the skin. This raises the possibility of using melanotan
to get a suntan without the risks of exposure to ultraviolet light. A second synthetic version of MSH dubbed Melanotan II also
darkened the skin of male volunteers. Unexpectedly, it also caused many of them to develop penile erections. This has raised the
possibility of using MSH to cure impotence.

MSH and appetite

Humans have no intermediate lobe in their pituitary gland, and MSH may not be a circulating hormone for us. However, α-MSH is
produced by POMC neurons in the brain where it acts to suppress appetite. Some cases of extreme obesity have been traced to
mutations in the brain receptor for α-MSH. Presumably these people are unable to respond to the appetite-suppressing effect of
their α-MSH.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 15.6.1.13: Melanocyte Stimulating Hormone (MSH) is shared under a CC BY 3.0 license and was authored, remixed, and/or
curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is
available upon request.

15.6.1.13.2 https://bio.libretexts.org/@go/page/5487
15.6.2: Insect Hormones
Because of their rigid exoskeleton, insects can only grow by periodically shedding their exoskeleton - called molting. Molting
occurs repeatedly during larval development. At the final molt, the adult emerges. In several insect orders, notably
ants and bees (Hymenoptera) — example the honeybee
flies (Diptera) — example Drosophila melanogaster
butterflies and moths (Lepidoptera) such as the silkworm moth
the adult looks entirely different from the larva that preceded it. This marked transformation is called complete metamorphosis.

Figure 15.6.2.1 Development cycles of silkworm moth

Complete metamorphosis takes place during a seemingly-dormant stage called the pupa. In fact, intense biological activity is going
on within the pupal case. The cells of virtually all the differentiated larval structures muscles, salivary glands, gut, etc. die by
apoptosis. The nutrients they release are then available for the further development of nests of cells - the imaginal discs - that have
been quietly developing within the larval body. Their differentiation produces the structures of the adult - legs, wings, compound
eyes, etc.
The sequence ending in the center panel (B) shows the larval, pupal, and adult stages during normal development of the domestic
silkworm moth, Bombyx mori.

Prothoracicotropic Hormone (PTTH)

Molting and pupation require the hormone, PTTH, secreted by a two pairs of cells in the brain of the larva. If these cells are cut out
of the brain of a full-grown larva, pupation does not occur. This is not because of the trauma of surgery; if transplanted somewhere
else in the caterpillar's body, pupation occurs normally. PTTH is a homodimer of two polypeptides of 109 amino acids. PTTH does
not drive pupation directly but, as its name suggests, acts on the prothoracic glands.

Ecdysone
There are two prothoracic glands located in the thorax. Under the influence of PTTH, they secrete the steroid hormone ecdysone.
Acting together, PTTH and ecdysone trigger every molt: larva-to-larva as well as pupa-to-adult. What, then, accounts for the
dramatic changes of metamorphosis?

Figure 15.6.2.2 ECdysone

15.6.2.1 https://bio.libretexts.org/@go/page/5464
Juvenile Hormone (JH)
Juvenile hormone is secreted by two tiny glands behind the brain, the corpora allata. As long as there is enough JH, ecdysone
promotes larva-to-larva molts. With lower amounts of JH, ecdysone promotes pupation. Complete absence of JH results in
formation of the adult.

Figure 15.6.2.3 Corpora allata

So if the corpora allata are removed from an immature silkworm, it immediately spins a cocoon and becomes a small pupa. A
miniature adult eventually emerges (shown in panel (A) above). Conversely, if the corpora allata of a young silkworm are place in
the body of a fully-mature larva, metamorphosis does not occur. The next molt produces an extra-large caterpillar (panel (C)
above).

JH affects gene expression

Adult insects do not normally molt, but if extra amounts of PTTH are given to an adult Rhodnius (the "kissing bug"), it is forced
into an extra molt. The English insect physiologist V. B. Wigglesworth showed that if juvenile hormone is first applied to the
insect's exoskeleton, the regions affected by it revert to larval type after this extra molt.

Figure 15.6.2.4 Juvenile hormone applied to insects. These images (courtesy of Dr. Wigglesworth) show his results. Left:
application of a band of juvenile hormone to the cuticle of an adult Rhodnius results in the formation of larval cuticle (speckled
band) when the insect is forced to undergo an extra molt. Right: Dr. Wigglesworth has printed his initials with juvenile hormone.
What a beautiful example of the power of a single molecule to unleash a different pattern of gene expression! Presumably, JH
interacts with hormone receptors in the cells to produce a new set of transcription factors.

Insect hormones and pest control

Knowledge of insect hormones has provided a number of opportunities to enlist them or molecules related to them in the battle
against insect pests.

This page titled 15.6.2: Insect Hormones is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.6.2.2 https://bio.libretexts.org/@go/page/5464
 SECTION OVERVIEW
15.7: Sexual Reproduction
Sexual reproduction is the formation of a new individual following the union of two gametes. In humans and the majority of other
eukaryotes plants as well as animals the two gametes differ in structure ("anisogamy") and are contributed by different parents.
Gametes need motility to be able to meet and unite and food to nourish the developing embryo. In animals (and some plants), these
two rather contrasting needs are met by anisogametes: sperm that are motile (and small) and eggs that contain food.

Topic hierarchy

15.7A: Sexual Reproduction

15.7B: Asexual Reproduction in Animals

15.7C: Birth Control

15.7D: Prenatal Screening

15.7E: Extraembryonic Membranes and the Physiology of the Placenta

15.7F: Genetic Mosaics

15.7G: Human Cloning

This page titled 15.7: Sexual Reproduction is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.7.1 https://bio.libretexts.org/@go/page/5367
15.7A: Sexual Reproduction
Sexual reproduction is the formation of a new individual following the union of two gametes. In humans and the majority of other
eukaryotes plants as well as animals the two gametes differ in structure ("anisogamy") and are contributed by different parents.
Gametes need motility to be able to meet and unite and food to nourish the developing embryo. In animals (and some plants), these
two rather contrasting needs are met by anisogametes: sperm that are motile (and small) and eggs that contain food.

Sex Organs of the Human Male

The reproductive system of the male has two major functions: (1) production of sperm and (2) delivery of these to the reproductive
tract of the female. Sperm production - spermatogenesis - takes place in the testes. Each testis is packed with seminiferous tubules
(laid end to end, they would extend more than 20 meters) where spermatogenesis occurs.

Figure 15.7.1.1 Male reproductive system

Spermatogenesis
The walls of the seminiferous tubules consist of diploid spermatogonia, stem cells that are the precursors of sperm. Spermatogonia
divide by mitosis to produce more spermatogonia or differentiate into spermatocytes. Meiosis of each spermatocyte produces 4
haploid spermatids. This process takes over three weeks to complete. Then the spermatids differentiate into sperm, losing most of
their cytoplasm in the process.

15.7A.1 https://bio.libretexts.org/@go/page/5496
 Figure 15.7.1.2 Spermatogenesis. During spermatogenesis, four sperm result from each primary spermatocyte, which divides into
two haploid secondary spermatocytes; these cells will go through a second meiotic division to produce four spermatids. (CC BY;
OpenStax).
For simplicity, the figure shows the behavior of just a single pair of homologous chromosomes with a single crossover. With 22
pairs of autosomes and an average of two crossovers between each pair, the variety of gene combinations in sperm is very great.

Sperm
Sperm cells are little more than flagellated nuclei. Each consists of a head, which has an acrosome at its tip and contains a haploid
set of chromosomes in a compact, inactive, state, a midpiece containing mitochondria and a single centriole, and a tail which is a
flagellum. This electron micrograph (courtesy of Dr. Don W. Fawcett and Susumu Ito) shows the sperm cell of a bat. Note the
orderly arrangement of the mitochondria. They supply the ATP to power the whiplike motion of the tail.

Figure 15.7.1.3 Bat sperm

15.7A.2 https://bio.libretexts.org/@go/page/5496
An adult male manufactures over 100 million sperm cells each day. These gradually move into the epididymis where they undergo
further maturation. The acidic environment in the epididymis keeps the mature sperm inactive. In addition to making sperm, the
testis is an endocrine gland. Its principal hormone, testosterone, is responsible for the development of the secondary sex
characteristics of men such as the beard, deep voice, and masculine body shape. Testosterone is also essential for making sperm.
Testosterone is made in the interstitial cells (also called Leydig cells) that lie between the seminiferous tubules.

LH
Interstitial cells are, in turn, the targets for a hormone often called interstitial cell stimulating hormone (ICSH). It is a product of
the anterior lobe of the pituitary gland. However, ICSH is identical to the luteinizing hormone (LH) found in females, and I prefer
to call it LH.

FSH
Follicle-stimulating hormone (also named for its role in females) acts directly on spermatogonia to stimulate sperm production
(aided by the LH needed for testosterone synthesis).

Sex Organs of the Human Female

The responsibility of the female mammal for successful reproduction is considerably greater than that of the male.

Figure 15.7.1.4 Female reproductive system

She must
manufacture eggs
be equipped to receive sperm from the male
provide an environment conducive to fertilization and implantation
nourish the developing baby not only before birth but after too

Oogenesis
Egg formation takes place in the ovaries. In contrast to males, the initial steps in egg production occur prior to birth. Diploid stem
cells called oogonia divide by mitosis to produce more oogonia and primary oocytes. By the time the fetus is 20 weeks old, the
process reaches its peak and all the oocytes that she will ever possess (~4 million of them) have been formed (*). By the time she is
born, only about 1 million of these remain (the others eliminated by apoptosis). Each has begun the first steps of the first meiotic
division stopping at the diplotene stage of meiosis I.

15.7A.3 https://bio.libretexts.org/@go/page/5496
 Figure 15.7.1.5 Oogenesis
No further development occurs until years later when the girl becomes sexually mature. Then the primary oocytes recommence
their development, usually one at a time and once a month. The primary oocyte grows much larger and completes meiosis I,
forming a large secondary oocyte and a small polar body that receives little more than one set of chromosomes. Which
chromosomes end up in the egg and which in the polar body is entirely a matter of chance.
In humans (and most vertebrates), the first polar body does not go on to meiosis II, but the secondary oocyte does proceed as far as
metaphase of meiosis II and then stops.
Only if fertilization occurs will meiosis II ever be completed. Entry of the sperm restarts the cell cycle breaking down MPF (M-
phase promoting factor) and turning on the anaphase-promoting complex (APC). Completion of meiosis II converts the secondary
oocyte into a fertilized egg or zygote (and also a second polar body). As in the diagram for spermatogenesis, the behavior of the
chromosomes is greatly simplified.

Figure 15.7.1.6 Polar body formation during oogenesis

The photomicrograph (courtesy of Turtox) shows polar body formation during oogenesis in the whitefish. Even allowing for the
fact that fish eggs are larger than mammalian eggs, you can readily see how the polar body gets little more than one set of
chromosomes.
These events take place within a follicle, a fluid-filled envelope of cells surrounding the developing egg. The ripening follicle also
serves as an endocrine gland. Its cells make a mixture of steroid hormones collectively known as estrogen. Estrogen is
responsible for the development of the secondary sexual characteristics of a mature woman, e.g.,
a broadening of the pelvis
development of the breasts
growth of hair around the genitals and in the armpits
development of adipose tissue leading to the more rounded body contours of adult women.
Estrogen continues to be secreted throughout the reproductive years of women During this period, it plays an essential role in the
monthly menstrual cycle.

Ovulation
Ovulation occurs about two weeks after the onset of menstruation. In response to a sudden surge of LH, the follicle ruptures and
discharges a secondary oocyte. This is swept into the open end of the fallopian tube and begins to move slowly down it.

15.7A.4 https://bio.libretexts.org/@go/page/5496
Copulation and Fertilization
For fertilization to occur, sperm must be deposited in the vagina within a few (5) days before or on the day of ovulation. Sperm
transfer is accomplished by copulation. Sexual excitation dilates the arterioles supplying blood to the penis. Blood accumulates in
three cylindrical spongy sinuses that run lengthwise through the penis. The resulting pressure causes the penis to enlarge and erect
and thus able to penetrate the vagina. Movement of the penis back and forth within the vagina causes sexual tension to increase to
the point of ejaculation. Contraction of the walls of each vas deferens propels the sperm along. Fluid is added to the sperm by the
seminal vesicles, Cowper's glands, and the prostate gland. These fluids provide
a source of energy (fructose)
an alkaline environment to activate the sperm
perhaps in other ways provide an optimum chemical environment for them
The mixture of sperm and accessory fluids is called semen. It passes through the urethra and is expelled into the vagina.
Physiological changes occur in the female as well as the male in response to sexual excitement, although these are not as readily
apparent. In contrast to the male, however, such responses are not a prerequisite for copulation and fertilization to occur. Once
deposited within the vagina, the sperm proceed on their journey into and through the uterus and on up into the fallopian tubes. It is
here that fertilization may occur if an "egg" is present (strictly speaking, it is still a secondary oocyte until after completion of
meiosis II).
Although sperm can swim several millimeters each second, their trip to and through the fallopian tubes may be assisted by
muscular contraction of the walls of the uterus and the tubes. The trip is fraught with heavy mortality. An average human ejaculate
contains over one hundred million sperm, but only a few dozen complete the journey, arriving within 15 minutes of ejaculation.
And of these, only one will succeed in fertilizing the egg.
Sperm swim towards the egg by chemotaxis following a gradient of progesterone secreted by cells surrounding the egg.
Progesterone opens CatSper ("cation sperm") channels in the plasma membrane surrounding the anterior portion of the sperm tail.
This allows an influx of Ca2+ ions which causes the flagellum to beat more rapidly and vigorously. Fertilization begins with the
binding of a sperm head to the glycoprotein coating of the egg (called the zona pellucida). Exocytosis of the acrosome at the tip of
the sperm head releases enzymes that digest a path through the zona and enable the sperm head to bind to the plasma membrane of
the egg. The binding is mediated by the binding of two membrane proteins:
Izumo1 on the surface of the sperm
Juno, its receptor on the egg surface
Fusion of their respective membranes allows the entire contents of the sperm to be drawn into the cytosol of the egg. Even though
the sperm's mitochondria enter the egg, they are almost always destroyed by autophagy and do not contribute their genes to the
embryo. So human mitochondrial DNA is almost always inherited from mothers only. Within moments, enzymes released from the
egg cytosol act on the zona making it impermeable to other sperm that arrive. Soon the nucleus of the successful sperm enlarges
into the male pronucleus. At the same time, the egg (secondary oocyte) completes meiosis II forming a second polar body and
the female pronucleus.
The male and female pronuclei move toward each other while duplicating their DNA in S phase. Their nuclear envelopes
disintegrate. A spindle is formed (following replication of the sperm's centriole), and a full set of dyads assembles on it. The
fertilized egg or zygote is now ready for its first mitosis. When this is done, 2 cells each with a diploid set of chromosomes are
formed.
In sea urchins, the block to additional sperm entry and the fusion of the pronuclei are triggered by nitric oxide generated in the egg
by the sperm acrosome.

Pregnancy
Development begins while the fertilized egg is still within the fallopian tube. Repeated mitotic divisions produces a solid ball of
cells called a morula. Further mitosis and some migration of cells converts this into a hollow ball of cells called the blastocyst.
Approximately one week after fertilization, the blastocyst embeds itself in the thickened wall of the uterus, a process called
implantation, and pregnancy is established.

15.7A.5 https://bio.libretexts.org/@go/page/5496
Fig.15.7.1.7 Blastocyst
The blastocyst produces two major collections of cells:
Three or four blastocyst cells develop into the inner cell mass, which will form 3 extraembryonic membranes: amnion, yolk
sac, and (a vestigial) allantois and in about 2 months, become the fetus and, ultimately, the baby.
The remaining 100 or so cells form the trophoblast, which will develop into the chorion that will go on to make up most of the
placenta. All the extraembryonic membranes play vital roles during development but will be discarded at the time of birth.
The placenta grows tightly fused to the wall of the uterus. Its blood vessels, supplied by the fetal heart, are literally bathed in the
mother's blood. Although there is normally no mixing of the two blood supplies, the placenta does facilitate the transfer of a variety
of materials between the fetus and the mother such as
receiving food
receiving oxygen and discharging carbon dioxide
discharging urea and other wastes
receiving antibodies (chiefly of the IgG class). These remain for weeks after birth, protecting the baby from the diseases to
which the mother is immune.
But the placenta is not simply a transfer device. Using raw materials from the mother's blood, it synthesizes large quantities of
proteins and also some hormones. The metabolic activity of the placenta is almost as great as that of the fetus itself. The umbilical
cord connects the fetus to the placenta. It receives deoxygenated blood from the iliac arteries of the fetus and returns oxygenated
blood to the liver and on to the inferior vena cava.

Figure 15.7.1.8 Foramen ovale

Because its lungs are not functioning, circulation in the fetus differs dramatically from that of the baby after birth. While within the
uterus, blood pumped by the right ventricle bypasses the lungs by flowing through the foramen ovale and the ductus arteriosus.
Although the blood in the placenta is in close contact with the mother's blood in the uterus, intermingling of their blood does not
normally occur. However, some of the blood cells of the fetus usually do escape into the mother's circulation — where they have
been known to survive for decades. This raises the possibility of doing prenatal diagnosis of genetic disorders by sampling the
mother's blood rather than having to rely on the more invasive procedures of amniocentesis and chorionic villus sampling (CVS).
Fragments of fetal DNA (~ 300 bp long) from apoptotic cells of the placenta are also found in the mother's plasma as early as 5
weeks after implantation. These can be tested for various forms of aneuploidy, e.g. the trisomy 21 of Down syndrome. Far rarer is
the leakage of mother's blood cells into the fetus. However, it does occur. A few pregnant women with leukemia or lymphoma have
transferred the malignancy to their fetus. Some babies have also acquired melanoma from the transplacental passage of these
highly-malignant cells from their mother.

15.7A.6 https://bio.libretexts.org/@go/page/5496
During the first 2 months of pregnancy, the basic structure of the baby is being formed. This involves cell division, cell migration,
and the differentiation of cells into the many types found in the baby. During this period, the developing baby - called an embryo -
is very sensitive to anything that interferes with the steps involved. Virus infection of the mother, e.g., by rubella ("German
measles") virus or exposure to certain chemicals may cause malformations in the developing embryo. Such agents are called
teratogens ("monster-forming"). The tranquilizer, thalidomide, taken by many pregnant European women between 1954 and 1962,
turned out to be a potent teratogen and was responsible for the birth of several thousand deformed babies.
After about two months, all the systems of the baby have been formed, at least in a rudimentary way. From then on, development of
the fetus, as it is now called, is primarily a matter of growth and minor structural modifications. The fetus is less susceptible to
teratogens than is the embryo. Pregnancy involves a complex interplay of hormones.

The placenta is an allograft

One of the greatest unsolved mysteries in immunology is how the placenta survives for 9 months without being rejected by the
mother's immune system. Every cell of the placenta carries the father's genome (a haploid set of his chromosomes); including one
of his #6 chromosomes where the genes for the major histocompatibility antigens (HLA) are located.
One partial exception: none of the genes on the father's X chromosome are expressed. While X-chromosome inactivation is random
in the cells of the fetus, it is NOT random in the cells of the trophoblast. In every cell of the trophoblast — and its descendants — it
is the paternal X chromosome that is inactivated. But this does not solve our problem because the genes for all the major
histocompatibility antigens are located on chromosome 6, which is not inactivated.
Thus the placenta is immunologically as foreign to the mother as a kidney transplant would be. Yet it thrives. Despite a half-century
of research, the mechanism for this immunologically privileged status remains uncertain. But one thing is clear - The mother is not
intrinsically tolerant of the father's antigens. She will promptly reject a skin transplant from the father. She develops antibodies
against his histocompatibility antigens expressed by the fetus. In fact, women who have borne several children by the same father
are often excellent sources of anti-HLA serum for use in tissue typing. So what accounts for the phenomenon? Some possibilities:
The placenta does not express class II histocompatibility antigens.
Nor does it express the strongly-immunogenic class I histocompatibility antigens (HLA-A, HLA-B). It does express HLA-C,
but this is only weakly immunogenic.
The cells of the placenta secrete progesterone, which is immunosuppressive.
In lab rats the embryos (and the mother's endometrium) secrete corticotropin-releasing hormone (CRH). This hormone induces
the expression of Fas ligand (FasL) on the cells of the placenta. Activated T cells express Fas so any threatening T cells would
commit suicide by apoptosis when they encounter FasL on their target.
In laboratory mice the cells of the placenta degrade the amino acid tryptophan. Tryptophan is essential for T-cell function.
When mice are treated with an inhibitor of the Trp-degrading enzyme, their fetuses are promptly aborted by the action of the
mother's lymphocytes. (D. H. Munn, et. al., Science, 281: 1191, 21 Aug 1998.)
In mice, expression of genes encoding cytokines needed to attract effector T cells (e.g., CTLs) into a tissue is suppressed in the
cells of the placenta.
Perhaps most important of all is the increased production in the mother of immunosuppressive regulatory T cells (Treg).
Depletion of Treg cells in pregnant mice leads to spontaneous abortion while
injection of Treg cells into mice that are otherwise prone to abortion enables them to carry their fetuses to term.
In humans, the number of Treg cells rises during pregnancy (in the fetus as well as the mother).

 In vitro fertilization

On July 25, 2013 Louise Brown celebrated her 35th birthday. She was the first of what today number some four million
(worldwide) "test tube babies"; that is, she developed from an egg that was fertilized outside her mother's body - the process
called in vitro fertilization (IVF). IVF involves
Harvesting mature eggs from the mother. This is not an easy process. The mother must undergo hormonal treatments to
produce multiple eggs, which then must be removed (under anesthesia) from her ovaries.
Harvesting sperm from the father. Harvesting is usually no problem, but often the sperm are defective in their ability to
fertilize (so setting the stage for ICSI).
Mixing sperm and eggs in a culture vessel ("in vitro").
Culturing the fertilized eggs for several days until they have developed to at least the 8-cell stage.

15.7A.7 https://bio.libretexts.org/@go/page/5496
 Placing two or more of these into the mother's uterus (which her hormone treatments have prepared for implantation).
Keeping one's fingers crossed as only about one-third of the attempts result in a successful pregnancy.
Intra cytoplasmic Sperm Injection (ICSI)
Successful IVF assumes the availability of healthy sperm. But many cases of infertility arise from defects in the father's sperm.
Often these can be overcome by directly injecting a single sperm into the egg. In the U.S. today, some two-thirds of ART
procedures employ ICSI (even though as many as half of these do not involve male infertility).
Ooplasmic Transfer
Infertility in some cases may stem from defects in the cytoplasm of the mother's egg. To circumvent these, cytoplasm can be
removed from the egg of a young, healthy woman ("Donor egg") and injected along with a single sperm into the prospective
mother's egg. Although a few healthy children have been born following ooplasmic transfer, the jury is still out on its safety,
and it is not approved for use in the U.S. One reason for concern is that ooplasmic transfer results in an egg carrying both the
mother's mitochondria and mitochondria from the donor (in normal fertilization, all the mitochondria in the father's sperm are
destroyed in the egg). This condition called heteroplasmy creates a child having two different mitochondrial DNA genomes in
all of its cells.

Fig.15.7.1.9 ooplasmic transfer

In rare, but important, cases, the defect in the prospective mother's cytoplasm is the result of her having mitochondria with a
mutant gene. Ooplasmic transfer is of no help in these cases because the fertilized egg will still contain a preponderance of the
mother's defective mitochondria. But three techniques worked out on laboratory animals show promise of being adapted to aid
such women to produce healthy young.

Three Possible Ways to Prevent Transmission of Mitochondrial Diseases

Maternal Spindle Transfer

Researchers in Oregon reported in the 17 September 2009 issue of Nature that they had been able to produce 4 healthy rhesus
monkeys with no mitochondria from their biological mother.

Figure 15.7.1.10 Maternal spindle transfer

Their procedure:
Remove the spindle with all its attached chromosomes from the mother's oocyte at metaphase II of meiosis. They managed to
do this without any of her mitochondria being withdrawn as well.

15.7A.8 https://bio.libretexts.org/@go/page/5496
 Enucleate the oocyte of the mitochondria donor and then insert the mother's chromosomes — still attached to the spindle —
into it. Then inject a sperm from the father.
Allow the fertilized egg to develop into a blastocyst.
Implant this in the uterus of a surrogate mother.
The result: 4 healthy babies each with the nuclear genes of their mother and father but none of the mitochondria of their mother.
Pronuclear Transfer

In this procedure,
An egg containing mutant mitochondria is fertilized by IVF.
The two pronuclei are removed and injected into a fertilized egg with healthy mitochondria and whose own pronuclei have been
removed.
Allow the egg to develop into a blastocyst.
Implant this in the uterus.
Both procedures (1) and (2) are under investigation for use in humans.
Polar Body Transfer
Both the first polar body (formed before fertilization) and the second polar body (formed after fertilization) contain a genome
equivalent to that of the secondary oocyte and zygote respectively. However, they contain few, if any, mitochondria. In mice,
transfer of either polar body to an enucleated recipient egg (with healthy mitochondria) yield young mice with few, if any, of the
donor mother's mitochondria with their defective mtDNA. So in mice, at least, this technique produces offspring with less
heteroplasmy than the other two techniques.
If any of these techniques can be applied to humans (there are safety and regulatory hurdles still to be overcome), it would allow
women carrying defective mitochondria to bear babies free of the ailment.

The Upside of ART

It has allowed some four million previously-infertile couples to have children.
It permits screening (on one cell removed from the 8-celled morula) for the presence of genetic disorders - thus avoiding
starting a pregnancy if a disorder is found.
One can use frozen sperm allowing fatherhood for a man who is no longer able to provide fresh sperm.
Because a number of morulas are created, the extras can be frozen, stored, and used later
if the initial attempt fails (the prospective mother must still receive hormones to prepare her uterus for implantation and the
success rate is lower with thawed morulas).
Where regulations permit, the extras can be used as a source of embryonic stem (ES) cells.

The Downside of ART

Although improving, the success rate is still sufficiently low (~35%) that the process often has to be repeated (which is
physically demanding as well as very expensive).
Because several morulas are usually transferred, multiple births are common (about 50%), and as is often the case with multiple
births, the babies are born early and weigh less (~one-third of all ART babies in the U.S. are born early). To reduce the number
of twins, triplets, etc., more ART centers are turning to "single-embryo transfer" (SET). Some ART centers find that they can
increase the success rate and thus rely more on SET by culturing the morulas for 5–6 days, instead of the usual 2–3 days, before
transferring them (by now they have become blastocysts) to the mother.
The risk of birth defects may be increased slightly (from ~6% in "normal" pregnancies to ~8% in ART pregnancies).
ART procedures in experimental animals often result in a failure of correct gene imprinting. Whether this will pose a problem
for humans remains to be seen.

Birth and Lactation

Exactly what brings about the onset of labor is still not completely understood. Probably a variety of integrated hormonal controls
are at work. A growing body of evidence implicates a rise in the level of fetal DNA in the mother's blood as a trigger for the onset
of labor. The first result of labor is the opening of the cervix. With continued powerful contractions, the amnion ruptures and the
amniotic fluid (the "waters") flows out through the vagina. The baby follows, and its umbilical cord can be cut. The infant's lungs
expand, and it begins breathing. This requires a major switchover in the circulatory system. Blood flow through the umbilical cord,

15.7A.9 https://bio.libretexts.org/@go/page/5496
ductus arteriosus, and foramen ovale ceases, and the adult pattern of blood flow through the heart, aorta, and pulmonary arteries
begins. In some infants, the switchover is incomplete, and blood flow through the pulmonary arteries is inadequate. Failure to
synthesize enough nitric oxide (NO) is one cause. Shortly after the baby, the placenta and the remains of the umbilical cord (the
"afterbirth") are expelled.

Figure 15.7.1.11 Fetus at full term

At the time of birth, and for a few days after, the mother's breasts contain a fluid called colostrum. It is rich in calories and
proteins, including antibodies that provide passive immunity for the newborn infant. Three or four days after delivery, the breasts
begin to secrete milk.
Its synthesis is stimulated by the pituitary hormone prolactin (PRL).
Its release is stimulated by a rise in the level of oxytocin when the baby begins nursing.
Milk also contains an inhibitory peptide. If the breasts are not fully emptied, the peptide accumulates and inhibits milk
production. This autocrine action thus matches supply with demand.

Birth Control
The following table summarizes the various birth control method available and in use today.
Popularity (% using the method) and relative effectiveness of several methods of birth control among U. S. women using contraceptives. The
pregnancy rate is the number of pregnancies per 100 women in the first year of using the method.
Method Popularity Pregnancy Rate

Natural family planning (rhythm) 1% 25

Male condom 16% 17

Oral contraceptives ("the pill") 28% 0.3–8.7*

Intrauterine devices (IUD) 8.5% 0.1–1.0*

Implants, e.g., Implanon® ~1% 0.05–1.0*

DMPA injections ~3.5% 6.7

Male + Female Sterilization 37% <<1%

None 85

* The lower value is found under ideal conditions; i.e., among highly-motivated women receiving good medical care.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 15.7A: Sexual Reproduction is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.7A.10 https://bio.libretexts.org/@go/page/5496
15.7B: Asexual Reproduction in Animals
Asexual reproduction is the formation of new individuals from the cell(s) of a single parent. It is very common in plants; less so in
animals.

Asexual Reproduction in Plants

All plant organs have been used for asexual reproduction, but stems are the most common.

Stems

Figure 15.7.2.1 Stolons of strawberry plant

In some species, stems arch over and take root at their tips, forming new plants. The horizontal above-ground stems (called
stolons) of the strawberry produce new daughter plants at alternate nodes. Underground stems such as rhizomes, bulbs, corms and
tubers are used for asexual reproduction as well as for food storage. Irises and day lilies, for example, spread rapidly by the growth
of their rhizomes.

Leaves

Figure 15.7.2.2 Leaves of bryophyllum

The above photo shows the leaves of the common ornamental plant Bryophyllum (also called Kalanchoë). Mitosis at meristems
along the leaf margins produce tiny plantlets that fall off and can take up an independent existence.

Roots
Some plants use their roots for asexual reproduction. The dandelion is a common example. Trees, such as the poplar or aspen, send
up new stems from their roots. In time, an entire grove of trees may form - all part of a clone of the original tree.

Plant Propagation
Commercially-important plants are often deliberately propagated by asexual means in order to keep particularly desirable traits
(e.g., flower color, flavor, resistance to disease). Cuttings may be taken from the parent and rooted.
Grafting

Figure 15.7.2.3 Grafting

Grafting is widely used to propagate a desired variety of shrub or tree. All apple varieties, for example, are propagated this way.

15.7B.1 https://bio.libretexts.org/@go/page/5497
Apple seeds are planted only for the root and stem system that grows from them. After a year's growth, most of the stem is
removed and a twig (scion) taken from a mature plant of the desired variety is inserted in a notch in the cut stump (the stock). So
long the cambiums of scion and stock are united and precautions are taken to prevent infection and drying out, the scion will grow.
It will get all its water and minerals from the root system of the stock. However, the fruit that it will eventually produce with be
identical (assuming that it is raised under similar environmental conditions) to the fruit of the tree from which the scion was taken.

Apomixis
Citrus trees and many other species of angiosperms use their seeds as a method of asexual reproduction; a process called apomixis.
In one form, the egg is formed with 2n chromosomes and develops without ever being fertilized.
In another version, the cells of the ovule (2n) develop into an embryo instead of - or in addition to - the fertilized egg.
Hybridization between different species often yields infertile offspring. But in plants, this does not necessarily doom the offspring.
Many such hybrids use apomixis to propagate themselves. The many races of Kentucky bluegrass growing in lawns across North
America and the many races of blackberries are two examples of sterile hybrids that propagate successfully by apomixis. Recently,
an example of apomixis in gymnosperms was discovered (see Pichot, C., et al, in the 5 July 2001 issue of Nature). In a rare
cypress, the pollen grains are diploid, not haploid, and can develop into an embryo when they land on either
the female cones of their own species (rare) or
those of a much more common species of cypress.
Is this paternal apomixis in a surrogate mother a desperate attempt to avoid extinction?
Breeding apomictic crop plants
Many valuable crop plants (e.g., corn) cannot be propagated by asexual methods like grafting.
Agricultural scientists would dearly love to convert these plants to apomixis: making embryos that are genetic clones of themselves
rather than the product of sexual reproduction with its inevitable gene reshuffling. After 20 years of work, an apomictic corn
(maize) has been produced, but it does not yet produce enough viable kernels to be useful commercially.

Asexual Reproduction in Animals

Budding
Here, offspring develop as a growth on the body of the parent. In some species, e.g., jellyfishes and many echinoderms, the buds
break away and take up an independent existence. In others, e.g., corals, the buds remain attached to the parent and the process
results in colonies of animals. Budding is also common among parasitic animals, e.g., tapeworms.

Fragmentation
As certain tiny worms grow to full size, they spontaneously break up into 8 or 9 pieces. Each of these fragments develops into a
mature worm, and the process is repeated.

Parthenogenesis
In parthenogenesis ("virgin birth"), the females produce eggs, but these develop into young without ever being fertilized.
Parthenogenesis occurs in some fishes, several kinds of insects, and a few species of frogs and lizards. It does not normally occur in
mammals because of their imprinted genes. However, using special manipulations to circumvent imprinting, laboratory mice have
been produced by parthenogenesis.
In a few nonmammalian species it is the only method of reproduction, but more commonly animals turn to parthenogenesis only
under certain circumstances. Examples:
Aphids use parthenogenesis in the spring when they find themselves with ample food. In this species, reproduction by
parthenogenesis is more rapid than sexual reproduction, and the use of this mode of asexual reproduction permits the animals to
quickly exploit the available resources.
Female Komodo dragons (the largest lizard) can produce offspring by parthenogenesis when no male is available for sexual
reproduction. Their offspring are homozygous at every locus including having identical sex chromosomes. Thus the females
produce all males because, unlike mammals, females are the heterogametic sex (ZW) while males are homogametic (ZZ).

15.7B.2 https://bio.libretexts.org/@go/page/5497
Parthenogenesis is forced on some species of wasps when they become infected with bacteria (in the genus Wolbachia). Wolbachia
can pass to a new generation through eggs, but not through sperm, so it is advantageous to the bacterium for females to be made
rather that males. In these wasps (as in honeybees), fertilized eggs (diploid) become females and unfertilized (haploid) eggs
become males. However, in Wolbachia-infected females, all their eggs undergo endoreplication producing diploid eggs that
develop into females without fertilization, by parthenogenesis. Treating the wasps with an antibiotic kills off the bacteria and
"cures" the parthenogenesis!

 Apis mellifera capensis

Occasionally worker honeybees develop ovaries and lay unfertilized eggs. Usually these are haploid, as you would expect, and
develop into males. However, workers of the subspecies Apis mellifera capensis (the Cape honeybee) can lay unfertilized
diploid eggs that develop into females (who continue the practice). The eggs are produced by meiosis, but then the polar body
nucleus fuses with the egg nucleus restoring diploidy (2n). The phenomenon is called automictic thelytoky.

Cape honey bees gorging on honey. (CC BY-SA 3.0; Discott)

Why Choose Asexual Reproduction?

Perhaps the better question is: Why not? After all, asexual reproduction would seem a more efficient way to reproduce. Sexual
reproduction requires males but they themselves do not produce offspring. Two general explanations for the overwhelming
prevalence of sexually-reproducing species over asexual ones are:
Perhaps sexual reproduction has kept in style because it provides a mechanism to weed out (through the recombination process
of meiosis) harmful mutations that arise in the population reducing its fitness. Asexual reproduction leads to these mutations
becoming homozygous and thus fully exposed to the pressures of natural selection.
Perhaps it is the ability to adapt quickly to a changing environment that has caused sex to remain the method of choice for most
living things.

Purging Harmful Mutations

Most mutations are harmful - changing a functional allele to a less or nonfunctional one. An asexual population tends to be
genetically static. Mutant alleles appear but remain forever associated with the particular alleles present in the rest of that genome.
Even a beneficial mutation will be doomed to extinction if trapped along with genes that reduce the fitness of that population. But
with the genetic recombination provided by sex, new alleles can be shuffled into different combinations with all the other alleles
available to the genome of that species. A beneficial mutation that first appears alongside harmful alleles can, with recombination,
soon find itself in more fit genomes that will enable it to spread through a sexual population.
Evidence (from Paland and Lynch in the 17 February 2006 issue of Science): Some strains of the water flea Daphnia pulex (a tiny
crustacean) reproduce sexually, others asexually. The asexual strains accumulate deleterious mutations in their mitochondrial genes
four times as fast as the sexual strains.
Evidence (from Goddard et al. in the 31 March 2005 issue of Nature): Budding yeast missing two genes essential for meiosis
adapt less rapidly to growth under harsh conditions than an otherwise identical strain that can undergo genetic recombination.
Under good conditions, both strains grow equally well.
Evidence (from Rice and Chippindale in the 19 October 2001 issue of Science):
Using experimental Drosophila populations, they found that a beneficial mutation introduced into chromosomes that can
recombine did over time increase in frequency more rapidly than the same mutation introduced into chromosomes that could not
recombine.

15.7B.3 https://bio.libretexts.org/@go/page/5497
So sex provides a mechanism for testing new combinations of alleles for their possible usefulness to the phenotype:
deleterious alleles weeded out by natural selection
useful ones retained by natural selection
Some organisms may still gain the benefits of genetic recombination while avoiding sex. Many mycorrhizal fungi use asexual
reproduction only. However, at least two species have been shown to have multiple — similar — copies of the same gene; that is,
are polyploid. Perhaps recombination between these (during mitosis?) enables these organisms to avoid the hazards of
accumulating deleterious mutations. (See the paper by Pawlowska and Taylor in the 19 Feb 2004 issue of Nature.) But there are
many examples of populations that thrive without sex, at least while they live in a stable environment.

Red Queen hypothesisnment

As we have seen (above), populations without sex are genetically static. They may be well-adapted to a given environment, but will
be handicapped in evolving in response to changes in the environment. One of the most potent environmental forces acting on a
species environment is its parasites. The speed with which parasites like bacteria and viruses can change their virulence may
provide the strongest need for their hosts to have the ability to make new gene combinations. So sex may be virtually universal
because of the never-ending need to keep up with changes in parasites.
Evidence:
Some parasites interfere with sexual reproduction in their host:
Wolbachia-induced parthenogenesis discussed above is an example.
Several types of fungi block wind pollination of their grass hosts forcing them to inbreed with its resulting genetic
uniformity.
There is some evidence that genetically uniform populations are at increased risk of devastating epidemics and population
crashes.
Flour beetles (Tribolium castaneum) parasitized by the microsporidium Nosema whitei increase the rate of recombination
during meiosis.
Drosophila females parasitized by bacteria produce more recombinant offspring than non-infected mothers do.
The idea that a constantly-changing environment, especially with respect to parasites, drives evolution is often called the Red
Queen hypothesis. It comes from Lewis Carroll's book Through the Looking Glass, where the Red Queen says "Now here, you see,
it takes all the running you can do to keep in the same place".
The possibilities outlined above are not mutually exclusive and a recent study [see Morran, L. T., et al., in Nature, 462:350, 19
November 2009] suggests that both forces are at work in favoring sexual reproduction over its alternatives.
The organism for testing these theories was Caenorhabditis elegans. While C. elegans does not reproduce asexually, most worms
are hermaphrodites and usually reproduce by self-fertilization with each individual fertilizing its own eggs. This quickly results in
its genes becoming homozygous and thus fully-exposed to natural selection just as they are in asexually-reproducing species.
Hermaphrodites have two X chromosomes and self-fertilization ("selfing") usually produces more of the same; that is,
hermaphrodites produce more hermaphrodites. However, an occasional nondisjunction generates an embryo with a single X
chromosome and this develops into a male. These males can mate with hermaphrodites (their sperm is preferred over the
hermaphrodites own) and, in fact, such "outcrossing" produces a larger number of offspring. It also produces 50% hermaphrodites
and 50% males.
Testing the role of outcrossing vs. self-fertilization in maintaining fitness in the face of an increased mutation rate
These workers developed six strains of worms:
two that could reproduce only by selfing
two that could reproduce only by crossing a male with an hermaphrodite ("outcrossing")
"wild-type" worms
All the strains were exposed to a chemical mutagen that increased the spontaneous mutation rate some fourfold.
The results: After 50 generations, the
the strains of worms that could reproduce only by selfing suffered a serious decline in fitness
the strains of worms that could reproduce only by outcrossing suffered no decline

15.7B.4 https://bio.libretexts.org/@go/page/5497
 the wild-type worms with intermediate levels of outcrossing (20–30%) suffered only moderate declines in fitness
Fitness was measured by placing the worms in a petri dish with a barrier that they had to cross to reach their food (E. coli).
The conclusion: the genetic recombination provided by outcrossing protected the worms from loss of fitness even in the face of an
increase in mutation rate.
Testing the role of outcrossing vs. self-fertilization in the speed of adaptation to a changed environment
For these tests, one of each category of mating types was exposed over 40 generations to a pathogenic bacterium (Serratia
marcescens) that killed most worms when eaten by them.
The results: After 40 generations,
the strain of worms that could reproduce only by selfing were just as susceptible to the pathogen as they were at the start while
the strain of worms that could reproduce only by outcrossing had evolved a high degree of resistance to the pathogen
the wild-type worms only developed a modest increase in their resistance to the bacteria.
Since these studies were reported, the same team has expanded their experiments to examine the effects of evolution in the
pathogen (Serratia marcescens), that is, to look for evidence of coevolution of host and parasite. (Reported by Morran, L. T., et al.,
in Science, 333: 216, 8 July 2011.)
Over 30 generations of worms, they harvested and tested the bacteria recovered from the bodies of worms that had died within 24
hours of infection. They found that:
Worms that can maintain genetic variability by outcrossing suffered substantially lower mortality from the coevolved parasite
that did worms from the starting population (kept frozen until used).
Worms that could only reproduce by selfing became so susceptible to the evolving strain of Serratia marcescens that they died
out within 20 generations.
Curiously, the selection pressure of the increasing virulence of Serratia marcescens caused wild-type worms to increase their
rate of outcrossing from the normal 20–30% to over 80%. So one response to the pressure of this coevolving parasite was to
promote sex in its host.

 Reproduction in Rotifers

Rotifers are microscopic invertebrates. They are assigned a phylum of their own (not discussed elsewhere in these pages). The
phylum includes:
a class of ~1,500 species called monogonont rotifers (they have only a single gonad). The monogonont rotifers can choose
either asexual or sexual reproduction as circumstances warrant.
a class of ~350 species called bdelloid rotifers. The bdelloid rotifers are limited to asexual reproduction only. Even after
years of study, neither males nor haploid eggs have ever been found in any members of this group. It looks as though they
gave up sexual reproduction millions of years ago.

A bdelloid rotifer. (CC BY-SA 3.0; Bob Blaylock)

Laboratory studies show that monogonont rotifers favor asexual reproduction when they are living in a stable environment but
shift to more sexual reproduction when placed in a varied or unfavorable environment. As they adapt to the new environment,
they gradually switch back to asexual reproduction.

15.7B.5 https://bio.libretexts.org/@go/page/5497
 But how have the bdelloid rotifers that never engage in sexual reproduction managed to survive? How have they avoided the
demands of the Red Queen; that is, avoided extinction at the hands of parasites?
One study (Wilson, C. G. and Sherman, P. W., Science, 327:574, 29 January 2010) reveals a mechanism. These tiny animals
can be completely desiccated (dried out) and remain in suspended animation for years. In the desiccated state, they can be
blown vast distances (some species are worldwide in their distribution). Once deposited in a moist environment (a few drops of
water are sufficient), they resume an active life. Wilson and Sherman have shown that the desiccation that is harmless to the
rotifers is lethal to their fungal parasite. So once dried, they are not only cured of their parasite, but can then be blown to a spot
where they can resume an active life with no parasites present.
Another way in which these rotifers can avoid the evolutionary dead-end expected of asexually-reproducing organisms has
been revealed by DNA sequencing of their genome. It turns out that they can purge their genome of deleterious alleles by gene
conversion (during mitosis).
In any case despite its disadvantages sexual reproduction is here to stay
reducing the effect of harmful mutations
increasing the speed with which populations can adapt to changes in their environment

Contibutors
John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.
\

This page titled 15.7B: Asexual Reproduction in Animals is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

15.7B.6 https://bio.libretexts.org/@go/page/5497
15.7C: Birth Control
Mechanical and/or Chemical Barriers
Male Condom
a sheath of thin, flexible material (e.g., latex) worn over the penis
effective if used carefully
also protects against sexually-transmitted disease (STD) agents such as
HIV, the cause of AIDs
herpes virus
human papilloma virus (HPV)
chlamydiae
Neisseria gonorrhoeae, the cause of gonorrhea

Female Condom
a thin-walled pouch inserted into the vagina
protects against sexually-transmitted diseases (STDs)
less effective than the male condom

Diaphragm
rubber dome placed at the upper end of the vagina
may be used along with spermicides

Cervical Cap
impermeable cap fitted over the cervix
best used with spermicides

Spermicides
chemicals, such as nonoxynol 9, that inactivate sperm. Inserted into the vagina — often incorporated in a sponge — prior to
intercourse.
not very effective if used alone

Hormonal Contraception
Oral Contraceptives - the "Pill"
Many formulations combining varying amounts of a synthetic estrogen and a synthetic progestin (progesterone-like steroid)
taken for 3 weeks, then stopped to allow menstruation
most widely-used reversible method

Skin ("Transdermal") Patch

The Ortho Evra® patch releases an estrogen and a progestin through the skin.
A fresh patch is applied each week for 3 weeks, and then a week without allows menstruation.
The failure rate is about 9%.

Vaginal Ring
a small plastic ring inserted into the vagina
NuvaRing® releases both an estrogen and a progestin.
It is left in place for 3 weeks and then removed for a week to allow menstruation.
The failure rate is about 9%.

Injectable Contraceptive
An injection containing a synthetic progestin (depot medroxyprogesterone acetate or "DMPA")(Depo-Provera®)
One injection given every three months inhibits the release of GnRH, thus inhibiting the synthesis of FSH and LH and blocking
ovulation.

15.7C.1 https://bio.libretexts.org/@go/page/5498
 One of the most reliable methods of birth control.

Contraceptive Implant
Implanon® and Nexplanon®, each a tiny (40 x 2 mm) flexible plastic rod that releases a synthetic progestin is inserted under
the skin (requiring a local anesthetic).
Prevents pregnancy for up to 3 years.
If pregnancy is desired sooner, is easily removed (again requiring a small incision and a local anesthetic) and normal fertility
quickly returns.
Although used by only ~1% of U.S. women, implants are among the most effective of the birth control methods.

"Morning After" Pill

The most popular formulation in the U.S., called Plan B One-Step®, contains a high dose of a progestin. If taken within 72 hours
after unprotected intercourse, the drug interferes with ovulation and, if ovulation has occurred, with fertilization.
If so many days have elapsed that implantation has occurred, RU-486 may be used. RU-486 is a synthetic steroid related to
progesterone. Unlike the progestins discussed above, that mimic the action of progesterone, RU-486 blocks the action of
progesterone. (Synthetic molecules that mimic the action of a natural molecule are called agonists; those that oppose it are
antagonists.) RU-486 (also known as mifepristone) is a progesterone antagonist. It binds to the progesterone receptor, and in so
doing prevents progesterone itself from occupying its receptor. Thus the gene transcription normally turned on by progesterone is
blocked, and the proteins necessary to begin and maintain pregnancy are not synthesized. Because RU-486 is used after
implantation, it is causing an early abortion and thus has been subjected to controversy.

Intrauterine Devices (IUD)

The intrauterine device (IUD) is a device, usually T-shaped, inserted into the uterus by a physician.
Two types available in the U.S.:
ParaGard®, which is coated with copper wire and can be left in place for 10 years;
Mirena®, which releases a progestin and can be left in place for up to 5 years.
Although used by only 8.5% of U.S. women, IUDs are among the most effective of the birth control methods. Only about 1
woman in a thousand becomes pregnant during her first year of using Mirena®.

Natural Family Planning - Rhythm Methods

An egg must be fertilized on the day of ovulation.
Sperm can live in the female reproductive tract for up to 6 days.
So copulation that takes place more than 5 days before or a day after ovulation is unlikely to lead to pregnancy.
Abstinence during this period is called natural family planning or the rhythm method.
Its success (which is low) depends upon being able to determine accurately just when ovulation occurs.
Highly-motivated women can do this by
monitoring their body temperature (which rises slightly at ovulation)
the amount and consistency of the mucus secreted by their uterus, and more recently
measuring the concentration of estrogen and/or progesterone in the urine (which mirrors the level in the blood).
It is favored by those who do not currently want a baby, but do not wish to use contraceptive devices (about 1% of U.S.
couples).

Abortion
the deliberate removal of the embryo or fetus before it is ready for birth
Done
mechanically
using a suction device (during the first 3 months of pregnancy)
using surgery (later in pregnancy)
or
chemically (using RU-486 and prostaglandins) during the first 7 weeks of pregnancy
All methods of birth control have been the subject of controversy (except for natural family planning).

15.7C.2 https://bio.libretexts.org/@go/page/5498
 In general, the controversy over a given method is proportional to the lateness of the stage of the reproductive process.
So not surprisingly abortion is a particularly controversial procedure especially when it is induced in the later stages of
pregnancy.
Nevertheless, worldwide some 46 million pregnancies are terminated each year by induced abortion.

Sterilization
Roughly one-third of U.S. couples still in their reproductive years have chosen for one or the other to be sterilized.

Tubal Ligation

Figure 15.7.3.1 Tubal ligation

Both fallopian tubes (oviducts) are cut and tied so that no egg can be fertilized.
Requires incision(s) and so must be done under anesthesia.

Vasectomy
Each vas deferens is cut near the top of the scrotum.
Can be done in the doctor's office, with a local anesthetic, in 30-40 minutes.
Testosterone secretion by the testes is not inhibited.
Does not stop the production of the various glandular secretions that make up the bulk of the semen.
Copulation and ejaculation proceed normally.
Sometimes the operation can be reversed, but don't count on it.

Quinacrine Sterilization (QS)

Pellets of the antimalarial drug quinicrine are placed (by a physician) in the uterus
Done twice, a month apart.
Causes scarring of the fallopian tubes
Clinical trials are in progress in the U.S.

Summary
Popularity (% using the method) and relative effectiveness of several methods of birth control among U. S. women using contraceptives. The
pregnancy rate is the number of pregnancies per 100 women in the first year of using the method.

Method Popularity Pregnancy Rate

Natural family planning (rhythm) 1% 25

Male condom 16% 17

Oral contraceptives ("the pill") 28% 0.3–8.7*

Intrauterine devices (IUD) 8.5% 0.1–1.0*

Implants, e.g., Implanon® ~1% 0.05–1.0*

DMPA injections ~3.5% 6.7

Male + Female Sterilization 37% <<1%

None 85

* The lower value is found under ideal conditions; i.e., among highly-motivated women receiving good medical care.

15.7C.3 https://bio.libretexts.org/@go/page/5498
The bottom line: The failure rate of the pill, patch, and vaginal ring, as they are commonly used, is 20 times that in women using an
IUD, or implant.

Future Prospects
Not too bright because pharmaceutical houses are reluctant to invest the huge amounts of money and time needed to develop
products that expose them to controversy, put them at risk of lawsuits and whose largest market is in countries too poor to afford
them.
Research on possible male birth control pills is going on. However, it is not yet easy to see how spermatogenesis can be blocked
without causing undesirable side-effects.
Some research is proceeding on contraceptive vaccines; that is, using the immune system to block one or another step in the
process (e.g. fertilization). Examples: vaccines to raise antibodies
against gonadotropin-releasing hormone, GnRH (for males)
against human chorionic gonadotropin, HCG (for females)
to immobilize sperm (also for females)
But, what risks such antibodies might present is not at all clear.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 15.7C: Birth Control is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.7C.4 https://bio.libretexts.org/@go/page/5498
15.7D: Prenatal Screening
Many tests are now available to detect genetic diseases such as sickle cell disease, cystic fibrosis and phenylketonuria (PKU). Most
of these tests can not only be performed on cells removed from adults but also on cells removed from the fetus and even from a
pre-implantation embryo.

Amniocentesis
During its development, the fetus sheds cells into the amniotic fluid. After 14–22 weeks of pregnancy, a small volume of this fluid
can be removed (using a needle inserted through the abdominal wall).

Figure 15.7.4.1 Ultrasound prior to amniocentesis

Using ultrasound to locate the position of the placenta prior to amniocentesis. These sonograms are made by recording the echoes
received from structures within the abdomen. A, amniotic cavity; B, urinary bladder; F, part of the fetus; P, placenta. Both
longitudinal (left) and transverse (right) scans are needed for accurate localization of the placenta. (Courtesy of the Downstate
Medical Center of the State University of New York.)
Separating the cells and culturing them enables the clinician to look for
chromosome abnormalities (e.g., the three number 21 chromosomes of Down syndrome)
certain enzymatic defects (e.g., an inability to metabolize galactose, hence milk)
the sex of the fetus
Over 100 genetic abnormalities can be diagnosed by amniocentesis and the pregnancy deliberately ended if the parents wish it.

Chorionic Villus Sampling (CVS)

This is an alternate method of prenatal diagnosis. A small amount of placental tissue is sucked out by a tube inserted through the
abdominal wall or through the vagina (the latter avoiding the need for an incision). For some tests the fetal cells can be examined
immediately without the need to culture them. Another advantage of CVS is that it can be performed earlier in pregnancy (after
only 10–12 weeks) than amniocentesis. If an abortion is to be performed, it is a simpler process early in pregnancy.

Non-Invasive Prenatal Genetic Testing (NIPT)

Although the blood vessels of the placenta are in close contact with the mother's blood vessels in the uterus, intermingling of their
blood does not normally occur. However some of cells of the fetus do manage to get into the mother's circulation where they may

15.7D.1 https://bio.libretexts.org/@go/page/5499
represent 1 in a million of her white blood cells (so only some 2–6 cells per ml of blood). Fragments of fetal DNA (~ 300 bp long)
from apoptotic cells of the placenta are also found in the mother's plasma as early as 5 weeks after implantation. This raises the
possibility of using genetic tests (e.g., PCR) to identify mutations or chromosomal abnormalities in the fetus using a small (~10 ml)
sample of blood drawn from the mother.
Two home blood test kits for determining the sex of the fetus are already on the market. The collected drops of blood are sent to a
laboratory to determine whether any Y-chromosome-specific DNA (e.g., SRY) is present. Tests of fetal DNA for Down syndrome
(trisomy 21), as well as for trisomy 13 and 18, have both higher sensitivity (false negatives <0.1%) and specificity (false positives
<0.2%) than amniocentesis and CVS.
In several European countries, Rh-negative mothers can now have their blood screened for the presence of an Rh-positive fetus.
The time will surely come when such NIPT screening will become available for many genetic disorders. The procedure is also
called non-invasive prenatal diagnosis - NIPD.
The level of fetal DNA in the mother's blood rises to a peak at the time of birth and some evidence suggests that this rise may be a
trigger to start the birth process.

Preimplantation Genetic Diagnosis (PGD)

Genetic Analysis of Blastomeres
One of the remarkable facts about mammalian development is that all the cells in the early (e.g., 8-cell) embryo are not needed to
produce a healthy fetus (which is why a single fertilized egg can on occasions produce identical twins, triplets, etc.). So couples
using in vitro fertilization (IVF) also can take advantage of genetic screening. While the embryo is in culture, one or two cells can
safely be removed and tested for their genotype. For example:
The sex of the embryo can be determined with a probe for Y-specific DNA. This permits prospective mothers carrying a severe
X-linked trait like hemophilia A to choose a female rather than a male embryo for attempted implantation.
Fluorescent probes specific for the DNA of particular chromosomes can detect (by FISH) if there is an abnormal number
(aneuploidy) such as the three #21 chromosomes of Down syndrome.
In fact the entire karyotype of the embryo can be determined. Random fragments of DNA prepared by the polymerase chain
reaction (PCR) of all the DNA of a cell from the embryo can be
given a fluorescent label
applied to the metaphase chromosomes of a standard reference cell that has a normal karyotype along with
DNA fragments from the reference cell labelled with a different color.
Comparing the intensity of the two colors from each chromosome shows whether the embryo has the normal amount of DNA
for that chromosome or is aneuploid containing either:
too much (e.g. 3 copies of #21 — trisomy)
too little (only a single copy of #14 — monosomy)

Genetic Analysis of Polar Bodies

As meiosis I is completed, one set of duplicated chromosomes (dyads) is extruded into the first polar body. The DNA of the polar
body can be amplified by the polymerase chain reaction (PCR) and tested.

Figure 15.7.4.2 Polar body screening

If the mother is heterozygous for a trait, and no crossover has occurred, and the polar body contains the mutant alleles (see figure),
the egg can be safely fertilized. (For simplicity, the figure shows only the pair of homologues carrying the locus of concern.)
However, if crossing over has occurred, the first polar body would contain one mutant and one healthy allele. In that case, there is a
50:50 chance that, after fertilization, the other copy of the mutant allele will end up in the egg (instead of in the second polar body).
So the second polar body should also be tested to see if it also contains the mutant allele. Only if it does can the egg be safely used.

15.7D.2 https://bio.libretexts.org/@go/page/5499
Contributors and Attributions
John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 15.7D: Prenatal Screening is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.7D.3 https://bio.libretexts.org/@go/page/5499
15.7E: Extraembryonic Membranes and the Physiology of the Placenta

Figure 15.7.5.1 Amniotic egg

The embryos of reptiles, birds, and mammals produce 4 extraembryonic membranes - amnion, yolk sac, chorion and allantois. In
birds and most reptiles, the embryo with its extraembryonic membranes develops within a shelled egg.
The amnion protects the embryo in a sac filled with amniotic fluid.
The yolk sac contains yolk — the sole source of food until hatching. Yolk is a mixture of proteins and lipoproteins.
The chorion lines the inner surface of the shell (which is permeable to gases) and participates in the exchange of O2 and CO2
between the embryo and the outside air.
The allantois stores metabolic wastes (chiefly uric acid) of the embryo and, as it grows larger, also participates in gas exchange.
With these four membranes, the developing embryo is able to carry on essential metabolism while sealed within the egg.
Surrounded by amniotic fluid, the embryo is kept as moist as a fish embryo in a pond. Although (most) mammals do not make a
shelled egg, they do also enclose their embryo in an amnion. For this reason, the reptiles, birds, and mammals are collectively
referred to as the amniota.

Amniotic Egg groups in Mammals

Mammals fall into three groups that differ in the way they use the amniotic egg.
These primitive mammals produce a shelled egg like their reptilian ancestors. Only four species exist today: three species of
spiny anteater (echidna) and the duckbill platypus.
Marsupials

Figure 15.7.5.2 Newborn baby opossums courtesy of Dr. Carl G. Hartman

Marsupials do not produce a shelled egg. The egg, which is poorly supplied with yolk, is retained for a time within the
reproductive tract of the mother. The embryo penetrates the wall of the uterus. The yolk sac provides a rudimentary
connection to the mother's blood supply from which it receives food, oxygen, and other essentials. However, this interface
between the tissues of the uterus and the extraembryonic membranes never becomes elaborately developed, and the young
are born in a very immature state.
The photo shows 18 newborn baby opossums fitting easily into a teaspoon. Despite their tiny size, they are able to crawl
into a pouch on the mother's abdomen, attach themselves to nipples, and drink milk from her mammary glands. Marsupials
are still abundant in Australia, but only the opossum is found in North America.
Placental mammals
In placental mammals, the extraembryonic membranes form a placenta and umbilical cord, which connect the embryo to the
mother's uterus in a more elaborate and efficient way. The blood supply of the developing fetus is continuous with that of the
placenta. The placenta extracts food and oxygen from the uterus. Carbon dioxide and other wastes (e.g., urea) are transferred to
the mother for disposal by her excretory organs.
Humans are placental mammals.

15.7E.1 https://bio.libretexts.org/@go/page/5500
This page titled 15.7E: Extraembryonic Membranes and the Physiology of the Placenta is shared under a CC BY 3.0 license and was authored,
remixed, and/or curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed
edit history is available upon request.

15.7E.2 https://bio.libretexts.org/@go/page/5500
15.7F: Genetic Mosaics
A genetic mosaic is a creature whose body is built of a mixture of cells of two or more different genotypes. In mammals they arise
by several different mechanisms:
The fusion of two different zygotes, or early embryos, into one. (The reverse of the process that produces identical twins!) The
resulting animal is called a chimera (after the monster in Greek mythology with a lion's head, goat's body, and serpent's tail).
The tetraparental mouse is a chimera formed this way. But on rare occasions, the same process can occur spontaneously in
humans (especially those using in vitro fertilization).
The sharing of blood supplies by separate embryos. This occurs with the occasional fraternal cattle twins and also — less often
— with human fraternal twins who have shared the same placenta. Blood stem cells of each twin seed the bone marrow of the
other. Only their blood cells are mosaic.
During early development, errors during mitosis can produce stem cells that go on to populate a tissue or organ with, for
example, a chromosomal aberration (e.g., aneuploid).
Example: Occasionally a baby is born with blood cells that have three copies of chromosome 21 (the same set responsible for
Down syndrome). This can produce a leukemia-like illness that, fortunately, often disappears as that cell population declines.
All female mammals are mosaic for the genes on the X chromosome because of the random inactivation of one or the other X
chromosome in all their somatic cells.
Anyone unlucky enough to have a cancer is a genetic mosaic because all cancers are made up of the descendants of cells
carrying a suite of mutations not found in normal cells.
Recent advances have enabled the coding portions of the genome of single cells to be sequenced. Early results indicate than
even normal cells in an adult have accumulated a suite of somatic mutations that differs from cell to cell. So all of us are genetic
mosaics! However, the rate of somatic mutations in these normal cells is only a fourth of that in cancer cells.

The Tetraparental Mouse

As the name suggests, tetraparental mice have four parents: two fathers and two mothers (not including the foster mother that gives
birth to them!). This is how they are made:
Early embryos at the 8-cell stage are removed from two different pregnant mice and placed in tissue culture medium.
Two different embryos are gently pushed together and, often, will fuse into a single embryo.
After a period of further growth in culture, the fused embryo is implanted in a foster mother (whose uterus has been prepared
for implantation by mating her with a vasectomized male).
The mouse that is born is a chimera, all (usually) of whose organs are made of some cells derived from one pair of parents and
some cells derived from the other pair.

Figure 15.7.6.1 Tetraparental mouse courtesy of the late Dr. Thomas G. Wegmann
The photograph shows a tetraparental mouse derived from a pair of inbred mice with black fur and a pair with white fur. Note the
intermingling of black and white patches. This mouse is not the same as an F1 hybrid produced by mating a white mouse with a
black one. In that case, all the cells would be of the same genotype, and the coat would have been a uniform brown.

A Tetragametic Human
A report by Yu, et. al. in the May 16, 2002 issue of The New England Journal of Medicine documents the discovery of a
tetragametic woman; that is a woman derived from four different gametes, not just two. She came to the doctors' attention because
she needed a kidney transplant.

15.7F.1 https://bio.libretexts.org/@go/page/5501
 Figure 15.7.6.3 Chimera formation
Tissue typing, which is done with blood cells, showed her to have inherited the "1" HLA region of her father (who was 1,2) and
the "3" region of her mother (who was 3,4).
She had two brothers,
One who inherited 1 from their father and 3 from their mother
The other who inherited 2 from their father and 3 from their mother.
Her husband typed 5,6
Of her three sons,
One was 1,6 which was to be expected
the other two were both 2,5. The 5 they got from their father, but where did the 2 come from?
The first thought was that she could not have been their mother, but clearly she knew better. (Paternity may sometimes be in
doubt, but not maternity.)
A clue came from typing other tissues. DNA analysis of her skin cells, hair follicles, thyroid cells, bladder cells, and cells
scraped from inside her mouth revealed not only 1 and 3 but also 2 and 4. It is not clear why her bone marrow was an exception
- containing only 1,3 stem cells.
How were these results possible? The most reasonable explanation is that
Her mother had simultaneously ovulated two eggs one containing a chromosome 6 with HLA 3 and the other with HLA 4.
Her father would, of course, have produced equal numbers of 1-containing and 2-containing sperm.
A 1-sperm fertilized the 3-egg.
A 2-sperm fertilized the 4-egg.
Soon thereafter the resulting early embryos fused into a single embryo.
As this embryo developed into a fetus, both types of cells participated in constructing her various organs including her oogonia
(but not, apparently, the blood stem cells in her bone marrow).
Although she was a mosaic for the HLA (and other) genes on chromosome 6, all her cells were XX. So both the father's
successful sperm cells had carried his X chromosome.
However, tetraparental humans have been found that were mosaic for sex chromosomes as well; that is, some of their cells were
XX; the other XY. In some cases this mosaic pattern results in a hermaphrodite - a person with a mixture of male and female
sex organs.

So what are her chances for finding a suitable kidney donor?

The HLA region on chromosome 6 carries a set of genes that encode the major transplantation antigens; that is, the antigens that
trigger graft rejection. Ordinarily, there is only a 1 in 4 chance that two siblings share the same transplantation antigens if both
parents were heterozygous as in her case. But because this woman has all four sets of transplantation antigens, she can accept a
kidney from any one of her brothers as well as her mother (her father was dead) without fear of rejecting it.Laboratory tests
confirmed that she was unable to generate T cells able to react against the cells of either brother or her mother.

15.7F.2 https://bio.libretexts.org/@go/page/5501
 Rat-Mouse Chimeras

Figure 15.7.6.4 Rat-Mouse chimeras

In the 3 September 2010 issue of Cell, Kobayashi et al. report the creation of healthy rat-mouse chimeras:
mice with functioning rat tissues
rats with functioning mouse tissues.
Their procedure:
Generate induced pluripotent stem cells (iPSCs) from embryonic fibroblasts of each species.
Inject:
mouse iPSCs into rat blastocysts
rat iPSCs into mouse blastocysts.
Implant these blastocysts into the uterus of pseudopregnant foster mothers of the same species as the blastocyst.

The Pdx-1−/− Mouse

Pdx-1 encodes a transcription factor that is essential for the development of the pancreas. Transgenic mice lacking a functioning
Pdx-1 gene (Pdx-1−/−) die shortly after birth.
However, Kobayashi et al. found that injecting rat induced pluripotent stem cells (iPSCs) into mouse Pdx-1−/− blastocysts
produced a few viable mouse chimeras complete with a pancreas made up almost exclusively of rat cells. The pancreas was fully
functional producing both exocrine secretions (e.g., pancreatic amylase) and endocrine secretions (e.g., insulin, glucagon, and
somatostatin).

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 15.7F: Genetic Mosaics is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.7F.3 https://bio.libretexts.org/@go/page/5501
15.7G: Human Cloning
In February 1997, a research team at the Roslin Institute in Edinburgh, Scotland, headed by Dr. I. Wilmut, reported (in the 27
February 1997 issue of Nature) that they had succeeded in producing a healthy lamb, named Dolly, from the nucleus of a cell taken
from an adult sheep.

In February 1997, a research team at the Roslin Institute in Edinburgh, Scotland, headed by Dr. I. Wilmut, reported (in the 27
February 1997 issue of Nature) that they had succeeded in producing a healthy lamb, named Dolly, from the nucleus of a cell
taken from an adult sheep.
Why has this achievement created such a stir?
After all, all the cells in an adult are
descended from the fertilized egg
have been produced by mitosis

Figure 15.7.7.1 Gray crescent

Many years earlier, the German embryologist Hans Spemann showed that even after 5 divisions of the fertilized egg, the nuclei
retained the potential to program the complete development of an adult. Using strands of baby hair, he tied loops around fertilized
amphibian (newt) eggs so that they were constricted into two halves with the nucleus confined to one half and a narrow bridge of
cytoplasm connecting the two halves.
He found that:
At first only the half containing the zygote nucleus would divide by mitosis.
Eventually a nucleus would cross into the other half and it, too, would begin dividing.
So long as both halves contained some of a cytoplasmic region called the gray crescent, the second half would then go on to
develop into a second perfectly-formed embryo.

Figure 15.7.7.3 How Dolly was made

Enucleate the eggs produced by Scottish Blackface ewes (female sheep).
Treat the ewes with gonadotropin-releasing hormone (GnRH) to cause them to produce oocytes ready to be fertilized. Like
all mammals, these are arrested at metaphase of the second meiotic division (meiosis II).

15.7G.1 https://bio.libretexts.org/@go/page/5502
 Plunge a micropipette into the egg over the polar body and suck out not only the polar body but the haploid pronucleus
within the egg.
Fuse each enucleated egg with a diploid cell growing in culture.
Cells from the mammary gland of an adult Finn Dorset ewe (they have white faces) are grown in tissue culture.
Five days before use, the nutrient level in the culture is reduced so that the cells stop dividing and enter G0 of the cell cycle.
Donor cells and enucleated recipient cells are placed together in culture.
The cultures are exposed to pulses of electricity to
cause their respective plasma membranes to fuse;
stimulate the resulting cell to begin mitosis (by mimicking the stimulus of fertilization).
Culture the cells until they have grown into a morula (solid mass of cells) or even into a blastocyst (6 days).
Transfer several of these into the uterus of each (of 13, in this case) Scottish Blackface ewes (previously treated with GnRH to
prepare them for implantation.
Wait (with your fingers crossed).
The result: One ewe gave birth (148 days later) to Dolly.
What made Dolly different?
The Wilmut group also used the same technique to produce healthy lambs using cells from lamb embryos (9 days after
fertilization) and lamb fetuses (26 days after fertilization). But in these experiments, there was no way to know the phenotype of
the nuclear donor because it had not yet been born. So, too, the recent cloning of monkeys from embryo nuclei represents simply an
expansion of nature's ability to produce identical twins, etc. whose traits we will not know until they are born and grow up. But the
nucleus that made Dolly came from an adult animal whose phenotypic traits were there to be seen.
How do we know that Dolly is not the progeny of an unsuspected mating of the foster mother?
She has a white face and the foster mother is a Scottish Blackface
DNA fingerprinting reveals bands found in Finn Dorset sheep (the breed that supplied the mammary cells), not those of Scottish
Blackface sheep
What accounts for this remarkable achievement?
Besides years of hard work, we do not know. Perhaps:
Using cells in G0 demethylates inactive genes and makes it possible once again for them to be expressed.
The mammary gland cells were not truly differentiated epithelial cells but primitive stem cells present in the mammary gland.

This page titled 15.7G: Human Cloning is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.7G.2 https://bio.libretexts.org/@go/page/5502
 SECTION OVERVIEW
15.8: Nervous System
Topic hierarchy

15.8A: Neurons

15.8B: Synapses

15.8C: The Human Central Nervous System

15.8D: The Peripheral Nervous System

15.8E: Drugs and the Nervous System

15.8F: Nitric Oxide (NO)

15.8G: Prion Diseases

This page titled 15.8: Nervous System is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.8.1 https://bio.libretexts.org/@go/page/5368
15.8A: Neurons
Excitable cells are those that can be stimulated to create a tiny electric current. Muscle fibers and nerve cells (neurons) are
excitable. The color photo is of a single interneuron in the retina of a rabbit. The cell has been injected with a fluorescent dye to
reveal all its branches. Each of the small knobs at the tips of the branches makes a synapse with another cell in the retina.

Figure 15.8.1.1: Neuron in a rabbit retina courtesy Julie H. Sandell and Richard H. Masland
The electric current in neurons is used to rapidly transmit signals through the animal, while the current in muscles is used to initiate
contraction.

The Resting Potential

All cells (not just excitable cells) have a resting potential: an electrical charge across the plasma membrane, with the interior of the
cell negative with respect to the exterior. The size of the resting potential varies, but in excitable cells runs about −70 millivolts
(mv). The resting potential arises from two activities:
The sodium/potassium ATPase: This pump pushes only two potassium ions (K+) into the cell for every three sodium ions (Na+)
it pumps out of the cell so its activity results in a net loss of positive charges within the cell.
Some potassium channels in the plasma membrane are "leaky" allowing a slow facilitated diffusion of K+ out of the cell (red
arrow).

Figure 15.8.1.2: Resting potential

Ionic Relations in the Cell

The sodium/potassium ATPase produces
a concentration of Na+ outside the cell that is some 10 times greater than that inside the cell
a concentration of K+ inside the cell some 20 times greater than that outside the cell.
The concentrations of chloride ions (Cl−) and calcium ions (Ca2+) are also maintained at greater levels outside the cell EXCEPT
that some intracellular membrane-enclosed compartments may also have high concentrations of Ca2+ (green oval).

Depolarization
Certain external stimuli reduce the charge across the plasma membrane.
mechanical stimuli (e.g., stretching, sound waves) activate mechanically-gated sodium channels
certain neurotransmitters (e.g., acetylcholine) open ligand-gated sodium channels
In each case, the facilitated diffusion of sodium into the cell reduces the resting potential at that spot on the cell creating an
excitatory postsynaptic potential or EPSP. If the potential is reduced to the threshold voltage (about −50 mv in mammalian
neurons), an action potential is generated in the cell.

15.8A.1 https://bio.libretexts.org/@go/page/5646
Action Potentials
If depolarization at a spot on the cell reaches the threshold voltage, the reduced voltage now opens up hundreds of voltage-gated
sodium channels in that portion of the plasma membrane. During the millisecond that the channels remain open, some 7000 Na+
rush into the cell. The sudden complete depolarization of the membrane opens up more of the voltage-gated sodium channels in
adjacent portions of the membrane. In this way, a wave of depolarization sweeps along the cell. This is the action potential. (In
neurons, the action potential is also called the nerve impulse.)

Figure 15.8.1.3 Action potential

The nerve impulse: (Figure 15.8.1.3) In the resting neuron, the interior of the axon membrane is negatively charged with respect to
the exterior (A). As the action potential passes (B), the polarity is reversed. Then the outflow of K+ ions quickly restores normal
polarity (C). At the instant pictured in the diagram, the moving spot, which has traced these changes on the oscilloscope as the
impulse swept past the intracellular electrode, is at position C.

The refractory period

A second stimulus applied to a neuron (or muscle fiber) less than 0.001 second after the first will not trigger another impulse. The
membrane is depolarized (position B), and the neuron is in its refractory period. Not until the −70 mv polarity is reestablished
(position C) will the neuron be ready to fire again. Repolarization is first established by the facilitated diffusion of potassium ions
out of the cell. Only when the neuron is finally rested are the sodium ions that came in at each impulse actively transported back
out of the cell. In some human neurons, the refractory period lasts only 0.001–0.002 second. This means that the neuron can
transmit 500–1000 impulses per second.

The action potential is all-or-none

The strength of the action potential is an intrinsic property of the cell. So long as they can reach the threshold of the cell, strong
stimuli produce no stronger action potentials than weak ones. However, the strength of the stimulus is encoded in the frequency of
the action potentials that it generates.

Myelinated Neurons
The axons of many neurons are encased in a fatty sheath called the myelin sheath. It is the greatly expanded plasma membrane of
an accessory cell called the Schwann cell. Where the sheath of one Schwann cell meets the next, the axon is unprotected. The
voltage-gated sodium channels of myelinated neurons are confined to these spots (called nodes of Ranvier).

Figure 15.8.1.4 Nodes of Ranvier

The inrush of sodium ions at one node creates just enough depolarization to reach the threshold of the next. In this way, the action
potential jumps from one node to the next. This results in much faster propagation of the nerve impulse than is possible in
nonmyelinated neurons.

15.8A.2 https://bio.libretexts.org/@go/page/5646
Multiple sclerosis
This autoimmune disorder results in the gradual destruction of myelin sheaths. Despite this, transmission of nerve impulses
continues for a period as the cell inserts additional voltage-gated sodium channels in portions of the membrane formerly protected
by myelin.

Hyperpolarization
Despite their name, some neurotransmitters inhibit the transmission of nerve impulses. They do this by opening chloride channels
and/or potassium channels in the plasma membrane. In each case, opening of the channels increases the membrane potential by
letting negatively-charged chloride ions (Cl−) IN and positively-charged potassium ions (K+) OUT. This hyperpolarization is
called an inhibitory postsynaptic potential (IPSP) because it counteracts any excitatory signals that may arrive at that neuron.
Although the threshold voltage of the cell is unchanged, it now requires a stronger excitatory stimulus to reach threshold.
Example: Gamma amino butyric acid (GABA). This neurotransmitter is found in the brain and inhibits nerve transmission by
both mechanisms:
binding to GABAA receptors opens chloride channels in the neuron
binding to GABAB receptors opens potassium channels

Integrating Signals

Figure 15.8.1.5 Neuron synapsing and EPSP

A single neuron, especially one in the central nervous system (see color photo at top), may have thousands of other neurons
synapsing on it. Some of these release activating (depolarizing) neurotransmitters; others release inhibitory (hyperpolarizing)
neurotransmitters.
The receiving cell is able to integrate these signals. The diagram shows how this works in a motor neuron.
The EPSP created by a single excitatory synapse is insufficient to reach the threshold of the neuron.
EPSPs created in quick succession, however, add together ("summation"). If they reach threshold, an action potential is
generated.
The EPSPs created by separate excitatory synapses (A + B) can also be added together to reach threshold.

15.8A.3 https://bio.libretexts.org/@go/page/5646
 Activation of inhibitory synapses (C) makes the resting potential of the neuron more negative. The resulting IPSP may also
prevent what would otherwise have been effective EPSPs from triggering an action potential.
Normally, the number of EPSPs needed to reach threshold is greater than shown here.
One might expect that depolarization at one point on the plasma membrane would generate an action potential irrespective of
inhibitory signals elsewhere. However, this is avoided in many neurons by the axon hillock and the axon initial segment (the
AIS). This is the region where the axon emerges from the cell body and is unmyelinated. The portion of the plasma membrane in
this region has few or no synapses of its own and a lower threshold than elsewhere on the cell.
Neurons can establish such distinctive domains on their plasma membrane by anchoring (with actin filaments) transmembrane
proteins as barriers to block the free diffusion of membrane proteins from the cell body to the axon. The action potential is usually
generated in the axon initial segment. Having neither excitatory nor inhibitory synapses of its own, it is able to evaluate the total
picture of EPSPs and IPSPs created in the dendrites and cell body. Only if, over a brief interval, the sum of depolarizing signals
minus the sum of the hyperpolarizing signals exceeds the threshold of the axon initial segment will an action potential be
generated.
This method for the neuron to evaluate a mix of positive and negative signals occurs rapidly. It turns out, however, that neurons
also have a long-term way to integrate a mix of positive and negative signals converging on them. This long-term response
involves changes in gene activity leading to changes in the number and activity of the cell's many synapses.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 15.8A: Neurons is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.8A.4 https://bio.libretexts.org/@go/page/5646
15.8B: Synapses
The coordination of cellular activities in animals is usually considered to involve the endocrine system (where the response is to
hormones: chemicals secreted into the blood by endocrine glands and carried by the blood to the responding cell) and a nervous
system (response to electrical impulses passing from the central nervous system to muscles and glands). However, in fact,
coordination by the nervous system is also chemical. Most neurons achieve their effect by releasing chemicals, the
neurotransmitters, on a receiving cell: another neuron (a "postsynaptic" neuron), a muscle cell and a gland cell. So the real
distinction between nervous and endocrine coordination is that nervous coordination is faster and more localized. Neurotransmitters
are chemicals that act in a paracrine fashion.
The junction between the axon terminals of a neuron and the receiving cell is called a synapse. Synapses at muscle fibers are also
called neuromuscular junctions or myoneural junctions.

Figure 15.8.2.1: Synapses The neuron, synaptic transmission, and neurotransmitters. In R. M. Julien, A primer of drug action: A
comprehensive guide to the actions, uses, and side effects of psychoactive drugs (pp. 60-88). New York, NY, USA: Worth
Publishers. (CC-BY-SA-3.0; Nrets).
Action potentials travel down the axon of the neuron to its end(s), the axon terminal(s).
Each axon terminal is swollen forming a synaptic knob.
The synaptic knob is filled with membrane-enclosed vesicles containing a neurotransmitter.
Arrival of an action potential at the synaptic knob opens Ca2+ channels in the plasma membrane.
The influx of Ca2+ triggers the exocytosis of some of the vesicles.
Their neurotransmitter is released into the synaptic cleft.
The neurotransmitter molecules bind to receptors on the postsynaptic membrane.
These receptors are ligand-gated ion channels.

Excitatory synapses
The neurotransmitter at excitatory synapses depolarizes the postsynaptic membrane (of a neuron in this diagram). Example:
acetylcholine (ACh)
Binding of acetylcholine to its receptors on the postsynaptic cell opens up ligand-gated sodium channels.
These allow an influx of Na+ ions, reducing the membrane potential.
This reduced membrane potential is called an excitatory postsynaptic potential or EPSP.
If depolarization of the postsynaptic membrane reaches threshold, an action potential is generated in the postsynaptic cell.

Inhibitory synapses
The neurotransmitter at inhibitory synapses hyperpolarizes the postsynaptic membrane. Example: gamma aminobutyric acid
(GABA) at certain synapses in the brain.
The GABA receptor is a ligand-gated chloride channel. Binding of GABA to the receptors increases the influx of chloride (Cl−)
A
ions into the postsynaptic cell raising its membrane potential and thus inhibiting it. (The neurotransmitter glycine acts in the same
way at synapses in the spinal cord and the base of the brain.) This is a fast response - taking only about 1 millisecond. Binding of
GABA to GABAB receptors activates an internal G protein and a "second messenger" that leads to the opening of nearby
potassium (K+) channels. As you might expect, this is a slower response, taking as long as 1 second.
In both cases, the resulting facilitated diffusion of ions (chloride IN; potassium OUT) increases the membrane potential (to as
much as −80 mv). This increased membrane potential is called an inhibitory postsynaptic potential (IPSP) because it counteracts
any excitatory signals that may arrive at that neuron. A hyperpolarized neuron appears to have an increased threshold. Actually, the

15.8B.1 https://bio.libretexts.org/@go/page/5647
threshold voltage (about −50 mv) has not changed. It is simply a question of whether the depolarization produced by excitatory
synapses on the cell minus the hyperpolarizing effect of inhibitory synapses can reach this value or not.

Neurotransmitters
Acetylcholine (ACh)
Widely used at synapses in the peripheral nervous system. Released at the terminals of
all motor neurons activating skeletal muscle.
all preganglionic neurons of the autonomic nervous system.
the postganglionic neurons of the parasympathetic branch of the autonomic nervous system.
Also mediates transmission at some synapses in the brain. These include synapses involved in the acquisition of short-term
memory. Drugs that enhance ACh levels - acetylcholinesterase inhibitors - are now used in elderly patients with failing memory
(e.g., Alzheimer's patients).
Nicotinic vs. Muscarinic Acetylcholine Receptors

ACh acts on two different types of receptor:

Nicotinic receptors are
found at the neuromuscular junction of skeletal (only) muscles
on the post-ganglionic neurons of the parasympathetic nervous system
on many neurons in the brain (e.g. neurons in the hypothalamus whose activation by nicotine suppresses appetite)
Nicotine is an agonist (hence the name)
Curare is an antagonist (hence its ability to paralyze skeletal muscles)
Muscarinic receptors are
Found at the neuromuscular junctions of cardiac and smooth muscle as well as on glands and on the post-ganglionic neurons
of the sympathetic nervous system.
Muscarine (a toxin produced by certain mushrooms) is an agonist.
Atropine is an antagonist (hence its use in acetylcholinesterase poisoning).

Amino acids
Glutamic acid (Glu); used at excitatory synapses in the central nervous system (CNS). Essential for long term potentiation
(LTP), a form of memory.
Like GABA, Glu acts on two types of CNS synapses:
FAST (~1 msec) with Glu opening ligand-gated Na+ channels;
SLOW (~1 sec) with Glu binding to G-protein-coupled receptors receptors that turn on a "second messenger" cascade of
biochemical changes that open channels allowing Na+ into the cell.
Gamma aminobutyric acid (GABA); used at inhibitory synapses in the CNS.
Glycine (Gly). Also used at inhibitory synapses in the CNS. In fact, both GABA and glycine are released together at some
inhibitory synapses.

Catecholamines
Synthesized from tyrosine (Tyr).
Noradrenaline (also called norepinephrine). Released by postganglionic neurons of the sympathetic branch of the autonomic
nervous system. Also used at certain synapses in the CNS.
Dopamine. Used at certain synapses in the CNS.

Other monoamines
Serotonin (also known as 5-hydroxytryptamine or 5HT). Synthesized from tryptophan (Trp).
Histamine
Both of these neurotransmitters are confined to synapses in the brain. However, serotonin is also secreted from the duodenum,
where it acts in a paracrine manner to stimulate intestinal peristalsis, and as a circulating hormone, where it is taken up by platelets
and also suppresses bone formation.

15.8B.2 https://bio.libretexts.org/@go/page/5647
Peptides
A selection of 9 of the 40 or more peptides that are suspected to serve as neurotransmitters in the brain. The first six also serve as
hormones.
Vasopressin
Oxytocin
Somatostatin
Gonadotropin-releasing hormone (GnRH)
Angiotensin II
Cholecystokinin (CCK)
Substance P
Two enkephalins
Met-enkephalin (Tyr-Gly-Gly-Phe-Met)
Leu-enkephalin (Tyr-Gly-Gly-Phe-Leu)

ATP
ATP - probably along with another neurotransmitter is released at some synapses in the brain.

Synaptic Plasticity
Most neurons release a single neurotransmitter at the synapses at their axon terminals. However, some exceptions have been found.
neurons that release one transmitter at some of their terminals, a different one at others
neurons that switch from one neurotransmitter to a different one when the stimulus reaching them changes. Example:
interneurons in the hypothalamus of the rat that release dopamine when the rats are exposed to short-day photoperiods (which
these nocturnal animals like) but switch to releasing somatostatin when the rats are exposed to long days (which they don't like).

Turning Synapses Off

Once its job is done, the neurotransmitter must be removed from the synaptic cleft to prepare the synapse for the arrival of the next
action potential. Two methods are used:
Reuptake. The neurotransmitter is taken back into the synaptic knob of the presynaptic neuron by active transport. All the
neurotransmitters except acetylcholine use this method.
Acetylcholine is removed from the synapse by enzymatic breakdown into inactive fragments. The enzyme used is
acetylcholinesterase.
Nerve gases used in warfare (e.g., sarin) and the organophosphate insecticides (e.g., parathion) achieve their effects by
inhibiting acetylcholinesterase thus allowing ACh to remain active. Atropine is used as an antidote because it blocks ACh
muscarinic receptors.

Drugs and Synapses

Many drugs that alter mental state achieve at least some of their effects by acting at synapses.

GABA Receptors
The GABAA receptor is a ligand-gated chloride channel. Activation of the receptors increases the influx of chloride (Cl−) ions into
the postsynaptic cell raising its membrane potential and thus inhibiting it. A number of drugs bind to the GABAA receptor. They
bind at sites different from the spot where GABA itself binds, but increase the strength of GABA's binding to its site. Thus they
enhance the inhibitory effect of GABA in the CNS. These drugs include sedatives like phenobarbital and anti-anxiety drugs like
Valium, Librium, Halcion (all members of a group called benzodiazepines). In view of their common action, it is not surprising that
they act additively; taken together these drugs can produce dangerous overdoses. The recreational (and illegal) drug γ-
hydroxybutyrate binds to the GABAB receptor.

Catecholamine synapses
Many antidepressant drugs (the so-called tricyclic antidepressants like amitriptyline ["Elavil"]) interfere with the reuptake of
noradrenaline and serotonin from their synapses and thus enhance their action at the synapse. The popular antidepressant

15.8B.3 https://bio.libretexts.org/@go/page/5647
fluoxetine ("Prozac"), seems to block only the reuptake of serotonin.

Dopamine synapses
One class of dopamine receptor is bound by such drugs as chlorpromazine and haloperidol. Binding of these drugs leads to
increased synthesis of dopamine at the synapse and eases some of the symptoms of schizophrenia.

Synapses blocking pain signals

The two enkephalins are released at synapses on neurons involved in transmitting pain signals back to the brain. The enkephalins
hyperpolarize the postsynaptic membrane thus inhibiting it from transmitting these pain signals. The ability to perceive pain is
vital. However, faced with massive, chronic, intractable pain, it makes sense to have a system that decreases its own sensitivity.
Enkephalin synapses provide this intrinsic pain-suppressing system.
Opiates such as heroin, morphine, codeine, and methadone bind these same receptors. This makes them excellent pain killers.
However, they are also highly addictive.
By binding to enkephalin receptors, they enhance the pain-killing effects of the enkephalins.
A homeostatic reduction in the sensitivity of these synapses compensates for continued exposure to opiates.
This produces tolerance, the need for higher doses to achieve the prior effect.
If use of the drug ceases, the now relatively insensitive synapses respond less well to the soothing effects of the enkephalins,
and the painful symptoms of withdrawal are produced.

Electrical Synapses
Electrical synapses are a rare exception to the general rule that neurons signal other neurons by release of chemical
neurotransmitters. Some properties of electrical synapses:
The two neurons are connected by gap junctions, the space between them being much smaller (~2 nm) than that at chemical
synapses (~20 nm).
In many cases, transmission of action potentials can pass in either direction.
Transmission between neurons is as much as ten times faster than in chemical synapses.
Thus electrical synapses can mediate, for example, the very rapid escape response of crayfish that encounter a threat.
Electrical synapses in the CNS permit groups of interneurons to fire together.
They are found in vertebrates (e.g. in the hippocampus of the brain) as well as in invertebrates like the crayfish.

This page titled 15.8B: Synapses is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.8B.4 https://bio.libretexts.org/@go/page/5647
15.8C: The Human Central Nervous System
The central nervous system is made up of the spinal cord and brain. The spinal cord conducts sensory information from the
peripheral nervous system (both somatic and autonomic) to the brain. It also conducts motor information from the brain to our
various effectors: skeletal muscles, cardiac muscle, smooth muscle, glands, and serves as a minor reflex center. The brain receives
sensory input from the spinal cord as well as from its own nerves (e.g., olfactory and optic nerves) and devotes most of its volume
(and computational power) to processing its various sensory inputs and initiating appropriate and coordinated motor outputs

White Matter vs. Gray Matter

Both the spinal cord and the brain consist of white matter (bundles of axons each coated with a sheath of myelin) and gray matter
(masses of the cell bodies and dendrites each covered with synapses). In the spinal cord, the white matter is at the surface, the gray
matter inside. In the brain of mammals, this pattern is reversed. However, the brains of "lower" vertebrates like fishes and
amphibians have their white matter on the outside of their brain as well as their spinal cord.

The Meninges
Both the spinal cord and brain are covered in three continuous sheets of connective tissue, the meninges. From outside in, these are
thedura mater — pressed against the bony surface of the interior of the vertebrae and the cranium, the arachnoid, nd the pia mater.
The region between the arachnoid and pia mater is filled with cerebrospinal fluid (CSF).

The Interstitial Fluid of the Central Nervous System

The cells of the central nervous system are bathed in a fluid, called cerebrospinal fluid (CSF), that differs from that serving as the
interstitial fluid (ISF) of the cells in the rest of the body. Cerebrospinal fluid leaves the capillaries in the choroid plexus of the brain.
It contains far less protein than "normal" because of the blood-brain barrier, a system of tight junctions between the endothelial
cells of the capillaries. This barrier creates problems in medicine as it prevents many therapeutic drugs from reaching the brain.
CSF flows uninterrupted throughout the central nervous system through the central cerebrospinal canal of the spinal cord and
through an interconnected system of four ventricles in the brain.
CSF returns to the blood through lymphatic vessels draining the brain.In mice, the flow of CSF increases by 60% when they are
asleep. Perhaps one function of sleep is to provide the brain a way of removing potentially toxic metabolites accumulated during
waking hours.

The Spinal Cord

31 pairs of spinal nerves arise along the spinal cord. These are "mixed" nerves because each contain both sensory and motor
axons. However, within the spinal column, all the sensory axons pass into the dorsal root ganglion where their cell bodies are
located and then on into the spinal cord itself. All the motor axons pass into the ventral roots before uniting with the sensory
axons to form the mixed nerves.

Figure 15.8.3.1 Spinal cord

The spinal cord carries out two main functions:
It connects a large part of the peripheral nervous system to the brain. Information (nerve impulses) reaching the spinal cord
through sensory neurons are transmitted up into the brain. Signals arising in the motor areas of the brain travel back down the
cord and leave in the motor neurons.
The spinal cord also acts as a minor coordinating center responsible for some simple reflexes like the withdrawal reflex.

15.8C.1 https://bio.libretexts.org/@go/page/5648
The interneurons carrying impulses to and from specific receptors and effectors are grouped together in spinal tracts.

Crossing Over of the Spinal Tracts

Impulses reaching the spinal cord from the left side of the body eventually pass over to tracts running up to the right side of the
brain and vice versa. In some cases this crossing over occurs as soon as the impulses enter the cord. In other cases, it does not take
place until the tracts enter the brain itself.

The Brain

Figure 15.8.3.2 Brain of vertebrates

The brain of all vertebrates develops from three swellings at the anterior end of the neural tube of the embryo. From front to back
these develop into the
forebrain (also known as the prosencephalon — shown in light color)
midbrain (mesencephalon — gray)
hindbrain (rhombencephalon — dark color) The human brain is shown from behind so that the cerebellum can be seen.
The human brain receives nerve impulses from the spinal cord and 12 pairs of cranial nerves:
Some of the cranial nerves are "mixed", containing both sensory and motor axons
Some, e.g., the optic and olfactory nerves (numbers I and II) contain sensory axons only
Some, e.g. number III that controls eyeball muscles, contain motor axons only.

The Hindbrain

Figure 15.8.3.3 The Hindbrain

The main structures of the hindbrain (rhombencephalon) are the medulla oblongata, pons and cerebellum.

Medulla oblongata
The medulla looks like a swollen tip to the spinal cord. Nerve impulses arising here rhythmically stimulate the intercostal muscles
and diaphragm thus making breathing possible. It also regulate heartbeats and regulate the diameter of arterioles thus adjusting
blood flow. The neurons controlling breathing have mu (µ) receptors, the receptors to which opiates, like heroin, bind. This
accounts for the suppressive effect of opiates on breathing. Destruction of the medulla causes instant death.

15.8C.2 https://bio.libretexts.org/@go/page/5648
Pons
The pons seems to serve as a relay station carrying signals from various parts of the cerebral cortex to the cerebellum. Nerve
impulses coming from the eyes, ears and touch receptors are sent on the cerebellum. The pons also participates in the reflexes that
regulate breathing.
The reticular formation is a region running through the middle of the hindbrain (and on into the midbrain). It receives sensory
input (e.g., sound) from higher in the brain and passes these back up to the thalamus. The reticular formation is involved in sleep,
arousal (and vomiting).

Cerebellum
The cerebellum consists of two deeply-convoluted hemispheres. Although it represents only 10% of the weight of the brain, it
contains as many neurons as all the rest of the brain combined. Its most clearly-understood function is to coordinate body
movements. People with damage to their cerebellum are able to perceive the world as before and to contract their muscles, but their
motions are jerky and uncoordinated. So the cerebellum appears to be a center for learning motor skills (implicit memory).
Laboratory studies have demonstrated both long-term potentiation (LTP) and long-term depression (LTD) in the cerebellum.

The Midbrain
The midbrain (mesencephalon) occupies only a small region in humans (it is relatively much larger in "lower" vertebrates). We
shall look at only three features:
the reticular formation: collects input from higher brain centers and passes it on to motor neurons.
the substantia nigra: helps "smooth" out body movements; damage to the substantia nigra causes Parkinson's disease.
the ventral tegmental area (VTA): packed with dopamine-releasing neurons that are activated by nicotinic acetylcholine
receptors and whose projections synapse deep within the forebrain.The VTA seems to be involved in pleasure: nicotine,
amphetamines and cocaine bind to and activate its dopamine-releasing neurons and this may account at least in part for their
addictive qualities.
The midbrain along with the medulla and pons are often referred to as the "brainstem".

The Forebrain
The human forebrain (prosencephalon) is made up of a pair of large cerebral hemispheres, called the telencephalon. Because of
crossing over of the spinal tracts, the left hemisphere of the forebrain deals with the right side of the body and vice versa. A group
of structures located deep within the cerebrum make up the diencephalon.

Diencephalon
We shall consider four of its structures:
Thalamus.
All sensory input (except for olfaction) passes through these paired structures on the way up to the somatic-sensory regions
of the cerebral cortex and then returns to them from there.
Signals from the cerebellum pass through them on the way to the motor areas of the cerebral cortex.
Lateral geniculate nucleus (LGN). All signals entering the brain from each optic nerve enter a LGN and undergo some
processing before moving on the various visual areas of the cerebral cortex.
Hypothalamus.
The seat of the autonomic nervous system. Damage to the hypothalamus is quickly fatal as the normal homeostasis of body
temperature, blood chemistry, etc. goes out of control.
The source of 8 hormones, two of which pass into the posterior lobe of the pituitary gland.
Posterior lobe of the pituitary.
Receives vasopressin and oxytocin from the hypothalamus and releases them into the blood.

The Cerebral Hemispheres

15.8C.3 https://bio.libretexts.org/@go/page/5648
 Figure 15.8.3.4 The Cerebral hemisphere
Each hemisphere of the cerebrum is subdivided into four lobes visible from the outside:
frontal
parietal
occipital
temporal
Hidden beneath these regions of each cerebral cortex is
An olfactory bulb; they receive input from the olfactory epithelia.
A striatum; they receive input from the frontal lobes and also from the limbic system (below). At the base of each striatum is a
nucleus accumbens (NA).

Figure 15.8.3.5 Striatum

The pleasurable (and addictive) effects of amphetamines, cocaine, and perhaps other psychoactive drugs seem to depend on
their producing increasing levels of dopamine at the synapses in the nucleus accumbens (as well as the VTA).
a limbic system; they receives input from various association areas in the cerebral cortex and pass signals on to the nucleus
accumbens. Each limbic system is made up of a:
hippocampus. It is essential for the formation of long-term memories.
The amygdala appears to be a center of emotions (e.g., fear). It sends signals to the hypothalamus and medulla which can
activate the flight or fight response of the autonomic nervous system. In rats, at least, the amygdala contains receptors for
vasopressin whose activation increases aggressiveness and other signs of the flight or fight response
oxytocin whose activation lessens the signs of stress
The amygdala receives a rich supply of signals from the olfactory system, and this may account for the powerful effect that
odor has on emotions (and evoking memories).

Mapping the Functions of the Brain

It is estimated that the human brain contains some 86 billion (8.6 x 1010) neurons averaging 10,000 synapses on each; that is,
almost 1015 connections. How to unravel the workings of such a complex system?
Several methods have been useful.

Histology
Microscopic examination with the aid of selective stains has revealed many of the physical connections created by axons in the
brain.

15.8C.4 https://bio.libretexts.org/@go/page/5648
The Electroencephalograph (EEG)
This device measures electrical activity (brain "waves") that can be detected at the surface of the scalp. It can distinguish between,
for example, sleep and excitement. It is also useful in diagnosing brain disorders such as a tendency to epileptic seizures.

Damage to the Brain

Many cases of brain damage from, for example,
strokes (interruption of blood flow to a part of the brain)
tumors in the brain
mechanical damage (e.g., bullet wounds)
have provided important insights into the functions of various parts of the brain.
Example 1:
Battlefield injury to the left temporal lobe of the cerebrum interferes with speech.

 Example 2: Phineas P. Gage

In 1848, an accidental explosion drove a metal bar completely through the frontal lobes of Phineas P. Gage. Not only did he
survive the accident, he never even lost consciousness or any of the clearly-defined functions of the brain. However, over the
ensuing years, he underwent a marked change in personality. Formerly described as a reasonable, sober, conscientious person,
he became — in the words of those observing him — "thoughtless, irresponsible, fitful, obstinate, and profane". In short, his
personality had changed, but his vision, hearing, other sensations, speech, and body coordination were unimpaired. (Similar
personality changes have since been often observed in people with injuries to their prefrontal cortex.)

Figure 15.8.3.6 Gage skull

The photograph (courtesy of the Warren Anatomical Museum, Harvard University Medical School) shows Gage's skull where
the bar entered (left) and exited (right) in the accident (which occurred 12 years before he died of natural causes in 1861).

Stimulating the exposed brain with electrodes

Figure 15.8.3.7 Motor and sensory area

There are no pain receptors on the surface of the brain, and some humans undergoing brain surgery have volunteered to have their
exposed brain stimulated with electrodes during surgery. When not under general anesthesia, they can even report their sensations
to the experimenter. Experiments of this sort have revealed a band of cortex running parallel to and just in front of the fissure of
Rolando that controls the contraction of skeletal muscles. Stimulation of tiny spots within this motor area causes contraction of
the muscles.
The area of motor cortex controlling a body part is not proportional to the size of that part but is proportional to the number of
motor neurons running to it. The more motor neurons that activate a structure, the more precisely it can be controlled. Thus the

15.8C.5 https://bio.libretexts.org/@go/page/5648
areas of the motor cortex controlling the hands and lips are much larger than those controlling the muscles of the torso and legs. A
similar region is located in a parallel band of cortex just behind the fissure of Rolando. This region is concerned with sensation
from the various parts of the body. When spots in this sensory area are stimulated, the patient reports sensations in a specific area
of the body. A map can be made based on these reports. When portions of the occipital lobe are stimulated electrically, the patient
reports light. However, this region is also needed for associations to be made with what is seen. Damage to regions in the occipital
lobe results in the person's being perfectly able to see objects but incapable of recognizing them.
The centers of hearing — and understanding what is heard — are located in the temporal lobes.

CT = X-ray C omputed T omography

This is an imaging technique that uses a series of X-ray exposures taken from different angles. Computer software can integrate
these to produce a three-dimensional picture of the brain (or other body region). CT scanning is routinely used to quickly diagnose
strokes.

PET = P ositron-E mission T omography

This imaging technique requires that the subject be injected with a radioisotope that emits positrons.
Water labeled with oxygen-15 (H215O) is used to measure changes in blood flow (which increases in parts of the brain that are
active). The short half-life of 15O (2 minutes) makes it safe to use.
Deoxyglucose labeled with fluorine-18. The brain has a voracious appetite for glucose (although representing only ~2% of our
body weight, the brain receives ~15% of the blood pumped by the heart and consumes ~20% of the energy produced by cellular
respiration when we are at rest). When supplied with deoxyglucose, the cells are tricked into taking in this related molecule and
phosphorylating it in the first step of glycolysis. But no further processing occurs so it accumulates in the cell. By coupling a
short-lived radioactive isotope like 18F to the deoxyglucose and using a PET scanner, it is possible to visualize active regions of
the brain.
The images in fig. 15.8.3.8 (courtesy of Michael E. Phelps from Science 211:445, 1981) were produced in a PET scanner. The
dark areas are regions of high metabolic activity. Note how the metabolism of the occipital lobes (arrows) increases when visual
stimuli are received.
Similarly, sounds increase the rate of deoxyglucose uptake in the speech areas of the temporal lobe.
The image in fig. 15.8.3.9 on the right (courtesy of Gary H. Duncan from Talbot, J. D., et. al., Science 251: 1355, 1991) shows
activation of the cerebral cortex by a hot probe (which the subjects describe as painful) applied to the forearm.

Figure 15.8.3.9 Cerebral cortex activation

Most cancers consume large amounts of glucose (cellular respiration is less efficient than in normal cells so they must rely more on
the inefficient process of glycolysis). Therefore PET scanning with 18F-fluorodeoxyglucose is commonly used to monitor both the
primary tumor and any metastases.

MRI = M agnetic R esonance I maging

This imaging technique uses powerful magnets to detect magnetic molecules within the body. These can be endogenous molecules
or magnetic substances injected into a vein.

15.8C.6 https://bio.libretexts.org/@go/page/5648
fMRI = Functional Magnetic Resonance Imaging
fMRI exploits the changes in the magnetic properties of hemoglobin as it carries oxygen. Activation of a part of the brain increases
oxygen levels there increasing the ratio of oxyhemoglobin to deoxyhemoglobin.
The probable mechanism:
The increased demand for neurotransmitters must be met by increased production of ATP.
Although this consumes oxygen (needed for cellular respiration),
it also increases the blood flow to the area.
So there is an increase and not a decrease in the oxygen supply to the region, which provides the signal detected by fMRI.

Magnetoencephalography (MEG)
MEG detects the tiny magnetic fields created as individual neurons "fire" within the brain. It can pinpoint the active region with a
millimeter, and can follow the movement of brain activity as it travels from region to region within the brain. MEG is noninvasive
requiring only that the subject's head lie within a helmet containing the magnetic sensors.

This page titled 15.8C: The Human Central Nervous System is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by
John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

15.8C.7 https://bio.libretexts.org/@go/page/5648
15.8D: The Peripheral Nervous System

Figure 15.8.4.1 Nervous system

The nervous system is divided into the peripheral nervous system (PNS) and the central nervous system (CNS).
The PNS consists of
sensory neurons running from stimulus receptors that inform the CNS of the stimuli
motor neurons running from the CNS to the muscles and glands - called effectors - that take action.
The CNS consists of the spinal cord and the brain.
The peripheral nervous system is subdivided into the
sensory-somatic nervous system and the
autonomic nervous system

The Sensory-Somatic Nervous System

The sensory-somatic system consists of 12 pairs of cranial nerves and 31 pairs of spinal nerves.

The Cranial Nerves

Nerves Type Function

I
sensory olfaction (smell)
Olfactory

vision
II
sensory (Contain 38% of all the axons connecting to the
Optic
brain.)

III
motor* eyelid and eyeball muscles
Oculomotor

IV
motor* eyeball muscles
Trochlear

V Sensory: facial and mouth sensation

mixed
Trigeminal Motor: chewing

VI
motor* eyeball movement
Abducens

Sensory: taste
VII
mixed Motor: facial muscles and
Facial
salivary glands

VIII
sensory hearing and balance
Auditory

IX Sensory: taste
mixed
Glossopharyngeal Motor: swallowing

X main nerve of the

mixed
Vagus parasympathetic nervous system (PNS)

XI
motor swallowing; moving head and shoulder
Accessory

15.8D.1 https://bio.libretexts.org/@go/page/5649
 XII
motor* tongue muscles
Hypoglossal

Figure 15.8.4.2 Autonomic nervous system

The autonomic nervous system consists of sensory neurons and motor neurons that run between the central nervous system
(especially the hypothalamus and medulla oblongata) and various internal organs such as the heart, lungs, viscera and the glands
(both exocrine and endocrine). It is responsible for monitoring conditions in the internal environment and bringing about
appropriate changes in them. The contraction of both smooth muscle and cardiac muscle is controlled by motor neurons of the
autonomic system. The actions of the autonomic nervous system are largely involuntary (in contrast to those of the sensory-
somatic system). It also differs from the sensory-somatic system as it is using two groups of motor neurons to stimulate the
effectors instead of one. First, the preganglionic neurons arise in the CNS and run to a ganglion in the body. Here they synapse
with postganglionic neurons, which run to the effector organ (cardiac muscle, smooth muscle, or a gland).
The autonomic nervous system has two subdivisions:
sympathetic nervous system
parasympathetic nervous system.

The Sympathetic Nervous System

Figure 15.8.4.3 Sympathetic nervous system

The preganglionic motor neurons of the sympathetic system (shown in black) arise in the spinal cord. They pass into sympathetic
ganglia which are organized into two chains that run parallel to and on either side of the spinal cord. The preganglionic neuron may
do one of three things in the sympathetic ganglion:
synapse with postganglionic neurons (shown in white) which then reenter the spinal nerve and ultimately pass out to the sweat
glands and the walls of blood vessels near the surface of the body.
pass up or down the sympathetic chain and finally synapse with postganglionic neurons in a higher or lower ganglion

15.8D.2 https://bio.libretexts.org/@go/page/5649
 leave the ganglion by way of a cord leading to special ganglia (e.g. the solar plexus) in the viscera. Here it may synapse with
postganglionic sympathetic neurons running to the smooth muscular walls of the viscera. However, some of these preganglionic
neurons pass right on through this second ganglion and into the adrenal medulla. Here they synapse with the highly-modified
postganglionic cells that make up the secretory portion of the adrenal medulla.
The neurotransmitter of the preganglionic sympathetic neurons is acetylcholine (ACh). It stimulates action potentials in the
postganglionic neurons. The neurotransmitter released by the postganglionic neurons is noradrenaline (also called
norepinephrine). The action of noradrenaline on a particular gland or muscle is excitatory is some cases, inhibitory in others. At
excitatory terminals, ATP may be released along with noradrenaline.
The release of noradrenaline
stimulates heartbeat
raises blood pressure
dilates the pupils
dilates the trachea and bronchi
stimulates glycogenolysis — the conversion of liver glycogen into glucose
shunts blood away from the skin and viscera to the skeletal muscles, brain, and heart
inhibits peristalsis in the gastrointestinal (GI) tract
inhibits contraction of the bladder and rectum
and, at least in rats and mice, increases the number of AMPA receptors in the hippocampus and thus increases long-term
potentiation (LTP).
In short, stimulation of the sympathetic branch of the autonomic nervous system prepares the body for emergencies: for "fight or
flight" (and, perhaps, enhances the memory of the event that triggered the response).
Activation of the sympathetic system is quite general because
a single preganglionic neuron usually synapses with many postganglionic neurons
the release of adrenaline from the adrenal medulla into the blood ensures that all the cells of the body will be exposed to
sympathetic stimulation even if no postganglionic neurons reach them directly.

The Parasympathetic Nervous System

Figure 15.8.4.4 Loewi's stimulation

The Nobel Prize winning physiologist Otto Loewi discovered (in 1920) that the effect of both sympathetic and parasympathetic
stimulation is mediated by released chemicals. He removed the living heart from a frog with its sympathetic and parasympathetic
nerve supply intact. As expected, stimulation of the first speeded up the heart while stimulation of the second slowed it down.
Loewi found that these two responses would occur in a second frog heart supplied with a salt solution taken from the stimulated
heart. Electrical stimulation of the vagus nerve leading to the first heart not only slowed its beat but, a short time later, slowed that
of the second heart also. The substance responsible was later shown to be acetylcholine. During sympathetic stimulation, adrenaline
(in the frog) is released.
Parasympathetic stimulation causes

15.8D.3 https://bio.libretexts.org/@go/page/5649
 slowing down of the heartbeat (as Loewi demonstrated)
lowering of blood pressure
constriction of the pupils
increased blood flow to the skin and viscera
peristalsis of the GI tract
In short, the parasympathetic system returns the body functions to normal after they have been altered by sympathetic stimulation.
In times of danger, the sympathetic system prepares the body for violent activity. The parasympathetic system reverses these
changes when the danger is over. The vagus nerves also help keep inflammation under control. Inflammation stimulates nearby
sensory neurons of the vagus. When these nerve impulses reach the medulla oblongata, they are relayed back along motor fibers to
the inflamed area. Release of acetylcholine suppresses the release of inflammatory cytokines, e.g., tumor necrosis factor (TNF),
from macrophages in the inflamed tissue.
Although the autonomic nervous system is considered to be involuntary, this is not entirely true. A certain amount of conscious
control can be exerted over it as has long been demonstrated by practitioners of Yoga and Zen Buddhism. During their periods of
meditation, these people are clearly able to alter a number of autonomic functions including heart rate and the rate of oxygen
consumption. These changes are not simply a reflection of decreased physical activity because they exceed the amount of change
occurring during sleep or hypnosis.

This page titled 15.8D: The Peripheral Nervous System is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

15.8D.4 https://bio.libretexts.org/@go/page/5649
15.8E: Drugs and the Nervous System
The activity of the nervous system is mediated by many kinds of interneurons releasing one or another neurotransmitter such as
noradrenaline
gamma aminobutyric acid (GABA)
dopamine
glutamate (Glu)
acetylcholine (ACh)
serotonin
Presynaptic neurons synthesize and package their neurotransmitter in vesicles for release (by exocytosis) at the synapse. They
often have "reuptake" transporters that reclaim the transmitter back into the cell when it has done its job. Postsynaptic neurons
display receptors to which the neurotransmitter binds. All of this machinery provides many targets for alteration by exogenous
chemicals; that is, psychoactive chemicals introduced into the body. These drugs fall into several distinct families.

Stimulants
The most widely used stimulants are
caffeine (in coffee, tea, and cola beverages)
nicotine (in cigarettes)
amphetamines
cocaine
All of these drugs mimic the stimulation provided by the sympathetic nervous system.
Nicotine binds to a subset of acetylcholine (ACh) receptors. ACh is a neurotransmitter at synapses early in the pathways of
sympathetic stimulation. Although a weak drug in one sense, nicotine is strongly addictive. The use of e-cigarettes, chewing gum
and skin patches containing nicotine is designed to satisfy the craving for nicotine while avoiding the serious health effects of other
ingredients in cigarette smoke.
Amphetamines and cocaine bind to — thus blocking — transporters used for the reuptake of dopamine (and noradrenaline) into
presynaptic neurons. This causes the level of dopamine to rise in the synapses. High levels of dopamine in an area of the brain
called the nucleus accumbens appear to mediate the pleasurable effects associated with these (as well as other) psychoactive drugs.
Table 1: Some amphetamines
Generic name Trade name

dextroamphetamine sulfate Dexedrine

methylphenidate Ritalin

pemoline Cylert

mixture of 4 amphetamines Adderall

The chief medical uses for amphetamines and amphetamine-like drugs are to help people lose weight (because they suppress
appetite) and to help children with attention deficit/hyperactivity disorder (ADHD) to perform better in school. At first glance, this
second use seems counterproductive. This controversial procedure seems to work by increasing the alertness of the child so that it
can focus its energies more effectively on the tasks in front of it.

Fen-Phen
Fen-Phen refers to a mixture of two amphetamine-like drugs fenfluramine and phentermine that were prescribed for losing
weight. Because of reports of occasional very serious side effects, the mixture is no longer available and fenfluramine has been
removed from the U.S. market.

Cocaine
Cocaine has been used for thousands of years by certain tribes in the Andes of South America. Cocaine and some of its relatives
have legitimate medical uses as local anesthetics (e.g., lidocaine). However, the widespread recreational use of cocaine has created

15.8E.1 https://bio.libretexts.org/@go/page/5650
serious social problems. In order to achieve its effects, cocaine must cross the so-called blood-brain barrier. If antibodies are
bound to the cocaine molecule, it cannot cross. This has raised the possibility of immunizing people against cocaine. It works in
mice.

Sedatives
Sedatives induce sleep. They include
ethanol (beverage alcohol)
barbiturates, such as
phenobarbital
secobarbital (Seconal®)
meprobamate (Miltown®, Equanil®)

Ethanol
Ethyl alcohol (ethanol) is, by a wide margin, the most widely used drug in most of the world. Its popularity comes not from its
sedative effect but from the sense of well-being that it induces at low doses. Perhaps low doses sedate those parts of the brain
involved with, for example, tension and anxiety and in this way produce a sense of euphoria. However, higher doses depress brain
centers involved in such important functions as pain sensation, coordination, and balance. At sufficiently high doses, the reticular
formation can be depressed enough to cause loss of consciousness.
Ethanol increases the release of the neurotransmitter GABA activating GABAA receptors and directly inhibits NMDA receptors.

Barbiturates
Barbiturates are often prescribed as sleeping pills and also to prevent seizures. Barbiturates mimic some of the action of ethanol,
particularly in their ability to depress the reticular formation (thus promoting sleep) and, in high doses, the medulla oblongata (thus
stopping breathing).
Barbiturates bind to a subset of GABA receptors designated GABAA receptors. These are ligand-gated channels that enhance the
flow of chloride ions (Cl−) into the postsynaptic neuron, thus increasing its resting potential and making it less likely to fire. By
binding to the GABAA receptor, barbiturates (and perhaps ethanol) increase the natural inhibitory effect of GABA synapses.
Barbiturates and alcohol act additively — the combination producing a depression greater than either one alone. The combination
is a frequent cause of suicide, both accidental and planned.

Meprobamate
Meprobamate is prescribed as a tranquilizer, but its action is quite different from the tranquilizers discussed below. Its molecular
activity is like that of other sedatives and in combination with them can produce a lethal overdose. All sedatives produce two
related physiological effects:
tolerance — the necessity for a steadily-increasing dose to achieve the same physiological and psychological effects
physical dependence — withdrawal of the drug precipitates unpleasant physical and psychological symptoms.
These traits are also shared with nicotine, opioids, and other psychoactive drugs.

Local Anesthetics
These chemical relatives of cocaine act by blocking the voltage-gated Na+ channels of sensory neurons preventing them from
generating action potentials. They are injected or applied topically and block transmission not only in pain-conducting neurons but
in others as well (causing general numbness).
Examples:
lidocaine (Xylocaine®)
procaine (Novocaine®)

Inhaled Anesthetics
Most of these are volatile hydrocarbons or ethers. Diethyl ether and chloroform are seldom used today, having been replaced by
safer alternatives such as isofluorane, a fluorinated ether. Some, like isofluorane, bind to inhibitory GABA receptors) in the brain

15.8E.2 https://bio.libretexts.org/@go/page/5650
hyperpolarizing, and thus decreasing the sensitivity of, postsynaptic neurons. Others, like ketamine, block the activity of excitatory
glutamate receptors.

Other Hydrocarbons
1,4-Butanediol is a common solvent. When ingested, it is converted into γ-hydroxybutyrate, an increasingly-popular (and illegal)
"club drug". γ-Hydroxybutyrate acts on GABAB receptors. Conversion of 1,4-butanediol to γ-hydroxybutyrate requires the enzyme
alcohol dehydrogenase, the same enzyme used to metabolize ethanol. Ingesting both ethanol and 1,4-butanediol delays the effects
of the latter.

Opioids
These are substances isolated from the opium poppy or synthetic relatives. (They are also called opiates.)
Examples:
morphine
codeine
heroin
fentanyl (a synthetic that is ~80 times more potent than morphine)
methadone
oxycodone
Opioids depress nerve transmission in sensory pathways of the spinal cord and brain that signal pain. This explains why opioids
are such effective pain killers. Opioids also inhibit brain centers controlling coughing, breathing, and intestinal motility. Both
morphine and codeine are used as pain killers, and codeine is also used in cough medicine. Opioids are exceedingly addictive,
quickly producing tolerance and dependence. Although heroin is even more effective as a painkiller than morphine and codeine, it
is so highly addictive that its use is illegal. Methadone is a synthetic opioid that is used to break addiction to heroin (and replace it
with addiction to methadone).

Figure 15.8.5.1 Pain signal transmission

Opioids bind to so-called mu (µ) receptors . These G-protein-coupled receptors are located on the subsynaptic membrane of
neurons involved in the transmission of pain signals. Their natural ligands are two pentapeptides (containing five amino acids):
Met-enkephalin (Tyr-Gly-Gly-Phe-Met-COO-)
Leu-enkephalin (Tyr-Gly-Gly-Phe-Leu-COO-)
Release of enkephalins suppresses the transmission of pain signals. Little is to be gained by having the perception of pain increase
indefinitely in proportion to the amount of damage done to the body. Beyond a certain point, it makes sense to have a system that
decreases its own sensitivity in the face of massive, intractable pain.
By binding to mu (µ) receptors, opioids like morphine enhance the pain-killing effects of enkephalin neurons. Opioid tolerance can
be explained, at least in part, as a homeostatic response that reduces the sensitivity of the system to compensate for continued
exposure to high levels of morphine or heroin. When the drug is stopped, the system is no longer as sensitive to the soothing effects
of the enkephalin neurons and the pain of withdrawal is produced.

15.8E.3 https://bio.libretexts.org/@go/page/5650
Mu (µ) receptors are also found on the cells in the medulla oblongata that regulate breathing. This accounts for the suppressive
effect opioids have on breathing.

Opioid antagonists
Opioid antagonists such as naloxone (Narcan®) and naltrexone (ReVia®) bind to µ receptors but instead of activating them, they
prevent the binding of the opioids themselves. In fact, if the receptors are already occupied by, for example, heroin molecules,
naloxone will push the heroin molecules off and quickly rescue the patient from a drug overdose. Naltrexone is used to help
recovering heroin addicts stay drug-free.

Antipsychotics
Antipsychotics (also called "neuroleptics") are used to treat schizophrenia, a common and devastating mental disease. They act by
binding to one class of receptors for the neurotransmitter dopamine. There are two groups currently in use:
"Typical" antipsychotics (sometimes referred to as "major tranquilizers"). Examples:
chlorpromazine (Thorazine®)
haloperidol (Haldol®)
"Atypical" antipsychotics (also referred to as "second generation" antipsychotics). Examples:
risperidone (Risperdal®)
olanzapine (Zyprexa®)
quetiapine (Seroquel®)

Tranquilizers
Tranquilizers act like sedatives in reducing anxiety and tensions. Most belong to a group called benzodiazepines and include such
commonly-prescribed drugs as Xanax® and Klonopin®. The benzodiazepines act on interneurons that use the inhibitory
neurotransmitter GABA. By binding to GABAA receptors on the postsynaptic membrane, they enhance the action of GABA at the
synapse.This is the same receptor to which barbiturates (and perhaps ethanol) bind. Thus although benzodiazepines seem safe
enough when used alone, combining them with ethanol or barbiturates can be (and often has been) lethal.

Antidepressants
Antidepressants fall into four chemical categories (of which we shall examine three). Most share a common property: they increase
the amount of serotonin at synapses that use it as a neurotransmitter.

Monoamine oxidase inhibitors (MAOIs)

These drugs act on a mitochondrial enzyme that breaks down monoamines such as noradrenaline and serotonin. By inhibiting the
enzyme in presynaptic serotonin-releasing neurons, more noradrenaline and serotonin is deposited in the synapse. Some examples:
Parnate®, Nardil®, Marplan®. For several reasons, MAO inhibitors are not used much anymore.

Tricyclic antidepressants (TCAs)

These drugs block the reuptake of noradrenaline, dopamine, and serotonin causing an increase in the level of these
neurotransmitters in the synapse.
Examples:

Generic name Trade name

imipramine Tofranil®

clomiprimine Anafranil®

amitriptyline Elavil®

Although tricyclics are still prescribed for pain relief, their role as antidepressants has largely been taken over by the serotonin
reuptake inhibitors (SRIs).

15.8E.4 https://bio.libretexts.org/@go/page/5650
Selective serotonin reuptake inhibitors (SSRIs)
These drugs inhibit the reuptake of serotonin but not of noradrenaline.
Examples:

Generic name Trade name

fluoxetine Prozac®

paroxetine Paxil®

sertraline Zoloft®

Although all these drugs quickly increase the amount of serotonin in the brain, there is more to the story than that. Unlike most
psychoactive drugs, antidepressants do not relieve the symptoms of depression until a week or more after dosing begins. During
this period, the number of serotonin receptors on the postsynaptic membranes decreases. How this translates into relief of
symptoms is not yet understood.

Serotonin and norepinephrine reuptake inhibitors (SNRIs)

Because they act on the reuptake of both serotonin and noradrenaline (norepinephrine), this category of antidepressants is also
known as dual reuptake inhibitors.
Examples: venlafaxine (Effexor®) and duloxetine (Cymbalta®).

Bupropion
Bupropion (Wellbutrin®) is a novel drug that blocks the reuptake of noradrenaline and dopamine. Although it does not interfere
with the uptake of serotonin, it also appears to be an effective antidepressant.

Atomoxetine
This drug (Strattera®) selectively interferes with the reuptake of noradrenaline. It is used in children with attention
deficit/hyperactivity disorder (ADHD).

Psychedelics
Psychedelic drugs distort sensory perceptions, especially sight and sound. Some such as mescaline, psilocybin and
dimethyltryptamine (DMT) are natural plant products.

Figure 15.8.5.2 Peyote cactus courtesy of Dr. Richard Evans Schultes

The photograph shows the peyote cactus in flower. The cactus head contains several psychedelic chemicals, of which mescaline is
the most important. Dried cactus heads ("mescal buttons") have been used since pre-Columbian times in the religious ceremonies
of native peoples in Mexico. About a century ago, this religious use spread to some tribes in the United States and Canada who, in
1922, became incorporated into the Native American Church. Other psychedelic drugs are synthetic. These include
lysergic acid diethylamide (LSD)
dimethoxymethylamphetamine (DOM or "STP")
methylenedioxymethamphetamine (MDMA or "ecstasy")
As their name suggests, DOM and MDMA also share the stimulant qualities of amphetamines. All the psychedelics have a
molecular structure that resembles serotonin and probably bind to serotonin receptors on the postsynaptic membrane.

15.8E.5 https://bio.libretexts.org/@go/page/5650
Phencyclidine (PCP)
PCP is used as an anesthetic in veterinary medicine. Used (illicitly) by humans (called "crystal" or "angel dust"), it can produce a
wide variety of powerful reactions resembling those of stimulants as well as psychedelics. Unlike the other psychedelics, it binds to
(and inhibits) NMDA receptors (in the hippocampus and other parts of the forebrain).

Marijuana
The main psychoactive ingredient in marijuana is delta-9-tetrahydrocannabinol (Δ9-THC). It binds to
CB1 receptors (G-protein-coupled receptors) that are present on presynaptic membranes in many parts of the brain.
CB2 receptors are also found in the brain as well as being highly-expressed on cells of the immune system (e.g., B cells and T
cells).
THC produces the drowsiness of sedatives like alcohol, the dulling of pain (like opioids) and in high doses, the perception-
distorting effects of the psychedelics. Unlike sedatives and opioids, however, tolerance to THC does not occur. In fact, the drug is
excreted so slowly from the body that, with repeated use, a given response is achieved by a lower dose.
The natural ligands of the CB receptors are the endocannabinoids - anandamide and 2-arachidonylglycerol (2-AG). Both of these
compounds are produced from phospholipids.
What are these natural ligands doing? They probably will turn out to have multiple effects, but the clearest ones so far are their
effects on
appetite. Mice given anandamide eat more than normal while those whose genes for the CB1 receptor have been "knocked
out" eat less than normal.These findings will be no surprise to the ill humans (e.g., with cancer or AIDS) who find that
marijuana improves their appetite. Rimonabant (Acomplia®), a drug that blocks the ability of the body's natural CB1 ligands to
bind the CB1 receptor was sold for a time in Europe as an appetite suppressant. (Because of its side effects, it was never
approved for use in the U.S. and was removed from the European market in 2008.)
development of correct synaptic connections in the embryonic brain. Mice whose genes for the CB1 receptor have been
knocked out develop defects in the wiring pattern of interneurons in their brain (which may account for the cognitive defects
that have been reported in the children of women who used marijuana during pregnancy).
neuronal activity in the adult brain. Mice whose genes for the CB1 receptor have been knocked out are more susceptible to
epileptic seizures. Marijuana has been used for centuries to control epileptic seizures in humans.
suppressing contact dermatitis. Knockout mice lacking CB1 and CB2 receptors mount a more vigorous allergic inflammatory
response to agents (like nickel) that elicit contact sensitivity.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 15.8E: Drugs and the Nervous System is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.8E.6 https://bio.libretexts.org/@go/page/5650
15.8F: Nitric Oxide (NO)
Nitric oxide is a gas. It is highly reactive; that is, it participates in many chemical reactions. (It is one of the nitrogen oxides
("NOx") in automobile exhaust and plays a major role in the formation of photochemical smog.) But NO also has many
physiological functions.

Figure 15.8.6.1 NO Synthase

They share these features:
NO is synthesized within cells by an enzyme NO synthase (NOS).
The human (and mouse) genome contains 3 different genes encoding NO synthases.
nNOS (or NOS-1): found in neurons (hence the "n").
eNOS (or NOS-3): found in the endothelial (hence the "e") cells that line the lumen of blood vessels.
iNOS (or NOS-2): found in macrophages. (the "i" stands for "inducible"). Whereas the levels of nNOS and eNOS are
relatively steady, expression of iNOS genes awaits an appropriate stimulus (e.g., invasion by a pathogen).
All types of NOS produce NO from arginine with the aid of molecular oxygen and NADPH.
NO diffuses freely across cell membranes.
There are so many other molecules with which it can interact, that it is quickly consumed close to where it is synthesized.
Thus NO acts in a paracrine or even autocrine fashion - affecting only cells near its point of synthesis.
This page examines some of the functions of NO.

Blood Flow
NO relaxes the smooth muscle in the walls of the arterioles. At each systole, the endothelial cells that line the blood vessels release
a puff of NO. This diffuses into the underlying smooth muscle cells causing them to relax and thus permit the surge of blood to
pass through easily. Mice whose genes for the NO synthase found in endothelial cells (eNOS) has been "knocked out" suffer from
hypertension.
Nitroglycerine, which is often prescribed to reduce the pain of angina, does so by generating nitric oxide, which relaxes the walls of
the coronary arteries and arterioles. NO also inhibits the aggregation of platelets and thus keeps inappropriate clotting from
interfering with blood flow.

Kidney Function
Release of NO around the glomeruli of the kidneys increases blood flow through them thus increasing the rate of filtration and
urine formation.

Penile Erection
The erection of the penis during sexual excitation is mediated by NO released from nerve endings close to the blood vessels of the
penis. Relaxation of these vessels causes blood to pool in the blood sinuses producing an erection. Three popular prescription drugs
enhance this effect by the mechanism described below.
Recent evidence suggests that NO's job in reproduction is not finished with producing an erection. At the moment of contact,
release of NO by the acrosome of the sperm activates the egg to complete meiosis II and the other steps of fertilization.

15.8F.1 https://bio.libretexts.org/@go/page/5651
Other Actions on Smooth Muscle
Peristalsis
The wavelike motions of the gastrointestinal tract are aided by the relaxing effect of NO on the smooth muscle in its walls.

Birth
NO also inhibits the contractility of the smooth muscle wall of the uterus. As the moment of birth approaches, the production of
NO decreases. Nitroglycerine has helped some women who were at risk of giving birth prematurely to carry their baby to full term.

NO and Inflammation
The NO produced by eNOS (NOS-3) inhibits inflammation in blood vessels. It does this by blocking the exocytosis of mediators of
inflammation from the endothelial cells. NO may also block exocytosis in other types of cells such as macrophages and cytotoxic T
lymphocytes (CTL).

Effects on Secretion
NO affects secretion from several endocrine glands.
For examples, it stimulates
the release of Gonadotropin-releasing hormone (GnRH) from the hypothalamus
the release of pancreatic amylase from the exocrine portion of the pancreas
the release of adrenaline from the adrenal medulla

NO and the Nervous System

NO and the Autonomic Nervous System
Some motor neurons of the parasympathetic branch of the autonomic nervous system release NO as their neurotransmitter. The
actions of NO on penile erection and peristalsis are probably mediated by these nerves.

NO and the Medulla Oblongata

Hemoglobin transports NO at the same time it carries oxygen. When it unloads oxygen in the tissues, it also unloads NO. In severe
deoxygenation, NO-sensitive cells in the medulla oblongata respond to this release by increasing the rate and depth of breathing.

NO and the Brain

In laboratory animals (mice and rats), NO is released by neurons in the CA1 region of the hippocampus and stimulates the NMDA
receptors there that are responsible for long-term potentiation (LTP) - a type of memory (and learning). The ease with which NO
diffuses away from the synapse where it is generated enables it to affect nearby synapses. So what may have begun as a localized
action becomes magnified.
Laboratory rats treated with inhibitors of NOS synthesis fail to develop and/or retain learned responses such as the conditioned
response. Mice whose genes for nNOS have been knocked out are healthy but display abnormal behavior, e.g., they kill other males
and try to mate with nonreceptive females.

NO and Fertilization
The acrosome at the tip of sperm heads activates its NO synthase when it enters the egg. The resulting release of NO in the egg is
essential (at least in sea urchins) for triggering the next steps in the process :
blocking the entry of additional sperm
orienting the pronuclei for fusion.

Killing Pathogens
NO aids in the killing of engulfed pathogens (e.g., bacteria) within the lysosomes of macrophages.
Mice whose genes for the NO synthase found in macrophages (iNOS) have been knocked out are more susceptible to infections by
intracellular bacteria like Listeria monocytogenes. Th1 cells, the ones responsible for an inflammatory response against invaders,
secrete NO. Harmless bacteria, living as commensals at the rear of our throat, convert nitrates in our food into nitrites. When these

15.8F.2 https://bio.libretexts.org/@go/page/5651
reach the stomach, the acidic gastric juice (pH ~1.4) generates NO from them. This NO kills almost all the bacteria that have been
swallowed in our food.
Since the dawn of recorded human history, nitrites have been used to preserve meat from bacterial spoilage.

NO and Longevity
Mice whose genes for eNos have been knocked out
show signs of premature aging
have a shortened life span
fail to benefit from the life-extending effect of a calorie-restricted (CR) diet

Mechanisms of NO Action
The signaling functions of NO begin with its binding to protein receptors on or in the cell. The binding sites can be either:In either
case, binding triggers an allosteric change in the protein which, in turn, triggers the formation of a "second messenger" within the
cell. The most common protein target for NO seems to be guanylyl cyclase, the enzyme that generates the second messenger cyclic
GMP (cGMP).
Three prescription drugs sildenafil (Viagra®), vardenafil (Levitra®) and tadalafil (Cialis®) enhance the effects of NO by inhibiting
the enzyme that normally breaks down cGMP.

Fireflies Use NO To Turn On their Flashes

Bioluminescence

Plants Also Use NO

NO has been implicated in many plant activities. It is a weapon against invading pathogens. Infection of the plant triggers the
formation of a NOS that, like the animal versions, makes NO from arginine. Release of NO by the infected cell induces a number
of defense responses. A gradient of NO may also guide the pollen tube to its destination in the ovule. The popular prescription drug
sildenafil citrate (Viagra®) enhances the effect of NO on pollination (just as it does on penile erection). NO inhibits flowering. NO
promotes recovery from etiolation.

This page titled 15.8F: Nitric Oxide (NO) is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.8F.3 https://bio.libretexts.org/@go/page/5651
15.8G: Prion Diseases
Prion diseases are transmissible from host to host of a single species and, sometimes, even from one species to another (such as a
laboratory animal). They destroy brain tissue giving it a spongy appearance. For these reasons, prion diseases are also called
transmissible spongiform encephalopathies or TSEs.
Some examples:

Creutzfeldt-Jakob Disease CJD humans

variant Creutzfeldt-Jakob Disease vCJD humans; acquired from cattle with BSE

Bovine Spongiform Encephalopathy BSE "mad cow disease"

infectious; in humans who practiced

Kuru
cannibalism in Papua New Guinea

Gerstmann-Sträussler-Scheinker disease GSS inherited disease of humans

Fatal Familial Insomnia FFI inherited disease of humans

Scrapie infectious disease of sheep and goats

other animal TSEs cats, mink, elk, mule deer

Before the victim dies of a TSE, the damage to the brain is reflected in such signs as loss of coordination and in humans dementia.
Injections of ground-up brain tissue from an animal or human patient with a prion disease into another animal (of the appropriate
species) transmits the disease. This suggests that the disease is caused by an infectious agent such as a virus. But viruses have a
genome and despite intense efforts no evidence of a virus has ever been found in these brain extracts. In fact, treating the extracts
with agents (e.g., ultraviolet light) that destroy DNA does not reduce their infectiousness.
To date, the evidence indicates that the infectious agent in the TSEs is a protein. Stanley Prusiner who pioneered in the study of
these proteins and was awarded the Nobel Prize in 1997 for his efforts has named them prion proteins (designated PrP) or simply
prions. It turns out that prions are molecules of a normal body protein that have changed their three-dimensional configuration.

PrPC
The normal protein
is called PrPC (for cellular)
is a glycoprotein normally anchored to the surface of cells.
has its secondary structure dominated by alpha helices (probably 3 of them)
is easily soluble
is easily digested by proteases
is encoded by a gene designated (in humans) PRNP located on our chromosome 20.

PrPSc
The abnormal, disease-producing protein
is called PrPSc (for scrapie)
has the same amino acid sequence as the normal protein; that is, their primary structures are identical but
its secondary structure is dominated by beta conformation
is insoluble in all but the strongest solvents
is highly resistant to digestion by proteases
When PrPSc comes in contact with PrPC, it converts the PrPC into more of itself (even in the test tube).
These molecules bind to each other forming aggregates.
It is not yet clear if these aggregates are themselves the cause of the cell damage or are simply a side effect of the underlying
disease process.

15.8G.1 https://bio.libretexts.org/@go/page/5652
Inherited Prion Diseases
Creutzfeldt-Jakob Disease (CJD)
10–15% of the cases of CJD are inherited; that is, the patient comes from a family in which the disease has appeared before. The
disease is inherited as an autosomal dominant. The patients have inherited at least one copy of a mutated PRNP gene. Some of the
most common mutations are:
a change in codon 200 converting glutamic acid (E) at that position to lysine (K) (thus designated "E200K")
a change from aspartic acid (D) at position 178 in the protein to asparagine (D178N) when it is accompanied by a
polymorphism in both PRNP genes that encodes valine at position 129. When the polymorphism at codon 129 is Met on both
genes, the D178N mutation produces Fatal Familial Insomnia instead.
a change from valine (V) at position at position 210 to isoleucine (V210I)
Extracts of autopsied brain tissue from these patients can transmit the disease to
apes (whose PRNP gene is probably almost identical to that of humans).
transgenic mice who have been given a Prnp gene that contains part of the human sequence.
These results lead to the important realization that prion diseases can only be transmitted to animals that already carry a PRNP gene
with a sequence that is at least similar to the one that encoded the PrPSc. In fact, knockout mice with no Prnp genes at all cannot be
infected by PrPSc.
Gerstmann-Sträussler-Scheinker disease (GSS)
This prion disease is caused by the inheritance of a PRNP gene with a mutations encoding most commonly
leucine instead of proline at position 102 (P102L) or
valine instead of alanine at position 117 (A117V)
Again, the disease is also strongly associated with homozygosity for a polymorphism at position 129 (both residues being
methionine).
Brain extracts from patients with GSS can transmit the disease to
monkeys and apes
transgenic mice containing a portion of the human PRNP gene.
Transgenic mice expressing the P102L gene develop the disease spontaneously.
Fatal Familial Insomnia (FFI)
People with this rare disorder have inherited
a PRNP gene with asparagine instead of aspartic acid encoded at position 178 (D178N)
the susceptibility polymorphism of methionine at position 129 of the PRNP genes.
Extracts from autopsied brains of FFI victims can transmit the disease to transgenic mice.

Infectious Prion Diseases

Kuru
Kuru was once found among the Fore tribe in Papua New Guinea whose rituals included eating the brain tissue of recently
deceased members of the tribe. Since this practice was halted, the disease has disappeared. Before then, the disease was studied by
transmitting it to chimpanzees using injections of autopsied brain tissue from human victims.
Scrapie
This disease of sheep (and goats) was the first TSE to be studied. It seems to be transmitted from animal to animal in feed
contaminated with nerve tissue. It can also be transmitted by injection of brain tissue.
Bovine Spongiform Encephalopathy (BSE) or "Mad Cow Disease"
An epidemic of this disease began in Great Britain in 1985 and before it was controlled, some 800,000 cattle were sickened by it.
Its origin appears to have been cattle feed that contained brain tissue from sheep infected with scrapie and had been treated in a
new way that no longer destroyed the infectiousness of the scrapie prions.

15.8G.2 https://bio.libretexts.org/@go/page/5652
The use of such food was banned in 1988 and after peaking in 1992, the epidemic declined quickly.
Creutzfeldt-Jakob Disease (CJD)
A number of humans have acquired CJD through accidental exposure to material contaminated with CJD prions.
Grafts of dura mater taken from patients with inherited CJD have transmitted the disease to 228 recipients.
Corneal transplants have also inadvertently transmitted CJD.
Instruments used in brain surgery on patients with CJD have transmitted the disease to other patients. Two years after their
supposed sterilization, these instruments remained infectious.
226 people have acquired CJD from injections of human growth hormone (HGH) or human gonadotropins prepared from
pooled pituitary glands that inadvertently included glands taken from humans with CJD.
Now that both HGH and human gonadotropins are available through recombinant DNA technology, such disastrous accidents need
never recur.
Variant Creutzfeldt-Jakob Disease (vCJD)
This human disorder appeared some years after the epidemic of BSE (Mad Cow Disease) swept through the cattle herds in Great
Britain. Even though the cow and human PRNP genes differ at 30 codons, the sequence of their prions suggests that these patients
(155 by 2005) acquired the disease from eating contaminated beef.
All the patients are homozygous for the susceptibility polymorphism of methionine at position 129. The BSE epidemic has waned,
and slaughter techniques that allow cattle nervous tissue in beef for human consumption have been banned since 1989. Now we
must wait to see whether more cases of vCJD are going to emerge or whether the danger is over.
Miscellaneous Infectious Prion Diseases
A number of TSEs have been found in other animals. Cats are susceptible to Feline Spongiform Encephalopathy (FSE). Mink are
also susceptible to a TSE. Even though mad cow disease has not been seen in North America, a similar disease is found in elk and
mule deer in the Rocky Mountains of the U.S.

Sporadic Prion Diseases

CJD and FFI occasionally occur in people who have no family history of the disease and no known exposure to infectious prions.
The cause of their disease is uncertain.
Perhaps a spontaneous somatic mutation has occurred in one of the PRNP genes in a cell.
Perhaps their normal PrPC protein has spontaneously converted into the PrPSc form.
Or perhaps the victims were simply unknowingly exposed to infectious prions, and sporadic prion diseases do not exist!
Whatever the answer, all the cases are found in people with a susceptibility polymorphism in their PRNP genes.

Prions in Yeast
Two proteins in yeast (Saccharomyces cerevisiae)
the Sup35 protein ("Sup35p") and
the Ure2 protein (Ure2p)
are able to form prions; that is, they can exist either
in a PrPC-like form that is functional or
in a PrPSc-like form that is not.
The greater ease with which yeast can be studied has proved that only protein is involved in prion formation and provided insight
into the need for PrPSc to find PrPC molecules of a similar primary structure in order to be able to convert them into the PrPSc
form.

Evidence that prions are a "protein-only" phenomenon

A few molecules of a PrPSc form of the Sup35 protein, when introduced into yeast cells, convert the yeast cell's own Sup35
protein into prion aggregates. The resulting "disease" phenotype is then passed on to the cell's daughters.
The introduced protein was synthesized in bacteria making it unlikely that it could be contaminated by any gene-containing
infectious agent of yeast.

15.8G.3 https://bio.libretexts.org/@go/page/5652
 Yeast can be "cured" of their prion "disease" by increasing the activity of their chaperones. Presumably the chaperone helps
maintain the folded state (with alpha helices) of the protein.
When the gene for the glucocorticoid receptor is altered to include sequences coding for one part (domain) of the Sup35 protein,
the resulting protein forms prions and produces an entirely new phenotype.

Possible basis of species specificity of prions

A particular PrPSc can only convert PrPC molecules of the same or at least similar primary structure.
This requirement of "like-with-like" resides in a short sequence at the N-terminal of the protein (rather like an antibody
epitope).
Yeasts engineered to form two types of prion form two types of "pure" aggregates within the cell.
Even in the test tube, each type of prion finds and aggregates with others of its own type.

Figure 15.8.7.1 PrP

So the picture that emerges is that a molecule of PrP acts as a "seed" providing a template for converting PrPC to more PrPSc.
Sc

These interact with each other to form small soluble aggregates. These interact with each other to form large insoluble deposits.
Although only a small portion of the prion protein is responsible for its specificity, other parts of the molecule are needed for
flipping the molecule from the alpha-helical to the beta conformation. All prion proteins contain tracts of repeated Gln-Asn
residues which appear to be essential for the conversion process.

Other Pathogenic Prion-like Proteins

The deposits of PrPScin the brain are called amyloid. Amyloid deposits are also found in other diseases.
Examples:
Alzheimer's disease is characterized by amyloid deposits of
the peptide amyloid-beta (Aβ)
the protein tau
in the brain.
The brains of Parkinson's disease patients have deposits of α-synuclein.
Deposits of the protein huntingtin are found in the brains of victims of Huntington's disease.
Amyloid deposits of the protein transthyretin are found in peripheral nerves, the kidney, and other organs.
With all of these diseases there is evidence that their amyloid-forming proteins, like PrPSc, can act as a "seed" converting a
correctly-folded protein into an incorrectly-folded one and have this effect spread from cell to cell. However, they do not seem to
be able to be spread from person to person (unlike the TSEs). Perhaps this is because they are not so incredibly resistant to
degradation as PrPSc is.
Most cells, including neurons in the brain, contain proteasomes that are responsible for degrading misfolded or aggregated
proteins. In the various brain diseases characterized by a build-up of amyloid deposits, it appears that as the small insoluble
amyloid precursors accumulate, they bind to proteasomes but cannot be degraded by them. Furthermore, this binding blocks the
ability of the proteasomes to process other proteins that are normal candidates for destruction. Because of the critical role of
proteasomes in many cell functions, such as mitosis, it is easy to see why this action leads to death of the cell.

Prion-like proteins not always harmful

Evidence:
Yeast are not harmed when Sup35p and Ure2p form prions.
The role of CPEB.
CPEB ("cytoplasmic polyadenylation element binding protein") is a protein that
is found in neurons of the central nervous system (as well as elsewhere)

15.8G.4 https://bio.libretexts.org/@go/page/5652
 stimulates messenger RNA (mRNA) translation
is needed for long-term facilitation (LTF)
accumulates at activated (by serotonin) synapses
has the ability to undergo a change in tertiary structure that
persists for long periods
induces the same conformational change in other molecules of CPEB forming prion-like aggregates
Perhaps the accumulation of these aggregates at a stimulated synapse causes a long-term change in its activity (memory).

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 15.8G: Prion Diseases is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.8G.5 https://bio.libretexts.org/@go/page/5652
 SECTION OVERVIEW
15.9: Senses
15.9A: Mechanoreceptors

15.9B: Hearing

15.9C: Vision

15.9D: Processing Visual Information

15.9E: Vision in Arthropods

15.9F: Heat, Cold, and Pain Receptors

15.9G: Taste

15.9H: Olfaction - The Sense of Smell

15.9I: Electric Organs and Electroreceptors

15.9J: Magnetoreceptors

This page titled 15.9: Senses is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.9.1 https://bio.libretexts.org/@go/page/5369
15.9A: Mechanoreceptors
We and other animals have several types of receptors of mechanical stimuli. Each initiates nerve impulses in sensory neurons when
it is physically deformed by an outside force such as: touch, pressure, stretching, sound waves, and motion. Mechanoreceptors
enable us to detect touch, monitor the position of our muscles, bones, and joints — the sense of proprioception and detect sounds
and the motion of the body.

Touch
Light touch is detected by receptors in the skin. Many of these are found next to hair follicles so even if the skin is not touched
directly, movement of the hair is detected. Touch receptors are not distributed evenly over the body. The fingertips and tongue may
have as many as 100 per cm2; the back of the hand fewer than 10 per cm2. This can be demonstrated with the two-point threshold
test. With a pair of dividers like those used in mechanical drawing, determine (in a blindfolded subject) the minimum separation of
the points that produces two separate touch sensations. The ability to discriminate the two points is far better on the fingertips than
on, say, the small of the back. The density of touch receptors is also reflected in the amount of somatosensory cortex in the brain
assigned to that region of the body.

Proprioception
Proprioception is our "body sense". It enables us to unconsciously monitor the position of our body. It depends on receptors in the
muscles, tendons, and joints. If you have ever tried to walk after one of your legs has "gone to sleep," you will have some
appreciation of how difficult coordinated muscular activity would be without proprioception.

Four Mechanoreceptors
1: The Pacinian Corpuscle
Pacinian corpuscles are pressure receptors. They are located in the skin and also in various internal organs. Each is connected to a
sensory neuron. Because of its relatively large size, a single Pacinian corpuscle can be isolated and its properties studied.
Mechanical pressure of varying strength and frequency is applied to the corpuscle by the stylus. The electrical activity is detected
by electrodes attached to the preparation.

Figure 15.9.1.1 Pacinian

Deforming the corpuscle creates a generator potential in the sensory neuron arising within it. This is a graded response: the greater
the deformation, the greater the generator potential. If the generator potential reaches threshold, a volley of action potentials (also
called nerve impulses) are triggered at the first node of Ranvier of the sensory neuron. Once threshold is reached, the magnitude of
the stimulus is encoded in the frequency of impulses generated in the neuron. So the more massive or rapid the deformation of a
single corpuscle, the higher the frequency of nerve impulses generated in its neuron.
2: Adaptation
When pressure is first applied to the corpuscle, it initiates a volley of impulses in its sensory neuron. However, with continuous
pressure, the frequency of action potentials decreases quickly and soon stops. This is the phenomenon of adaptation. Adaptation
occurs in most sense receptors. It is useful because it prevents the nervous system from being bombarded with information about
insignificant matters like the touch and pressure of our clothing. Stimuli represent changes in the environment. If there is no
change, the sense receptors soon adapt. But note that if we quickly remove the pressure from an adapted Pacinian corpuscle, a fresh
volley of impulses will be generated. This is why Pacinian corpuscles respond especially well to vibrations.
The speed of adaptation varies among different kinds of receptors. Receptors involved in proprioception such as spindle fibers
adapt slowly if at all.

15.9A.1 https://bio.libretexts.org/@go/page/5682
3: Meissner Corpuscles
Meissner corpuscles, like Pacinian corpuscles, adapt quickly to a sustained stimulus but are activated again when the stimulus is
removed. Thus they are especially sensitive to movement across the skin.
4: Merkel Cells
Merkel cells are transducers of light touch, responding to the texture and shape of objects indenting the skin. Unlike Pacinian and
Meissner corpuscles, they do not adapt rapidly to a sustained stimulus; that is, they continue to generate nerve impulses so long as
the stimulus remains. They are found in the skin often close to hairs. They form synapses with Aβ sensory neurons leading back to
the CNS.
In the rat, light movement of a hair triggers a generator potential in a Merkel cell. If this reaches threshold, an influx of Ca++ ions
through voltage-gated calcium channels generate action potentials in the Merkel cell. These cause the release of neurotransmitters
at the synapse with its Aβ sensory neuron. (This neuron may also have its own mechanically-gated ion channels able to directly
generate action potentials more rapidly than Merkel cells can.)

 The knee jerk Reflex

The knee jerk is a stretch reflex. Your physician taps you just below the knee with a rubber-headed hammer. You respond with
an involuntary kick of the lower leg.
The hammer strikes a tendon that inserts an extensor muscle in the front of the thigh into the lower leg.
Tapping the tendon stretches the thigh muscle.
This activates stretch receptors within the muscle called muscle spindles. Each muscle spindle consists of
sensory nerve endings wrapped around
special muscle fibers called spindle fibers (also called intrafusal fibers)
Stretching a spindle fiber initiates a volley of impulses in the sensory neuron (called an "I-a" neuron) attached to it.
The impulses travel along the sensory axon to the spinal cord where they form several kinds of synapses:
Some of the branches of the I-a axons synapse directly with alpha motor neurons (Pacinian Corpuscle). These carry
impulses back to the same muscle causing it to contract. The leg straightens.
Some of the branches of the I-a axons synapse with inhibitory interneurons in the spinal cord (Meissner Corpuscles).
These, in turn, synapse with motor neurons leading back to the antagonistic muscle, a flexor in the back of the thigh.
By inhibiting the flexor, these interneurons aid contraction of the extensor.
Still other branches of the I-a axons synapse with interneurons leading to brain centers, e.g., the cerebellum, that
coordinate body movements (Merkel Cells).

Figure 15.9.1.2 Kneejerk reflex

15.9A.2 https://bio.libretexts.org/@go/page/5682
This page titled 15.9A: Mechanoreceptors is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.9A.3 https://bio.libretexts.org/@go/page/5682
15.9B: Hearing
The sense of hearing is the ability to detect the mechanical vibrations we call sound. Sound waves pass down the auditory canal of
the outer ear and strike the eardrum (tympanic membrane) causing it to vibrate. These vibrations are transmitted across the middle
ear by three tiny linked bones, the ossicles:
hammer (malleus)
anvil (incus)
stirrup (stapes)
The ossicles also magnify the amplitude of the vibrations.

Figure 15.9.2.1 Ear

The middle ear is filled with air and is connected to the outside air by the eustachian tube, which opens into the nasopharynx.
Opening of the tube during swallowing or yawning equalizes the air pressure on either side of the eardrum. Allergies or a head cold
may inflame the walls of the eustachian tubes making them less easily opened. Rapid changes in pressure at such times — such as
descending in an aircraft or during a SCUBA dive, may be quite painful because of the unequal pressure against the eardrums.

The Inner Ear

Vibrations of the innermost ossicle, the stirrup, are transmitted through a flexible membrane, the oval window to the cochlea of the
inner ear. The cochlea is a tube, about 3.5 cm long, that is coiled like a snail shell and filled with a special fluid called endolymph.
The most dramatic difference in the composition of endolymph from other lymph in the body is its high concentration of potassium
(K+) ions. Running through the cochlea for its entire length is a plate of bone and an inner tube that is also filled with endolymph.
These structures divide the outer tube of the cochlea into two separate chambers.

Figure 15.9.2.2 Inner ear

Because liquids are practically incompressible, it is necessary to have some way of relieving the pressures created when the oval
window is pushed in and out. The flexible round window does this by moving in the opposite direction.

The organ of Corti

The organ of Corti lies within the middle chamber of the cochlea. It contains thousands of hair cells, which are the actual vibration
receptors. The apical surface of the hair cells contains an array of stereocilia, which give the hair cells their name. Stereocilia are
not built from the "9+2" arrangement of microtubules that are found in true cilia. The hair cells are located between the basilar and
tectorial membranes. Vibrations of the endolymph cause vibrations of the basilar membrane. This moves stereocilia at the tips of
the hair cells against the tectorial membrane and open potassium channels in them. The influx of K+ from the endolymph
depolarizes the cell.

15.9B.1 https://bio.libretexts.org/@go/page/5684
You should note that hair cells differ from most "excitable cells" (neurons and muscle fibers) in their use of potassium ions, not
sodium ions, to depolarize the cell. Depolarization of the hair cell causes the release of a neurotransmitter (probably glutamate) at
its basal surface and the initiation of nerve impulses in a sensory neuron that synapses with it. These impulses travel back along the
auditory nerve (the 8th cranial nerve) to the brain.
Many people, especially when young, can hear sounds with frequencies (pitches) from as low as 16 to as high as 20,000 hertz
(cycles per second). Detection of a given frequency is a function of the location of the hair cells along the organ of Corti with the
highest frequencies detected near the base of the cochlea, and the remainder of the sound spectrum detected in a progressive
fashion with the lowest frequencies detected by hair cells near the tip.

Deafness
Deafness may be acquired or inherited.

Acquired deafness
If a laboratory animal is exposed to very intense, pure tones, it eventually becomes deaf to those frequencies, but its ability to hear
other pitches is unimpaired. Examination of its organ of Corti reveals destroyed hair cells in a single area whose location can be
easily correlated with the pitch of the destructive sound. Similar deficits occur in humans who are exposed to intense noises for
long periods. A trained audiologist can tell by looking at the frequency response whether a patient flies private aircraft.

Inherited deafness
About 1 newborn in a thousand is born deaf because of a genetic defect. As the years go by, many of us (~16%) suffer a
progressive loss of hearing because of genetic defects. Literally scores of genes have been identified in recent years whose mutant
versions result in hearing loss.

Figure 15.9.2.3 K - cycle

Mutations in a transcription factor have been associated with a stirrup (stapes) that cannot move freely and thus cannot transmit
vibrations to the oval window. The proper organization of the stereocilia involves actin, a form of myosin (called myosin VIIA),
and cadherins.also cause deafness. Mutations in the gene encoding a protein that helps with actin polymerization cause deafness.
Mutations in the myosin VIIA gene and mutations in the gene encoding cadherin 23.
The potassium that enters the hair cells must be removed from them and recycled back to the endolymph for hearing to continue.
Scores of mutations in the necessary transport molecules have been linked to inherited deafness. Mutations in genes encoding the
K+ channels that allows K+ to leave the hair cell through its basolateral surface (shown in green ). (These same channels are found
in the loops of Henle in the kidneys so the mutations can produce defects in kidney function as well as deafness.) Mutations in the
connexins (magenta) that form the gap junctions through which the K+ passes from cell to cell on its way back to the secretory
cells that will deposit it back in the endolymph. Mutations in the sodium-potassium-chloride cotransporter (shown in yellow) that
actively transports K+ against its concentration gradient into the secretory cells. Mutations in the K+ channels (shown in lavender)
that allow for the facilitated diffusion of K+ out of the secretory cells and into the endolymph.

Equilibrium
The inner ear also detects:
the position of the body with respect to gravity
the motion of the body.
Just above the cochlea are two interconnecting chambers filled with endolymph, the sacculus and utriculus. On their inner surface
are patches of hair cells to which are attached thousands of tiny spheres of calcium carbonate (CaCO3). Gravity pulls these

15.9B.2 https://bio.libretexts.org/@go/page/5684
downward. As the head is oriented in different directions, these ear stones or otoliths shift their position. The action potentials
initiated in the hair cells are sent back to the brain.
Motion of the body is detected in the three semicircular canals at the top of each inner ear, each one oriented in a different plane.
There is a small chamber at one end of each canal containing hair cells. Whenever the head is moved, the fluid within the canals
lags in its motion so that there is relative motion between the walls and the endolymph. This stimulates the hair cells to send
impulses back to the brain.
When the hair cells send messages that are incongruent with what the eyes are seeing and our body is feeling, as may occur in a
boat or aircraft during rough weather, motion sickness can result. Some people also suffer severe dizziness because otoliths have
become dislodged from their utriculus (e.g. following a blow to the head) and settled in a semicircular canal.

Echolocation
Bats can hear frequencies as high as 150,000 hertz. Sound at these ultrasonic (to us) frequencies travels in fairly straight lines. Bats
flying in complete darkness are able to locate obstacles and even insect prey by emitting pulses of this ultrasonic sound and then
adjusting the course of flight to the echo that returns to their ears. Such a system of echolocation works on the same principle as
sonar for submarine detection.

Figure 15.9.2.4 Echolocation of a blindfolded bat

A blindfolded bat can fly between the wires touching them only rarely. A bat whose ears are plugged collides repeatedly with the
wires.

Figure 15.9.2.5 Hunter and hunted

Hunter and hunted. In the top photo, a moth (bright streak) takes successful evasive action upon detecting the approach of a bat
(broad streak across the photo). (The diffuse image is a tree in the background.) In the bottom photo, the two streaks intersect,
indicating that this time the moth was unable to escape capture by the bat. (Photos by Frederic A. Webster, courtesy of the late Prof.
Kenneth D. Roeder.)

This page titled 15.9B: Hearing is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.9B.3 https://bio.libretexts.org/@go/page/5684
15.9C: Vision
The human eye is wrapped in three layers of tissue:
the sclerotic coat. This tough layer creates the "white" of the eye except in the front where it forms the transparent cornea. The
corneaThe surface of the cornea is kept moist and dust-free by secretions from the tear glands.
admits light to the interior of the eye and
bends the light rays to that they can be brought to a focus.
the choroid coat. This middle layer is deeply pigmented with melanin. It reduces reflection of stray light within the eye. The
choroid coat forms the iris in the front of the eye. This, too, is pigmented and is responsible for eye "color". The size of its
opening, the pupil, is variable and under the control of the autonomic nervous system. In dim light (or when danger threatens),
the pupil opens wider letting more light into the eye. In bright light the pupil closes down. This not only reduces the amount of
light entering the eye but also improves its image-forming ability (as does "stopping down" the iris diaphragm of a camera).
the retina The retina is the inner layer of the eye. It contains the light receptors, the rods and cones (and thus serves as the
"film" of the eye). The retina also has many interneurons that process the signals arising in the rods and cones before passing
them back to the brain. (Note: the rods and cones are not at the surface of the retina but lie underneath the layer of
interneurons.)

Figure 15.9.3.1 Human eye

 The blind spot

All the nerve impulses generated in the retina travel back to the brain by way of the axons in the optic nerve (above). At the
point on the retina where the approximately 1 million axons converge on the optic nerve, there are no rods or cones. This spot,
called the blind spot, is thus insensitive to light.

Figure 15.9.3.2 Blind spot

You can demonstrate the presence of the blind spot. Cover your right eye with your hand and stare at the red circle as you
move closer to the screen (the square will disappear). Or cover your left eye and stare at the red square as you move.

The Lens
The lens is located just behind the iris. It is held in position by zonules extending from an encircling ring of muscle. When this
ciliary muscle is relaxed, its diameter increases, the zonules are put under tension, and the lens is flattened and when contracted,
its diameter is reduced, the zonules relax, and the lens becomes more spherical. These changes enable the eye to adjust its focus
between far objects and near objects.

15.9C.1 https://bio.libretexts.org/@go/page/5686
 Figure 15.9.3.3 Eye corrections
Farsightedness. If the eyeball is too short or the lens too flat or inflexible, the light rays entering the eye — particularly those from
nearby objects — will not be brought to a focus by the time they strike the retina. Eyeglasses with convex lenses can correct the
problem. Farsightedness is called hypermetropia.
Nearsightedness. If the eyeball is too long or the lens too spherical, the image of distant objects is brought to a focus in front of the
retina and is out of focus again before the light strikes the retina. Nearby objects can be seen more easily. Eyeglasses with concave
lenses correct this problem by diverging the light rays before they enter the eye. Nearsightedness is called myopia.
Cataracts One or both lenses often become cloudy as one ages. When a cataract seriously interferes with seeing, the cloudy lens is
easily removed and a plastic one substituted. The entire process can be done in a few minutes as an outpatient under local
anesthesia.
The iris and lens divide the eye into two main chambers:
the front chamber is filled with a watery liquid, the aqueous humor
the rear chamber is filled with a jellylike material, the vitreous body

The Retina
Four kinds of light-sensitive receptors are found in the retina:
rods
three kinds of cones, each "tuned" to respond best to light from a portion of the spectrum of visible light
cones that absorb long-wavelength light (red)
cones that absorb middle-wavelength light (green)
cones that absorb short-wavelength light (blue)
This scanning electron micrograph (courtesy of Scott Mittman and David R. Copenhagen) shows rods and cones in the retina of the
tiger salamander. Each type of receptor has its own special pigment for absorbing light. Each consists of a transmembrane protein
called opsin coupled to the prosthetic group retinal. Retinal is a derivative of vitamin A (which explains why night blindness is
one sign of vitamin A deficiency) and is used by all four types of receptors.

Figure 15.9.3.4 The retina

The amino acid sequence of each of the four types of opsin are similar, but the differences account for their differences in
absorption spectrum. The retina also contains a complex array of interneurons:
bipolar cells and ganglion cells that together form a path from the rods and cones to the brain

15.9C.2 https://bio.libretexts.org/@go/page/5686
 a complex array of other interneurons that form synapses with the bipolar and ganglion cells and modify their activity.
Ganglion cells are always active. Even in the dark they generate trains of action potentials and conduct them back to the brain
along the optic nerve. Vision is based on the modulation of these nerve impulses. There is not the direct relationship between
visual stimulus and an action potential that is found in the senses of hearing, taste, and smell. In fact, action potentials are not even
generated in the rods and cones.

Rod Vision
Rhodopsin is the light-absorbing pigment of the rods. This G-protein-coupled receptor (GPCR) is incorporated in the membranes
of disks that are neatly stacked (some 1000 or more of them) in the outer portion of the rod. This arrangement is reminiscent of the
organization of thylakoids, another light-absorbing device.

Fig.15.9.3.5 Rod cells of kangaroo bat

The electron micrograph (courtesy of Keith Porter) shows the rod cells of the kangaroo rat. The outer segments of the rods contain
the orderly stacks of membranes which incorporate rhodopsin. The inner portion contain many mitochondria. The two parts of the
rod are connected by a stalk (arrow) that has the same structure as a primary cilium. Although the disks are initially formed from
the plasma membrane, they become separated from it. Thus signals generated in the disks must be transmitted by a chemical
mediator (a "second messenger" called cyclic GMP (cGMP) to alter the potential of the plasma membrane of the rod. Rhodopsin
consists of an opsin of 348 amino acids coupled to retinal. Like all G-protein-coupled receptors, opsin has 7 segments of alpha
helix that pass back and forth through the lipid bilayer of the disk membrane.

Retinal

Figure 15.9.3.6 Retinal

Retinal consists of a system of alternating single and double bonds. In the dark, the hydrogen atoms attached to the #11 and #12
carbon atoms of retinal (red arrows) point in the same direction producing a kink in the molecule. This configuration is designated
cis. When light is absorbed by retinal, the molecule straightens out forming the all-trans isomer.
This physical change in retinal triggers the following chain of events culminating in a change in the
pattern of impulses sent back along the optic nerve.
1. Formation of all-trans retinal activates its opsin.
2. Activated rhodopsin, in turn, activates many molecules of a G protein called transducin.
3. Transducin activates an enzyme that breaks down cyclic GMP.
+

15.9C.3 https://bio.libretexts.org/@go/page/5686
 4. The drop in cGMP closes Na+ channels in the plasma membrane of the rod. Because these positive ions can no longer enter, the
interior of the cell becomes more negative (hyperpolarized) increasing its membrane potential from about −30 to some −70 mV.
5. This slows the release of the neurotransmitter glutamate at synapses between the rod and interneurons (e.g., bipolar cells).
6. This reduction in glutamate release activates some interneuron pathways, inhibits others.
7. The interplay of excited and inhibited interneurons modulates the spontaneous firing of the ganglion cells to which they are
connected and gives rise to the ability of the retina to discriminate shapes.
So the retina is not simply a sheet of photocells, but a tiny brain center that carries out complex information processing before
sending signals back along the optic nerve. In fact, the retina really is part of the brain and grows out from it during embryonic
development.

Rod vision is acute but coarse

Rods do not provide a sharp image for several reasons.
Adjacent rods are connected by gap junctions and so share their changes in membrane potential.
Several nearby rods often share a single circuit to one ganglion cell.
A single rod can send signals to several different ganglion cells.
So if only a single rod is stimulated, the brain has no way of determining exactly where on the retina it was. However, rods are
extremely sensitive to light. A single photon (the minimum unit of light) absorbed by a small cluster of adjacent rods is sufficient to
send a signal to the brain. So although rods provide us with a relatively grainy, colorless image, they permit us to detect light that is
over a billion times dimmer than what we see on a bright sunny day.

Cone Vision
Although cones operate only in relatively bright light, they provide us with our sharpest images and enable us to see colors. Most of
the 3 million cones in each retina are confined to a small region just opposite the lens called the fovea. So our sharpest and colorful
images are limited to a small area of view. Because we can quickly direct our eyes to anything in view that interests us, we tend not
to be aware of just how poor our peripheral vision is.
The three types of cones provide us the basis of color vision. Cones are "tuned" to different portions of the visible spectrum.
red absorbing cones; those that absorb best at the relatively long wavelengths peaking at 565 nm
green absorbing cones with a peak absorption at 535 nm
blue absorbing cones with a peak absorption at 440 nm.
Retinal is the prosthetic group for each pigment. Differences in the amino acid sequence of their opsins accounts for the differences
in absorption. The response of cones is not all-or-none. Light of a given wavelength (color), say 500 nm (green), stimulates all
three types of cones, but the green-absorbing cones will be stimulated most strongly. Like rods, the absorption of light does not
trigger action potentials but modulates the membrane potential of the cones.

Color Blindness
The term color blindness is something of a misnomer. Very few (~1 in 105) people cannot distinguish colors at all. Most "color-
blind" people actually have abnormal color vision such as confusing the red and green of traffic lights. As high as 8% of the males
in some populations have an inherited defect in their ability to discriminate reds and greens. These defects are found almost
exclusively in males because the genes that encode the red-absorbing and green-absorbing opsins are on the X chromosome.

15.9C.4 https://bio.libretexts.org/@go/page/5686
 Figure 15.9.3.7 Red - Green genes
The X chromosome normally carries a cluster of from 2 to 9 opsin genes. The minimum basis for normal red-green vision is one
gene whose opsin absorbs efficiently in the red and one that absorbs well in the green (chromosome 1 in the figure). Multiple
copies of these genes are also fine (2 and 3). Males with either a "green gene" or "red gene" missing are severely color blind (4 and
5). However, if all the red genes carry mutations (this seldom seems to be the case for the green genes — nobody knows why), then
they may have red-green color blindness that ranges from mild to severe depending on the particular mutations involved (6). The
rule seems to be that the more the mutations shift the pigment towards green, the more serious the defect. However, a large number
of mutations don't always produce serious defects. Multiple mutations in a single gene may offset each other producing only mild
defects. And as long as one normal copy of each gene is present, the presence of additional mutated genes seldom produce a serious
problem (7).
Why do some males have as many as 9 copies of genes encoding the red and green opsins, when two are enough? The sequences of
the red and green genes are the same at 98% of their nucleotides. This high degree of similarity creates the risk of mismatches in
synapsis during meiosis with unequal crossing over.

Blue vision
Abnormal blue sensitivity occasionally occurs in humans but is much rarer than abnormalities in red-green vision. The gene for the
blue-cone opsin is located on chromosome 7. Thus this trait shows an autosomal pattern of inheritance being found in females as
often as in males.

This page titled 15.9C: Vision is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.9C.5 https://bio.libretexts.org/@go/page/5686
15.9D: Processing Visual Information

Figure 15.9.4.2 Ganglion cells

By inserting an electrode in a single ganglion cell, it was shown (by Stephen W. Kuffler) that
Even in the dark, ganglion cells have a slow, steady rate of firing.
Diffuse light directed on the retina has little effect on this rate.
But a tiny spot of light falling on a small circular area of the retina can greatly increase the firing rate of some ganglion cells
(left) while
a spot directed around the perimeter of such an "on" area suppresses that ganglion cell (center).
Light shining on both areas produces no effect (right).
Other ganglion cells have a central "off" area surrounded by an "on" area.

Figure 15.9.4.3 Lateral geniculate nucleus

Two associates of Kuffler, David H. Hubel and Torsten N. Wiesel inserted electrodes in these areas but instead of directing light
into the eye, they projected images on a screen in front of the animal (an anesthetized cat or monkey). Using this procedure, they
found that
cells of the lateral geniculate nucleus (LGN) respond about the same way that ganglion cells do; that is, to circular spots of
light.
But the cells in the visual cortex receiving input from the LGN no longer respond to circles of light but only to bars of light (or
dark) or to straight-line edges between dark and light areas.
One of these "simple cortical cells" will only respond when the stimulus is directed at a particular area of the screen and at a
specific angle. However, an ineffective position for one of these cortical cells is an effective position for another.

Figure 15.9.4.4 LGN

15.9D.1 https://bio.libretexts.org/@go/page/5688
The diagram shows this mechanism by which the circular response areas of ganglion and LGN cells can be converted into the
rectangular response areas found in the cells of the visual cortex. Other cells ("complex cortical cells") still want their edges
oriented in one direction, but the edges can now be moved across the screen. As the figure shows, this can be explained if a set of
simple cortical cells all responding to an edge of the same slope but each responsible for a different part of the visual field converge
on a single "complex cortical cell". Thus these complex cortical cells continue to respond to the stimulus even though its absolute
position on the retina changes.
While these studies provide only the tiniest glimpse into the workings of the brain, they provide some clues of what will be found:
At each step of processing, the inputs of a number of interneurons are funneled into a single output.
So, at each step, some of the information is selectively destroyed.
A simple cortical cell, for example, fires only if a number of LGN cells converging on it are simultaneously active. Otherwise,
the excitation dies out at the synapses.
In this way, each level of the brain acts as a filtering device and, in doing so, provides a mechanism by which certain features of
what might be a very complex stimulus can be discriminated..
So instead of responding to particular impulses in particular circuits, the mammalian brain seems to respond to the spatial and
temporal organization of many impulses passing along many converging circuits.
The importance of these studies was recognized by the award of a Nobel Prize in 1981 to Hubel and Wiesel (too late for Kuffler,
who died in 1980).

This page titled 15.9D: Processing Visual Information is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.9D.2 https://bio.libretexts.org/@go/page/5688
15.9E: Vision in Arthropods
The arthropod (e.g., insects, crustaceans) eye is built quite differently from the vertebrate eye (and mollusk eye). Arthropod eyes
are called compound eyes because they are made up of repeating units, the ommatidia, each of which functions as a separate
visual receptor. Each ommatidium consists of
a lens (the front surface of which makes up a single facet)
a transparent crystalline cone
light-sensitive visual cells arranged in a radial pattern like the sections of an orange
pigment cells which separate the ommatidium from its neighbors.
The pigment cells ensure that only light entering the ommatidium parallel (or almost so) to its long axis reaches the visual cells and
triggers nerve impulses. Thus each ommatidium is pointed at just a single area in space and contributes information about only one
small area in the field of view. There may be thousands of ommatidia in a compound eye with their facets spread over most of the
surface of a hemisphere.
The photo, courtesy Carolina Biological Supply Company, shows the compound eye of Drosophila melanogaster. The composite
of all their responses is a mosaic image — a pattern of light and dark dots rather like the halftone illustrations in a newspaper or
magazine. And just as in those media, the finer the pattern of dots, the better the quality of the image.

Figure 15.9E. 1: A photograph of the head of a woodworm beetle (Anobium punctatum) showing the compound eye and
ommatidia. Photograph by Siga licensed under Creative Commons.
Grasshopper eyes, with relatively few ommatidia must produce a coarse, grainy image. The honeybee and dragonfly have many
more ommatidia and a corresponding improvement in their ability to discriminate ("resolve") detail. Even so, the resolving ability
of the honeybee eye is poor in comparison with that of most vertebrate eyes and only 1/60 as good as that of the human eye; that is,
two objects that we could distinguish between at 60 feet (18 m) could only be discriminated by the bee at a distance of one foot (0.3
m).

Flicker effect
The compound eye is excellent at detecting motion. As an object moves across the visual field, ommatidia are progressively turned
on and off. Because of the resulting "flicker effect", insects respond far better to moving objects than stationary ones. Honeybees,
for example, will visit wind-blown flowers more readily than still ones.

15.9E.1 https://bio.libretexts.org/@go/page/5690
Resolution and Sensitivity
Arthropods that are apt to be active in dim light (e.g., crayfish, praying mantis) concentrate the screening pigments of their
ommatidia into the lower ends of the pigment cells. This shift enables light entering a single ommatidium at an angle to pass into
adjacent ommatidia and stimulate them also. With many ommatidia responding to a single area in the visual field, the image
becomes coarser. The praying mantis probably can do little more than distinguish light and dark in the evening.
The shift in pigments does, however, make it more sensitive to light than it is in the daytime as more ommatidia can detect a given
area of light.

Color vision
Some insects are able to distinguish colors. This requires two or more pigments, each of which absorbs best at a different
wavelength. In the honeybee:
four of the visual cells in each ommatidium respond best to yellow-green light (544 nm)
two respond maximally to blue light (436 nm)
the remaining two respond best to ultraviolet light (344 nm)
This system should enable the honeybee to distinguish colors (except red) and Figure 15.9E. 2 shows - behavioral studies verify
this.

Figure 15.9E. 2: Color vision in bees Courtesy of Dr. M. Renner

The above picture shows a demonstration of color vision in honeybees. After a period of feeding from a dish placed on blue
cardboard, the bees return to an empty dish on a clean blue card. They are able to distinguish the blue card from others of varying
shades of gray.

Ultraviolet vision
Why ultraviolet vision? Television camera tubes are also sensitive to ultraviolet, as well as visible light, but their glass lens is
opaque to ultraviolet. (This is why you cannot get tanned or synthesize calciferol Vitamin D2) from the sunlight passing through
window glass.) Using a special ultraviolet-transmitting lens (Figure 15.9E. 3), many insect-pollinated flowers appear to the
honeybee quite different from the way they appear to us. The sharp contrasts between flowers that appear similar to us partly
explains the efficiency with which honeybees secure nectar from only one species of flower at a time even when other species are
also in bloom.

Figure 15.9E. 3: Images of a Mimulus flower in visible light (left) and ultraviolet light (right) showing a dark nectar guide that is
visible to bees but not to humans. (CC BY-SA 3.0; Plantsurfer).
Monarch butterflies, which can migrate as much as 2500 miles (> 4000 km), navigate by ultraviolet light from the sun. When their
view of the sun is through a filter that blocks out only its ultraviolet rays, their flight path becomes disoriented. Ultraviolet vision is

15.9E.2 https://bio.libretexts.org/@go/page/5690
not limited to animals with compound eyes. A few marsupials, rodents, a bat that feeds on nectar, and many birds have also been
shown to have ultraviolet vision.

This page titled 15.9E: Vision in Arthropods is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.9E.3 https://bio.libretexts.org/@go/page/5690
15.9F: Heat, Cold, and Pain Receptors

This page examines the detection of heat, cold, and pain. Why pain? Because at least some of the receptors of heat and cold, when
the stimulus exceeds a certain threshold, transmit signals that the brain interprets as pain.

The Receptors
Few, if any, of the receptors of heat, cold, and pain are specialized transducers (in the way that, for example, the Pacinian corpuscle
is). Rather they are sensory neurons whose plasma membrane contains transmembrane proteins that are ion channels that open in
response to particular stimuli. A single neuron may contain several types of these ion channels and thus be able to respond to
several types of stimuli. Like all sensory spinal neurons, their axons travel to a dorsal root ganglion of the spinal cord, where their
cell bodies reside, and then on in to the gray matter of the spinal cord.
Three types of sensory neurons are found in the skin.
Aδ ("A-delta") fibers
These are thinly-myelinated.
They transmit signals in response to heat and touch. If the stimulus exceeds a certain threshold, the brain interprets these as
acute pain. This is "good pain" because it warns you to do something to take care of the problems, e.g., a hot saucepan.
C fibers
These are unmyelinated and thus conduct impulses slowly.
C fibers also respond to heat and touch. If the stimulus exceeds a certain threshold, the brain interprets these as diffuse, dull,
chronic pain. This is "bad pain" because it cannot be alleviated simply by removing the stimulus. It is pain generated by
such things as damaged tissue or pain that remains after the stimulus that caused acute pain has been removed.
Aβ ("A-beta") fibers
These are thickly-myelinated fibers.
They mostly respond to painless stimuli such as light touch.

Heat
There are several types of ion channels in the skin that respond to temperature. They are all transmembrane proteins in the plasma
membrane that open to let in both calcium ions and sodium ions (the latter the source of the action potential). Between them, they
cover a range of temperatures.
TRPV4
Warm (~27–34°C)
TRPV3
Warmer (~34–39°C)
TRPV1
Hot (≥43°C). Also activated by capsaicin, the active ingredient of hot chili peppers, by camphor, by acids (protons), and by
pain-inducing products of inflammation.
TRPV2
Painfully hot (>52°C)
Knockout mice lacking the TRPV1 receptor not only do not avoid water with capsaicin in it but have a diminished response to heat
and to substances that normal elicit itching. Birds also have TRPV1 receptors. Theirs also respond to heat (and acids), but do not
respond to capsaicin. This must explain why birds happily eat hot chili peppers (and so disperse their seeds). The vampire bat,
Desmodus rotundus, expresses normal TRPV1 receptors in the sensory neurons leading to the dorsal root ganglia, and these
respond normally to painful heat (> 43°C). However, these bats express a shortened version of TRPV1 (produced by alternative
splicing) in their trigeminal nerves that run from the bat's upper lip and nose. The shortened receptors respond to a lower
temperature (~30°C) enabling the bats to detect the warmth radiating from the skin of their victims.

15.9F.1 https://bio.libretexts.org/@go/page/5692
Cold
Two candidate receptors:
One, designated TRPM8, is a channel that admits Ca2+ and Na+ in response to moderate cold (<28°C) or menthol (the
ingredient that gives mint its "cool" touch and taste). Knockout mice lacking the gene encoding the TRPM8 receptor do not
avoid cold places as normal mice do.
A second, designated TRPA1, responds to lower temperatures (<18°C). It also responds to several irritant chemicals eliciting
signals that the brain interprets at pain. TRPA1 is found in the hair cells of the inner ear that respond to sound and changes in
position.) However, TRPA1 knockout mice respond normally to cold and seem to have normal hearing so the precise role of
these receptors is still uncertain for those stimuli.
TRPA1 channels serve a different function in pit vipers like rattlesnakes. These cold-blooded animals detect warm-blooded prey
using temperature-sensitive neurons at the base of pits in their head. The neurons contain TRPA1 channels that open wide when
radiant heat entering the pit raises their temperature above 27°C.

Pain
When sensory nerve fibers are exposed to extremes, they signal pain. Pain receptors are also called nociceptors.

Processing Pathways
All the neurons in the skin are part of the sensory-somatic branch of the peripheral nervous system. Their axons pass into the dorsal
root ganglion, where their cell body is located, and then on in to the gray matter of the spinal cord where they synapse with
interneurons.
Several different neurotransmitters have been implicated in pain pathways. Three of them:
glutamate. This seems to be the dominant neurotransmitter when the threshold to pain is first crossed. It is associated with acute
("good") pain.
substance P. This peptide (containing 11 amino acids) is released by C fibers. It is associated with intense, persistent, chronic -
thus "bad" pain.
glycine. It suppresses the transmission of pain signals in the dorsal root ganglion. Prostaglandins potentiate the pain of
inflammation by blocking its action.

Neuropathic Pain
This is pain caused by injury to the nerves themselves such as by mechanical damage, massive inflammation, and growing tumors.

Visceral Pain
The brain can also register pain from stimuli originating in sensory neurons of the autonomic nervous system. This so-called
visceral pain is not felt in a discrete location as pain signals transmitted by the sensory-somatic system are.

Treating pain with drugs

The weapons presently available to reduce pain are many in number but few in types. They are
Non-steroidal anti-inflammatory drugs (NSAIDs)
Opioids (also called opiates)
NSAIDs
Inflammation is caused by tissue damage and, among other things, causes pain. Damaged tissue releases prostaglandins and these
are potent triggers of pain. Prostaglandins are 20-carbon organic acids synthesized from unsaturated fatty acids.
There are at least three key enzymes that synthesize prostaglandins:
Cyclooxygenase 1 (Cox-1)
Cyclooxygenase 2 (Cox-2)
Cyclooxygenase 3 (Cox-3)
Most NSAIDs block the action of all three cyclooxygenases. They include:
aspirin

15.9F.2 https://bio.libretexts.org/@go/page/5692
 ibuprofen (Advil®, Motrin®)
naproxen (Aleve®)
and many others
Two NSAIDs celecoxib (Celebrex®) and rofecoxib (Vioxx®) were introduced in 1999 that selectively inhibit Cox-2 while leaving
Cox-1 untouched. It was hoped that these would provide pain relief without the gastrointestinal side effects associated with the
broad spectrum NSAIDs. However, the manufacturer of Vioxx® removed it from the market on 30 September 2004 because it
increases the risk of heart attacks and strokes.
Acetaminophen (Tylenol®)
This is also a nonsteroidal anti-inflammatory drug but its mode of action is different from the others. It selectively inhibits Cox-3
and provides pain relief without irritating the stomach. It is particularly useful for
people allergic to aspirin and its relatives
avoiding the risk of Reye's syndrome that has been associated with giving aspirin to children with viral infections.
Opioids
Opioids are extremely effective pain killers but are also addictive so their use is surrounded by controversy and regulation.
Some examples:
morphine
codeine
heroin
methadone
oxycodone
Opioids bind to receptors on interneurons in the pain pathways in the central nervous system. The natural ligands for these
receptors are two enkephalins — each a pentapeptide (5 amino acids):
Met-enkephalin (Tyr-Gly-Gly-Phe-Met)
Leu-enkephalin (Tyr-Gly-Gly-Phe-Leu)

Figure 15.9.6.1 Pain synapse

The drawing shows how this mechanism might work. The activation of enkephalin synapses suppresses the release of the
neurotransmitter (substance P) used by the sensory neurons involved in the perception of chronic and/or intense pain. The ability
to perceive pain is vital. However, faced with massive, chronic, intractable pain, it makes sense to have a system that decreases its
own sensitivity. Enkephalin synapses provide this intrinsic pain-suppressing system.
Morphine and the other opioids bind these same receptors. This makes them excellent pain killers.
However, they are also highly addictive.
By binding to enkephalin receptors, they enhance the pain-killing effects of the enkephalins.
A homeostatic reduction in the sensitivity of these synapses compensates for continued exposure to opioids.
This produces tolerance, the need for higher doses to achieve the prior effect.

15.9F.3 https://bio.libretexts.org/@go/page/5692
 If use of the drug ceases, the now relatively insensitive synapses respond less well to the soothing effects of the enkephalins,
and the painful symptoms of withdrawal are produced.

This page titled 15.9F: Heat, Cold, and Pain Receptors is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.9F.4 https://bio.libretexts.org/@go/page/5692
15.9G: Taste

Figure 15.9.7.1 Taste bud

There are five primary taste sensations:
salty
sour
sweet
bitter
umami

Properties of the taste system

A single taste bud contains 50–100 taste cells representing all 5 taste sensations (so the classic textbook pictures showing
separate taste areas on the tongue are wrong).
Each taste cell has receptors on its apical surface. These are transmembrane proteins which
admit the ions that give rise to the sensation of salty
bind to the molecules that give rise to the sensations of sweet, bitter, and umami
A single taste cell seems to be restricted to expressing only a single type of receptor (except for bitter receptors).
A stimulated taste receptor cell triggers action potentials in a nearby sensory neuron leading back to the brain.
However, a single sensory neuron can be connected to several taste cells in each of several different taste buds.
The sensation of taste like all sensations resides in the brain.
And in mice, at least, the sensory neurons for four of the tastes (not sour) transmit their information to four discrete areas of the
brain.

Salty
In mice, perhaps humans, the receptor for table salt (NaCl) is an ion channel that allows sodium ions (Na+) to enter directly into the
cell depolarizing it and triggering action potentials in a nearby sensory neuron.
In lab animals, and perhaps in humans, the hormone aldosterone increases the number of these salt receptors. This makes good
biological sense:
The main function of aldosterone is to maintain normal sodium levels in the body.
An increased sensitivity to sodium in its food would help an animal suffering from sodium deficiency (often a problem for
ungulates, like cattle and deer).

Sour
Sour receptors detect the protons (H+) liberated by sour substances (acids). This closes transmembrane K+ channels which leads to
depolarization of the cell, and the release of the neurotransmitter serotonin into its synapse with a sensory neuron.

Sweet
Sweet substances (like table sugar sucrose) bind to G-protein-coupled receptors (GPCRs) at the cell surface.
Each receptor contains 2 subunits designated T1R2 and T1R3 and is coupled to G proteins.

15.9G.1 https://bio.libretexts.org/@go/page/5694
 The complex of G proteins has been named gustducin because of its similarity in structure and action to the transducin that
plays such an essential role in rod vision.
Activation of gustducin triggers a cascade of intracellular reactions:
production of the second messengers inositol trisphosphate (IP3) and diacylglycerol (DAG)
this releases intracellular stores of Ca++
this allows in the influx of Na+ ions depolarizing the cell and causing the release of ATP
this triggers action potentials in a nearby sensory neuron.
The hormone leptin inhibits sweet cells by opening their K+ channels. This hyperpolarizes the cell making the generation of action
potentials more difficult. Could leptin, which is secreted by fat cells, be a signal to cut down on sweets?

Bitter
The binding of substances with a bitter taste, e.g., quinine, phenylthiocarbamide [PTC], also takes place on G-protein-coupled
receptors that are coupled to gustducin and the signaling cascade is the same as for sweet (and umami).
Humans have genes encoding 25 different bitter receptors ("T2Rs"), and each taste cell responsive to bitter expresses a number (4–
11) of these genes. (This is in sharp contrast to the system in olfaction where a single odor-detecting cell expresses only a single
type of odor receptor.)
Despite this — and still unexplained — a single taste cell seems to respond to certain bitter-tasting molecules in preference to
others.
The sensation of taste — like all sensations — resides in the brain. Transgenic mice that
express T2Rs in cells that normally express T1Rs (sweet) respond to bitter substances as though they were sweet
express a receptor for a tasteless substance in cells that normally express T2Rs (bitter) are repelled by the tasteless compound
So it is the activation of hard-wired neurons that determines the sensation of taste, not the molecules nor the receptors themselves.

Umami
Umami is the response to salts of glutamic acid — like monosodium glutamate (MSG) a flavor enhancer used in many processed
foods and in many Asian dishes. Processed meats and cheeses (proteins) also contain glutamate. The binding of amino acids,
including glutamic acid, takes place on G-protein-coupled receptors that are coupled to heterodimers of the protein subunits
T1R1 and T1R3. The signaling cascade that follows is the same as it is for sweet and bitter.

Taste Receptors in Other Locations

Taste receptors have been found in several other places in the body. Examples:
Bitter receptors (T2Rs) are found on the cilia and smooth muscle cells of the trachea and bronchi where they probably serve to
expel inhaled irritants;
Sweet receptors (T1Rs) are found in cells of the duodenum. When sugars reach the duodenum, the cells respond by releasing
incretins. These cause the beta cells of the pancreas to increase the release of insulin.
So the function of "taste" receptors appears to be the detection of chemicals in the environment - a broader function than simply
taste.

This page titled 15.9G: Taste is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.9G.2 https://bio.libretexts.org/@go/page/5694
15.9H: Olfaction - The Sense of Smell
Smell depends on sensory receptors that respond to airborne chemicals. In humans, these chemoreceptors are located in the
olfactory epithelium — a patch of tissue about the size of a postage stamp located high in the nasal cavity. The olfactory epithelium
is made up of three kinds of cells: sensory neurons each with a primary cilium supporting cells between them basal cells that divide
regularly producing a fresh crop of sensory neurons to replace those that die.

Figure 15.9.8.1 Olfactory epithelium

Smell depends on sensory receptors that respond to airborne chemicals. In humans, these chemoreceptors are located in the
olfactory epithelium — a patch of tissue about the size of a postage stamp located high in the nasal cavity. The olfactory
epithelium is made up of three kinds of cells:
sensory neurons each with a primary cilium
supporting cells between them
basal cells that divide regularly producing a fresh crop of sensory neurons to replace those that die (and providing an exception
to the usual rule that neurons seldom are replaced)

The sequence of events

Figure 15.9.8.2 Olfaction

The cilia of the sensory neurons are immersed in a layer of mucus. Odorant molecules (molecules that we can smell) dissolve
in the mucus.
These then bind to receptors on the cilia. These are "7-pass" transmembrane proteins.
Binding of the odorant activates a G protein coupled to the receptor on its cytoplasmic side.
This activates adenylyl cyclase, an enzyme embedded in the plasma membrane of the cilia.
Adenylyl cyclase catalyzes the conversion of ATP to the "second messenger" cyclic AMP (cAMP) in the cytosol.

 ). Some other examples of GPCRs:

receptors of peptide hormones
taste receptors
the light receptor rhodopsin
GABAB receptors at certain synapses in the brain

cAMP opens up ligand-gated sodium channels for the facilitated diffusion of Na+ into the cell
The influx of Na+ reduces the potential across the plasma membrane.
If this depolarization reaches threshold, it generates an action potential.
The action potential is conducted back along the olfactory nerve to the brain.
The brain evaluates this and other olfactory signals reaching it as a particular odor.

15.9H.1 https://bio.libretexts.org/@go/page/5696
How can one kind of cell enable us to discriminate among so many different odors?
Humans can discriminate between hundreds, perhaps thousands, of different odorant molecules, each with its own structure. How
can one kind of cell provide for this?
The mechanism:
Although a single olfactory neuron contains over a thousand receptor genes, there is only a single enhancer capable of binding
to the promoters of these genes and turning them on. There are, of course, two alleles of the enhancer but only one is active (one
is methylated; the other is not). Presumably, when the active enhancer encounters the promoter of an olfactory gene, it turns it
on and ceases its search. Thus only one olfactory receptor gene gets to be expressed in a single cell, but which one is a matter of
chance.
Now we have a mechanism for discriminating among a thousand or so odorants. However,
Each receptor is probably capable of binding to several different odorants — some more tightly than others. (The cells
described above also responded — although more weakly — to 3 related odorants.)
Each odorant is capable of binding to several different receptors.
This provides the basis for combinatorial diversity. It would work like this:
Assume that
Odorant A binds to receptors on neurons #3, #427, and #886.
Odorant B binds to receptors on neurons #2, #427, and #743.
The brain then would interpret the two different patterns of impulses as separate odors.
This mechanism appears capable of discriminating between as many as a trillion different mixtures of odorants.

This page titled 15.9H: Olfaction - The Sense of Smell is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

15.9H.2 https://bio.libretexts.org/@go/page/5696
15.9I: Electric Organs and Electroreceptors

Figure 15.9.9.1 Electroplate

At rest, the interior of each electrocyte, like a nerve or muscle cell, is negatively charged with respect to the two exterior surfaces.
The potential is about 0.08 volt, but because the charges alternate, no current flows. When a nerve impulse reaches the posterior
surface, the inflow of sodium ions momentarily reverses the charge just as it does in the action potential of nerves and muscles. (In
most fishes, electrocytes are, in fact, modified muscle cells.) Although the posterior surface is now negative, the anterior surface
remains positive. The charges now reinforce each other and a current flows just as it does through an electric battery with the cells
wired in "series".
With its several thousand electrocytes, the South American electric eel (Electrophorus electricus) produces voltages as high as 600
volts. The flow (amperage) of the current is sufficient (0.25–0.5 ampere) to stun, if not kill, a human. The pulse of current can be
repeated several hundred times each second.
Powerful electric organs like those of the electric eel are used as weapons to stun prey as well as potential predators.

The Mechanism
In the 5 December 2014 issue of Science, Kenneth Catania describes his experiments that revealed how the electric eel captures its
prey.
While exploring its environment, the eel emits a continuous series of low-voltage discharges. Periodically it interrupts these with a
discharge of 2 or 3 high-voltage pulses. These cause nearby prey, e.g. a fish, to twitch. Within a tiny fraction of a second (20–40
ms) of detecting the twitch, the eel unleashes a volley (~400 per second) of high-voltage discharges that stun the prey enabling the
eel to capture it.
Remarkably, both the twitch response and the immobilization are triggered by the prey's own motor neurons. A pair of pulses
induces a brief contraction while a volley of discharges induces tetanus.
Although action potentials in the prey's motor neurons were not measured directly, two pieces of evidence support this mechanism.
1. The responses remained intact even when the brain and spinal cord of the prey were destroyed thus eliminating the possibility
that the prey was relying on a sensory→cns→motor reflex.
2. Curare, which blocks the transmission of action potentials across the neuromuscular junction did block the prey's responses.
So hunting by the electric eel involves a preliminary 2 or 3 powerful pulses to - in Catania's words - answer the question "Are you
living prey?". If the answer is "yes", the prey is quickly stunned and ready to eat.

Weak Electric Organs

The electric organs of many fishes are too weak to be weapons. Instead they are used as signaling devices.
Many fishes, besides the electric eel, emit a continuous train of electric signals in order to detect objects in the water around them.
The system operates something like an underwater radar and requires that the fishes also have electroreceptors (which are located
in the skin). The presence of objects in the water distorts the electric fields created by the fish, and this alteration is detected by the
electroreceptors.
Electric fishes use their system of transmitter and receiver for such functions as
navigating in murky water and/or at night
locating potential mates

15.9I.1 https://bio.libretexts.org/@go/page/5698
 defense of their territory against rivals of the same species
attracting other members of their species into schools

This page titled 15.9I: Electric Organs and Electroreceptors is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by
John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

15.9I.2 https://bio.libretexts.org/@go/page/5698
15.9J: Magnetoreceptors
Evidence for an ability to alter their behavior in response to the earth's magnetic field has been found in many animals, including
sea turtles, birds, fish (especially common in those that migrate), honeybees, mice as well as in some bacteria.
Some examples:
Homing pigeons become disoriented when magnets are placed at the sides of their head. However, this disorientation occurs
only on cloudy days, suggesting that their ability to navigate by magnetic cues is a backup system.
Woodmice, taken from their home territory to a new location 40 meters away, normally orient toward home (left side of figure).
But if, while they are being moved, they are exposed to a magnetic field that is just the reverse of the earth's magnetic field —
and they are not allowed to see the surrounding terrain — they orient away from their home (right side of figure).

Figure 15.9.10.1 Magnetic sense

Left: orientation taken by individual woodmice after being removed from their home in a closed box. Right: same experiment
except that the mice were subjected to a reversed magnetic field as they were moved from their home. Each dot represents the
orientation taken by one mouse. The arrow within each circle indicates the average for all the mice. Mice transported in an open
box so they can see landmarks orient correctly whether or not they are exposed to an abnormal magnetic field. (Based on the work
of Mather and Baker, Nature, 291:152, 1981.)
Thrush nightingales (Luscinia luscinia) migrate in the fall from northern Europe to equatorial Africa. They interrupt their migration
with a stopover in northern Egypt where they feed and gain weight. This stopover presumably provides them with the energy stores
they need to fly without feeding across the Sahara Desert.
Fransson and colleagues report in the 1 November 2001 issue of Nature that when they confined naive birds (born in Sweden that
spring) in Sweden but exposed them to a magnetic field characteristic of northern Egypt, the birds proceeded to put on weight as
though they had arrived in Egypt (and three times more than control birds kept in the normal magnetic field of Sweden).

Receptors that detect magnetic fields

The location and mechanism of action of the receptors in these animals is still a puzzle. Microscopic grains of magnetite
(FeO.Fe2O3), a magnetic material, have been found in honeybees and pigeons, but whether and how these might function as
receptors is not known.
Certain bacteria orient themselves in magnetic fields as weak as those of the earth and this is mediated by grains of magnetite
within the cell. There is also evidence that birds and amphibians can supplement their magnetic sense using the interaction of light
and magnetic fields on cryptochrome molecules in their retina. The ability of Drosophila to respond to magnetic fields depends on
blue light and cryptochrome.
In the absence of blue light, the flies do not respond to a magnetic field.
Mutant flies that lack cryptochrome are likewise insensitive to magnetic fields.
However, mutant flies whose own cryptochrome genes have been replaced by the human gene respond normally to a magnetic
field while exposed to blue light.

How humans detect magnetic fields

The jury is still out. There is some evidence that humans can detect the orientation of magnetic fields. Both cryptochrome and
magnetite are found in humans, but their presence may have nothing to do with magnetoreception.

This page titled 15.9J: Magnetoreceptors is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.9J.1 https://bio.libretexts.org/@go/page/5700
 SECTION OVERVIEW
15.10: Muscles
Topic hierarchy

15.10A: Bones

15.10B: Muscles

15.10C: Testing the Sliding-Filament Hypothesis

This page titled 15.10: Muscles is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.10.1 https://bio.libretexts.org/@go/page/5370
15.10A: Bones
The vertebrate body is supported by an endoskeleton made of cartilage and bone. (Sharks and their relatives use only cartilage.)
The bones of the human skeleton perform several functions: support, protection of internal organs from mechanical damage (e.g.,
skull, ribs), reservoir of calcium and phosphate, and source of all the blood cells

Figure 15.10.1.1 Human bone skeleton

The vertebrate body is supported by an endoskeleton made of cartilage and bone. (Sharks and their relatives use only cartilage.)
The bones of the human skeleton perform several functions:
support
protection of internal organs from mechanical damage (e.g., skull, ribs)
reservoir of calcium and phosphate
source of all the blood cells

Structure

Figure 15.10.1.2 Bone structure

Periosteum. A tissue covering the bone that brings blood and lymph vessels, as well as nerves, to it.
Compact bone (also known as cortical bone). Dense deposits of minerals - mainly calcium phosphate and Type I collagen.
These are arranged in concentric circles around a central Haversian canal through which blood and lymph vessels as well as
nerves pass.

15.10A.1 https://bio.libretexts.org/@go/page/5760
 Figure 15.10.1.3 Haversian canal
Spongy bone (also known as trabecular or cancellous bone). The mineral deposits are arranged as a system of struts. Bone
marrow fill the spaces between.
Bone marrow. Some bones, such as the femur, also contain a central cavity filled with bone marrow. Bone marrow contains the
stem cells that gives rise to all the types of blood cells.
Epiphyseal plate. Until the end of puberty, this disk of cartilage produces more cartilage which then is converted into more
bone. In this way, the bone grows lengthwise.

Physiology
Looking at a skeleton, bone seems an inert thing. But in the living body it is anything but. The size and shape of bones not only
changes during growth, but for the rest one's life it is continuously being remodeled in response to the stresses put on it.
Approximately 10% of your bone mass is removed and replaced each year.
The remodeling of bone requires the coordinated activity of two types of cells:
Osteoclasts are derived from stem cells in the bone marrow - the same ones produce monocytes and macrophages.
Excess activity of osteoclasts (common after menopause in women) produces osteoporosis. The bones become weakened as
cortical bone gets thinner and the spaces in spongy bone get larger.
Reduced activity of osteoclasts produces osteopetrosis. This occurs when a person inherits a mutant version(s) of one or
another of the genes needed for normal osteoclast function. Inhibition of osteoclast function causes too much bone to form
leading to
extra-dense bone which actually is more brittle than normal bone thus leading to fractures
filling-in of the bone marrow cavity with bone thus interfering with the normal production of blood cells

Hormones and Bone

Many hormones affect bone growth and remodeling.
Growth hormone (GH). As its name suggests, GH drives the growth of bones until the adult size is reached.
Parathyroid hormone (PTH). It promotes the number and activity of osteoblasts.
Estrogens. Until the end of puberty, estrogens are needed for maturation of the skeleton (in males as well as females). In
women, after the menopause, taking supplemental estrogen slows up the bone loss that so often leads to osteoporosis. The
estrogen induces FasL in osteoclasts causing them to self-destruct by apoptosis and in this way slows up the destruction of
bone.
Calcitonin and thyroid stimulating hormone (TSH), both of which inhibit the activity of osteoclasts.
Calcitriol (1,25[OH]2 vitamin D3. Needed for the deposition of calcium into bone.
Osteoprotegerin is a protein secreted by osteoblasts and their precursors (thus a cytokine) that also inhibits the production and
activity of osteoclasts. Clinical trials of a recombinant version (made in E. coli) are underway as a possible treatment for
various bone-weakening disorders like osteoporosis and multiple myeloma.
Leptin, which regulates the balance between osteoblast and osteoclast activity.
Serotonin. Secreted by the duodenum, serotonin suppresses osteoblasts (at least in mice). This may account for the bone-
weakening effect in humans of prolonged use of selective serotonin reuptake inhibitors (SSRIs).
Bone also produces hormones thus is itself an endocrine organ.
Osteoblasts and their progeny produce a hormone — fibroblast growth factor 23 (FGF-23) — which reduces the reabsorption
of phosphate by the kidneys thus allowing more phosphate to pass out in the urine and lowering the phosphate level in the
blood. FGF-23 is also called phosphatonin.
Osteoblasts also secrete osteocalcin, a hormone that stimulates the beta cells of the pancreas to release insulin. This increases
the uptake of glucose by skeletal muscles thus enhancing exercise capacity. Calcitonin also stimulates the Leydig cells of the

15.10A.2 https://bio.libretexts.org/@go/page/5760
 testes to release testosterone. Osteocalcin crosses the blood-brain barrier and affects neurotransmitter levels, memory, and
behavior in mice and may do so in humans.

This page titled 15.10A: Bones is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.10A.3 https://bio.libretexts.org/@go/page/5760
15.10B: Muscles
Animals use muscles to convert the chemical energy of ATP into mechanical work. Three different kinds of muscles are found in
vertebrate animals.
Heart muscle also called cardiac muscle makes up the wall of the heart. Throughout our life, it contracts some 70 times per
minute pumping about 5 liters of blood each minute.
Smooth muscle is found in the walls of all the hollow organs of the body (except the heart). Its contraction reduces the size of
these structures. Thus it
regulates the flow of blood in the arteries
moves your breakfast along through your gastrointestinal tract
expels urine from your urinary bladder
sends babies out into the world from the uterus
regulates the flow of air through the lungs
The contraction of smooth muscle is generally not under voluntary control.
Skeletal muscle, as its name implies, is the muscle attached to the skeleton. It is also called striated muscle. The contraction of
skeletal muscle is under voluntary control.

Anatomy of Skeletal Muscle

Figure 15.10.2.1 Forearm

A single skeletal muscle, such as the triceps muscle, is attached at its
origin to a large area of bone; in this case, the humerus.
at its other end, the insertion, it tapers into a glistening white tendon which, in this case, is attached to the ulna, one of the
bones of the lower arm.
As the triceps contracts, the insertion is pulled toward the origin and the arm is straightened or extended at the elbow. Thus the
triceps is an extensor. Because skeletal muscle exerts force only when it contracts, a second muscle - a flexor - is needed to flex or
bend the joint. The biceps muscle is the flexor of the lower arm. Together, the biceps and triceps make up an antagonistic pair of
muscles. Similar pairs, working antagonistically across other joints, provide for almost all the movement of the skeleton.

The Muscle Fiber

Skeletal muscle is made up of thousands of cylindrical muscle fibers often running all the way from origin to insertion. The fibers
are bound together by connective tissue through which run blood vessels and nerves.Each muscle fibers contains:
an array of myofibrils that are stacked lengthwise and run the entire length of the fiber;
mitochondria;
an extensive smooth endoplasmic reticulum (SER);
many nuclei (thus each skeletal muscle fiber is a syncytium).
The multiple nuclei arise from the fact that each muscle fiber develops from the fusion of many cells (called myoblasts). The
number of fibers is probably fixed early in life. This is regulated by myostatin, a cytokine that is synthesized in muscle cells (and
circulates as a hormone later in life). Myostatin suppresses skeletal muscle development. (Cytokines secreted by a cell type that
inhibit proliferation of that same type of cell are called chalones.) Cattle and mice with inactivating mutations in their myostatin
genes develop much larger muscles. Some athletes and other remarkably strong people have been found to carry one mutant

15.10B.1 https://bio.libretexts.org/@go/page/5761
myostatin gene. These discoveries have already led to the growth of an illicit market in drugs supposedly able to suppress
myostatin.
In adults, increased muscle mass comes about through an increase in the thickness of the individual fibers and increase in the
amount of connective tissue. In the mouse, at least, fibers increase in size by attracting more myoblasts to fuse with them. The
fibers attract more myoblasts by releasing the cytokine interleukin 4 (IL-4). Anything that lowers the level of myostatin also leads
to an increase in fiber size.
Because a muscle fiber is not a single cell, its parts are often given special names such as
sarcolemma for plasma membrane
sarcoplasmic reticulum for endoplasmic reticulum
sarcosomes for mitochondria
sarcoplasm for cytoplasm
Although this tends to obscure the essential similarity in structure and function of these structures and those found in other cells.

Figure 15.10.2.2 Striated muscle

The nuclei and mitochondria are located just beneath the plasma membrane. The endoplasmic reticulum extends between the
myofibrils. Seen from the side under the microscope, skeletal muscle fibers show a pattern of cross banding, which gives rise to the
other name: striated muscle. The striated appearance of the muscle fiber is created by a pattern of alternating dark A bands and
light I bands.
The A bands are bisected by the H zone running through the center of which is the M line.
The I bands are bisected by the Z disk.
Each myofibril is made up of arrays of parallel filaments.
The thick filaments have a diameter of about 15 nm. They are composed of the protein myosin.
The thin filaments have a diameter of about 5 nm. They are composed chiefly of the protein actin along with smaller amounts
of two other proteins - troponin and tropomyosin.

The anatomy of a sarcomere

Figure 15.10.2.3 Sacromere

The entire array of thick and thin filaments between the Z disks is called a sarcomere.
The thick filaments produce the dark A band.

15.10B.2 https://bio.libretexts.org/@go/page/5761
 The thin filaments extend in each direction from the Z disk. Where they do not overlap the thick filaments, they create the light
I band.
The H zone is that portion of the A band where the thick and thin filaments do not overlap.
The M line runs through the exact center of the sarcomere. Molecules of the giant protein, titin, extend from the M line to the Z
disk. One of its functions is to provide elasticity to the muscle. It also provides a scaffold for the assembly of a precise number
of myosin molecules in the thick filament (294 in one case). It may also dictate the number of actin molecules in the thin
filaments.
Shortening of the sarcomeres in a myofibril produces the shortening of the myofibril and, in turn, of the muscle fiber of which it is
a part. [This electron micrograph of a single sarcomere was kindly provided by Dr. H. E. Huxley.]

Activation of Skeletal Muscle

The contraction of skeletal muscle is controlled by the nervous system. The Dying Lioness (an Assyrian relief dating from about
650 B.C.) shows this vividly. Injury to the spinal cord has paralyzed the otherwise undamaged hind legs. In this respect, skeletal
muscle differs from smooth and cardiac muscle. Both cardiac and smooth muscle can contract without being stimulated by the
nervous system. Nerves of the autonomic branch of the nervous system lead to both smooth and cardiac muscle, but their effect is
one of moderating the rate and/or strength of contraction.

Figure 15.10.2.4: The Dying Lionesssupplied through the courtesy of The Trustees of the British Museum

The Neuromuscular Junction

Nerve impulses (action potentials) traveling down the motor neurons of the sensory-somatic branch of the nervous system cause the
skeletal muscle fibers at which they terminate to contract. The junction between the terminal of a motor neuron and a muscle fiber
is called the neuromuscular junction. It is simply one kind of synapse. (The neuromuscular junction is also called the myoneural
junction.)

15.10B.3 https://bio.libretexts.org/@go/page/5761
 Figure 15.10.2.5 NM Junction
The terminals of motor axons contain thousands of vesicles filled with acetylcholine (ACh). Many of these can be seen in the
electron micrograph on the left (courtesy of Prof. B. Katz).
When an action potential reaches the axon terminal, hundreds of these vesicles discharge their ACh onto a specialized area of
postsynaptic membrane on the muscle fiber (the folded membrane running diagonally upward from the lower left). This area
contains a cluster of transmembrane channels that are opened by ACh and let sodium ions (Na+) diffuse in.
The interior of a resting muscle fiber has a resting potential of about −95 mV. The influx of sodium ions reduces the charge,
creating an end plate potential. If the end plate potential reaches the threshold voltage (approximately −50 mV), sodium ions
flow in with a rush and an action potential is created in the fiber. The action potential sweeps down the length of the fiber just as it
does in an axon. No visible change occurs in the muscle fiber during (and immediately following) the action potential. This period,
called the latent period, lasts from 3–10 msec.
Before the latent period is over,
the enzyme acetylcholinesterase
breaks down the ACh in the neuromuscular junction (at a speed of 25,000 molecules per second)
the sodium channels close, and
the field is cleared for the arrival of another nerve impulse.
the resting potential of the fiber is restored by an outflow of potassium ions.
The brief (1–2 msec) period needed to restore the resting potential is called the refractory period.

Tetanus
The process of contracting takes some 50 msec; relaxation of the fiber takes another 50–100 msec. Because the refractory period is
so much shorter than the time needed for contraction and relaxation, the fiber can be maintained in the contracted state so long as it
is stimulated frequently enough (e.g., 50 stimuli per second). Such sustained contraction is called tetanus.

15.10B.4 https://bio.libretexts.org/@go/page/5761
 Figure 15.10.2.6 Tetanus
In the above figure:
When shocks are given at 1/sec, the muscle responds with a single twitch.
At 5/sec and 10/sec, the individual twitches begin to fuse together, a phenomenon called clonus.
At 50 shocks per second, the muscle goes into the smooth, sustained contraction of tetanus.
Clonus and tetanus are possible because the refractory period is much briefer than the time needed to complete a cycle of
contraction and relaxation. Note that the amount of contraction is greater in clonus and tetanus than in a single twitch.
As we normally use our muscles, the individual fibers go into tetanus for brief periods rather than simply undergoing single
twitches.

The Sliding-Filament Model

Each molecule of myosin in the thick filaments contains a globular subunit called the myosin head. The myosin heads have
binding sites for the actin molecules in the thin filaments and ATP. Activation of the muscle fiber causes the myosin heads to bind
to actin. An allosteric change occurs which draws the thin filament a short distance (~10 nm) past the thick filament. Then the
linkages break (for which ATP is needed) and reform farther along the thin filament to repeat the process. As a result, the filaments
are pulled past each other in a ratchetlike action. There is no shortening, thickening, or folding of the individual filaments.
Electron microscopy supports this model.

Figure 15.10.2.7 Sliding - Filament model courtesy of Dr. H. E. Huxley

As a muscle contracts,
the Z disks come closer together
the width of the I bands decreases
the width of the H zones decreases
there is no change in the width of the A band
Conversely, as a muscle is stretched,
the width of the I bands and H zones increases
but there is still no change in the width of the A band

Coupling Excitation to Contraction

Calcium ions (Ca2+) link action potentials in a muscle fiber to contraction.
In resting muscle fibers, Ca2+ is stored in the endoplasmic (sarcoplasmic) reticulum.
Spaced along the plasma membrane (sarcolemma) of the muscle fiber are inpocketings of the membrane that form "T-
tubules". These tubules plunge repeatedly into the interior of the fiber.
The T-tubules terminate near the calcium-filled sacs of the sarcoplasmic reticulum.

15.10B.5 https://bio.libretexts.org/@go/page/5761
 Each action potential created at the neuromuscular junction sweeps quickly along the sarcolemma and is carried into the T-
tubules.

Figure 15.10.2.8 Sacrolemma

The arrival of the action potential at the ends of the T-tubules triggers the release of Ca2+.
The Ca2+ diffuses among the thick and thin filaments where it
binds to troponin on the thin filaments.
This turns on the interaction between actin and myosin and the sarcomere contracts.
Because of the speed of the action potential (milliseconds), the action potential arrives virtually simultaneously at the ends of all
the T-tubules, ensuring that all sarcomeres contract in unison.
When the process is over, the calcium is pumped back into the sarcoplasmic reticulum using a Ca2+ ATPase.

Isotonic versus Isometric Contractions

If a stimulated muscle is held so that it cannot shorten, it simply exerts tension. This is called an isometric ("same length")
contraction. If the muscle is allowed to shorten, the contraction is called isotonic ("same tension").

Motor Units
All motor neurons leading to skeletal muscles have branching axons, each of which terminates in a neuromuscular junction with a
single muscle fiber. Nerve impulses passing down a single motor neuron will thus trigger contraction in all the muscle fibers at
which the branches of that neuron terminate. This minimum unit of contraction is called the motor unit.
The size of the motor unit is small in muscles over which we have precise control. Examples:
a single motor neuron triggers fewer than 10 fibers in the muscles controlling eye movements
the motor units of the muscles controlling the larynx are as small as 2–3 fibers per motor neuron
In contrast, a single motor unit for a muscle like the gastrocnemius (calf) muscle may include 1000–2000 fibers (scattered
uniformly through the muscle).
Although the response of a motor unit is all-or-none, the strength of the response of the entire muscle is determined by the number
of motor units activated. Even at rest, most of our skeletal muscles are in a state of partial contraction called tonus. Tonus is
maintained by the activation of a few motor units at all times even in resting muscle. As one set of motor units relaxes, another set
takes over.

Fueling Muscle Contraction

15.10B.6 https://bio.libretexts.org/@go/page/5761
 Figure 15.10.2.9 Creatine
ATP is the immediate source of energy for muscle contraction. Although a muscle fiber contains only enough ATP to power a few
twitches, its ATP "pool" is replenished as needed. There are three sources of high-energy phosphate to keep the ATP pool filled.
creatine phosphate
glycogen
cellular respiration in the mitochondria of the fibers.

Creatine phosphate
The phosphate group in creatine phosphate is attached by a "high-energy" bond like that in ATP. Creatine phosphate derives its
high-energy phosphate from ATP and can donate it back to ADP to form ATP.
Creatine phosphate + ADP ↔ creatine + ATP
The pool of creatine phosphate in the fiber is about 10 times larger than that of ATP and thus serves as a modest reservoir of ATP.

Glycogen
Skeletal muscle fibers contain about 1% glycogen. The muscle fiber can degrade this glycogen by glycogenolysis producing
glucose-1-phosphate. This enters the glycolytic pathway to yield two molecules of ATP for each pair of lactic acid molecules
produced. Not much, but enough to keep the muscle functioning if it fails to receive sufficient oxygen to meet its ATP needs by
respiration.
However, this source is limited and eventually the muscle must depend on cellular respiration.

Cellular respiration
Cellular respiration not only is required to meet the ATP needs of a muscle engaged in prolonged activity (thus causing more rapid
and deeper breathing), but is also required afterwards to enable the body to resynthesize glycogen from the lactic acid produced
earlier (deep breathing continues for a time after exercise is stopped). The body must repay its oxygen debt.

Type I vs. Type II Fibers

Several different types of muscle fiber can be found in most skeletal muscles: Type I and and 3 subtypes of Type II fibers. Each
type differs in the myosin it uses and also in its structure and biochemistry.

Type I Fibers
loaded with mitochondria
depend on cellular respiration for ATP production
fatty acids the major energy source
resistant to fatigue
rich in myoglobin and hence red in color (the "dark" meat of the turkey)
activated by small-diameter, thus slow-conducting, motor neurons
also known as "slow-twitch" fibers
dominant in muscles used in activities requiring endurance (leg muscles) and those that depend on tonus, e.g., those responsible
for posture

15.10B.7 https://bio.libretexts.org/@go/page/5761
Type IIb Fibers
few mitochondria
rich in glycogen
depend on creatine phosphate and glycolysis for ATP production
fatigue easily with the production of lactic acid
low in myoglobin hence whitish in color (the white meat of the turkey)
activated by large-diameter, thus fast-conducting, motor neurons
also known as "fast-twitch" fibers
dominant in muscles used for rapid movement, e.g., those moving the eyeballs.
The other subtypes of Type II fibers have properties intermediate between those of Type IIb and Type I.
Most skeletal muscles contain some mixture of Type I and Type II fibers, but a single motor unit always contains one type or the
other, never both.
In mice, the number of Type I vs Type II fibers can be changed with exercise and drug treatment. Whether the same holds true for
humans remains to be seen. Perhaps training in humans does not alter the number of fibers of a particular type but may increase
the diameter of one type (e.g., Type I in marathoners, Type IIb in weight lifters) at the expense of the other types.

Cardiac Muscle

Figure 15.10.2.10 Cardiac muscle

Cardiac or heart muscle resembles skeletal muscle in some ways: it is striated and each cell contains sarcomeres with sliding
filaments of actin and myosin. However, cardiac muscle has a number of unique features that reflect its function of pumping blood.
The myofibrils of each cell (and cardiac muscle is made of single cells — each with a single nucleus) are branched.
The branches interlock with those of adjacent fibers by adherens junctions. These strong junctions enable the heart to contract
forcefully without ripping the fibers apart.
This electron micrograph (reproduced with permission from Keith R. Porter and Mary A. Bonneville, An Introduction to the
Fine Structure of Cells and Tissues, 4th ed., Lea & Febiger, Philadelphia, 1973) shows an adherens junction and several of
the other features listed here.
The action potential that triggers the heartbeat is generated within the heart itself. Motor nerves (of the autonomic nervous
system) do run to the heart, but their effect is simply to modulate — increase or decrease — the intrinsic rate and the strength of
the heartbeat. Even if the nerves are destroyed (as they are in a transplanted heart), the heart continues to beat.
The action potential that drives contraction of the heart passes from fiber to fiber through gap junctions.
Significance: all the fibers contract in a synchronous wave that sweeps from the atria down through the ventricles and
pumps blood out of the heart. Anything that interferes with this synchronous wave (such as damage to part of the heart
muscle from a heart attack) may cause the fibers of the heart to beat at random — called fibrillation. Fibrillation is the
ultimate cause of most deaths, and its reversal is the function of defibrillators that are part of the equipment in ambulances,
hospital emergency rooms, and even on U.S. air lines.
The refractory period in heart muscle is longer than the period it takes for the muscle to contract (systole) and relax (diastole).
Thus tetanus is not possible (a good thing, too!).
Cardiac muscle has a much richer supply of mitochondria than skeletal muscle. This reflects its greater dependence on cellular
respiration for ATP.

15.10B.8 https://bio.libretexts.org/@go/page/5761
 Cardiac muscle has little glycogen and gets little benefit from glycolysis when the supply of oxygen is limited.
Thus anything that interrupts the flow of oxygenated blood to the heart leads quickly to damage - even death - of the
affected part. This is what happens in heart attacks.

Smooth Muscle
Smooth muscle is made of single, spindle-shaped cells. It gets its name because no striations are visible in them. Nonetheless, each
smooth muscle cell contains thick (myosin) and thin (actin) filaments that slide against each other to produce contraction of the
cell. The thick and thin filaments are anchored near the plasma membrane (with the help of intermediate filaments).
Smooth muscle (like cardiac muscle) does not depend on motor neurons to be stimulated. However, motor neurons (of the
autonomic system) reach smooth muscle and can stimulate it or relax it depending on the neurotransmitter they release (e.g.
noradrenaline or nitric oxide, NO).
Smooth muscle can also be made to contract
by other substances released in the vicinity (paracrine stimulation)
Example: release of histamine causes contraction of the smooth muscle lining our air passages (triggering an attack of
asthma)
by hormones circulating in the blood
Example: oxytocin reaching the uterus stimulates it to contract to begin childbirth.
The contraction of smooth muscle tends to be slower than that of striated muscle. It also is often sustained for long periods. This,
too, is called tonus but the mechanism is not like that in skeletal muscle.

Muscle Diseases
The Muscular Dystrophies (MD)
Together myosin, actin, tropomyosin, and troponin make up over three-quarters of the protein in muscle fibers. Some two dozen
other proteins make up the rest. These serve such functions as attaching and organizing the filaments in the sarcomere and
connecting the sarcomeres to the plasma membrane and the extracellular matrix. Mutations in the genes encoding these proteins
may produce defective proteins and resulting defects in the muscles.
Among the most common of the muscular dystrophies are those caused by mutations in the gene for dystrophin. The gene for
dystrophin is huge, containing 79 exons spread out over 2.4 million base pairs of DNA. Thus this single gene represents about
0.1% of the entire human genome (3 x 109 bp) and is almost half the size of the entire genome of E. coli!
Duchenne muscular dystrophy (DMD)
Deletions or nonsense mutations that cause a frameshift usually introduce premature termination codons (PTCs) in the
resulting mRNA. Thus at best only a fragment of dystrophin is synthesized and DMD, a very severe form of the disease, results.
Becker muscular dystrophy (BMD).
If the deletion simply removes certain exons but preserves the correct reading frame, a slightly-shortened protein results that
produces BMD, a milder form of the disease.
The gene for dystrophin is on the X chromosome, so these two diseases strike males in a typical X-linked pattern of inheritance.
A treatment for DMD

15.10B.9 https://bio.libretexts.org/@go/page/5761
 Figure 15.10.2.11 Exon skipping
Deletions of one or more exons in the huge dystrophin gene are the cause of most of the cases of DMD. Exon 50 is a particularly
notorious offender. When it is deleted, splicing of the pre-mRNA introduces a frameshift which then introduces a premature
termination codon resulting in no functional dystrophin synthesized ("B"). However, an antisense oligonucleotide targeted to exon
51 causes the splicing mechanism to skip over it resulting in the stitching together of exons 49 and 52. This restores the correct
reading frame so that only a slightly-altered version of dystrophin is produced, i.e., a BMD-type dystrophin ("C"). Seventeen
weeks of weekly injections of 12 young DMD patients in the Netherlands with the oligonucleotide caused their muscles to
synthesize sufficient amounts of dystrophin to enable 8 of them to walk better than before. (See Goemans, N., et al., in the 21 April
2011 issue of The New England Journal of Medicine.

Three research groups have used the CRISPR-Cas9 genome editing system to remove a mutated exon in DMD mice. The treatment
restored dystrophin synthesis and improved skeletal and cardiac muscle function in the mice.

Myasthenia Gravis
Myasthenia gravis is an autoimmune disorder affecting the neuromuscular junction. Patients have smaller end plate potentials
(EPPs) than normal. With repeated stimulation, the EPPs become too small to trigger further action potentials and the fiber ceases
to contract. Administration of an inhibitor of acetylcholinesterase temporarily can restore contractility by allowing more ACh to
remain at the site.
Patients with myasthenia gravis have only 20% or so of the number of ACh receptors found in normal neuromuscular junctions.
This loss appears to be caused by antibodies directed against the receptors. Some evidence:
A disease resembling myasthenia gravis can be induced in experimental animals by immunizing them with purified ACh
receptors.
Anti-ACh receptor antibodies are found in the serum of human patients.
Experimental animals injected with serum from human patients develop the signs of myasthenia gravis.
Newborns of mothers with myasthenia gravis often show mild signs of the disease for a short time after their birth. This is the
result of the transfer of the mother's antibodies across the placenta during gestation.
The reason some people develop autoimmune antibodies against the ACh receptor is unknown.

The Cardiac Myopathies

Cardiac muscle, like skeletal muscle, contains many proteins in addition to actin and myosin. Mutations in the genes for these may
cause the wall of the heart to become weakened and, in due course, enlarged. Among the genes that have been implicated in these
diseases are those encoding:
actin
two types of myosin

15.10B.10 https://bio.libretexts.org/@go/page/5761
 troponin
tropomyosin
myosin-binding protein C (which links myosin to titin)
The severity of the disease varies with the particular mutation causing it (over 100 have been identified so far) . Some mutations
are sufficiently dangerous that they can lead to sudden catastrophic heart failure in seemingly healthy and active young adults.

This page titled 15.10B: Muscles is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.10B.11 https://bio.libretexts.org/@go/page/5761
15.10C: Testing the Sliding-Filament Hypothesis
The sliding-filament model postulates that when skeletal (or cardiac) muscle contracts, the thin and thick filaments in each
sarcomere slide along each other without their shortening, thickening, or folding and the strength of the relative motion between
the thick and thin filaments is determined by the number of cross-bridges that can form between the two.

The Testing

Figure 15.10.3.1 Isometric apparatus

This diagram shows apparatus with which to test the model.
An isolated muscle (e.g., the calf muscle of a frog) placed in this apparatus cannot shorten when stimulated by an electric shock.
Thus stimulation of the muscle produces an isometric ("same length") contraction.
The muscle is placed in the apparatus and stretched to the desired length.
It is then given a series of tetanizing shocks to measure its "active" tension; that is, the tension produced when it is stimulated.
The strain gauge measures the tension exerted by the muscle.
(Muscles are elastic, so if we stretch the muscle in putting it in the apparatus, it will already be exerting a "resting" tension.)
Now let us plot the effect of muscle length on the active tension that is produced.

The Results
The muscle produces the highest tension when held in the apparatus at the length it normally has in the intact animal.
If held at longer (or shorter) lengths, the active tension produced is less.
You may conclude from this that nature knows best. And, in fact she does. If a muscle is surgically reattached to an animal so that
its length is changed, the muscle gradually adapts to its new length and, after a few weeks, is able to exert its maximum isometric
contractions at the new length.

The Interpretation

Figure 15.10.3.2 Interpretation of the results

A muscle stretched beyond its normal length has less overlap between the thick and thin filaments.
Thus fewer cross-bridges can form to slide the filaments against each other.

15.10C.1 https://bio.libretexts.org/@go/page/5762
 In fact, if the muscle is stretched so far that the thin filaments are pulled entirely away from the thick filaments, the muscle
exerts no tension at all.
As for the effect of holding the muscle at shorter than normal length, the thin filaments extend so far across the sarcomere that
they interact with cross-bridges exerting force the opposite way — reducing the tension generated.

Figure 15.10.3.3 Striation patterns

These electron micrographs (courtesy of Dr. H. E. Huxley) show the pattern of striations in stretched muscle and resting muscle. In
the stretched muscle, there is less overlap of the thick and thin filaments.
Consequently
The light I bands and the H zone become wider.
The width of the dark A band remains unchanged.
We would not expect this pattern if sarcomere length involved a change in the length of the thick filaments.

This page titled 15.10C: Testing the Sliding-Filament Hypothesis is shared under a CC BY 3.0 license and was authored, remixed, and/or curated
by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available
upon request.

15.10C.2 https://bio.libretexts.org/@go/page/5762
 SECTION OVERVIEW
15.11: Behavior
Topic hierarchy

15.11.1: Innate Behavior

15.11.2: Taxis

15.11.3: Learned Behavior

15.11.4: Long-Term Potentiation (LTP)

15.11.5: Honeybee Navigation

15.11.6: Avoiding Predation

15.11.7: Pheromones

15.11.8: Circadian Rhythms in Drosophila and Mammals

This page titled 15.11: Behavior is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.11.1 https://bio.libretexts.org/@go/page/5371
15.11.1: Innate Behavior
Behavior is action that alters the relationship between an organism and its environment. Behavior may occur as a result of
an external stimulus (e.g., sight of a predator)
internal stimulus (e.g., hunger)
or, more often, a mixture of the two (e.g., mating behavior)
It is often useful to distinguish between
innate behavior = behavior determined by the "hard-wiring" of the nervous system. It is usually inflexible, a given stimulus
triggering a given response. A salamander raised away from water until long after its siblings begin swimming successfully will
swim every bit as well as they the very first time it is placed in the water. Clearly this rather elaborate response is "built in" in
the species and not something that must be acquired by practice.
learned behavior = behavior that is more or less permanently altered as a result of the experience of the individual organism
(e.g., learning to play baseball well).
However, careful analysis often reveals that any particular behavior is a combination of innate and learned components.
Examples of innate behavior:
taxes
reflexes
instincts

Taxes
Some organisms respond to a stimulus by automatically moving directly toward or away from or at some defined angle to it. These
responses are called taxes. They are similar to tropisms in plants except that actual locomotion of the entire organism is involved.
Link to a detailed discussion.

Reflexes
The Withdrawal Reflex
When you touch a hot object, you quickly pull you hand away using the withdrawal reflex.
These are the steps:
The stimulus is detected by receptors in the skin.
These initiate nerve impulses in sensory neurons leading from the receptors to the spinal cord.
The impulses travel into the spinal cord where the sensory nerve terminals synapse with interneurons.
Some of these synapse with motor neurons that travel out from the spinal cord entering mixed nerves that lead to the
flexors that withdraw your hand.
Others synapse with inhibitory interneurons that suppress any motor output to extensors whose contraction would interfere
with the withdrawal reflex.

The Stretch Reflex

The stretch reflex is examined (with a diagram) on a separate page. Link to it.

Instincts
Instincts are complex behavior patterns which, like reflexes, are inborn, rather inflexible, and valuable at adapting the animal to its
environment. They differ from reflexes in their complexity. The entire body participates in instinctive behavior, and an elaborate
series of actions may be involved.

15.11.1.1 https://bio.libretexts.org/@go/page/5763
 Figure 15.11.1.1 Instincts in animals and birds
The scratching behavior of a dog and a European bullfinch, shown here, is part of their genetic heritage. The widespread behavior
of scratching with a hind limb crossed over a forelimb in common to most birds, reptiles, and mammals. (Picture courtesy of
Rudolf Freund and Scientific American, 1958.) So instincts are inherited just as the structure of tissues and organs is. Another
example.
The African peach-faced lovebird carries nesting materials to the nesting site by tucking them in its feathers.
Its close relative, the Fischer's lovebird, uses its beak to transport nesting materials.
The two species can hybridize. When they do so, the offspring succeed only in carrying nesting material in their beaks.
Nevertheless, they invariably go through the motions of trying to tuck the materials in their feathers first.

Foraging Behavior
Foraging for food is a crucial behavior for animals. Like all behavior, it requires the interaction of many components. Nonetheless,
it turns out that in some animals, at least, foraging behavior can be altered by a single gene.

Drosophila melanogaster
The discovery of the genetic control of foraging in Drosophila began with the observations of Marla Sokolowski when she was an
undergraduate biology student at the University of Toronto.
She noticed that Drosophila larvae, feeding in her culture vessels, displayed one of two distinct feeding patterns:
"rovers" who moved rapidly over the surface of the culture medium
"sitters who fed at a much more leisurely pace
She went on to find that this "bimodal" pattern of behavior
continued when the larvae became adults
was present in populations of wild fruit flies, not just in her laboratory colonies
After further years of research, she has shown that the behavior is under the control of a single gene, named for ("foraging"). Two
alleles are present, at almost equal frequencies, that is, for is polymorphic.
forR, which is dominant
fors, the recessive
About 70% of natural populations are rovers being either homozygous for forR or heterozygous (forR/fors).
Sitters are homozygous for fors
Both alleles encode a PKG, a protein kinase (an enzyme that attaches phosphate groups to target proteins) that is activated by the
"second messenger" cyclic GMP (cGMP). The enzyme encoded by the forR allele is more active than that encoded by fors. She
and her colleagues have succeeded in inserting forR DNA into sitters who promptly become rovers.
Why this polymorphism? Why should alleles for two such different behaviors be maintained at such high frequency in the
population?
One possible answer: it permits the population to thrive under varying food conditions:
sitters are favored when food is abundant
rovers are favored when competition for food is strong, such as in crowded cultures

Honeybees
Honeybees have their version of the for gene, called Amfor ("Apis mellifera for"). It, too, encodes a cGMP-dependent protein
kinase (PKG). When worker bees first hatch, they remain in the hive tending to various housekeeping chores, such as feeding the
larvae. But when they are 2–3 weeks old, they leave the hive and begin foraging for nectar and pollen. This change in behavior

15.11.1.2 https://bio.libretexts.org/@go/page/5763
coincides with the increased expression of Amfor. When newly-hatched workers are treated with cGMP, the amount of PKG in
their brains goes up and they quickly begin foraging instead of doing housekeeping.

Interaction of Internal and External Stimuli

Figure 15.11.1.2 Mating rabbits

Instinctive behavior often depends on conditions in the internal environment. In many vertebrates courtship and mating behavior
will not occur unless sex hormones (estrogens in females, androgens in males) are present in the blood. The target organ is a small
region of the hypothalamus. When stimulated by sex hormones in its blood supply, the hypothalamus initiates the activities leading
to mating. The level of sex hormones is, in turn, regulated by the activity of the anterior lobe of the pituitary gland.
The above figure outlines the interactions of external and internal stimuli that lead an animal, such as a rabbit, to see a sexual
partner and mate with it.

Releasers of Instinctive Behavior

Figure 15.11.1.3 Breeding in a three-spined stickleback

Once the body is prepared for certain types of instinctive behavior, an external stimulus may be needed to initiate the response. N.
Tinbergen (who shared the 1973 Nobel Prize with Konrad Lorenz and Karl von Frisch) showed that the stimulus need not
necessarily be appropriate to be effective.
During the breeding season, the female three-spined stickleback normally follows the red-bellied male (a in the figure) to the
nest that he has prepared.
He guides her into the nest (b) and then
prods the base of her tail (c).
She then lays eggs in the nest.
After doing so, the male drives her from the nest, enters it himself, and fertilizes the eggs (d).

15.11.1.3 https://bio.libretexts.org/@go/page/5763
 Although this is the normal pattern, the female will follow almost any small red object to the nest, and once within the nest,
neither the male nor any other red object need be present.
Any object touching her near the base of her tail will cause her to release her eggs.
It is as though she were primed internally for each item of behavior and needed only one specific signal to release the behavior
pattern. For this reason, signals that trigger instinctive acts are called releasers. Once a particular response is released, it usually
runs to completion even though the stimulus has been removed. One or two prods at the base of her tail will release the entire
sequence of muscular actions involved in liberating her eggs.
Chemical signals (e.g., pheromones) serve as important releasers for the social insects: ants, bees, and termites. Many of these
animals emit several different pheromones which elicit, for example, alarm behavior, mating behavior, and foraging behavior in
other members of their species.
The mammary glands of domestic rabbit mothers emit a pheromone that releases immediate nursing behavior by their babies
(pups). A good thing, too, as mothers devote only 5–7 minutes a day to feeding their pups so they had better be quick about it.
The studies of Tinbergen and others have shown that animals can often be induced to respond to inappropriate releasers. For
example, a male robin defending its territory will repeatedly attack a simple clump of red feathers instead of a stuffed robin that
lacks the red breast of the males.
Although such behavior seems inappropriate to our eyes, it reveals a crucial feature of all animal behavior: animals respond
selectively to certain aspects of the total sensory input they receive. Animals spend their lives bombarded by myriad sights, sounds,
odors, etc. But their nervous system filters this mass of sensory data, and they respond only to those aspects that the evolutionary
history of the species has proved to be significant for survival.

This page titled 15.11.1: Innate Behavior is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.11.1.4 https://bio.libretexts.org/@go/page/5763
15.11.2: Taxis
Some organisms respond to a stimulus by automatically moving directly toward or away from or at some defined angle to it. These
responses are called taxes. They are similar to tropisms in plants except that actual locomotion of the entire organism is involved.

Chemotaxis

Figure 15.11.2.1: Chemotaxis. (courtesy of Dr. Julius Adler from Science, 26 December 1969)
When a capillary tube filled with glucose is placed in a medium containing E. coli, the bacteria alter their locomotion so that they
congregate near the opening of the tube. This chemotactic response does not depend on the bacteria being able to metabolize the
substance although presumably that is the value under normal conditions. E. coli responds strongly to a number of organic
molecules besides glucose, including galactose and the amino acids serine and aspartic acid. Figure Figure 15.11.2.1 shows how the
bacteria have congregated at the opening of a capillary tube filled with a weak solution of an amino acid.

Figure 15.11.2.2: Chemokines. This scanning electron micrograph (courtesy of Drs. Ralph Snyderman and C. A. Daniels) shows
two human monocytes migrating through the pores of a filter in response to a chemokine diffusing up from beneath.
Some of the motile cells of the immune system also display chemotaxis. The substances that attract them are called chemokines
(for chemotactic cytokines).

Phototaxis
Photosynthetic microorganisms often display phototaxis.

15.11.2.1 https://bio.libretexts.org/@go/page/5764
 Figure 15.11.2.3: Phototaxis in green alga.These photographs (courtesy of Dr. Mary Ella Feinleib of Tufts University) shows
phototaxis in the unicellular green alga Chlamydomonas.
In the left picture, randomly oriented tracks formed during 1/3 sec by the algae swimming about in red light to which the are
insensitive. In the right picture, upon adding a beam of blue-green light from one side, the tracks become oriented in its direction.

Magnetotaxis
Several species of bacteria swim in the direction of magnetic lines of force. Because of the inclination of the earth's magnetic lines
of force, this behavior causes the bacterium to swim downward and thus to return to the sediments in which it lives. For an
organism as tiny as a bacterium, gravity is of no consequence. So here is an alternate mechanism by which dislodged bacteria can
find their way back into their normal habitat.

Figure 15.11.2.4: Magnetotaxis. The electron micrograph (courtesy of R. B. Blakemore and N. Blakemore) is of the bacterium
Magnetospirillum magnetotacticum (the bar represents 1 µm.). The row of dark objects within the cell are particle of magnetite
(FeO.Fe2O3). These act like a compass needle, and in this species, which was found in a freshwater pond in New Hampshire
(USA), orient their owner toward the North Pole.
Magnetotactic bacteria in the Southern Hemisphere achieve the same result by swimming toward the South Pole. Particles
resembling these magnetite particles have been found in the Martian meteorite ALH84001. If they were not formed by a purely
chemical process (as some believe), they would be another entry in the hunt for evidence that Mars can (or could) support life.

This page titled 15.11.2: Taxis is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.11.2.2 https://bio.libretexts.org/@go/page/5764
15.11.3: Learned Behavior
Habituation
Habituation is a reduction in a previously-displayed response when no reward or punishment follows. If you make an unusual
sound in the presence of the family dog, it will respond usually by turning its head toward the sound. If the stimulus is given
repeatedly and nothing either pleasant or unpleasant happens to the dog, it will soon cease to respond. This lack of response is not a
result of fatigue or sensory adaptation and is long-lasting; when fully habituated, the dog will not respond to the stimulus even
though weeks or months have elapsed since it was last presented.

Sensitization
Sensitization is an increase in the response to an innocuous stimulus when that stimulus occurs after a punishing stimulus.

 Sensitization in sea slugs

When the siphon of the sea slug Aplysia is gently touched, the animal withdraws its gill for a brief period. However, if
preceded by an electrical shock to its tail, the same gentle touch to the siphon will elicit a longer period of withdrawal. The
sensitization response to a single shock (blue bar) dies out after about an hour, and returns to baseline after a day (yellow). So it
is an example of short-term memory.

Figure 15.11.3.1 Sensitization in a sea slug

However, if the animal is sensitized with multiple shocks given over several days, its subsequent response to a gentle touch on
the siphon is much larger and is retained longer (tan and gray bars). This is an example of long-term memory and requires
protein synthesis. (These findings are the work of Eric R. Kandel, who was awarded a Nobel Prize in 2000.)

Imprinting
If newly-hatched geese are exposed to a moving object of reasonable size and emitting reasonable sounds, they will begin to follow
it just as they would normally follow their mother. This is called imprinting. The time of exposure is quite critical. A few days
after hatching, imprinting no longer occurs. Prior to this time, though, the results can be quite remarkable. A gosling imprinted to a
moving box or clucking person will try to follow this object for the rest of its life. In fact, when the gosling reaches sexual maturity,
it will make the imprinted object - rather than a member of its own species - the goal of its sexual drive.

15.11.3.1 https://bio.libretexts.org/@go/page/5765
 Figure 15.11.3.2 Konrad Lorenz and his imprinted goslings
Much of our knowledge of imprinting was learned from the research of Konrad Lorenz, shown here with some of his imprinted
goslings. Lorenz shared a Nobel Prize in 1973 for his discoveries. (Photo by Tom McAvoy; courtesy of LIFE Magazine, ©1955,
Time, Inc.)
Male mice become imprinted with the odor of littermates during the first three weeks of life. When they reach sexual maturity, they
avoid mating with close relatives. The odor is controlled by the major histocompatibility complex (MHC).

The Conditioned Response (CR)

The conditioned response is probably the simplest form of learned behavior. It is a response that as a result of experience comes to
be caused by a stimulus different from the one that originally triggered it. The Russian physiologist Ivan Pavlov found that placing
meat powder in a dog's mouth would cause it to salivate.
The meat powder, an unconditioned stimulus (US), triggers a simple inborn reflex involving taste receptors, sensory neurons,
networks of interneurons in the brain, and autonomic motor neurons running to the salivary glands thus producing an
unconditioned response (UR).
Pavlov found that if he rang a bell every time he put the meat powder in the dog's mouth, the dog eventually salivated upon hearing
the bell alone. This is the conditioned response (CR). The dog has learned to respond to a substitute stimulus, the conditioned
stimulus (CS).
We assume that the physiological basis of the conditioned response is the transfer, by appropriate neurons, of nervous activity in the
auditory areas of the brain to the motor neurons controlling salivation. This involves the development and/or strengthening of
neural circuits, which - we may also assume - is characteristic of all forms of learning.
The conditioned response has proved to be an excellent tool for determining the sensory capabilities of other animals. For example,
honeybees can be conditioned to seek food on a piece of blue cardboard. By offering other colors to a blue-conditioned bee, Karl
von Frisch (who shared the 1973 Nobel Prize with Lorenz) found that honeybees can discriminate between yellow-green, blue-
green, blue-violet, and ultraviolet.

Instrumental Conditioning
Pavlov's dogs were restrained and the response being conditioned (salivation) was innate. But the principles of conditioning can
also be used to train animals to perform tasks that are not innate. In these cases, the animal is placed in a setting where it can move
about and engage in different activities. The experimenter chooses to reward only one, e.g., turning to the left. By first rewarding
(e.g., with a pellet of food) even the slightest movement to the left and then only more complete turns, a skilled experimenter can in
about 2 minutes train a naive pigeon to make a complete turn. A little more work and the pigeon will pace out a figure eight.
In the example shown here, the pigeon - presented with two spots of light - pecks at the brighter and reaches down to pick up the
grain of food that is its reward.

15.11.3.2 https://bio.libretexts.org/@go/page/5765
 Figure 15.11.3.3 Instrumental conditioning on pigeons. (Photos courtesy of Roy DeCarava and Scientific American.)
Such training is known as instrumental conditioning or operant conditioning. The latter term was coined by B. F. Skinner,
whose skill with the technique enabled him to train pigeons to play ping-pong and even a toy piano! It is also called trial-and-
error learning because the animal is free to try various responses before finding the one that is rewarded.

Figure 15.11.3.4 Chimpanzee solving a maze with a magnet

Maze problems are a form of instrumental conditioning in which the animal is faced with a sequence of alternatives.
In this photo (Courtesy of B. Rensch), Julia, a chimpanzee, uses a magnet to move an iron ring through a maze. Julia is able to
solve mazes like this on her first attempt most (86%) of the time and sometimes faster than biology students can!

Concepts
Although most animals solve mazes and other problems by trial and error, Julia (and biology students) usually make only one or
two random attempts at solving a problem and then, all of a sudden, "get it". They have made an abstract generalization about the
specific problem; that is, have formed a concept. Oddity problems are an example. This young rhesus monkey has learned that
food will be found - not under any particular object - but under whichever object is different from the others.

Figure 15.11.3.5 Oddity problems (Photo courtesy of H. F. Harlow, University of Wisconsin Primate Laboratory.)
In monkeys (and probably humans as well), concept formation depends on activity in the prefrontal cortex of the brain. Recent
research suggests that honeybees can also solve simple oddity problems!

This page titled 15.11.3: Learned Behavior is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.11.3.3 https://bio.libretexts.org/@go/page/5765
15.11.4: Long-Term Potentiation (LTP)
All learning depends on memory. The formation of memories appears to occur in two separate phases, first short-term memory.
(e.g., Humans undergoing electroshock treatment (to alleviate their depression) are unable to remember events that occurred just
prior to the treatment, but their memory of earlier events is unimpaired) that followed by formation of long-term memory. Damage
to the temporal lobes of the brain can result in the loss of the ability to remember new learning for more than about an hour. Two
systems that have been particularly useful in working out the cellular and molecular basis for memory formation are sensitization in
the sea slug Aplysia and the study of long-term potentiation (LTP).

Long-Term Potentiation (LTP)

Rats and mice can be trained to solve simple tasks. For example, if a mouse is placed in a pool of murky water, it will swim about
until it finds a hidden platform to climb out on. With repetition, the mouse soon learns to locate the platform more quickly.
Presumably it does so with the aid of visual cues placed around the perimeter of the pool because it cannot see or smell the
platform itself.

Figure 15.11.4.1 Mouse in murky water

Rats or mice who have had a part of their brain called the hippocampus damaged, cannot learn this task, although they continue to
solve it quickly if they were trained before their brain damage. This suggests that neurons in the hippocampus are needed for this
type of learning. In contrast to the rest of the brain, new neurons are produced in the hippocampus throughout life. They arise from
a pool of stem cells in the brain. The integration of newly-formed neurons into existing hippocampal circuitry facilitates the
learning of new memories (as well as the forgetting of old ones).

Demonstrating Long-Term Potentiation

The behavior of certain synapses in the "CA1" region of the hippocampus of the rat (or mouse) is consistent with their being
essential for this form of long-term memory. Slices of the hippocampus can be removed and its CA1 neurons studied in vitro with
recording electrodes. Rapid, intense stimulation of presynaptic neurons evokes action potentials in the postsynaptic neuron. This is
just what we would expect from the properties of synapses.

Figure 15.11.4.2 Synapse B response after intense stimulation

What is remarkable about this system is that over time these synapses become increasingly sensitive so that a constant level of
presynaptic stimulation becomes converted into a larger postsynaptic output (graph on right). This long-term potentiation can last
for weeks. Treatment of a slice of hippocampus with a drug called aminophosphonovaleric acid ("APV") blocks the formation of
LTP. This is because APV blocks the action of NMDA receptors, a subset of postsynaptic receptors that normally respond to the

15.11.4.1 https://bio.libretexts.org/@go/page/5766
excitatory neurotransmitter glutamate (Glu). NMDA receptors (synapse B above) are distinguished from other Glu-activated
receptors in being stimulated by the drug, N-methyl-D-aspartate (NMDA).
NMDA receptors contain a transmembrane channel that allows for the facilitated diffusion of calcium ions (Ca2+) across the
plasma membrane of the synapse. Binding of Glu (or NMDA) and D-serine released from a nearby astrocyte to these receptors
opens the channel allowing Ca2+ to flow in if — and only if — the same postsynaptic cell has been simultaneously depolarized by
other synapses on it (synapse A above). (The drawing is vastly-oversimplified: each CA1 neuron has tens of thousands of synapses
on it.)
The influx of Ca2+ into the neuron activates an enzyme called calcium-calmodulin-dependent kinase II (CaMKII). Kinases attach
phosphate groups to proteins and, in so doing, alter their functioning. In this case, CaMKII phosphorylates a second type of Glu
receptor called AMPA receptors, which makes them more permeable to sodium ions (Na+) thus lowering the resting potential of
the cell and making it more sensitive to incoming impulses. In addition, there is evidence that the activity of CaMKII increases the
number of AMPA receptors at the synapse.
The ability to make transgenic mice has provided tools to test this model of LTP.

 Mutant mice

Mice that are homozygous for a mutant CaMKII transgene fail to develop LTP. This was shown (by A. J. Silver, et. al., in
Science 257:206, 1992) in two ways:
by measuring the current in the postsynaptic cell of normal mice and mutant mice. The graph above(left) shows that mutant
mice do not develop the increase in current flow that normal mice (graph above) do.
The same failure of LTP occurs when the mice are tested on the hidden platform (graph right).

Figure 15.11.4.3 Mutant mice response to stimulus

 Transgenic mice
Transgenic mice that make extra-large amounts of NMDA receptors show enhanced LTP as shown by
greater postsynaptic currents in their hippocampus
their enhanced performance on the hidden-platform test
and enhanced performance in other tests of learning and memory
These findings were reported in the 2 September 1999 issue of Nature by Tang, Y-P, et al. The experiments described above
show that manipulations that affect the postsynaptic electrical response (EPSPs) of neurons stimulated electrically also affect
learned behavior. They do not show that learning induces increased EPSPs in postsynaptic neurons of the hippocampus. Now,
researchers at MIT have done just that.

15.11.4.2 https://bio.libretexts.org/@go/page/5766
 They used rats in which they implanted an array of closely-spaced recording electrodes in the CA1 region of the hippocampus.
These rats were then placed in a training apparatus where they learned in a single trial that moving from a lighted chamber to a
dark one would give them a shock.
In just 30 minutes some, but never all, of the recording electrodes picked up increased EPSPs in the CA1 neurons and the
number of AMPA receptors increased in the CA1 cells. So learning this conditioned response produced the electrical and
synaptic changes of LTP but only in certain regions of the hippocampus. Presumably other types of learning would produce
LTP in other parts of the CA1 region. (You can read the report of their work in Whitlock, J. R., et al., Science, 25 August
2006.)

Early LTP vs. Late LTP

LTP occurs in two phases:
an early one (in the first hour or so) which involves increased sensitivity of the synapse without any new gene transcription or
mRNA translation occurring
a late one which requires new gene transcription and mRNA translation and results in an increase in the number of AMPA
receptors accompanied by an increase in the size of the synaptic connection. These changes persist for many hours and even
many days. However, increased AMPA receptor formation seems to require continuous stimulation because (in rats, at least)
interfering with the process erases late LTP (and memory) even a month later.
This is yet more evidence that memories are acquired in two phases; early and late. Late LTP may involve not only the addition of
AMPA receptors to existing synapses but the formation of entirely new synapses. Researches in Geneva, Switzerland have
demonstrated that formation of LTP in rat brains coincides with the formation of additional synapses (at least one more) between
the presynaptic axon terminal and the dendrite it synapses with. (Report by Toni, N., et al, Nature, 25 Nov 99). Presumably this,
too, increases the efficiency of synaptic transmission.

Summary
Rapid, intense stimulation of CA1 neurons in the hippocampus depolarizes them.
Binding of Glu and D-serine to their NMDA receptors opens them.
Ca2+ ions flow into the cell through the NMDA receptors and bind to calmodulin.
This activates calcium-calmodulin-dependent kinase II (CaMKII).
CaMKII phosphorylates AMPA receptors making them more permeable to the inflow of Na+ ions and thus increasing the
sensitivity of the cell to depolarization.
In time CaMKII also increases the number of AMPA receptors at the synapse.
Increased gene expression (i.e., protein synthesis — perhaps of AMPA receptors) also occurs during the development of LTP.
Enlargement of the synaptic connections and perhaps the formation of additional synapses occur during the formation of LTP.
LTP has also been demonstrated in neurons of the cerebellum.

Long-Term Depression (LTD)

Slow, weak electrical stimulation of CA1 neurons also brings about long-term changes in the synapses, in this case, a reduction in
their sensitivity. This is called long-term depression or LTD. It reduces the number of AMPA receptors at the synapse. Long-term
depression also occurs in isolated preparations of neurons from the sea slug, Aplysia and the cerebellum of mice during the
development of an conditioned response (CR)

This page titled 15.11.4: Long-Term Potentiation (LTP) is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

15.11.4.3 https://bio.libretexts.org/@go/page/5766
15.11.5: Honeybee Navigation
The domestic honeybee, Apis mellifera, is a colonial insect living in hives containing one queen — a fertile female, a few drones
(males), and thousands of workers (infertile females). The workers are responsible for keeping the hive clean, building the wax
combs of the hive, tending the young and, when they get older (and when their for gene gets turned on), and foraging for food -
nectar and pollen.

Figure 15.11.5.1 Honeybee castes

ome 5–25% of the workers in the hive are scouts. Their job is to search for new sources of food for the other workers, the foragers,
to harvest. While both scouts and foragers look alike, recent research suggests that they represent stable subpopulations with
distinctive patterns of gene expression in their brains. (See Liang, Z. S., et al., in the 9 March 2012 issue of Science.)
When food is discovered by scouts, they return to the hive. Shortly after their return, many foragers leave the hive and fly directly
to the food. The remarkable thing about this is that the foragers do not follow the scouts back. The scouts may remain in the hive
for hours and those that leave continue to hunt for new sources of food even though the foragers are continuing to bring back ample
supplies of food from the sites the scouts discovered earlier. So the scout bees have communicated to the foragers the necessary
information for them to find the food on their own.
It turns out that the scouts can convey to the foragers information about
the odor of the food
its direction from the hive
its distance from the hive

Distance
When food is within 50–75 meters of the hive, the scouts dance the "round dance" on the surface of the comb (left). But when the
food is farther than 75 meters from the hive, the scouts dance the "waggle dance" (right). The waggle dance has two components:
(1) a straight run - the direction of which conveys information about the direction of the food and (2) the speed at which the dance
is repeated which indicates how far away the food is.

Figure 15.11.5.2 Round Dance

The graph shows the relationship between the speed of the dance and the distance to the food. It is based on data collected by the
German ethologist Karl von Frisch. It was he who discovered much of what we know today about honeybee communication (and
was honored with a Nobel Prize in 1973).

15.11.5.1 https://bio.libretexts.org/@go/page/5767
 Figure 15.11.5.3 von Frisch graph
How do the bees calculate distance? von Frisch thought they measured the distance by assessing the amount of energy it took to get
there. But the mechanism turns out to be quite different. The bees measure distance by the motion of images received by their eyes
as they fly.

Flicker Effect
Honeybees, like all insects, have compound eyes. These give little information about depth but are very sensitive to "flicker effect".
It has long been known to bee keepers that honeybees respond better to flowers
moving in the breeze
with complex petals
The importance of flicker effect can be demonstrated by training honeybees to visit food placed on cards with patterns. For
example, the bees can distinguish any figure in the top row from any figure in the bottom row more easily than they can distinguish
between any of the figures in either row.

Figure 15.11.5.4 Flicker patterns

Evidence of distance measuring

Working at the University of Notre Dame (Indiana), Esch and Burns found that when the hive and food were placed on top of tall
(50 m) buildings, the speed of the waggle dance indicated a distance only half of the distance indicated by bees travelling the same
distance (230 m) at ground level. Features of the scenery pass the retina faster when near than when far (compare the changes in
your view from an airliner at cruising altitude and as it approaches the runway).

Tests of Searching Behavior

Figure 15.11.5.5 Searching and Dancing behavior in bees

Working at the Australian National University, Srinivasan and his colleagues built tunnels decorating the interior walls with
patterns to create flicker. In these three experiments, the bees were first fed in the middle of the tunnel of standard diameter. Then

15.11.5.2 https://bio.libretexts.org/@go/page/5767
the food was removed.
1. Using the same tunnel, foragers came to same spot in the tunnel.
2. Using a narrower tunnel, foragers began searching for food near its entrance. Forced to fly closer to the vertical stripes, the
images moved by faster.
3. Using a tunnel with a larger diameter, foragers searched for food at its far end. Flying farther from the stripes, the images
moved by more slowly.

Tests of Dancing Behavior

All tunnels were 6 meters long and located 35 meters from the hive — well within the distance (50–75 m) that normally elicits the
round dance.
1. Bees were fed at the entrance. Back at the hive, they danced the round dance as you would expect.
2. Bees fed at end of tunnel. Back at the hive, they danced the waggle dance. Even though the total distance from the hive (41 m)
was still well within the "round" range, the complexity of the scenery passed in the last 6 m, elicited the waggle dance.
3. Bees fed at end of tunnel decorated with horizontal stripes. These created no flicker as the bees flew, and on their return to the
hive they danced the round dance.
You can read about this second set of experiments in Srinivasan, et. al., Science, 4 February 2000.

Recruits respond to the misinformation given by returning scouts

More recently, the Esch and Srinivasan groups have teamed up to show that naive foragers are fooled by the misinformation that
the returning scouts give them. When scouts were fed only 11 m from the hive but at the far end of a striped tunnel, they danced the
waggle dance back at the hive as though the food had been 70 m away. Most of the workers they recruited flew out (bypassing the
tunnel) 70 m looking for food. You can read about these experiments in Ungless, et. al., Nature, 31 May 2001.

Direction
By itself, the knowledge that food is 6 kilometers (3.7 miles) away is not very useful. But von Frisch also noted that the direction of
the straight portion of the waggle dance varied with the direction of the food source from the hive and the time of day.
At any one time, the direction changes with the location of the food.
With a fixed source of food, the direction changes by the same angle as the sun during its passage through the sky.
But
The sun is not visible within the hive.
The scouts dance on the vertical surface of the combs.
How, then, do they translate flight angles in the darkened hive?

Figure 15.11.5.6 Bee dance

The picture shows the relationship between the angle of the dance on the vertical comb and the bearing of the sun with respect to
the location of food. When the food and sun are in the same direction, the straight portion of the waggle dance is directed upward.
When the food is at some angle to the right (blue) or left (red) of the sun, the bee orients the straight portion of her dance at the
same angle to the right or left of the vertical.
Using radar to track individual bees recruited by the waggle dance, Riley, J. R., et al., (Nature, 12 May 2005) have shown that the
recruits do fly in the indicated direction. They even adjust their flight path to compensate for being blown off course by the wind.
However, their course is seldom so precise that they can find the food without the aid of vision and/or smell as they neared it.

15.11.5.3 https://bio.libretexts.org/@go/page/5767
Other features
Time Sense
When scouts remain in the hive for a long period, they shift the direction of the straight portion of the waggle dance as the day
wears on (and the direction of the sun shifts). But they cannot see the sun in the darkened hive. Evidently, they are "aware" of the
passing time and make the necessary corrections.

Figure 15.11.5.7 Time Sense

The time sense of honeybees has long been known to people who have sweet snacks in their garden at a set time every day. Within
minutes of the regular time, foraging bees arrive for their share of the jam. The speed of the bee's clock seems to be related to its
metabolic rate. If normally punctual bees are chilled (to lower their metabolic rate) or exposed to an anesthetizing concentration of
carbon dioxide they arrive late to the picnic table (graph above).

Polarized light
von Frisch also discovered that scouts (and foragers) don't actually have to see the sun to navigate. As long as they can see a small
patch of clear blue sky, they get along fine. This is because sky light is partially polarized, and the plane of polarization in any part
of the sky is determined by the location of the sun. Try it by rotating a pair of polaroid® sun glasses!

Swarming
Before a new queen emerges, the old queen leaves the hive, taking many of the workers with her. The swarm usually settles
somewhere, e.g., on a tree branch, while scouts go searching for a new home. Each scout that finds a promising site, returns to the
swarm and dances on it just as though she had found food. Eventually, the swarm departs for the location promoted most
vigorously. Once the new hive is established, many of the scouts that found the site will become food scouts.

Grooming
Workers have another type of dance — rapidly vibrating from side to side — that tells other workers that she needs help removing
dust, pollen, etc. from hard-to-reach places on her body.

This page titled 15.11.5: Honeybee Navigation is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.11.5.4 https://bio.libretexts.org/@go/page/5767
15.11.6: Avoiding Predation
Most animals get their food from preying on other organisms, and much of the life of animals involves eating and avoiding being
eaten. So it is not surprising to find many examples of adaptations that increase the effectiveness of predation and minimize the risk
of being preyed upon. We shall examine some of the devices that help their owners avoid being eaten.

Camouflage (cryptic coloration)

Many animals are patterned to blend in with their surroundings. Some examples include the peppered moth and the winter flounder.

Masquerade
Masquerading animals resemble some inanimate object and thereby escape detection by potential predators (or prey).

Figure 15.11.6.1 Twig caterpillar

The motionless twig caterpillar shown here (courtesy of Muriel V. Williams) complete with "buds" and "lenticels" escapes
detection by birds (but pays for its cleverness by occasionally having some other insect lay eggs on it by mistake).

Chemical Defenses
Many plants and animals use repellent chemicals to deter predation. Millipedes secrete hydrocyanic acid when disturbed. Some
beetles squirt potential predators with such mixtures as 85% acetic acid or 40% formic acid. The discharge of the skunk is another
familiar example.But what if you have a powerful defensive weapon but no potential predator notices until it has launched an
attack? One solution to this dilemma is the evolution of warning coloration (also called aposematic coloration).

Aposematic Coloration

Figure 15.11.6.2 Monarch larva

This is the larva of the monarch butterfly; an example of aposematic coloration. There is no question of camouflage here. Rather
this creature is advertising its presence. The milkweed leaves on which it is feeding contain cardiac glycosides that are toxic to
vertebrates because they block the activity of the Na+/K+ ATPase that is essential for many cell functions. The larva stores these
within its body and thus becomes unpalatable to vertebrate predators. The chemicals remain in the body even after metamorphosis,
so that adults are unpalatable as well.

15.11.6.1 https://bio.libretexts.org/@go/page/5768
 Figure 15.11.6.3 Blu jay
In these photographs (provided by Lincoln P. Brower) a blue jay eats a portion of a monarch butterfly (left) that had fed (in its
larval stage) on poisonous milkweed. A short time later, the blue jay vomits (right). Following this episode, the blue jay refused to
eat any other monarch offered to it.

Mimicry
Batesian Mimicry
If an animal is not noxious to potential predators, why not look like an animal that is? Some examples:
A number of harmless snakes closely mimic the bright warning coloration of the coral snake — the most poisonous snake in
the United States.
The harmless robber fly (right) resembles the bumblebee (left) even though the two are not closely related. The robber fly is a
dipteran, with only a single pair of wings, while the bumblebee is a hymenopteran with two pairs.
The viceroy butterfly (bottom) contains no toxic substances in its body and presumably is quite palatable (one entomologist
declared it tastes like dried toast). If so, the viceroy's striking resemblance to the monarch (top) enables it to capitalize on the
monarch's unpalatability. (Photos by, and courtesy of, Howard Hoople.)
This phenomenon is called Batesian mimicry (named after Henry W. Bates, a nineteenth-century naturalist who studied many such
cases).

Figure 15.11.6.4 Batesian mimicry in robberfly(left) and civeroy butterfly(right)

15.11.6.2 https://bio.libretexts.org/@go/page/5768
Müllerian Mimicry
Some unpalatable animals closely resemble other equally unpalatable species. Such mimicry is called Müllerian mimicry (in honor
of the German zoologist Fritz Müller, who studied it). Presumably each species gains a measure of protection from the occasional,
but educational, losses of the other species to predators. Lincoln Brower, who has studied the monarch and viceroy, believes that
the viceroy is as unpalatable to potential predators as the monarch, and thus is really an example of Müllerian mimicry.

Aggressive Mimicry
Some carnivores have evolved devices with which they mimic the prey (or potential mate) of other (usually smaller) predators.
They use these devices as lures.
Two examples:
The angler fish (Antennarius) displays a lure resembling a small fish. The lure is a development of the spine of the first dorsal
fin. This species of anglerfish, which was found in the Philippines, is 9.5 cm long. Note its use of camouflage: its texture (and
color) closely resemble the sponge- and algae-encrusted rocks found in its habitat.

Figure 15.11.6.5 Angler fish courtesy of David B. Grobecker from Pietsch, T. W. and D. B. Grobecker, Science, 201:369, 1978.)
Fireflies use their flashes to attract mates. The pattern differs from species to species. In one species, the females sometimes mimic
the pattern used by females of another species. When the males of the second species respond to these "femmes fatales", they are
eaten!

Group Behavior
Cooperation between members of a social species often reduces the severity of predation. Grazing ungulates are usually organized
so that the stronger are on the outside of the herd, the weaker within.

Figure 15.11.6.6 Musk oxen

In this photo (courtesy of Ted Grant, National Film Board of Canada), musk oxen have responded to a threat by forming a circle
with the females and young in the center. Both herds of ungulates and flocks of birds often have members who are extra-watchful,
ready to give the alarm if danger threatens. When alarmed, smelt (a kind of fish) release a pheromone into the water that warns
other members of the school. When a honeybee stings an intruder, she release isoamyl acetate, which excites other bees to join the
attack.

This page titled 15.11.6: Avoiding Predation is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.11.6.3 https://bio.libretexts.org/@go/page/5768
15.11.7: Pheromones
Pheromones are chemicals released by an organism into its environment enabling it to communicate with other members of its own
species.

Pheromones in Insects
Alarm Pheromone: When an ant is disturbed, it releases a pheromone that can be detected by other ants several centimeters away.
They are attracted by low concentrations of the pheromone and begin to move toward the region of increasing concentration. As
they get nearer to their disturbed nestmate, their response changes to one of alarm. The higher concentration causes them to run
about as they work to remedy the disturbance. Unless additional amounts of the alarm pheromone are released, it soon dissipates.
This ensures that once the emergency is over, the ants return quietly to their former occupations. Honeybees also have an alarm
pheromone (which is a good thing not to elicit around a colony of "Africanized" bees).
Trail Pheromone: Certain ants, as they return to the nest with food, lay down a trail pheromone. This trail attracts and guides other
ants to the food. It is continually renewed as long as the food holds out. When the supply begins to dwindle, trailmaking ceases.
The trail pheromone evaporates quickly so other ants stop coming to the site and are not confused by old trails when food is found
elsewhere. And at least in one species of ant, trails that no longer lead to food are also marked with a repellant pheromone.

Figure 15.11.7.1: Trail pheromone

A stick treated with the trail pheromone of an ant (left) can be used to make an artificial trail which is followed closely by other
ants emerging from their nest (right). The trail will not be maintained by other ants unless food is placed at its end. (Photos
courtesy of Sol Mednick and Scientific American).
Queen Pheromone: Honeybee queens spend their lives literally surrounded by a retinue of worker bees. The queen emits a
pheromone that is a complex mixture of unsaturated hydrocarbons, fatty acids, and other organic molecules. Among its effects:
inducing the workers to feed and groom her
inhibiting the workers from building queen cells and rearing new queens
inhibiting ovary development in the workers
Sex Attractants

Hundreds of pheromones are known with which one sex (usually the female) of an insect species attracts its mates. Many of these
sex attractants or their close chemical relatives are available commercially. They have proved useful weapons against insect pests
in two ways:
Male Confusion: Distributing a sex attractant throughout an area masks the insect's own attractant and thus may prevent the
sexes getting together. This "communication disruption" has been used successfully against a wide variety of important pests.
For example, the sex attractant of the cotton boll weevil has reduced the need for conventional chemical insecticides by more
than half in some cotton-growing areas.
Insect Monitoring: Insect sex attractants are also valuable in monitoring pest populations. By baiting traps with the appropriate
pheromone, a build-up of the pest population can be spotted early. Even if a conventional insecticide is the weapon chosen, its
early use reduces
the amount needed
damage to the crop
cost to the grower
possible damage to the environment.
Early detection of pest build-up is a key ingredient in the system known as integrated pest management (IPM).

15.11.7.1 https://bio.libretexts.org/@go/page/5769
 Figure 15.11.7.2 Gypsy moth
The photo (courtesy of USDA) shows the feathery antennae of a male gypsy moth. These detect the pheromone released by the
females (who do not fly). In some insects, a single molecule of sex attractant is enough to elicit a response.
Sexual Deception
By an animal: Many species of spiders prey exclusively on moths of certain species and only on the males. Studies of one
species of spider, Mastophora cornigera, show that it releases a mixture of volatile compounds that mimic the sex pheromone
of the moth species it preys upon. Male moths flying upwind in search of a female end up eaten instead!
By a plant: A number of species of orchids - each pollinated by the males of a single species of insect (wasps or bees) — emit
the same pheromone that is the sex attractant by which females of the insect species attract the males for mating.

Pheromones in Mammals
Releaser Pheromones: Many mammals (e.g., dogs and cats) deposit chemicals in and/or around their "territory". As these
vaporize, they signal to other members of the species of the presence of the occupant of the territory. Domestic rabbit mothers
release a mammary pheromone that triggers immediate nursing behavior by their babies (pups). A good thing, too, as mothers
devote only 5–7 minutes a day to feeding their pups so they had better be quick about it.
Many animals, including mammals, signal with alarm pheromones. Although neither the source nor the chemical nature of alarm
pheromones are known in any mammal, stressed animals release something that triggers quick behavior (e.g., flight or fight) in
other members of their species. The pheromone is detected in a special cluster of cells located at the very tip of the nose and thus in
a position to detected airborne molecules even before the vomeronasal organ (see below) or nasal epithelium can. The detectors on
these cells are primary cilia.
Primer Pheromones: Rats and mice give off pheromones that elicit mating behavior. However, the response is not immediate as it
is in the releaser pheromones of mother rabbits and insects. Instead, detection of the pheromone primes the endocrine system of the
recipient to make the changes, e.g., ovulation, needed for successful mating. Primer pheromones are detected by the olfactory
epithelium with which normal odors are detected and also in most mammals (but not humans) by the vomeronasal organ (VNO).
The VNO is a patch of receptor tissue in the nasal cavity distinct from the olfactory epithelium. The receptors are G-protein-
coupled transmembrane proteins similar to those that mediate olfaction, but encoded by entirely different genes. The neurons
leading from the VNO take a separate path into and through the brain.
Human pheromones: It has long been noticed that women living close together (e.g., college roommates) develop synchronous
menstrual cycles. This is thought to be because they release two (as yet uncharacterized) primer pheromones: (1) one prior to
ovulation that tends to speed up the onset of ovulation in others and (2) one after ovulation that tends to delay the onset of ovulation
in other women. Both pheromones are released from the armpits. The pheromones are not detected consciously as odors, but
presumably trigger the hormonal changes that mediate the menstrual cycle.

This page titled 15.11.7: Pheromones is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

15.11.7.2 https://bio.libretexts.org/@go/page/5769
15.11.8: Circadian Rhythms in Drosophila and Mammals

All eukaryotes and some microbes (e.g., cyanobacteria) display changes in gene activity, biochemistry, physiology, and behavior
that wax and wane through the cycle of days and nights.
Examples:
The level of the hormone melatonin that rises in your body during the night and falls during the day.
Fruit flies (Drosophila melanogaster) hatch in greatest numbers just at dawn.
Even when the organism is placed in constant conditions (e.g., continuous darkness), these rhythms persist. However, without
environmental cues, they tend to be somewhat longer or somewhat shorter than 24 hours giving rise to the name circadian rhythms
(L. circa = about; dies = day).
The genetics and molecular biology of circadian rhythms have been studied in several model organisms including
some unicellular eukaryotes
fungi
plants (Arabidopsis)
invertebrates (Drosophila)
mammals (mice, rats, and humans)
What has emerged are some remarkable similarities in mechanisms across these various groups. Let us take a detailed look at the
mechanism in Drosophila.

The Circadian Clock in Drosophila

A number of genes in Drosophila are turned on when the animal is exposed to light:
effector genes whose products mediate the animal's responses (e.g. hatching or molting)
clock genes whose products regulate the circadian clock. Two key members of this group are:
period (per)
timeless (tim)

Figure 15.11.8.1 Promoter

Activation of all of these genes requires that their promoters are bound by the protein transcription factors
CLOCK encoded by the gene clock (clk)
CYCLE encoded by the gene cycle (cyc)
(The names of proteins will be designated with capitalized Roman letters; the genes that encode them indicated in lower case
italics.)

15.11.8.1 https://bio.libretexts.org/@go/page/5770
The Mechanism

Fig.15.11.8.2 Mechanism

The PER and TIM proteins (synthesized on ribosomes in the cytoplasm) form dimers.
When the concentration of these gets high enough (early evening), they dissociate and are transported into the nucleus.
Here PER
binds to the CLK/CYC transcription factors, removing them from the promoters of the genes they activate; thus shutting off
transcription. Because these genes include per and tim, the result is a negative feedback loop; that is, the product of the per
gene inhibit its own synthesis (as well as that of tim). Just as the heat of a furnace turns through the thermostat - its own
production off, so a rising level of PER/TIM dimers turns off further synthesis of them. As the level then falls, this inhibition
is lifted and PER/TIM activity begins anew.
turns on clock gene expression.
The time required for the different effects results in the levels of PER/TIM and CLOCK oscillating in opposite phases with a
circadian (~24 hr) rhythm (figure).

Setting the Clock

Even without any external cues (e.g., alternating light and dark), the cycles persist although they tend to drift away from
environmental time.
Under natural conditions, the clocks are precise.
This is because they are "set" (synchronized) by environmental cues, of which light is one of the most important.
In Drosophila, it works like this.
Light (blue) is absorbed by the protein cryptochrome (CRY).
This causes an allosteric change in its conformation enabling it to bind to TIM and PER.
This causes TIM and PER to break down (in proteasomes) ending their inhibition of gene transcription.
If this happens when PER/TIM levels are rising (late in the "day"), it sets the clock back.
If it happens when PER/TIM levels are declining (late in the "night"), it sets the clock ahead.

The Circadian Clock in Mammals

Figure 15.11.8.3 Clock in mammals

The circadian clock in mammals resembles that in Drosophila in a number of ways with many of the participating genes being
homologous. However, there are some differences:

15.11.8.2 https://bio.libretexts.org/@go/page/5770
 The transcription factors that turn on the light-induced promoters are dimers of the CLOCK protein and a protein designated
BMAL1. These dimers turn on
three Per genes
two Cry genes, the genes encoding cryptochrome
hundreds of effector genes whose products control a wide variety of metabolic functions (e.g., cellular respiration,
glycolysis, gluconeogenesis, lipid metabolism)
The PER and CRY mRNAs are exported to the cytoplasm where they are translated.
The PER and CRY proteins then enter the nucleus where they inhibit CLOCK-BMAL1 thus turning OFF transcription of Per
and Cry, and are then degraded in proteasomes.
In due course these actions allow CLOCK and BMAL1 to once again stimulate transcription of Per and Cry. Thus this negative
feedback loop causes the levels of BMAL1 and PER/CRY to oscillate in opposite phases (as CLOCK and PER/TIM do in
Drosophila).
Many tissues in mammals, e.g., liver, skeletal muscle, and the beta cells of the pancreas have endogenous clocks. But all of these
are under the control of a "master clock", the suprachiasmatic nucleus (SCN) - clusters of neurons in the hypothalamus.
The blood levels of many hormones have strong circadian rhythms. Examples:
hormones synthesized in the hypothalamus, e.g. vasopressin
whose secretion is controlled by the hypothalamus such as growth hormone and cortisol
insulin

Setting the Clock

By light
Mice who are totally blind (lacking both rods and cones) have no trouble keeping their circadian clock on time.
They are able to do this because
Some 1–2% of the ganglion cells in their retina - instead of depending on signals arriving from rods and/or cones detect light
directly.
These ganglion cells have an extensive network of dendrites that contain the pigment melanopsin.
When exposed to light (diffuse light is fine), these ganglion cells become depolarized and send their signals back to the
suprachiasmatic nucleus (SCN).

By food
In mice, the SCN clock, set by light/dark cycles, is the master clock as long as food is available all the time (the normal situation in
the laboratory). However, if food is offered for only a 4-hour period when the mice would normally be asleep, they shift several
circadian activities so that, for example, once a day they begin running about just before they expect food to be given to them. This
rhythm continues even if the mice are kept in constant darkness.
The clock mechanism is the same as the light/dark-driven clock in the SCN, but the machinery that sets the clock by food is located
in a different part of the hypothalamus, the dorsomedial hypothalamic nuclei (DMH).
Mice with both copies of the Bmal1 gene knocked out, are unable to establish circadian rhythms to either light or food. However,
injections of an adeno-associated virus vector (AAV) containing the Bmal1 gene
into the SCN restores the light clock but not the food-set clock
into the DMH restores the food but not the light-set clock.

Sleep Disorders
Unlike mice, people who are totally blind cannot set the clock in their SCN. As a result, their circadian rhythm drifts out of phase
with the actual cycle of day and night. These people often are bothered by feeling sleepy during the day and wide awake when they
want to be asleep at night. A report in the 12 October 2000 issue of the New England Journal of Medicine tells of a group of
blind people who were able to set their clocks with the help of a dose (10 mg) of melatonin at bedtime. However, this treatment
worked only when the subject's circadian rhythm had drifted so that the normal rise in melatonin from the pineal gland was

15.11.8.3 https://bio.libretexts.org/@go/page/5770
occurring in the early evening; that is, the dose of melatonin had to be given when it could boost the endogenous level of the
hormone.
Some people suffer from a disorder called familial advanced sleep-phase syndrome (FASPS). As the name suggests, it is
inherited ("familial") and their circadian clocks run fast ("advanced"). Those afflicted tend to wake up several (up to four) hours
earlier than normal.
One cause of the disorder turns out to be a point mutation in the human PER2 gene. Exactly how this mutation causes shortening
of the circadian cycle is still under investigation.

Photoperiodism
Many plants and animals not only engage in a cycle of daily activities (opening of flowers, waking, feeding, etc.) but also in
seasonal activities.
In plants, such things as production of flowers and making buds dormant in preparation for winter.
In animals, such things as preparing to migrate and entering and leaving hibernation.
The most reliable clue to the change of season is length of day (temperature is far less reliable!). The farther a plant or animal lives
north or south of the equator, the more pronounced the changing ratio of daytime hours to nighttime hours with the changing
seasons.
It is not surprising then that both plants and animals mainly depend on photoperiod to prepare for changes in seasonal activities.
And what better way to measure the relative length of day and night than by enlisting the machinery by which circadian rhythms
are entrained?
As for animals, recent work with Drosophila suggests that this animal uses two circadian clocks to monitor the changing length of
day and night.
An "evening" clock that takes over in the long days of summer.
A"morning" clock that is inhibited by light but takes over when the nights are getting longer;
The molecular machinery (Cry, Tim, Per, etc.) for each clock is confined to separate neurons in two different parts of the brain.
In these experiments, Drosophila is using the two clocks to adapt daily — not seasonal — cycles of activity to the changing
seasons. But this machinery for measuring photoperiod could enable them to prepare for seasonal changes in activity, e.g., to stop
forming eggs at the end of the summer. However, other studies examining such seasonal changes in Drosophila find that the
photoperiodic response is independent of circadian responses. So we must await more experiments to resolve the question.

This page titled 15.11.8: Circadian Rhythms in Drosophila and Mammals is shared under a CC BY 3.0 license and was authored, remixed, and/or
curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is
available upon request.

15.11.8.4 https://bio.libretexts.org/@go/page/5770
 CHAPTER OVERVIEW
Unit 16: The Anatomy and Physiology of Plants
16.1: Plant Anatomy
16.1.1: Plant Tissues
16.1.2: Roots
16.1.3: Stems
16.1.4: The Leaf
16.1.5: Arabidopsis Thaliana
16.2: Plant Physiology
16.2A: Xylem
16.2B: Phloem
16.2C: Transpiration
16.2D: Gas Exchange in Plants
16.2E: Photorespiration and C4 Plants
16.2F: Tropisms
16.3: Reproduction in Plants
16.3A: Alternation of Generations in Plants
16.3B: Moss Life Cycle
16.3C: Fern Life Cycle
16.3D: Angiosperm Life Cycle
16.3E: Asexual Reproduction in Plants
16.3E: Self-incompatibility - How Plants Avoid Inbreeding
16.3F: Transgenic Plants
16.4: Plant Development - Fundamentals
16.4A: Plant Growth
16.4B: Germination of Seeds
16.4C: Etiolation
16.4D: Flowering
16.4E: Photoperiodism and Phytochrome
16.5: Plant Development - Hormones
16.5A: Abscisic acid (ABA)
16.5B: Auxin
16.5C: Cytokinins
16.5D: Ethylene
16.5E: Gibberellins
16.5F: Strigolactones

This page titled Unit 16: The Anatomy and Physiology of Plants is shared under a CC BY 3.0 license and was authored, remixed, and/or curated
by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available
upon request.

1
 SECTION OVERVIEW
16.1: Plant Anatomy
Topic hierarchy

16.1.1: Plant Tissues

16.1.2: Roots

16.1.3: Stems

16.1.4: The Leaf

16.1.5: Arabidopsis Thaliana

This page titled 16.1: Plant Anatomy is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.1.1 https://bio.libretexts.org/@go/page/5773
16.1.1: Plant Tissues

Figure 16.1.1.1 Types of plant tissues

Meristematic
The main function of meristematic tissue is mitosis. The cells are small, thin-walled, with no central vacuole and no specialized
features.
Meristematic tissue is located in
the apical meristems at the growing points of roots and stems.
the secondary meristems (lateral buds) at the nodes of stems (where branching occurs), and in some plants,
meristematic tissue, called the cambium, that is found within mature stems and roots.
The cells produced in the meristems soon become differentiated into one or another of several types.

Protective
Protective tissue covers the surface of leaves and the living cells of roots and stems. Its cells are flattened with their top and bottom
surfaces parallel. The upper and lower epidermis of the leaf are examples of protective tissue.

Parenchyma
The cells of parenchyma are large, thin-walled, and usually have a large central vacuole. They are often partially separated from
each other and are usually stuffed with plastids. In areas not exposed to light, colorless plastids predominate and food storage is the
main function. The cells of the white potato are parenchyma cells. Where light is present, e.g., in leaves, chloroplasts predominate
and photosynthesis is the main function.

Sclerenchyma
The walls of these cells are very thick and built up in a uniform layer around the entire margin of the cell. Often, the cell dies after
its cell wall is fully formed. Sclerenchyma cells are usually found associated with other cells types and give them mechanical
support.
Sclerenchyma is found in stems and also in leaf veins. Sclerenchyma also makes up the hard outer covering of seeds and nuts.

Collenchyma
Collenchyma cells have thick walls that are especially thick at their corners. These cells provide mechanical support for the plant.
They are most often found in areas that are growing rapidly and need to be strengthened. The petiole ("stalk") of leaves is usually
reinforced with collenchyma.

16.1.1.1 https://bio.libretexts.org/@go/page/5777
Xylem
Xylem conducts water and dissolved minerals from the roots to all the other parts of the plant.
In angiosperms, most of the water travels in the xylem vessels. These are thick-walled tubes that can extend vertically through
several feet of xylem tissue. Their diameter may be as large as 0.7 mm. Their walls are thickened with secondary deposits of
cellulose and are usually further strengthened by impregnation with lignin. The secondary walls of the xylem vessels are deposited
in spirals and rings and are usually perforated by pits. Xylem vessels arise from individual cylindrical cells oriented end to end. At
maturity the end walls of these cells dissolve away, and the cytoplasmic contents die. The result is the xylem vessel, a continuous
nonliving duct.
Xylem also contains tracheids. These are individual cells tapered at each end so the tapered end of one cell overlaps that of the
adjacent cell. Like xylem vessels, they have thick, lignified walls and, at maturity, no cytoplasm. Their walls are perforated so that
water can flow from one tracheid to the next. The xylem of ferns and conifers contains only tracheids.
In woody plants, the older xylem ceases to participate in water transport and simply serves to give strength to the trunk. Wood is
xylem. When counting the annual rings of a tree, one is counting rings of xylem.

Phloem
The main components of phloem are sieve elements and companion cells.
Sieve elements are so named because their end walls are perforated. This allows cytoplasmic connections between vertically-
stacked cells. The result is a sieve tube that conducts the products of photosynthesis - sugars and amino acids - from the place
where they are manufactured (a "source"), e.g., leaves, to the places ("sinks") where they are consumed or stored; such as
roots
growing tips of stems and leaves
flowers
fruits, tubers, corms, etc.
Sieve elements have no nucleus and only a sparse collection of other organelles. They depend on the adjacent companion cells for
many functions. Companion cells move sugars, amino acids and a variety of macromolecules into and out of the sieve elements. In
"source" tissue, such as a leaf, the companion cells use transmembrane proteins to take up - by active transport - sugars and other
organic molecules from the cells manufacturing them. Water follows by osmosis. These materials then move into adjacent sieve
elements through plasmodesmata. The pressure created by osmosis drives the flow of materials through the sieve tubes.
In "sink" tissue, the sugars and other organic molecules leave the sieve elements through plasmodesmata connecting the sieve
elements to their companion cells and then pass on to the cells of their destination. Again, water follows by osmosis where it may
leave the plant by transpiration or increase the volume of the cells or move into the xylem for recycling through the plant.

This page titled 16.1.1: Plant Tissues is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.1.1.2 https://bio.libretexts.org/@go/page/5777
16.1.2: Roots

Root Structure

Figure 16.1.2.1 The root

The Root Tip

The root tip consists of a
root cap — a sheath of cells that
protect the meristem from abrasion and damage as the root tip grows through the soil;
secrete the growth hormone auxin;
detect water and nutrients in the soil;
detect gravity and respond with gravitropism.
meristem - a region of rapid mitosis, which produces the new cells for root growth.
Because of the frequency of mitosis in the meristem, root tips are often used to demonstrate mitosis in the laboratory The inset is a
photo (courtesy of Carolina Biological Supply Co.) of anaphase in the meristem of an onion root tip.

The Region of Elongation

Here the cells produced by mitosis undergo a period of elongation in the direction of the axis of the root.

The Region of Differentiation

Here develop the differentiated tissues of the root.
Epidermis - A single layer of flattened cells at the surface. When first formed, epidermal cells have extensions — the root hairs
— which greatly increase the surface area available for the uptake of nutrients from the soil. The photo below shows the root
hairs in the region of differentiation of a germinating radish seed.

16.1.2.1 https://bio.libretexts.org/@go/page/5778
 Figure 16.1.2.2 Radish root
Cortex - A band of parenchyma cells that develops beneath the epidermis. It stores food. Its inner surface is bounded by a
single layer of cells, the
Endodermis
Stele
Pericycle - the outer boundary of the stele. Secondary roots branch from it.
Xylem - arranged in bundles in a spokelike fashion
Phloem - alternates with xylem
Cambium - In older parts of the root, another meristem forms between the xylem and phloem. Mitosis in the cambium
produces new "secondary xylem" to the inside and secondary phloem to the outside.

Water Uptake
Water enters the root through the epidermis. Once within the epidermis, water passes through the cortex, mainly traveling between
the cells. However, in order to enter the stele, it must pass through the cytoplasm of the cells of the endodermis.
Once within the stele, water is free again to move between cells as well as through them. In young roots, water enters directly into
the xylem. In older roots, it may have to pass first through a band of phloem and cambium. It does so by traveling through
horizontally-elongated cells, the xylem rays.

Mineral Uptake
One might have expected that minerals would enter the root dissolved in water. But, in fact, minerals enter separately:
Even when no water is being absorbed, minerals enter freely - mostly through the root hairs.
Minerals can enter against their concentration gradient; that is, by active transport. For example, plants can take up K+ from the
soil against a ten-thousand-fold concentration gradient; e.g., from as little as 10 µM in the soil to 100 mM in the cell.
Anything that interferes with the metabolism of root hairs interferes with mineral absorption.
The root hairs are also the point of entry of mycorrhizal fungi. These transport minerals - especially phosphorus - to the root
hair in exchange for carbohydrates from the plant.
In legumes, the root hairs are the point of entry of rhizobia that will establish the mutualistic partnership enabling the plant to
convert atmospheric nitrogen into protein.

Plants absorb their nutrients in inorganic form

For examples:
nitrogen enters as nitrate (NO3−) or ammonium ions (NH4+)
phosphorus as PO43−
potassium as K+
calcium as Ca2+
When you hear of the virtues of organic fertilizers, remember that such materials meet no nutritional need of the plant until their
constituents have been degraded to inorganic forms. Organic matter does play an important role in making good soil texture, but
only to the extent that it can yield inorganic ions can it meet the nutritional needs of the plant.

16.1.2.2 https://bio.libretexts.org/@go/page/5778
Once within the epidermis, inorganic ions pass inward from cell to cell, probably through plasmodesmata. The final step from the
cytoplasm of the pericycle cells to the xylem is probably accomplished once again by active transport.

This page titled 16.1.2: Roots is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.1.2.3 https://bio.libretexts.org/@go/page/5778
16.1.3: Stems
javascript:void('Remove Anchor')

The organization of the tissues of the stem differs between dicots and monocots.

The Woody Dicot Stem

The drawing shows a sector of a cross section through a 5-year old twig from a basswood tree (Tilia). The stem has three areas:
bark
wood
pith

Figure 16.1.3.1 Dicot stem

Bark
Cork - The outer part of the bark is protected by layers of dead cork cells impregnated with suberin. Suberin is waxy and cuts
down water loss from the stem. But suberin is as impervious to air as it is to water. The gas exchange needs of the living cells
beneath the cork are met by openings in the cork called lenticels.
Cortex - Layers of parenchyma cells. These store food (as they do in the root). In the very young stem (before cork has
formed), they may have chloroplasts and carry on photosynthesis.
Cork cambium - In older stems, a meristem forms between the cork and cortex. Mitosis of its cells produces more cork.
Expanded pith rays - Regions of parenchyma that store food.
Phloem - Bundles of sieve tubes surrounded and supported by sclerenchyma. Translocation of food through the stem takes
place in the sieve tubes.

Cambium
During the growing season, mitosis in this band of meristematic tissue produces new phloem to the outside and new xylem to the
inside.

Xylem
Xylem makes up the wood region. The xylem vessels made in the spring, when water is plentiful, have larger diameters than those
made later in the season. No xylem is made during the dormant season. The visual contrast between the late summer xylem of one
season and the spring xylem of the next creates the annual ring. Xylem serves two functions:
transport of water and minerals up the stem
support

16.1.3.1 https://bio.libretexts.org/@go/page/5779
 Figure 16.1.3.2 Monocot stem
The photograph (courtesy of Turtox) shows the organization of tissues in the corn (maize) stem, a typical monocot. The corn stem
consists of:
an external rind
an interior filled with pith.
Vascular bundles are scattered through the pith.
Each vascular bundle contains:
a layer of sclerenchyma that provides support
a bundle of phloem containing
sieve tubes used for food transport
their companion cells.
four xylem vessels
a group of xylem tracheids
both carry water and dissolved minerals up the stem

This page titled 16.1.3: Stems is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.1.3.2 https://bio.libretexts.org/@go/page/5779
16.1.4: The Leaf

Layers in a leaf

Figure 16.1.4.1 Leaf structure

Upper epidermis
This is a single layer of cells containing few or no chloroplasts. The cells are quite transparent and permit most of the light that
strikes them to pass through to the underlying cells. The upper surface is covered with a waxy, waterproof cuticle, which serves to
reduce water loss from the leaf.

Palisade layer
This consists of one or more layers of cylindrical cells oriented with their long axis perpendicular to the plane of the leaf. The cells
are filled with chloroplasts (usually several dozen of them) and carry on most of the photosynthesis in the leaf.

Spongy layer
Lying beneath the palisade layer, its cells are irregular in shape and loosely packed. Although they contain a few chloroplasts, their
main function seems to be the temporary storage of sugars and amino acids synthesized in the palisade layer. They also aid in the
exchange of gases between the leaf and the environment. During the day, these cells give off oxygen and water vapor to the air
spaces that surround them. They also pick up carbon dioxide from the air spaces. The air spaces are interconnected and eventually
open to the outside through pores called stomata (sing., stoma).
Collectively, the palisade and spongy layers make up the mesophyll.

Lower epidermis
Typically, most of the stomata (thousands per square centimeter) are located in the lower epidermis. Although most of the cells of
the lower epidermis resemble those of the upper epidermis, each stoma is flanked by two sausage-shaped cells called guard cells.
These differ from the other cells of the lower epidermis not only in their shape but also in having chloroplasts. The guard cells
regulate the opening and closing of the stomata. Thus they control the exchange of gases between the leaf and the surrounding
atmosphere.

Leaf Veins
Not only must the cells of the mesophyll be close to their air supply to secure CO2 and release O2 and the reverse in the dark but
they must be close to a leaf vein with its
xylem to supply water and minerals
phloem to remove synthesized food

16.1.4.1 https://bio.libretexts.org/@go/page/5780
 Figure 16.1.4.2 Network of leaf veins
The photo shows the network of leaf veins in a maple leaf. Probably no cell in the spongy layer is more than two cells away from a
vein.
The xylem and phloem of veins is often surrounded by layers of sclerenchyma cells. These impart strength to the vein providing a
stiff framework to support the soft tissues of the leaf blade.

This page titled 16.1.4: The Leaf is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.1.4.2 https://bio.libretexts.org/@go/page/5780
16.1.5: Arabidopsis Thaliana

Figure 16.1.5.1 Arabidopsis courtesy of Nicole Hanley Markelz of the Plant Genome Research Outreach Program at Cornell
University
This little plant has become to plant biology what Drosophila melanogaster and Caenorhabditis elegans are to animal biology.
Arabidopsis is an angiosperm, a dicot from the mustard family (Brassicaceae). It is popularly known as thale cress or mouse-ear
cress. While it has no commercial value - in fact is considered a weed - it has proved to be an ideal organism for studying plant
development.
Some of its advantages as a model organism:
It has one of the smallest genomes in the plant kingdom: 135 x 106 base pairs of DNA distributed in 5 chromosomes (2n = 10)
and almost all of which encodes its 27,407 genes.
Transgenic plants can be made easily using Agrobacterium tumefaciens as the vector to introduce foreign genes.
The plant is small - a flat rosette of leaves from which grows a flower stalk 6–12 inches high.
It can be easily grown in the lab in a relatively small space.
Development is rapid. It only takes 5– 6 weeks from seed germination to the production of a new crop of seeds.
It is a prolific producer of seeds (up to 10,000 per plant) making genetics studies easier.
Mutations can be easily generated (e.g., by irradiating the seeds or treating them with mutagenic chemicals).
It is normally self-pollinated so recessive mutations quickly become homozygous and thus expressed.
Other members of its family cannot self-pollinate. They have an active system of self-incompatibility. Arabidopsis,
however, has inactivating mutations in the genes - SRK and SCR - that prevent self-pollination in other members of the
family.
However, Arabidopsis can easily be cross-pollinated to
do genetic mapping
produce strains with multiple mutations.
Many of the findings about how plants work described throughout these pages were learned from studies with Arabidopsis.

This page titled 16.1.5: Arabidopsis Thaliana is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.1.5.1 https://bio.libretexts.org/@go/page/5781
 SECTION OVERVIEW
16.2: Plant Physiology
Topic hierarchy

16.2A: Xylem

16.2B: Phloem

16.2C: Transpiration

16.2D: Gas Exchange in Plants

16.2E: Photorespiration and C4 Plants

16.2F: Tropisms

This page titled 16.2: Plant Physiology is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.2.1 https://bio.libretexts.org/@go/page/5774
16.2A: Xylem
Most plants secure the water and minerals they need from their roots. The path taken is:
soil → roots → stems → leaves (16.2A.1)

The minerals (e.g., K+, Ca2+) travel dissolved in the water (often accompanied by various organic molecules supplied by root
cells), but less than 1% of the water reaching the leaves is used in photosynthesis and plant growth. Most of it is lost in
transpiration, which serve two useful functions- it provides the force for lifting the water up the stems and it cools the leaves. Water
and minerals enter the root by separate paths which eventually converge in the stele.

The Pathway of Water and Minerals

Soil water enters the root through its epidermis. It appears that water then travels in both the cytoplasm of root cells - called the
symplast (i.e., it crosses the plasma membrane and then passes from cell to cell through plasmodesmata) and in the nonliving parts
of the root - called the apoplast (i.e., in the spaces between the cells and in the cells walls themselves. This water has not crossed a
plasma membrane. However, the inner boundary of the cortex, the endodermis, is impervious to water because of a band of
lignified matrix called the casparian strip. Therefore, to enter the stele, apoplastic water must enter the symplasm of the endodermal
cells. From here it can pass by plasmodesmata into the cells of the stele. Once inside the stele, water is again free to move between
cells as well as through them. In young roots, water enters directly into the xylem vessels and/or tracheids. These are nonliving
conduits so are part of the apoplast.

Figure 16.2.1.1: Pathway of water

Once in the xylem, water with the minerals that have been deposited in it (as well as occasional organic molecules supplied by the
root tissue) move up in the vessels and tracheids. At any level, the water can leave the xylem and pass laterally to supply the needs
of other tissues. At the leaves, the xylem passes into the petiole and then into the veins of the leaf. Water leaves the finest veins and
enters the cells of the spongy and palisade layers. Here some of the water may be used in metabolism, but most is lost in
transpiration.
Minerals enter the root by active transport into the symplast of epidermal cells and move toward and into the stele through the
plasmodesmata connecting the cells. They enter the water in the xylem from the cells of the pericycle (as well as of parenchyma
cells surrounding the xylem) through specialized transmembrane channels.

What Forces Water Through the Xylem?

Observations
The mechanism is based on purely physical forces because the xylem vessels and tracheids are lifeless.
Roots are not needed. This was demonstrated over a century ago by a German botanist who sawed down a 70-ft (21 meters) oak
tree and placed the base of the trunk in a barrel of picric acid solution. The solution was drawn up the trunk, killing nearby
tissues as it went.
However, leaves are needed. When the acid reached the leaves and killed them, the upward movement of water ceased.
Removing a band of bark from around the trunk - a process called girdling - does not interrupt the upward flow of water.
Girdling removes only the phloem, not the xylem, and so the foliage does not wilt. (In due course, however, the roots - and thus
the entire plant - will die because the roots cannot receive any of the food manufactured by the leaves.)

16.2A.1 https://bio.libretexts.org/@go/page/5782
Transpiration-Pull
In 1895, the Irish plant physiologists H. H. Dixon and J. Joly proposed that water is pulled up the plant by tension (negative
pressure) from above. As we have seen, water is continually being lost from leaves by transpiration. Dixon and Joly believed that
the loss of water in the leaves exerts a pull on the water in the xylem ducts and draws more water into the leaf. But even the best
vacuum pump can pull water up to a height of only 34 ft (10.4 m) or so. This is because a column of water that high exerts a
pressure of ~15 lb/in2 (103 kilopascals, kPa) just counterbalanced by the pressure of the atmosphere. How can water be drawn to
the top of a sequoia (the tallest is 370 feet [113 meters] high)? Taking all factors into account, a pull of at least 270 lb/in2 (~1.9 x
103 kPa) is probably needed.
The answer to the dilemma lies the cohesion of water molecules; that is the property of water molecules to cling to each through
the hydrogen bonds they form. When ultrapure water is confined to tubes of very small bore, the force of cohesion between water
molecules imparts great strength to the column of water. It has been reported that tensions as great as 3000 lb/in2 (21 x 103 kPa)
are needed to break the column, about the value needed to break steel wires of the same diameter. In a sense, the cohesion of water
molecules gives them the physical properties of solid wires. Because of the critical role of cohesion, the transpiration-pull theory is
also called the cohesion theory.

support for Cohesion theory

If sap in the xylem is under tension, we would expect the column to snap apart if air is introduced into the xylem vessel by
puncturing it. This is the case.
If the water in all the xylem ducts is under tension, there should be a resulting inward pull (because of adhesion) on the walls of
the ducts. This inward pull in the band of sapwood in an actively transpiring tree should, in turn, cause a decrease in the
diameter of the trunk.

Figure 16.2.1.2 Transpiration in a monterey pine

The graph shows the results of obtained by D. T. MacDougall when he made continuous measurements of the diameter of a
Monterey pine. The diameter fluctuated on a daily basis reaching its minimum when the rate of transpiration reached its
maximum (around noon)
The rattan vine may climb as high as 150 ft (45.7 m) on the trees of the tropical rain forest in northeastern Australia to get its
foliage into the sun. When the base of a vine is severed while immersed in a basin of water, water continues to be taken up. A
vine less than 1 inch (2.5 cm) in diameter will "drink" water indefinitely at a rate of up to 12 ml/minute.
If forced to take water from a sealed container, the vine does so without any decrease in rate, even though the resulting vacuum
becomes so great that the remaining water begins to boil spontaneously. (The boiling temperature of water decreases as the air
pressure over the water decreases, which is why it takes longer to boil an egg in Denver than in New Orleans.)
Transpiration-pull enables some trees and shrubs to live in seawater. Seawater is markedly hypertonic to the cytoplasm in the
roots of the red mangrove (Rhizophora mangle), and we might expect water to leave the cells resulting in a loss in turgor and
wilting. In fact, the remarkably high tensions on the order of 500–800 lb/in2 (~3 to 5 thousand kPa) in the xylem can pull water
into the plant against this osmotic gradient. So mangroves literally desalt seawater to meet their needs.

Problems with the theory

When water is placed under a high vacuum, any dissolved gases come out of solution as bubbles (as we saw above with the rattan
vine) - this is called cavitation. Any impurities in the water enhance the process. So measurements showing the high tensile
strength of water in capillaries require water of high purity - not the case for sap in the xylem. So might cavitation break the
column of water in the xylem and thus interrupt its flow? Probably not so long as the tension does not greatly exceed 270 lb/in2
(~1.9 x 103 kPa).
By spinning branches in a centrifuge, it has been shown that water in the xylem avoids cavitation at negative pressures exceeding
225 lb/in2 (~1.6 x 103 kPa). And the fact that sequoias can successfully lift water 358 ft (109 m) - which would require a tension of
270 lb/in2 (~1.9 x 103 kPa) - indicates that cavitation is avoided even at that value. However, such heights may be approaching the
limit for xylem transport. Measurements close to the top of the tallest living sequoia (370 ft [=113 m] high) show that the high
tensions needed to get water up there have resulted in smaller stomatal openings, causing lower concentrations of CO2 in the

16.2A.2 https://bio.libretexts.org/@go/page/5782
needles, causing reduced photosynthesis, causing reduced growth (smaller cells and much smaller needles). (Reported by Koch, G.
W. et al., in Nature, 22 April 2004.) So the limits on water transport limit the ultimate height which trees can reach. The tallest tree
ever measured, a Douglas fir, was 413 ft. (125.9 meters) high.

Root Pressure
When a tomato plant is carefully severed close to the base of the stem, sap oozes from the stump. The fluid comes out under
pressure which is called root pressure. Root pressure is created by the osmotic pressure of xylem sap which is, in turn, created by
dissolved minerals and sugars that have been actively transported into the apoplast of the stele.

Figure 16.2.1.3: Root pressure

One important example is the sugar maple when, in very early spring, it hydrolyzes the starches stored in its roots into sugar. This
causes water to pass by osmosis through the endodermis and into the xylem ducts. The continuous inflow forces the sap up the
ducts.
Although root pressure plays a role in the transport of water in the xylem in some plants and in some seasons, it does not account
for most water transport.
Few plants develop root pressures greater than 30 lb/in2 (207 kPa), and some develop no root pressure at all.
The volume of fluid transported by root pressure is not enough to account for the measured movement of water in the xylem of
most trees and vines.
Those plants with a reasonably good flow of sap are apt to have the lowest root pressures and vice versa.
The highest root pressures occur in the spring when the sap is strongly hypertonic to soil water, but the rate of transpiration is
low. In summer, when transpiration is high and water is moving rapidly through the xylem, often no root pressure can be
detected.
So although root pressure may play a significant role in water transport in certain species (e.g., the coconut palm) or at certain
times, most plants meet their needs by transpiration-pull.

This page titled 16.2A: Xylem is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.2A.3 https://bio.libretexts.org/@go/page/5782
16.2B: Phloem
Food and other organic substances (e.g., some plant hormones and even messenger RNAs) manufactured in the cells of the plant
are transported in the phloem. Sugars (usually sucrose), amino acids and other organic molecules enter the sieve elements through
plasmodesmata connecting them to adjacent companion cells. Once within the sieve elements, these molecules can be transported
either up or down to any region of the plant moving at rates as high as 110 μm per second.
Two demonstrations:
Girdling. Girdling is removing a band of bark from the circumference of the tree. Girdling removes the phloem, but not the
xylem. If a tree is girdled in summer, it continues to live for a time. There is, however, no increase in the weight of the roots,
and the bark just above the girdled region accumulates carbohydrates. Unless a special graft is made to bridge the gap, the tree
eventually dies as its roots starve.

Figure 16.2.2.0: Girdling, also called ring barking or ring-barking, is the process of completely removing a strip of bark (consisting
of Secondary Phloem tissue, cork cambium, and cork) around a tree's outer circumference, causing its death. Here girdling occurs
by deliberate human action to give new habitats to species of dead woods (Lille, North of France, Parc de la Cidatelle (Bois de
Boulogne). (CC-BY-SA-3.0; Lamiot).
The pictures below are autoradiographs showing that the products of photosynthesis are transported in the phloem.

Figure 16.2.2.1 Products of photosynthesis transported in phloem courtesy of R. S. Gage and S. Aronoff
A cucumber leaf was supplied with radioactive water (3HOH) and allowed to carry on photosynthesis for 30 minutes. Then
slices were cut from the petiole of the leaf and covered with a photographic emulsion. Radioactive products of
photosynthesis darkened the emulsion where it was in contact with the phloem (upper left in both photos), but not where it
was in contact with the xylem vessels (center). In the photomicrograph on the left, the microscope is focused on the tissue in
order to show the cells clearly; on the right, the microscope has been focused on the photographic emulsion.
Some fruits, such as the pumpkin, receive over 0.5 gram of food each day through the phloem. Because the fluid is fairly dilute,
this requires a substantial flow. In fact, the use of radioactive tracers shows that substances can travel through as much as 100 cm of
phloem in an hour.

Mechanism that drives translocation of food through the phloem

16.2B.1 https://bio.libretexts.org/@go/page/5783
 Figure 16.2.2.2 Chilling petiole
Translocation through the phloem is dependent on metabolic activity of the phloem cells (in contrast to transport in the xylem).
Chilling its petiole slows the rate at which food is translocated out of the leaf (above).
Oxygen lack also depresses it.
Killing the phloem cells puts an end to it.

The Pressure-Flow Hypothesis

Figure 16.2.2.3 Pressure flow

The best-supported theory to explain the movement of food through the phloem is called the pressure-flow hypothesis.
It proposes that water containing food molecules flows under pressure through the phloem.
The pressure is created by the difference in water concentration of the solution in the phloem and the relatively pure water in the
nearby xylem ducts.
At their "source" - the leaves - sugars are pumped by active transport into the companion cells and sieve elements of the
phloem.
As sugars (and other products of photosynthesis) accumulate in the phloem, water enters by osmosis.
In the figure, sugar molecules are represented in black, water molecules in red.)
Turgor pressure builds up in the sieve elements (similar to the creation of root pressure).
As the fluid is pushed down (and up) the phloem, sugars are removed by the cortex cells of both stem and root (the "sinks") and
consumed or converted into starch.
Starch is insoluble and exerts no osmotic effect.
Therefore, the osmotic pressure of the contents of the phloem decreases.
Finally, relatively pure water is left in the phloem, and this leaves by osmosis and/or is drawn back into nearby xylem vessels
by the suction of transpiration-pull.
Thus it is the pressure gradient between "source" (leaves) and "sink" (shoot and roots) that drives the contents of the phloem up and
down through the sieve elements.

Tests of the theory

1. The contents of the sieve elements must be under pressure.

16.2B.2 https://bio.libretexts.org/@go/page/5783
This is difficult to measure because when a sieve element is punctured with a measuring probe, the holes in its end walls quickly
plug up. However, aphids can insert their mouth parts without triggering this response.

Figure 16.2.2.4 Pressure flow hypothesis in reality

Left: when it punctures a sieve element, sap enters the insect's mouth parts under pressure and some soon emerges at the other end
(as a drop of honeydew that serves as food for ants and bees).
Right: honeydew will continue to exude from the mouthparts after the aphid has been cut away from them.
2. The osmotic pressure of the fluid in the phloem of the leaves must be greater than that in the phloem of the food-receiving
organs such as the roots and fruits. Most measurements have shown this to be true.

Transport of Messenger RNA (mRNA) through the Phloem

Plant scientists at the Davis campus of the University of California (reported in the 13 July 2001 issue of Science) have
demonstrated that messenger RNAs can also be transported long distances in the phloem. They grafted normal tomato scions onto
mutant tomato stocks and found that mRNAs synthesized in the stock were transported into the scions. These mRNAs converted
the phenotype of the scion into that of the stock.

This page titled 16.2B: Phloem is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.2B.3 https://bio.libretexts.org/@go/page/5783
16.2C: Transpiration
Transpiration is the evaporation of water from plants. It occurs chiefly at the leaves while their stomata are open for the passage
of CO2 and O2 during photosynthesis. But air that is not fully saturated with water vapor (100% relative humidity) will dry the
surfaces of cells with which it comes in contact. So the photosynthesizing leaf loses substantial amount of water by evaporation.
This transpired water must be replaced by the transport of more water from the soil to the leaves through the xylem of the roots and
stem.
Transpiration is not simply a hazard of plant life. It is the "engine" that pulls water up from the roots to:
supply photosynthesis (1%-2% of the total)
bring minerals from the roots for biosynthesis within the leaf
cool the leaf

Figure 16.2.3.1 Potometer

Using a potometer (above), one can study the effect of various environmental factors on the rate of transpiration. As water is
transpired or otherwise used by the plant, it is replaced from the reservoir on the right. This pushes the air bubble to the left
providing a precise measure of the volume of water used.

Environmental factors that affect the rate of transpiration

1. Light
Plants transpire more rapidly in the light than in the dark. This is largely because light stimulates the opening of the stomata
(mechanism). Light also speeds up transpiration by warming the leaf.
2. Temperature
Plants transpire more rapidly at higher temperatures because water evaporates more rapidly as the temperature rises. At 30°C, a leaf
may transpire three times as fast as it does at 20°C.
3. Humidity
The rate of diffusion of any substance increases as the difference in concentration of the substances in the two regions
increases.When the surrounding air is dry, diffusion of water out of the leaf goes on more rapidly.
4. Wind
When there is no breeze, the air surrounding a leaf becomes increasingly humid thus reducing the rate of transpiration. When a
breeze is present, the humid air is carried away and replaced by drier air.
5. Soil water
A plant cannot continue to transpire rapidly if its water loss is not made up by replacement from the soil. When absorption of water
by the roots fails to keep up with the rate of transpiration, loss of turgor occurs, and the stomata close. This immediately reduces
the rate of transpiration (as well as of photosynthesis). If the loss of turgor extends to the rest of the leaf and stem, the plant wilts.
The volume of water lost in transpiration can be very high. It has been estimated that over the growing season, one acre of corn
(maize) plants may transpire 400,000 gallons (1.5 million liters) of water. As liquid water, this would cover the field with a lake 15
inches (38 cm) deep. An acre of forest probably does even better.

This page titled 16.2C: Transpiration is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.2C.1 https://bio.libretexts.org/@go/page/5784
16.2D: Gas Exchange in Plants
In order to carry on photosynthesis, green plants need a supply of carbon dioxide and a means of disposing of oxygen. In order to
carry on cellular respiration, plant cells need oxygen and a means of disposing of carbon dioxide (just as animal cells do). Unlike
animals, plants have no specialized organs for gas exchange (with the few inevitable exceptions!). The are several reasons they can
get along without them:
Each part of the plant takes care of its own gas exchange needs. Although plants have an elaborate liquid transport system, it
does not participate in gas transport.
Roots, stems, and leaves respire at rates much lower than are characteristic of animals. Only during photosynthesis are large
volumes of gases exchanged, and each leaf is well adapted to take care of its own needs.
The distance that gases must diffuse in even a large plant is not great. Each living cell in the plant is located close to the surface.
While obvious for leaves, it is also true for stems. The only living cells in the stem are organized in thin layers just beneath the
bark. The cells in the interior are dead and serve only to provide mechanical support.
Most of the living cells in a plant have at least part of their surface exposed to air. The loose packing of parenchyma cells in
leaves, stems, and roots provides an interconnecting system of air spaces. Gases diffuse through air several thousand times
faster than through water. Once oxygen and carbon dioxide reach the network of intercellular air spaces (arrows), they diffuse
rapidly through them.
Oxygen and carbon dioxide also pass through the cell wall and plasma membrane of the cell by diffusion. The diffusion of
carbon dioxide may be aided by aquaporin channels inserted in the plasma membrane.

Leaves
The exchange of oxygen and carbon dioxide in the leaf (as well as the loss of water vapor in transpiration) occurs through pores
called stomata (singular = stoma).

Figure 16.2.4.1 Stoma

Normally stomata open when the light strikes the leaf in the morning and close during the night. The immediate cause is a change
in the turgor of the guard cells. The inner wall of each guard cell is thick and elastic. When turgor develops within the two guard
cells flanking each stoma, the thin outer walls bulge out and force the inner walls into a crescent shape. This opens the stoma.
When the guard cells lose turgor, the elastic inner walls regain their original shape and the stoma closes.

Time Osmotic Pressure lb/in2

7 A.M. 212

11A.M. 456

5 P.M. 272

12 Midnight 191

16.2D.1 https://bio.libretexts.org/@go/page/5785
The table shows the osmotic pressure measured at different times of day in typical guard cells. The osmotic pressure within the
other cells of the lower epidermis remained constant at 150 lb/in2 (~1000 kilopascal, kPa). When the osmotic pressure of the guard
cells became greater than that of the surrounding cells, the stomata opened. In the evening, when the osmotic pressure of the guard
cells dropped to nearly that of the surrounding cells, the stomata closed.

Opening stomata
The increase in osmotic pressure in the guard cells is caused by an uptake of potassium ions (K+). The concentration of K+ in
open guard cells far exceeds that in the surrounding cells. This is how it accumulates:
Blue light is absorbed by phototropin which activates a proton pump (an H+-ATPase) in the plasma membrane of the guard
cell.
ATP, generated by the light reactions of photosynthesis, drives the pump.
As protons (H+) are pumped out of the cell, its interior becomes increasingly negative.
This attracts additional potassium ions into the cell, raising its osmotic pressure.

Closing stomata
Although open stomata are essential for photosynthesis, they also expose the plant to the risk of losing water through transpiration.
Some 90% of the water taken up by a plant is lost in transpiration. In angiosperms and gymnosperms (but not in ferns and
lycopsids), Abscisic acid (ABA) is the hormone that triggers closing of the stomata when soil water is insufficient to keep up with
transpiration (which often occurs around mid-day).
The mechanism:
ABA binds to receptors at the surface of the plasma membrane of the guard cells.
The receptors activate several interconnecting pathways which converge to produce
a rise in pH in the cytosol
transfer of Ca2+ from the vacuole to the cytosol
These changes stimulate the loss of negatively-charged ions (anions), especially NO3− and Cl−, from the cell and also the loss
of K+ from the cell.
The loss of these solutes in the cytosol reduces the osmotic pressure of the cell and thus turgor.
The stomata close.
Open stomata also provide an opening through which bacteria can invade the interior of the leaf. However, guard cells have
receptors that can detect the presence of molecules associated with bacteria called pathogen-associated molecular patterns
(PAMPs). LPS and flagellin are examples. When the guard cells detect these PAMPs, ABA mediates closure of the stoma and thus
close the door to bacterial entry.
This system of innate immunity resembles that found in animals.

Density of stomata
The density of stomata produced on growing leaves varies with such factors as the temperature, humidity, and light intensity
around the plant. It also depends on the the concentration of carbon dioxide in the air around the leaves. The relationship is
inverse; that is, as the concentration of CO2 goes up, the number of stomata produced goes down, and vice versa. Some evidence:
Plants grown in an artificial atmosphere with a high level of CO2 have fewer stomata than normal.
Herbarium specimens reveal that the number of stomata in a given species has been declining over the last 200 years — the
time of the industrial revolution and rising levels of CO2 in the atmosphere.
These data can be quantified by determining the stomatal index: the ratio of the number of stomata in a given area divided by the
total number of stomata and other epidermal cells in that same area.

 Q&A
How does the plant determine how many stomata to produce?
It turns out that the mature leaves on the plant detect the conditions around them and send a signal (its nature still unknown -
but see below*) that adjusts the number of stomata that will form on the developing leaves.

16.2D.2 https://bio.libretexts.org/@go/page/5785
 Two experiments (reported by Lake et al., in Nature, 411:154, 10 May 2001):
When the mature leaves of the plant (Arabidopsis) are encased in glass tubes filled with high levels (720 ppm) of CO2, the
developing leaves have fewer stomata than normal even though they are growing in normal air (360 ppm).
Conversely, when the mature leaves are given normal air (360 ppm CO2) while the shoot is exposed to high CO2 (720
ppm), the new leaves develop with the normal stomatal index.

*One signal that increases stomatal density in 2-day-old Arabidopsis seedlings (a different experimental setup than the one
above) is a 45-amino acid peptide called stomagen that is released by mesophyll cells and induces the formation of stomata in
the epidermis above.

 Stomata reveal past carbon dioxide levels

Because CO2 levels and stomatal index are inversely related, could fossil leaves tell us about past levels of CO2 in the
atmosphere? Yes. As reported by Gregory Retallack (in Nature, 411:287, 17 May 2001), his study of the fossil leaves of the
ginkgo and its relatives shows:
their stomatal indices were high late in the Permian period (275–290 million years ago) and again in the Pleistocene epoch
(1–8 million years ago). Both these periods are known from geological evidence to have been times of low levels of
atmospheric carbon dioxide and ice ages (with glaciers).
Conversely, stomatal indices were low during the Cretaceous period, a time of high CO2 levels and warm climate.
These studies also lend support to the importance of carbon dioxide as a greenhouse gas playing an important role in global
warming.

Roots and Stems

Woody stems and mature roots are sheathed in layers of dead cork cells impregnated with suberin — a waxy, waterproof (and
airproof) substance. So cork is as impervious to oxygen and carbon dioxide as it is to water. However, the cork of both mature roots
and woody stems is perforated by nonsuberized pores called lenticels. These enable oxygen to reach the intercellular spaces of the
interior tissues and carbon dioxide to be released to the atmosphere.

Figure 16.2.4.2 Lenticels. The photo shows the lenticels in the bark of a young stem.
In many annual plants, the stems are green and almost as important for photosynthesis as the leaves. These stems use stomata rather
than lenticels for gas exchange.

This page titled 16.2D: Gas Exchange in Plants is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.2D.3 https://bio.libretexts.org/@go/page/5785
16.2E: Photorespiration and C4 Plants
All plants carry on photosynthesis by adding carbon dioxide (CO2) to a phosphorylated 5-carbon sugar called ribulose
bisphosphate. This reaction is catalyzed by the enzyme ribulose bisphosphate carboxylase oxygenase (RUBISCO). The
resulting 6-carbon compound breaks down into two molecules of 3-phosphoglyceric acid (PGA). These 3-carbon molecules
serve as the starting material for the synthesis of glucose and other food molecules. The process is called the Calvin cycle and the
pathway is called the C3 pathway.

Photorespiration
As its name suggests, RUBISCO catalyzes two different reactions:
adding CO2 to ribulose bisphosphate — the carboxylase activity
adding O2 to ribulose bisphosphate — the oxygenase activity
Which one predominates depends on the relative concentrations of O2 and CO2 with
high CO2, low O2 favoring the carboxylase action
high O2, low CO2 favoring the oxygenase action
The light reactions of photosynthesis liberate oxygen and more oxygen dissolves in the cytosol of the cell at higher temperatures.
Therefore, high light intensities and high temperatures (above ~ 30°C) favor the second reaction.
The uptake of O2 by RUBISCO forms the 3-carbon molecule 3-phosphoglyceric acid, just as in the Calvin cycle, and the 2-carbon
molecule glycolate. The glycolate enters peroxisomes where it uses O2 to form intermediates that enter mitochondria where they
are broken down to CO2. So this process uses O2 and liberates CO2 as cellular respiration does which is why it is called
photorespiration. It undoes the good anabolic work of photosynthesis, reducing the net productivity of the plant. For this reason,
much effort so far largely unsuccessful has gone into attempts to alter crop plants so that they carry on less photorespiration. The
problem may solve itself. If atmospheric CO2 concentrations continue to rise, perhaps this will enhance the net productivity of the
world's crops by reducing losses to photorespiration.

C 4 Plants
Over 8,000 species of angiosperms have developed adaptations which minimize the losses to photorespiration. They all use a
supplementary method of CO2 uptake which forms a 4-carbon molecule instead of the two 3-carbon molecules of the Calvin cycle.
Hence these plants are called C4 plants. (Plants that have only the Calvin cycle are thus C3 plants). Some C4 plants - called CAM
plants - separate their C3 and C4 cycles by time, while other C4 plants have structural changes in their leaf anatomy so that their
C4 and C3 pathways are separated in different parts of the leaf with RUBISCO sequestered where the CO2 level is high; the O2
level low.
After entering through stomata, CO2 diffuses into a mesophyll cell. Being close to the leaf surface, these cells are exposed to high
levels of O2, but they have no RUBISCO so cannot start photorespiration (nor the dark reactions of the Calvin cycle).

Figure 16.2.5.1 C4 Anatomy

Instead the CO2 is inserted into a 3-carbon compound (C3) called phosphoenolpyruvic acid (PEP) forming the 4-carbon
compound oxaloacetic acid (C4). Oxaloacetic acid is converted into malic acid or aspartic acid (both have 4 carbons), which is
transported (by plasmodesmata) into a bundle sheath cell. Bundle sheath cells are deep in the leaf so atmospheric oxygen cannot

16.2E.1 https://bio.libretexts.org/@go/page/5786
diffuse easily to them and often have thylakoids with reduced photosystem II complexes (the one that produces O2). Both of these
features keep oxygen levels low in Bundle sheath cells, which is where the 4-carbon compound is broken down into carbon
dioxide, which enters the Calvin cycle to form sugars and starch, and pyruvic acid (C3), which is transported back to a mesophyll
cell where it is converted back into PEP.
These C4 plants are well adapted to (and likely to be found in) habitats with high daytime temperatures and intense sunlight. Some
examples crabgrass, corn (maize), sugarcane, and sorghum. Although only ~3% of the angiosperms, C4 plants are responsible for
~25% of all the photosynthesis on land.

 4 cells in C3 plants
The ability to use the C4 pathway has evolved repeatedly in different families of angiosperms - a remarkable example of
convergent evolution. Perhaps the potential is in all angiosperms.
A report in the 24 January 2002 issue of Nature (by Julian M. Hibbard and W. Paul Quick) describes the discovery that
tobacco, a C3 plant, has cells capable of fixing carbon dioxide by the C4 path. These cells are clustered around the veins
(containing xylem and phloem) of the stems and also in the petioles of the leaves. In this location, they are far removed from
the stomata that could provide atmospheric CO2. Instead, they get their CO2 and/or the 4-carbon malic acid in the sap that has
been brought up in the xylem from the roots.
If this turns out to be true of many C3 plants, it would explain why it has been so easy for C4 plants to evolve from C3
ancestors.

CAM Plants
CAM plants are also C4 plants (CAM stands for crassulacean acid metabolism because it was first studied in members of the plant
family Crassulaceae.). However, instead of segregating the C4 and C3 pathways in different parts of the leaf, CAM plants separate
them in time instead (Table 1).
Table 1
Night Morning

CAM plants take in CO2 through their open stomata (they tend to The stomata close (thus conserving moisture as well as reducing the
have reduced numbers of them). inward diffusion of oxygen).
The CO2 joins with PEP to form the 4-carbon oxaloacetic acid. The accumulated malic acid leaves the vacuole and is broken down
This is converted to 4-carbon malic acid that accumulates during to release CO2.
the night in the central vacuole of the cells. The CO2 is taken up into the Calvin (C3) cycle.

These adaptations also enable their owners to thrive in conditions of high daytime temperatures, intense sunlight, and low soil
moisture. Some examples of CAM plants include cacti, Bryophyllum, the pineapple and all epiphytic bromeliads, sedums, and the
"ice plant" that grows in sandy parts of the scrub forest biome.

Figure 1: Cultivated cacti in the Singapore Botanic Gardens. (CC SA-Y 3.0; Calvin Teo).

16.2E.2 https://bio.libretexts.org/@go/page/5786
C 4 Diatoms
On 26 October 2000, Nature reported the discovery of both the C3 and C4 pathways in a marine diatom. In this unicellular
organism, the two paths are kept separate by having the C4 path in the cytosol, and the C3 path confined to the chloroplast. The
presence of a C4 pathway probably reflects the frequent low concentrations of CO2 in ocean waters.

This page titled 16.2E: Photorespiration and C4 Plants is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.2E.3 https://bio.libretexts.org/@go/page/5786
16.2F: Tropisms
A tropism is a growth movement whose direction is determined by the direction from which the stimulus strikes the plant. There
are two forms: Positive = the plant, or a part of it, grows in the direction from which the stimulus originates. and Negative =
growth away from the stimulus.

A tropism is a growth movement whose direction is determined by the direction from which the stimulus strikes the plant.
Positive = the plant, or a part of it, grows in the direction from which the stimulus originates.
Negative = growth away from the stimulus.
Plants respond to:
Light = phototropism
Stems are positively phototropic.
Roots are negatively phototropic.
Gravity = gravitropism
Stems are negatively gravitropic while
roots are positively gravitropic.
The adaptive value of these tropisms is clear.
Roots growing down and/or away from light are more likely to find the soil, water, and minerals they need.
Stems growing up and toward the light will be able to expose their leaves so that photosynthesis can occur.

The Mechanism of Phototropism

The Darwin Experiments

Figure 16.2.6.2 Darwins experiment

If they placed an opaque cover over the tip, phototropism failed to occur even though the rest of the coleoptile was illuminated
from one side. However, when they buried the plant in fine black sand so that only its tip was exposed, there was no interference
with the tropism — the buried coleoptile bent in the direction of the light.
From these experiments, it seemed clear that
the stimulus (light) was detected at one location (the tip)
the response (bending) was carried out at another (the region of elongation)

Figure 16.2.6.3 Boysen - Jensen experiment

The Danish plant physiologist Boysen-Jensen showed (in 1913) that the signal was a chemical passing down from the tip of the
coleoptile.
He

16.2F.1 https://bio.libretexts.org/@go/page/5787
 cut off the tip of the coleoptile
covered the stump with a layer of gelatin
replaced the tip.

Figure 16.2.6.9 Roots vs Shoots

The graph (based on the work of K. V. Thimann) shows the effect of auxin concentration on root and stem growth. The difference
between the behavior of roots and stems lies in the difference in the sensitivity of their cells to auxin. Auxin concentrations high
enough to stimulate stem growth inhibit root growth.

Possible Mechanism of Gravitropism in Roots

When a root is placed on its side,
Statoliths (organelles containing starch grains) settle by gravity to the bottom of cells in the root tip.
This causes PIN proteins to redistribute to the underside of the cell where they pump auxin out of the cell.
The auxin then accumulates along the under side of the root.
This INHIBITS root cell elongation (see graph).
So the cells at the top surface of the root elongate, causing the root to grow down.

This page titled 16.2F: Tropisms is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.2F.2 https://bio.libretexts.org/@go/page/5787
 SECTION OVERVIEW
16.3: Reproduction in Plants
Topic hierarchy

16.3A: Alternation of Generations in Plants

16.3B: Moss Life Cycle

16.3C: Fern Life Cycle

16.3D: Angiosperm Life Cycle

16.3E: Asexual Reproduction in Plants

16.3E: Self-incompatibility - How Plants Avoid Inbreeding

16.3F: Transgenic Plants

This page titled 16.3: Reproduction in Plants is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.3.1 https://bio.libretexts.org/@go/page/5775
16.3A: Alternation of Generations in Plants
This page titled 16.3A: Alternation of Generations in Plants is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by
John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

16.3A.1 https://bio.libretexts.org/@go/page/5788
16.3B: Moss Life Cycle
Mosses and liverworts are traditionally classified together in the Division Bryophyta on the basis of their sharing a similar life
cycle (alternation of generations), similar reproductive organs (antheridia and archegonia), and a lack of vascular tissue (xylem and
phloem).

Figure 16.3.2.1: A thallose liverwort, Lunularia cruciata. Imaged used with permission (Public Domain; Velela).
Some 23,000 species of living mosses and liverworts have been identified. These are small, fairly simple, plants usually found in
moist locations. Liverworts have a thin, leathery body that grows flat on moist soil or, in some cases, the surface of still water. The
above photo is of a common liverwort, Ricciocarpus natans. Mosses have an erect shoot bearing tiny leaflike structures arranged in
spirals. Neither mosses nor liverworts have any woody tissue so they never grow very large. They have neither xylem nor phloem
for the transport of water and food through the plant.

The Gametophyte Generation

Fig.16.3.2.2 Moss life cycle

The leafy shoot of mosses is haploid and thus part of the gametophyte generation.
In the common haircap moss, Polytrichum commune (shown here), there are three kinds of shoots:
Female, which develop archegonia at their tip.
A single egg forms in each archegonium.
Male, which develop antheridia at their tip.
Multiple swimming sperm form in each antheridium.

16.3B.1 https://bio.libretexts.org/@go/page/5789
 Sterile, which do not form sex organs.
In early spring, raindrops splash sperm from male to female plants. These swim down the canal in the archegonium to the chamber
containing the egg. The resulting zygote begins the sporophyte generation.

The Sporophyte Generation

Figure 16.3.2.3 Moss sporophyte

Mitosis of the zygote produces an embryo that grows into the mature sporophyte generation. It consists of:
A foot, which absorbs water, minerals, and food from the parent gametophyte
A stalk, at the tip of which is formed a sporangium (the brownish objects in the photo).
The sporangium is
filled with spore mother cells
sealed by an operculum
covered with a calyptra. The calyptra develops from the wall of the old archegonium and so is actually a part of the
gametophyte generation. It is responsible for the common name ("haircap moss") of this species.
During the summer, each spore mother cell undergoes meiosis, producing four haploid spores - the start of the new gametophyte
generation. Late in the summer, the calyptra and operculum become detached from the sporangium allowing the spores to be
released. These tiny spores are dispersed so effectively by the wind that many mosses are worldwide in their distribution. If a spore
reaches a suitable habitat, it germinates to form a filament of cells called a protonema. Soon buds appear and develop into the
mature leafy shoots.
Thus the gametophyte generation is responsible for sexual reproduction. The sporophyte generation is responsible for dispersal.

Evolutionary Position of the Bryophytes

Evidence from the chloroplast genome
The chloroplasts of mosses and liverworts, like those of all photosynthetic eukaryotes, contain multiple copies of a small genome:
circular DNA molecules encoding some - but not all of the genes needed for their own replication and photosynthesis. Chloroplast
genomes have been sequenced from representatives of most of the plant groups. Although they all contain the same genes, they fall
into two distinct groups with respect to the organization of their genes.

Figure 16.3.2.4 Chloroplast gene

One group is illustrated by the figure, which shows the organization of the genome in Marchantia polymorpha, a liverwort.
Between the two arrowheads is a stretch of some 30,000 base pairs. The order of the genes in this region is also found in

16.3B.2 https://bio.libretexts.org/@go/page/5789
 mosses (supporting the idea that mosses and liverworts are, indeed, close relatives), and in the lycopsids — vascular plants
(they have xylem and phloem) that have a fossil record going back over 400 million years.
In all the other groups of plants, the same genes are present but in inverted order.

Evidence from the mitochondrial genome (mtDNA)

However, the mitochondrial DNA of plants suggests a different evolutionary scenario. The mtDNA of all plants including mosses
and lycopsids but NOT liverworts (nor green algae) contain certain shared introns. This suggests that:
mosses and liverworts are not close relatives
liverworts and lycopsids are not close relatives
liverworts may have been the first group of plants to evolve from algal ancestors

This page titled 16.3B: Moss Life Cycle is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.3B.3 https://bio.libretexts.org/@go/page/5789
16.3C: Fern Life Cycle
Ther are over 10,000 species of ferns. Most are found in the tropics where tree ferns with their above-ground stems may grow as
high as 40 feet. In temperate regions, the stems of ferns called rhizome grow underground. The leaves called fronds grow up from
the rhizome each spring.

Alternation of Generations
The Sporophyte Generation

Figure 16.3.3.1 Fern life cycle

The plant we recognize as a fern is the diploid sporophyte generation. Sori form on the fronds. Each contains many sporangia
mounted on stalks. Within each sporangium, the spore mother cells undergo meiosis producing four haploid spores each.
When the humidity drops,
The thin-walled lip cells of each sporangium separate.
The annulus slowly straightens out.
Then the annulus snaps forward expelling the spores.

Figure 16.3.3.2 Sori on a fern leaflet

The photo shows the sori on the underside of the leaflets of Polystichum acrostichoides, the Christmas fern.

The Gametophyte Generation

If a spore is blown to a suitable moist location, it germinates into a filament of cells. This may grow into a prothallus with
1. rhizoids, which absorb water and minerals from the soil,
2. archegonia, which produce a single egg (by mitosis) or

16.3C.1 https://bio.libretexts.org/@go/page/5790
 3. antheridia, which form swimming sperm (again, by mitosis) or
4. both.

Fertilization
If moisture is plentiful, the sperm swim to archegonia - usually on another prothallus because the two kinds of sex organs generally
do not mature at the same time on a single prothallus. Another method for promoting cross-fertilization: The first spores to
germinate develop into prothallia with archegonia. These prothallia secrete a gibberellin into their surroundings. This is absorbed
by younger prothallia and causes them to produce antheridia exclusively. Fertilization restores the diploid number and begins a new
sporophyte generation. The embryo sporophyte develops a foot that penetrates the tissue of the prothallus and enables the
sporophyte to secure nourishment until it becomes self-sufficient. Although it is tiny, the haploid fern prothallus is a fully-
independent, autotrophic plant.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 16.3C: Fern Life Cycle is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.3C.2 https://bio.libretexts.org/@go/page/5790
16.3D: Angiosperm Life Cycle
Angiosperms are the flowering plants (today the most abundant and diverse plants on earth). Most are terrestrial and all lack
locomotion. This poses several problems. Gametes are delicate single cells. For two plants to cross fertilize, there must be a
mechanism for the two gametes to reach each other safely. Moreover, there must also be a mechanism to disperse their offspring far
enough away from the parent so that they do not have to compete with the parent for light, water, and soil minerals. The functions
of the flower solve both of these problems.

The Flower and Its Pollination

In angiosperms, meiosis in the sporophyte generation produces two kinds of spores: (1) microspores which develop in the
microsporangium and will germinate and develop into the male gametophyte generation and (2) megaspores that develop in the
megasporangium will develop into the female gametophyte generation. Both types of sporangia are formed in flowers. In most
angiosperms, the flowers are perfect: each has both microsporangia and megasporangia, although some angiosperms are
imperfect, having either microsporangia or megasporangia but not both.
Monoecious plants have both types of imperfect flower on the same plant.
Dioecious plants have imperfect flowers on separate plants; that is, some plants are male, some female. Examples include
willows, poplars, and the date palm. Most dioecious plants use an X-Y system of of sex determination like that in mammals.
However, a few species use an X-to-autosome ratio system like that of Drosophila, and a very few use a ZW system like that of
birds and lepidoptera.

Figure 16.3.4.1 Flower

Flowers develop from flower buds. Each bud contains 4 concentric whorls of tissue. From the outer to the inner, these develop into
a whorl of sepals (collectively called the calyx)
a whorl of petals (collectively called the corolla)
stamens in which the microsporangia form
carpels in which the megasporangia form.

Stamens
Each stamen consists of a lobed anther, containing the microsporangia and supported by a thin filament. Meiosis of the diploid
microspore mother cells in the anther produces four haploid microspores. Each of these develops into a pollen grain consisting of
a larger vegetative cell (also called the tube cell) inside of which is a a smaller germ cell (also called the generative cell). At some
point, depending on the species, the germ cell divides by mitosis to produce 2 sperm cells.

Carpels
Carpels consist of a stigma, usually mounted at the tip of a style with an ovary at the base. Often the entire whorl of carpels is
fused into a single pistil. The megasporangia, called ovules, develop within the ovary. Meiosis of the megaspore mother cell in
each ovule produces 4 haploid cells, a large megaspore and 3 small cells that disintegrate.

Development of the megaspore

The nucleus of the megaspore undergoes three successive mitotic divisions. The 8 nuclei that result are distributed and partitioned
off by cell walls to form the embryo sac. This is the mature female gametophyte generation. The egg cell will start the new
sporophyte generation if it is fertilized. It is flanked by 2 synergid cells. In several (perhaps all) angiosperms, they secrete an
attractant that guides the pollen tube through the micropyle into the embryo sac. The large central cell, which in most angiosperms
contains 2 polar nuclei, will after its fertilization develop into the endosperm of the seed. It also contains 3 antipodal cells.

16.3D.1 https://bio.libretexts.org/@go/page/5791
 Figure 16.3.4.2 Embryo sac

Pollination
When a pollen grain reaches the stigma, it germinates into a pollen tube. If it hasn't done so already, the germ cell divides by
mitosis forming 2 sperm cells. These, along with the tube nucleus (also known as the vegetative nucleus), migrate down the pollen
tube as it grows through the style, the micropyle, and into the ovule chamber.
In Arabidopsis the pollen tube follows a gradient of increasing concentration of a small defensin-like protein secreted by the
synergids. The pollen tube with its contents makes up the mature male gametophyte generation.

Double fertilization
The pollen tube enters the ovule through the micropyle and ruptures. One sperm cell fuses with the egg forming the diploid zygote.
The other sperm cell fuses with the polar nuclei forming the endosperm nucleus. Most angiosperms have two polar nuclei so the
endosperm is triploid (3n). The tube nucleus disintegrates.
Most angiosperms have mechanisms by which they avoid self-fertilization.

Seeds

Figure 16.3.4.3 Bean seed

After double fertilization, each ovule develops into a seed, which consists of
a plumule, made up of two embryonic leaves, which will become the first true leaves of the seedling, and a terminal (apical)
bud. The terminal bud contains the meristem at which later growth of the stem takes place.
One or two cotyledons which store food that will be used by the germinating seedling. Angiosperms that produce seeds with
two cotyledons are called dicots. Examples include beans, squashes, Arabidopsis. Angiosperms whose seeds contain only a
single cotyledon are monocots. Examples include corn and other grasses.
The hypocotyl and radicle, which will grow into the part of the stem below the first node ("hypocotyl" = below the cotyledons)
and primary root respectively. The development of each of the parts of the plant embryo depends on gradients of the plant
hormone, auxin.
In addition to the embryo plant (derived from the zygote), each seed is covered with protective seed coats derived from the
walls of the ovule.

16.3D.2 https://bio.libretexts.org/@go/page/5791
 Figure 16.3.4.4 Corn kernel
The food in the cotyledons is derived from the endosperm which, in turn, received it from the parent sporophyte. In many
angiosperms (e.g., beans), when the seeds are mature, the endosperm has been totally consumed and its food transferred to the
cotyledons. In others (some dicots and all monocots), the endosperm persists in the mature seed.
The seed is thus a dormant embryo sporophyte with stored food and protective coats. Its two functions are
dispersal of the species to new locations (aided in angiosperms by the fruit)
survival of the species during unfavorable climatic periods (e.g., winter). "Annual" plants (e.g., beans, cereal grains, many
weeds) can survive freezing only as seeds. When the parents die in the fall, the seeds remain alive — though dormant— over
the winter. When conditions are once more favorable, germination occurs and a new generation of plants develops.

Fruits
Fruits are a development of the ovary wall and sometimes other flower parts as well. As seeds mature, they release the hormone
auxin, which stimulates the wall of the ovary to develop into the fruit. In fact, commercial fruit growers may stimulate fruit
development in unpollinated flowers by applying synthetic auxin to the flower.

Figure 16.3.4.5 Fruit

Fruits promote the dispersal of their content of seeds in a variety of ways.
Wind. The maple "key" and dandelion parachute are examples.
Water. Many aquatic angiosperms and shore dwellers (e.g., the coconut palm) have floating fruits that are carried by water
currents to new locations.
Hitchhikers. The cocklebur and sticktights achieve dispersal of their seeds by sticking to the coat (or clothing) of a passing
animal.
Edible fruits. Nuts and berries entice animals to eat them. Buried and forgotten (nuts) or passing through their g.i. tract
unharmed (berries), the seeds may end up some distance away from the parent plant.
Mechanical. Some fruits, as they dry, open explosively expelling their seeds. The pods of many legumes (e.g., wisteria) do this.

This page titled 16.3D: Angiosperm Life Cycle is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.3D.3 https://bio.libretexts.org/@go/page/5791
16.3E: Asexual Reproduction in Plants
Asexual reproduction is the formation of new individuals from the cell(s) of a single parent. It is very common in plants, less so in
animals.

Asexual Reproduction in Plants

All plant organs have been used for asexual reproduction, but stems are the most common.

Stems
In some species, stems arch over and take root at their tips, forming new plants.

Figure 16.3.5.1 Strawberry stolon

The horizontal above-ground stems (called stolons) of the strawberry (shown here) produce new daughter plants at alternate nodes.
Underground stems such as rhizomes, bulbs, corms and tubers are used for asexual reproduction as well as for food storage.
Irises and day lilies, for example, spread rapidly by the growth of their rhizomes.

Leaves

Figure 16.3.5.2 Leaves of Bryophyllum

This photo shows the leaves of the common ornamental plant Bryophyllum (also called Kalanchoë) . Mitosis at meristems along
the leaf margins produce tiny plantlets that fall off and can take up an independent existence.

Roots
Some plants use their roots for asexual reproduction. The dandelion is a common example. Trees, such as the poplar or aspen, send
up new stems from their roots. In time, an entire grove of trees may form - all part of a clone of the original tree.

Plant Propagation
Commercially-important plants are often deliberately propagated by asexual means in order to keep particularly desirable traits
(e.g., flower color, flavor, resistance to disease). Cuttings may be taken from the parent and rooted.

Figure 16.3.5.3 Grafting

16.3E.1 https://bio.libretexts.org/@go/page/5792
Grafting is widely used to propagate a desired variety of shrub or tree. All apple varieties, for example, are propagated this way.
Apple seeds are planted only for the root and stem system that grows from them. After a year's growth, most of the stem is
removed and a twig (scion) taken from a mature plant of the desired variety is inserted in a notch in the cut stump (the stock). So
long the cambiums of scion and stock are united and precautions are taken to prevent infection and drying out, the scion will grow.
It will get all its water and minerals from the root system of the stock. However, the fruit that it will eventually produce with be
identical (assuming that it is raised under similar environmental conditions) to the fruit of the tree from which the scion was taken.

Apomixis
Citrus trees and many other species of angiosperms use their seeds as a method of asexual reproduction; a process called apomixis.
In one form, the egg is formed with 2n chromosomes and develops without ever being fertilized.
In another version, the cells of the ovule (2n) develop into an embryo instead of - or in addition to - the fertilized egg.
Hybridization between different species often yields infertile offspring. But in plants, this does not necessarily doom the offspring.
Many such hybrids use apomixis to propagate themselves.
The many races of Kentucky bluegrass growing in lawns across North America and the many races of blackberries are two
examples of sterile hybrids that propagate successfully by apomixis.
Recently, an example of apomixis in gymnosperms was discovered (see Pichot, C., et al, in the 5 July 2001 issue of Nature). In a
rare cypress, the pollen grains are diploid, not haploid, and can develop into an embryo when they land on either the female cones
of their own species (rare) or those of a much more common species of cypress.
Is this paternal apomixis in a surrogate mother a desperate attempt to avoid extinction?

Breeding apomictic crop plants

Many valuable crop plants (e.g., corn) cannot be propagated by asexual methods like grafting.
Agricultural scientists would dearly love to convert these plants to apomixis: making embryos that are genetic clones of themselves
rather than the product of sexual reproduction with its inevitable gene reshuffling. After 20 years of work, an apomictic corn
(maize) has been produced, but it does not yet produce enough viable kernels to be useful commercially.

Asexual Reproduction in Animals

Budding
Here, offspring develop as a growth on the body of the parent. In some species, e.g., jellyfishes and many echinoderms, the buds
break away and take up an independent existence. In others, e.g., corals, the buds remain attached to the parent and the process
results in colonies of animals. Budding is also common among parasitic animals, e.g., tapeworms.

Fragmentation
As certain tiny worms grow to full size, they spontaneously break up into 8 or 9 pieces. Each of these fragments develops into a
mature worm, and the process is repeated.

Parthenogenesis
In parthenogenesis ("virgin birth"), the females produce eggs, but these develop into young without ever being fertilized.
Parthenogenesis occurs in some fishes, several kinds of insects, and a few species of frogs and lizards. It does not normally occur in
mammals because of their imprinted genes. However, using special manipulations to circumvent imprinting, laboratory mice have
been produced by parthenogenesis.
In a few nonmammalian species it is the only method of reproduction, but more commonly animals turn to parthenogenesis only
under certain circumstances. Examples:
Aphids use parthenogenesis in the spring when they find themselves with ample food. In this species, reproduction by
parthenogenesis is more rapid than sexual reproduction, and the use of this mode of asexual reproduction permits the animals to
quickly exploit the available resources.
Female Komodo dragons (the largest lizard) can produce offspring by parthenogenesis when no male is available for sexual
reproduction. Their offspring are homozygous at every locus including having identical sex chromosomes. Thus the females
produce all males because, unlike mammals, females are the heterogametic sex (ZW) while males are homogametic (ZZ).

16.3E.2 https://bio.libretexts.org/@go/page/5792
Parthenogenesis is forced on some species of wasps when they become infected with bacteria (in the genus Wolbachia). Wolbachia
can pass to a new generation through eggs, but not through sperm, so it is advantageous to the bacterium for females to be made
rather that males.
In these wasps (as in honeybees),
fertilized eggs (diploid) become females
unfertilized (haploid) eggs become males
However, in Wolbachia-infected females, all their eggs undergo endoreplication producing diploid eggs that develop into females
without fertilization; that is, by parthenogenesis.
Treating the wasps with an antibiotic kills off the bacteria and "cures" the parthenogenesis!
Apis mellifera capensis
Occasionally worker honeybees develop ovaries and lay unfertilized eggs. Usually these are haploid, as you would expect, and
develop into males. However, workers of the subspecies Apis mellifera capensis (the Cape honeybee) can lay unfertilized diploid
eggs that develop into females (who continue the practice). The eggs are produced by meiosis, but then the polar body nucleus
fuses with the egg nucleus restoring diploidy (2n). (The phenomenon is called automictic thelytoky.)

Why Choose Asexual Reproduction?

Perhaps the better question is: Why not?
After all, asexual reproduction would seem a more efficient way to reproduce. Sexual reproduction requires males but they
themselves do not produce offspring.
Two general explanations for the overwhelming prevalence of sexually-reproducing species over asexual ones are:
Perhaps sexual reproduction has kept in style because it provides a mechanism to weed out (through the recombination process
of meiosis) harmful mutations that arise in the population reducing its fitness. Asexual reproduction leads to these mutations
becoming homozygous and thus fully exposed to the pressures of natural selection.
Perhaps it is the ability to adapt quickly to a changing environment that has caused sex to remain the method of choice for most
living things.

Purging Harmful Mutations

Most mutations are harmful - changing a functional allele to a less or nonfunctional one. An asexual population tends to be
genetically static. Mutant alleles appear but remain forever associated with the particular alleles present in the rest of that genome.
Even a beneficial mutation will be doomed to extinction if trapped along with genes that reduce the fitness of that population.
But with the genetic recombination provided by sex, new alleles can be shuffled into different combinations with all the other
alleles available to the genome of that species. A beneficial mutation that first appears alongside harmful alleles can, with
recombination, soon find itself in more fit genomes that will enable it to spread through a sexual population.
Evidence (from Paland and Lynch in the 17 February 2006 issue of Science):
Some strains of the water flea Daphnia pulex (a tiny crustacean) reproduce sexually, others asexually. The asexual strains
accumulate deleterious mutations in their mitochondrial genes four times as fast as the sexual strains.
Evidence (from Goddard et al. in the 31 March 2005 issue of Nature):
Budding yeast missing two genes essential for meiosis adapt less rapidly to growth under harsh conditions than an otherwise
identical strain that can undergo genetic recombination. Under good conditions, both strains grow equally well.
Evidence (from Rice and Chippindale in the 19 October 2001 issue of Science):
Using experimental Drosophila populations, they found that a beneficial mutation introduced into chromosomes that can
recombine did - over time increase in frequency more rapidly than the same mutation introduced into chromosomes that could not
recombine.
So sex provides a mechanism for testing new combinations of alleles for their possible usefulness to the phenotype:
deleterious alleles weeded out by natural selection
useful ones retained by natural selection

16.3E.3 https://bio.libretexts.org/@go/page/5792
Some organisms may still gain the benefits of genetic recombination while avoiding sex. Many mycorrhizal fungi use asexual
reproduction only. However, at least two species have been shown to have multiple - similar - copies of the same gene; that is, are
polyploid. Perhaps recombination between these (during mitosis?) enables these organisms to avoid the hazards of accumulating
deleterious mutations. (See the paper by Pawlowska and Taylor in the 19 Feb 2004 issue of Nature.)
But there are many examples of populations that thrive without sex, at least while they live in a stable environment.

Rapid Adaptation to a Changing Environment

As we have seen (above), populations without sex are genetically static. They may be well-adapted to a given environment, but will
be handicapped in evolving in response to changes in the environment. One of the most potent environmental forces acting on a
species environment is its parasites.
The speed with which parasites like bacteria and viruses can change their virulence may provide the strongest need for their hosts
to have the ability to make new gene combinations. So sex may be virtually universal because of the never-ending need to keep up
with changes in parasites.
Evidence:
Some parasites interfere with sexual reproduction in their host:
Wolbachia-induced parthenogenesis discussed above is an example.
Several types of fungi block wind pollination of their grass hosts forcing them to inbreed with its resulting genetic
uniformity.
There is some evidence that genetically uniform populations are at increased risk of devastating epidemics and population
crashes.
Flour beetles (Tribolium castaneum) parasitized by the microsporidium Nosema whitei increase the rate of recombination
during meiosis.
Drosophila females parasitized by bacteria produce more recombinant offspring than non-infected mothers do.
The idea that a constantly-changing environment, especially with respect to parasites, drives evolution is often called the Red
Queen hypothesis. It comes from Lewis Carroll's book Through the Looking Glass, where the Red Queen says "Now here, you see,
it takes all the running you can do to keep in the same place".
The possibilities outlined above are not mutually exclusive and a recent study [see Morran, L. T., et al., in Nature, 462:350, 19
November 2009] suggests that both forces are at work in favoring sexual reproduction over its alternatives.
The organism for testing these theories was Caenorhabditis elegans. While C. elegans does not reproduce asexually, most worms
are hermaphrodites and usually reproduce by self-fertilization with each individual fertilizing its own eggs. This quickly results in
its genes becoming homozygous and thus fully-exposed to natural selection just as they are in asexually-reproducing species.
Hermaphrodites have two X chromosomes and self-fertilization ("selfing") usually produces more of the same; that is,
hermaphrodites produce more hermaphrodites. However, an occasional nondisjunction generates an embryo with a single X
chromosome and this develops into a male. These males can mate with hermaphrodites (their sperm is preferred over the
hermaphrodites own) and, in fact, such "outcrossing" produces a larger number of offspring. It also produces 50% hermaphrodites
and 50% males.
Testing the role of outcrossing vs. self-fertilization in maintaining fitness in the face of an increased mutation rate.
These workers developed six strains of worms:
two that could reproduce only by selfing
two that could reproduce only by crossing a male with an hermaphrodite ("outcrossing")
"wild-type" worms
All the strains were exposed to a chemical mutagen that increased the spontaneous mutation rate some fourfold.
The results: After 50 generations, the
the strains of worms that could reproduce only by selfing suffered a serious decline in fitness
the strains of worms that could reproduce only by outcrossing suffered no decline
the wild-type worms with intermediate levels of outcrossing (20–30%) suffered only moderate declines in fitness.

16.3E.4 https://bio.libretexts.org/@go/page/5792
Fitness was measured by placing the worms in a petri dish with a barrier that they had to cross to reach their food (E. coli).
The conclusion: the genetic recombination provided by outcrossing protected the worms from loss of fitness even in the face of an
increase in mutation rate.
Testing the role of outcrossing vs. self-fertilization in the speed of adaptation to a changed environment.
For these tests, one of each category of mating types was exposed over 40 generations to a pathogenic bacterium (Serratia
marcescens) that killed most worms when eaten by them.
The results: After 40 generations,
the strain of worms that could reproduce only by selfing were just as susceptible to the pathogen as they were at the start while
the strain of worms that could reproduce only by outcrossing had evolved a high degree of resistance to the pathogen
the wild-type worms only developed a modest increase in their resistance to the bacteria.
Since these studies were reported, the same team has expanded their experiments to examine the effects of evolution in the
pathogen (Serratia marcescens), that is, to look for evidence of coevolution of host and parasite. (Reported by Morran, L. T., et al.,
in Science, 333: 216, 8 July 2011.)
Over 30 generations of worms, they harvested and tested the bacteria recovered from the bodies of worms that had died within 24
hours of infection. They found that:
Worms that can maintain genetic variability by outcrossing suffered substantially lower mortality from the coevolved parasite
that did worms from the starting population (kept frozen until used).
Worms that could only reproduce by selfing became so susceptible to the evolving strain of Serratia marcescens that they died
out within 20 generations.
Curiously, the selection pressure of the increasing virulence of Serratia marcescens caused wild-type worms to increase their
rate of outcrossing from the normal 20–30% to over 80%. So one response to the pressure of this coevolving parasite was to
promote sex in its host.

Reproduction in Rotifers
Rotifers are microscopic invertebrates. They are assigned a phylum of their own (not discussed elsewhere in these pages). The
phylum includes:
a class of ~1,500 species called monogonont rotifers (they have only a single gonad). The monogonont rotifers can choose
either asexual or sexual reproduction as circumstances warrant.
a class of ~350 species called bdelloid rotifers. The bdelloid rotifers are limited to asexual reproduction only. Even after years
of study, neither males nor haploid eggs have ever been found in any members of this group. It looks as though they gave up
sexual reproduction millions of years ago.
Laboratory studies show that monogonont rotifers favor asexual reproduction when they are living in a stable environment but shift
to more sexual reproduction when placed in a varied or unfavorable environment. As they adapt to the new environment, they
gradually switch back to asexual reproduction.
But how have the bdelloid rotifers that never engage in sexual reproduction managed to survive? How have they avoided the
demands of the Red Queen; that is, avoided extinction at the hands of parasites?
One study (Wilson, C. G. and Sherman, P. W., Science, 327:574, 29 January 2010) reveals a mechanism. These tiny animals can be
completely desiccated (dried out) and remain in suspended animation for years. In the desiccated state, they can be blown vast
distances (some species are worldwide in their distribution). Once deposited in a moist environment (a few drops of water are
sufficient), they resume an active life. Wilson and Sherman have shown that the desiccation that is harmless to the rotifers is lethal
to their fungal parasite. So once dried, they are not only cured of their parasite, but can then be blown to a spot where they can
resume an active life with no parasites present.
Another way in which these rotifers can avoid the evolutionary dead-end expected of asexually-reproducing organisms has been
revealed by DNA sequencing of their genome. It turns out that they can purge their genome of deleterious alleles by gene
conversion (during mitosis).
But in any case despite its disadvantages sexual reproduction is here to stay
reducing the effect of harmful mutations

16.3E.5 https://bio.libretexts.org/@go/page/5792
 increasing the speed with which populations can adapt to changes in their environment

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 16.3E: Asexual Reproduction in Plants is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

16.3E.6 https://bio.libretexts.org/@go/page/5792
16.3E: Self-incompatibility - How Plants Avoid Inbreeding
Evolution seems to favor (and be favored by) genetic variability. Genetic variability is promoted by outbreeding - sexual
reproduction between genetically dissimilar parents. Just why sexual reproduction is so popular throughout the world of living
things is still a hotly-debated question, but the fact remains. Plants, being anchored in position, have a special problem in this
regard. Many employ the services of animals (e.g., insects, birds, bats) to transfer pollen from plant to plant. But if the flowers have
both sex organs:what is to prevent the pollen from fertilizing its own eggs?
A variety of solutions have been tried in the plant kingdom. These include:
Having imperfect flowers; that is, flowers that are either male or female.
Dioecy. The imperfect flowers are present on separate plants. Dioecy is the equivalent of the separate sexes of most animals.
But it is rather rare. Some examples include poplars and hollies.
Monoecy. The imperfect flowers are present on the same plant. But if they mature at different times, self-fertilization is
avoided. Corn (maize) is a common example.
But the vast majority of angiosperms have perfect flowers; that is containing both male and female sex organs. So how do they
avoid self-fertilization?
Heteromorphic flowers.
The flowers are perfect but come in two structural types; for example
long stamens with a short style
short stamens with a long style
Homomorphic flowers. All flowers have exactly the same structure. Avoidance of self-fertilization depends on
genetic/biochemical mechanisms. There are two quite different types of self-incompatibility.
Sporophytic self-incompatibility (SSI)
Gametophytic self-incompatibility (GSI)

Sporophytic Self-Incompatibility (SSI)

This form of self-incompatibility has been studied intensively in members of the mustard family (Brassica), including turnips,
rape, cabbage, broccoli, and cauliflower.

16.3E.1 https://bio.libretexts.org/@go/page/5793
 Figure 16.3.6.1 S Loci
In this system,

Rejection of self pollen is controlled by the diploid genotype of the sporophyte generation.
The control lies in the "S-locus", which is actually a cluster of three tightly-linked loci:
SLG (S-Locus Glycoprotein) which encodes part of a receptor present in the cell wall of the stigma;
SRK (S-Receptor Kinase), which encodes the other part of the receptor. Kinases attach phosphate groups to other proteins.
SRK is transmembrane protein embedded in the plasma membrane of the stigma cell.
SCR (S-locus Cysteine-Rich protein), which encodes a soluble ligand for the same receptor which is secreted by the pollen.
Because the plants cannot fertilize themselves, they tend to be heterozygous; that is, carry a pair of different S loci (here
designated S1 and S2).
However, dozens of different S alleles may be present in the population of the species; that is; the S-locus in the species is
extremely polymorphic (analogous to the major histocompatibility locus of vertebrates).
The difference between the alleles is concentrated in certain "hypervariable regions" of the receptor (analogous to the
hypervariable regions that provide the great binding diversity of antibodies

Figure 16.3.6.3 Pollen Stigma SSI

The rules:

Pollen will not germinate on the stigma (diploid) of a flower that contains either of the two alleles in the sporophyte parent that
produced the pollen.
This holds true even though each pollen grain being haploid contains only one of the alleles.
In the example shown here, the S2 pollen, which was produced by a S1S2 parent, cannot germinate on an S1S3 stigma.

The explanation:

The S1S2 pollen-producing sporophyte synthesizes both SCR1 and SCR2 for incorporation in (and later release from) both S1
and S2 pollen grains.
If either SCR molecule can bind to either receptor on the pistil, the kinase triggers a series of events that lead to failure of the
stigma to support germination of the pollen grain. Among these events is the ubiquination of proteins targeting them for
destruction in proteasomes.
If this path is not triggered (e.g., pollen from an S1S2 parent on an S3S4 stigma, the pollen germinates successfully.

Gametophytic Self-Incompatibility (GSI)

16.3E.2 https://bio.libretexts.org/@go/page/5793
 Figure 16.3.6.4 GSI
This form of self-incompatibility is more common than SSI but not so well understood. It occurs in nearly one-half of all the
families of angiosperms, including
the Solanaceae (potatoes, tomatoes [wild, not cultivated], and tobacco)
petunias
beets (Beta vulgaris)
buttercups (Ranunculus)
lilies
roses
many grasses
The rules:
The S loci are (as in SSI plants) extremely polymorphic; that is, there is an abundance of multiple alleles in the population.
Incompatibility is controlled by the single S allele in the haploid pollen grain.
Thus a pollen grain will grow in any pistil that does not contain the same allele (so, as shown here and in contrast to what
happens in SSI, S2 pollen from an S1S2 parent will grow down an S1S3 style.
This appears to be the mechanism in the petunia:
All pollen grains - incompatible as well as compatible - germinate forming pollen tubes that begin to grow down the style.
However, growth of incompatible pollen tubes stops in the style while compatible tubes go on to fertilize the egg in the ovary.
The block within incompatible pollen tubes is created by an S-locus-encoded ribonuclease (S-RNase), which is synthesized
within the style, enters the pollen tube and destroys its RNA molecules halting pollen tube growth.
The RNase molecules contain a hypervariable region, each encoded by a different allele, which establishes each S specificity
(S1, S2, S3, etc.).
The pollen tube expresses a protein designated SLF that binds S-RNase. SLF also exists in different S specificities (S1, S2, S3,
etc.).
In compatible ("nonself") tubes, the SCF triggers the degradation (in proteasomes) of the S-RNase thus permitting RNAs in the
Switching
pollen tubefrom Cross-Pollination
to survive to Self-Pollination
and growth to continue.
In incompatible
A substantial ("self")
minority tubes the interaction
of angiosperms of, for example,
have abandoned the S1 SCF
cross-pollination with the S1 S-RNase
for self-pollination. blocks itswhile
For example, degradation
its wildsorelatives
the
RNAstoofbethe
continue pollen tube are the
cross-pollinated, destroyed
domesticandtomato
growthisisnot.
halted.
Two steps are needed for this change:
An entirely-different
1. abandoning mechanism
its mechanism of of gametophytic self-incompatibility is found in poppies (Papaver rhoeas).
self-incompatibility
2. changes in flower structure to reduce the chance that pollinators will transfer pollen from another plant to its stigma.
Unlike its wild relatives, the stigma of the domestic tomato does not protrude beyond the anthers. Of the several genes involved in
this change, the most important one is Style2.1. The mutation in Style2.1 responsible for the change in phenotype in our cultivated
tomatoes is found in the promoter region - the protein-encoding portion of the gene is exactly the same as in wild tomatoes.
Here, again, is evidence that much of the diversity of life arises not from mutations in the protein-coding portion of the genes that
we share but mutations in their regulatory regions (promoters and enhancers).

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

16.3E.3 https://bio.libretexts.org/@go/page/5793
This page titled 16.3E: Self-incompatibility - How Plants Avoid Inbreeding is shared under a CC BY 3.0 license and was authored, remixed,
and/or curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history
is available upon request.

16.3E.4 https://bio.libretexts.org/@go/page/5793
16.3F: Transgenic Plants
Progress is being made on several fronts to introduce new traits into plants using recombinant DNA technology. The genetic
manipulation of plants has been going on since the dawn of agriculture, but until recently this has required the slow and tedious
process of cross-breeding varieties. Genetic engineering promises to speed the process and broaden the scope of what can be done.

Making transgenic plants

There are several methods for introducing genes into plants, including infecting plant cells with plasmids as vectors carrying the
desired gene or shooting microscopic pellets containing the gene directly into the cell. In contrast to animals, there is no real
distinction between somatic cells and germline cells. Somatic tissues of plants, e.g., root cells grown in culture, can be transformed
in the laboratory with the desired gene or grown into mature plants with flowers. If all goes well, the transgene will be incorporated
into the pollen and eggs and passed on to the next generation. In this respect, it is easier to produce transgenic plants than
transgenic animals.

Some Achievements
Improved Nutritional Quality
Milled rice is the staple food for a large fraction of the world's human population. Milling rice removes the husk and any beta-
carotene it contained. Beta-carotene is a precursor to vitamin A, so it is not surprising that vitamin A deficiency is widespread,
especially in the countries of Southeast Asia. The synthesis of beta-carotene requires a number of enzyme-catalyzed steps. In
January 2000, a group of European researchers reported that they had succeeded in incorporating three transgenes into rice that
enabled the plants to manufacture beta-carotene in their endosperm.

Insect Resistance
Bacillus thuringiensis is a bacterium that is pathogenic for a number of insect pests. Its lethal effect is mediated by a protein toxin it
produces. Through recombinant DNA methods, the toxin gene can be introduced directly into the genome of the plant where it is
expressed and provides protection against insect pests of the plant.

Disease Resistance
Genes that provide resistance against plant viruses have been successfully introduced into such crop plants as tobacco, tomatoes,
and potatoes.

Figure 16.3.7.1 Tomatoes

Tomato plants infected with tobacco mosaic virus (which attacks tomato plants as well as tobacco). The plants in the back row
carry an introduced gene conferring resistance to the virus. The resistant plants produced three times as much fruit as the sensitive
plants (front row) and the same as control plants.

Herbicide Resistance
Questions have been raised about the safety - both to humans and to the environment - of some of the broad-leaved weed killers
like 2,4-D. Alternatives are available, but they may damage the crop as well as the weeds growing in it. However, genes for
resistance to some of the newer herbicides have been introduced into some crop plants and enable them to thrive even when
exposed to the weed killer.

16.3F.1 https://bio.libretexts.org/@go/page/5794
 Figure 16.3.7.2 Effect of bromoxynil on tobacco courtesy of Calgene, Davis, CA
Effect of the herbicide bromoxynil on tobacco plants transformed with a bacterial gene whose product breaks down bromoxynil
(top row) and control plants (bottom row). "Spray blank" plants were treated with the same spray mixture as the others except the
bromoxynil was left out.

Salt Tolerance
A large fraction of the world's irrigated crop land is so laden with salt that it cannot be used to grow most important crops.
However, researchers at the University of California Davis campus have created transgenic tomatoes that grow well in saline soils.
The transgene was a highly-expressed sodium/proton antiport pump that sequestered excess sodium in the vacuole of leaf cells.
There was no sodium buildup in the fruit.

"Terminator" Genes
This term is used (by opponents of the practice) for transgenes introduced into crop plants to make them produce sterile seeds (and
thus force the farmer to buy fresh seeds for the following season rather than saving seeds from the current crop). The process
involves introducing three transgenes into the plant:
A gene encoding a toxin which is lethal to developing seeds but not to mature seeds or the plant. This gene is normally inactive
because of a stretch of DNA inserted between it and its promoter.
A gene encoding a recombinase — an enzyme that can remove the spacer in the toxin gene thus allowing to be expressed.
A repressor gene whose protein product binds to the promoter of the recombinase thus keeping it inactive.
How they work
When the seeds are soaked (before their sale) in a solution of tetracycline
Synthesis of the repressor is blocked.
The recombinase gene becomes active.
The spacer is removed from the toxin gene and it can now be turned on.
Because the toxin does not harm the growing plant - only its developing seeds - the crop can be grown normally except that its
seeds are sterile.
The use of terminator genes has created much controversy:
Farmers - especially those in developing countries - want to be able to save some seed from their crop to plant the next season.
Seed companies want to be able to keep selling seed.

Transgenes Encoding Antisense RNA

These are discussed in a separate page. Link to it

Biopharmaceuticals
The genes for proteins to be javascript:void('Remove anchor')used in human (and animal) medicine can be inserted into plants and
expressed by them.
Advantages:
Glycoproteins can be made (bacteria like E. coli cannot do this).
Virtually unlimited amounts can be grown in the field rather than in expensive fermentation tanks.
It avoids the danger from using mammalian cells and tissue culture medium that might be contaminated with infectious agents.
Purification is often easier.

16.3F.2 https://bio.libretexts.org/@go/page/5794
Corn is the most popular plant for these purposes, but tobacco, tomatoes, potatoes, rice and carrot cells grown in tissue culture are
also being used. Some of the proteins that have been produced by transgenic crop plants:
human growth hormone with the gene inserted into the chloroplast DNA of tobacco plants
humanized antibodies against such infectious agents as
HIV
respiratory syncytial virus (RSV)
sperm (a possible contraceptive)
herpes simplex virus, HSV, the cause of "cold sores"
Ebola virus, the cause of the often-fatal Ebola hemorrhagic fever
protein antigens to be used in vaccines
An example: patient-specific antilymphoma (a cancer) vaccines. B-cell lymphomas are clones of malignant B cells
expressing on their surface a unique antibody molecule. Making tobacco plants transgenic for the RNA of the variable
(unique) regions of this antibody enables them to produce the corresponding protein. This can then be incorporated into a
vaccine in the hopes (early trials look promising) of boosting the patient's immune system - especially the cell-mediated
branch - to combat the cancer.
other useful proteins like lysozyme and trypsin
However, as of April 2012, the only protein to receive approval for human use is glucocerebrosidase, an enzyme lacking in
Gaucher's disease. It is synthesized by transgenic carrot cells grown in tissue culture.

Controversies
The introduction of transgenic plants into agriculture has been vigorously opposed by some. There are a number of issues that
worry the opponents. One of them is the potential risk of transgenes in commercial crops endangering native or nontarget species.
Examples:
A gene for herbicide resistance in, e.g. maize (corn), escaping into a weed species could make control of the weed far more
difficult.
The gene for Bt toxin expressed in pollen might endanger pollinators like honeybees.
To date, field studies on Bt cotton and maize show that the numbers of some nontarget insects are reduced somewhat but not as
much as in fields treated with insecticides.
Another worry is the inadvertent mixing of transgenic crops with nontransgenic food crops. Although this has occurred
periodically, there is absolutely no evidence of a threat to human health.
Despite the controversies, farmers around the world are embracing transgenic crops. Currently in the United States over 80% of the
corn, soybeans, and cotton grown are genetically modified (GM) — principally to provide
resistance to the herbicide glyphosate ("Roundup Ready®") thus making it practical to spray the crop with glyphosate to kill
weeds without harming the crop
resistance to insect attack (by expressing the toxin of Bacillus thuringiensis)

This page titled 16.3F: Transgenic Plants is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.3F.3 https://bio.libretexts.org/@go/page/5794
 SECTION OVERVIEW
16.4: Plant Development - Fundamentals
16.4A: Plant Growth

16.4B: Germination of Seeds

16.4C: Etiolation

16.4D: Flowering

16.4E: Photoperiodism and Phytochrome

This page titled 16.4: Plant Development - Fundamentals is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

16.4.1 https://bio.libretexts.org/@go/page/5776
16.4A: Plant Growth
Growth in plants occurs chiefly at meristems where rapid mitosis provides new cells. As these cells differentiate, they provide new
plant tissue.

Stem Growth
In stems, mitosis in the apical meristem of the shoot apex (also called the terminal bud) produces cells that enable the stem to
grow longer and, periodically, cells that will give rise to leaves. The point on the stem where leaves develop is called a node. The
region between a pair of adjacent nodes is called the internode. The internodes in the terminal bud are very short so that the
developing leaves grow above the apical meristem that produced them and thus protect it. New meristems, the lateral buds,
develop at the nodes, each just above the point where a leaf is attached. When the lateral buds develop, they produces new stem
tissue, and thus branches are formed.

Figure 16.4.1.2 Horse chestnut

Under special circumstances (such as changes in photoperiod), the apical meristem is converted into a flower bud. This develops
into a flower. The conversion of the apical meristem to a flower bud "uses up" the meristem so that no further growth of the stem
can occur at that point. However, lateral buds behind the flower can develop into branches.
The drawing is of a typical woody dicot, the horse chestnut, as seen during the dormant season. The leaves have dropped off,
leaving a leaf scar; the dots inside each leaf scar show where the vascular bundles (xylem and phloem) had entered the petiole of
the leaf. A flower had been produced the season before, so that during the season just ended two branches had grown out on either
side of the flower bud scar. Lenticels are openings that allow oxygen and carbon dioxide to diffuse between the living cells of the
stem and the air.
The growth of roots in described in a separate page,

This page titled 16.4A: Plant Growth is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.4A.1 https://bio.libretexts.org/@go/page/5795
16.4B: Germination of Seeds
Germination is the resumption of growth of the embryo plant inside the seed.
Requirements:
proper temperature
Water is always needed to allow vigorous metabolism to begin. It is also sometimes needed to leach away a germination
inhibitor within the seed. This is especially common among desert annuals. The inhibitor is often abscisic acid (ABA).
oxygen
a preceding period of dormancy (often).
The seeds of many temperate-climate angiosperms will germinate only after a prolonged period of cold. An inhibitor within the
seed (probably abscisic acid - ABA) is gradually broken down at low temperatures until finally there is not enough to prevent
germination when other conditions become favorable. This mechanism is of obvious survival value in preventing seeds from
germinating during an unseasonably warm spell in the autumn or winter.
Correct photoperiod (often).

Germination in a Dicot

Figure 16.4.2.1 Germination of a bean seed

The primary root emerges through the seed coats while the seed is still buried in the soil.
The hypocotyl ("below the cotyledons") emerges from the seed coats and pushes its way up through the soil. It is bent in a
hairpin shape - the hypocotyl arch- as it grows up. The two cotyledons protect the plumule- the epicotyl ("above the
cotyledons") and first leaves - from mechanical damage.
Once the hypocotyl arch emerges from the soil, it straightens out. This response is triggered by light. Both red light, absorbed
by phytochrome and blue light, absorbed by cryptochrome can do the job.
The cotyledons spread apart exposing the epicotyl with the apical meristem at its tip, and two primary leaves
In many dicots, the cotyledons not only transfer their food stores to the developing plant but also turn green and make more
food by photosynthesis until they drop off.
The above image (courtesy of the Pittsburgh Plate Glass Co.) is a time-lapse photograph showing three stages in the germination of
a bean seed.

Germination in Monocots

Figure 16.4.2.2 Coleoptile of an oat seed

When grass seeds like corn (maize) or oats (shown here) germinate,

16.4B.1 https://bio.libretexts.org/@go/page/5796
 The primary root pierces the seed (and fruit) coverings and grows down.
The primary leaf of the plant grows up. It is protected as it pushes up through the soil by the coleoptile - a hollow, cylindrical
structure.
Once the seedling has grown above the surface, the coleoptile stops growing and the primary leaf pierces it.
The coleoptile of grass (e.g., oat) seedlings has been a favorite experimental object for studing phototropism.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 16.4B: Germination of Seeds is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.4B.2 https://bio.libretexts.org/@go/page/5796
16.4C: Etiolation
The stems of plants raised in the dark elongate much more rapidly than normal, a phenomenon called etiolation. It is a mechanism
that increases the probability of the plant reaching the light.

Figure 16.4.4.1 Etiolation

Once light shines on it,
the cotyledons spread apart
the primary leaves
grow to full size
turn green
the plant begins to produce internodes of normal size.
The image shows seedlings of the common garden bean grown in the light (left) and in darkness (right). The pale color of the dark-
grown plant is caused by the lack of chlorophyll. When the food reserves of its seed are used up, the seedling will die (unless
placed in the light).
Each seedling has three nodes (the bottom ones where the cotyledons were attached), but the internodes are greatly elongated in the
dark-grown seedling. This response is NOT dependent on photosynthesis, because light too dim to be useful in photosynthesis
nevertheless halts etiolation. Exposure to dim red light (660 nm) or blue light can halt etiolation. The effect of blue light is
mediated by cryptochrome. The red light effect is mediated by phytochrome.

How does phytochrome work?

The prevention of etiolation in Arabidopsis is mediated by phytochrome B.
When sunlight (660 nm) converts PR into PFR, the PFR moves from the cytoplasm into the nucleus.
There it stimulates the activity of DELLA proteins.
These bind to members of a group of helix-loop-helix proteins called PIFs ("phytochrome-interacting factors").
PIFs, like many helix-loop-helix proteins, are transcription factors. They bind to and turn on promoters of genes that, among
other effects, stimulate cell and thus stem elongation.
However, when DELLA proteins bind PIFs, the PIFs are prevented from binding to the promoters of their target genes.
The result: reduced cell elongation and so no etiolation.
Gibberellins are plant hormones that promote stem elongation thus mimicking the etiolation response. They do this by triggering
the degradation of DELLA proteins thus freeing PIFS to bind to the promoters of genes needed for cell elongation.

The Shade-Avoidance Response

Natural sunlight contains about the same amount of red (660 nm) as far-red (735 nm) light. However, chlorophyll absorbs 660 nm
light strongly, so that the light that filters through a canopy of foliage is enriched in far-red light.
This is absorbed by PFR converting it into inactive PR and relieving the inhibition of PIFs.
The now-active PIFs turn on the genes needed for the synthesis of auxin.
Auxin stimulates stem elongation.
The shade-avoidance response helps ensure that the plant reaches enough sunlight to be able to carry on photosynthesis.

16.4C.1 https://bio.libretexts.org/@go/page/5804
Contributors and Attributions
John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 16.4C: Etiolation is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.4C.2 https://bio.libretexts.org/@go/page/5804
16.4D: Flowering
The flowering plants (angiosperms) go through a phase of vegetative growth producing more stems and leaves and a flowering
phase where they produce the organs for sexual reproduction. In "annuals", like the snapdragon, the vegetative phase begins with
germination of the seed. Flowering follows and ends with the senescence and death of the plant. In biennials, the vegetative phase
takes up the first year; flowering followed by death occurs the second year. In perennials, flowering typically occurs year after
year when conditions are appropriate.

Figure 16.4.5.1 Meristem

Vegetative growth of the above-ground part of the plant — the shoot — occurs at the apical meristem. This is a mass of
undifferentiated cells at the tip of the stem. Mitosis of these cells produces cells that differentiate to form more stem, leaves and
secondary meristems. Also called lateral buds, these form in the axils of the leaves and will form branches.

The Signal to Flower

Flowering involves the conversion of the apical meristem into a floral meristem, from which all the parts of the flower will be
produced. Signals that change the fate of the apical meristem include:
maturity of the plant
temperature
the arrival of the plant hormone gibberellin
for many plants, photoperiod - the relative length of day and night.

Temperature
Many annual plants (e.g., winter wheat) and biennial plants have their time of flowering delayed unless they have undergone a
preceding period of wintertime cold. The change brought about by this prolonged exposure to the cold is called vernalization.
In the "model" plant Arabidopsis thaliana, vernalization works like this.
A gene designated Flowering Locus C (FLC) encodes a transcription factor that blocks the expression of the genes needed for
flowering.
The level of FLC mRNA is high in the fall.
But with the onset of cold temperatures, production of an antisense transcript of FLC (called COOLAIR) increasesas does, later,
a sense transcript of part of the FLC gene.
Both of these RNAs are non-coding; that is, they are not translated into protein.
But they cooperate in suppressing the production of FLC mRNA and its translation into FLC protein.
With the arrival of spring, there is no FLC protein remaining to suppress flowering so flowering can begin.

16.4D.1 https://bio.libretexts.org/@go/page/5805
 Figure 16.4.5.2 Lilac
The buds of many species of woody angiosperms found in temperate climates, such as apples and lilacs, also need a preceding
period of cold weather before they can develop into flowers. So these plants cannot be grown successfully at lower latitudes
because the winters never get cold enough (a few days at 0–10°C). This bud dormancy is localized. Prior chilling of one bud on a
lilac stem enables it to flower while the other, nonchilled, buds on the stem remain dormant.

Photoperiod
Photoperiod is detected in the leaves. The cocklebur, drawn here, needs at least 8.5 hours of darkness in order to flower. Even if
only a part of one leaf is exposed to the correct photoperiod, the entire plant will bloom (middle figure).

Figure 16.4.5.3 Photoperiod demonstration

The leaves produce a chemical signal called florigen that is transmitted to the apical meristems to start their conversion into floral
meristems. The right-hand drawing shows that grafting a cocklebur (B) that receives the required period of darkness to one (A) that
does not causes flowering in both. Evidently the florigen signal passes from B to A through their connected vascular systems.
The chemical nature of florigen has been sought for decades. The most recent evidence suggests that at least one component is the
protein encoded by the gene FLOWERING LOCUS T (FT).

Converting the Apical Meristem to a Floral Meristem

In the nucleus of the meristem cells, the FT protein binds to the transcription factor FD and turns on the expression of genes needed
for flowering, e.g., APETALA1 and LEAFY.

Structure of the Flower

Figure 16.4.5.4 Floral meristem

The floral meristem differentiates into four concentric groups of cells that form the four parts of the flower.
1. The cells in whorl 1 develop into a whorl of sepals. These form at the lowest level. Collectively they make up the calyx.
2. Whorl 2 forms above the calyx, forming the petals. Collectively these make up the corolla of the flower (the part that most
ornamentals are grown for).
3. Whorl 3 develops into the stamens, the male reproductive organs.
4. The innermost whorl, 4, forms carpels, the female reproductive organs. Carpels often fuse to form a single structure, which
some botanists call the pistil.

16.4D.2 https://bio.libretexts.org/@go/page/5805
What triggers the various parts of the floral meristem to enter one or another of these four developmental pathways?

The ABC Model of Flower Development

Genetic analysis of mutants especially those found in the dicots Arabidopsis thaliana and in the snapdragon (Antirrhinum) support
the ABC model of flowering. This model postulates a group of genes that encode the transcription factors needed to turn on the
genes for sepal, petal, etc. development. The "master switches" fall into 3 groups: A, B, and C.

Figure 16.4.5.5 ABC Model

These are the rules:
Cells in which only A genes are expressed develop into sepals. This occurs at the lowest level of the floral meristem.
Cells in which both A and B genes are expressed develop into petals. This occurs at the next higher level.
Expression of B and C genes turns on the developmental program to form stamens.
Expression of C genes alone turns on the development of carpels in the innermost band of cells.
Examples of A, B and C group genes involved in flowering - these have been identified in Arabidopsis thaliana

APETALA1 (AP1) and

A group
APETALA2 (AP2)
APETALA3 (AP3) and
B group
PISTILLATA (PI)

C group AGAMOUS (AG)

The transcription factor LEAFY plays a major role in turning on the A, B, and C group genes in the appropriate locations.
The LEAFY protein alone turns on AP1 in whorls 1 and 2.
LEAFY plus a protein encoded by the gene UFO (for "unusual floral organs") turn on AP3 in whorls 2 and 3.
LEAFY and a second, still unidentified, protein turn on AG in whorls 3 and 4.
If LEAFY protein alone is sufficient to turn on AP1, why isn't AP1 expressed in all four whorls?
The answer: AGAMOUS blocks the expression of AP1, so any cell expressing AGAMOUS cannot express AP1. In fact, the
antagonism is reciprocal: AP2 in whorls 1 and 2 (A group) inhibits AGAMOUS so the gene expression in whorls 3 and 4 remains
distinct from that in whorls 1 and 2.
The proteins encoded by APETALA3 and PISTILLATA (Group B) form a heterodimer that binds to
the APETALA1 protein to form petals
the AGAMOUS protein to form stamens
Aided by a fourth transcription factor encoded by the gene SEPALLATA3, these quaternary complexes bind to specific sequences of
DNA turning on the expression of the various genes needed to form whorls 2 and 3. Further research may reveal similar behavior
for the other genes.
SEPALLATA3 (SEP3) is one of four SEP genes in Arabidopsis. If all but SEP4 are inactivated, a flower with only sepals is formed
(hence the name). If all four are inactivated, no flowers are formed at all.
So formation of a flower requires a cascade of sequential gene activity that gradually converts a mass of undifferentiated cells
(the apical meristem) into the parts of a flower. The genes encode transcription factors that act as master switches, turning on (or
off) downstream genes that ultimately make each part of the flower in its appropriate location. This same strategy of genetic control
of developmental pathways is seen in animal development.

This page titled 16.4D: Flowering is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.4D.3 https://bio.libretexts.org/@go/page/5805
16.4E: Photoperiodism and Phytochrome
Many angiosperms flower at about the same time every year. This occurs even though they may have started growing at different
times. Their flowering is a response to the changing length of day and night as the season progresses. The phenomenon is called
photoperiodism. It helps promote cross pollination.
In 1920 two employees of the U. S. Department of Agriculture, W. W. Garner and H. A. Allard, discovered a mutation in tobacco -
a variety called Maryland Mammoth - that prevented the plant from flowering in the summer as normal tobacco plants do.
Maryland Mammoth would not bloom until late December. Experimenting with artificial lighting in winter and artificial darkening
in summer, they found that Maryland Mammoth was affected by photoperiod. Because it would flower only when exposed to short
periods of light, they called it a short-day plant. Some other short-day plants are
chrysanthemums (bloom in the fall)
rice (Oryza sativa)
poinsettias
morning glory (Pharbitis nil)
the cocklebur (Xanthium)
Some plants such as spinach, Arabidopsis, sugar beet and the radish flower only after exposure to long days and hence are called
long-day plants. Still other plants, e.g. the tomato, are day neutral; that is, flowering is not regulated by photoperiod.
Photoperiodism also explains why some plant species can be grown only in a certain latitude. Spinach, a long-day plant, cannot
flower in the tropics because the days never get long enough (14 hours). Ragweed, a short-day plant, fails to thrive in northern
Maine because by the time the days become short enough to initiate flowering, a killing frost in apt to occur before reproduction
and the formation of seeds is completed.

Photoperiodism in a Short-Day Plant

Figure 16.4.6.1 Cocklebur chart

Experiments with the cocklebur have shown that the term short-day is something of a misnomer; what the cocklebur needs is a
sufficiently long night.
Cockleburs (adapted to the latitude of Michigan) will flower only if they have been kept in the dark for at least 8.5 hours — the
critical period. (A and B).
Interruption of an otherwise long night by light — red (660 nm) rays are particularly effective — prevents flowering. (C)
unless
it is followed by irradiation with far-red (730 nm) light (D).
An intense exposure to far-red light at the start of the night reduces the dark requirement by 2 hours (E).
These response are mediated by phytochrome.

Phytochrome

Figure 16.4.6.2 Pr_Pfr

16.4E.1 https://bio.libretexts.org/@go/page/5806
 Phytochrome is a homodimer: two identical protein molecules each conjugated to a light-absorbing molecule (compare
rhodopsin).
Plants make 5 phytochromes: PhyA, PhyB, as well as C, D, and E.
There is some redundancy in function of the different phytochromes, but there also seem to be functions that are unique to one
or another. The phytochromes also differ in their absorption spectrum; that is, which wavelengths (e.g., red vs. far-red) they
absorb best.
Phytochromes exist in two interconvertible forms
PR because it absorbs red (R; 660 nm) light
PFR because it absorbs far-red (FR; 730 nm) light
These are the relationships:
Absorption of red light by PR converts it into PFR.
Absorption of far-red light by PFR converts it into PR.
In the dark, PFR spontaneously converts back to PR.

The Hourglass Model

The behavior of phytochrome provided the first model - called the hourglass model - of the mechanism of photoperiodism in short-
day plants.
Sunlight is richer in red (660 nm) than far-red (730 nm) light, so at sundown all the phytochrome is PFR.
During the night, the PFR converts back to PR.
The PR form is needed for the release of the flowering signal.
Therefore, the cocklebur needs 8.5 hours of darkness in which to
convert all the PFR present at sundown into PR
carry out the supplementary reactions leading to the release of the flowering signal ("florigen").
If this process is interrupted by a flash of 660-nm light, the PR is immediately reconverted to PFR and the night's work is
undone (C)
A subsequent exposure to far-red (730 nm) light converts the pigment back to PR and the steps leading to the release of
"florigen" can be completed (D)
Exposure to intense far-red light at the beginning of the night sets the clock ahead about 2 hours or so by eliminating the need
for the spontaneous conversion of PFR to PR (E).

The Circadian Rhythm Model

Recent work mostly in the long-day plant, Arabidopsis - supports a different model of photoperiodism. This work suggests that the
photoperiodic response is governed by the interaction of daylight with innate circadian rhythms of the plant.
Virtually all eukaryotes have innate circadian rhythms.
These are rhythms of biological activities that fluctuate over a period of approximately 24 hours (L. circa = about; dies = day)
even under constant environmental conditions (e.g. continuous darkness). Under constant conditions, the cycles may drift out
of phase with the environment.
However, when exposed to the environment (e.g., alternating day and night), the rhythms become entrained; that is, they now
cycle in lockstep with the cycle of day and night with a period of exactly 24 hours.
In Arabidopsis, the entrainment of the rhythms requires that light is detected by the
phytochromes (absorb red light)
cryptochromes (absorb blue light)

Long-Day Plants
Arabidopsis is a long-day plant and has provided many clues about the mechanism involved in this photoperiodic response. Any
response to photoperiod requires a method of keeping time; that is, a clock. Plants, like so many other organisms, have an innate
circadian rhythm that regulates the expression of many genes. Among these in Arabidopsis is CONSTANS (CO), a gene that
encodes a zinc-finger transcription factor whose levels of mRNA rise and fall with a circadian rhythm.

16.4E.2 https://bio.libretexts.org/@go/page/5806
 Figure 16.4.6.3 Co_mRNA
Translation of CONSTANS mRNA produces the transcription factor that turns on a number of genes, including FLOWERING
LOCUS T (FT), a gene needed to start the conversion of apical buds into flower buds.
CONSTANS messenger RNA (mRNA) is abundant early in the morning, declines during the middle part of the day and then rises
to another peak late in the afternoon.
However,
the CONSTANS protein is quickly degraded (in proteasomes) during the morning and middle part of the day and also during
the night.
The degradation triggered by morning light (rich in 660 nm rays) is mediated by phytochrome B (PhyB).
By late in the afternoon, if the day has been long enough,
transcription of the CO gene increases producing a rise in CO mRNA
translation of the CO mRNA produces more CO protein which is
no longer degraded.
These effects are mediated by the absorption of
red (enriched in far-red) light by phytochrome A (PhyA)
blue light by cryptochrome.
Now with the CONSTANS protein accumulating, it is available to turn on the gene transcription (e.g., FT) needed for the induction
of the flowering. In short days, with darkness falling before the rise in CONSTANS mRNA, there is not enough CONSTANS
protein synthesized to induce flowering. So flowering in Arabidopsis seems to require the interaction of daylight perceived by
phytochromes and cryptochromes with the intrinsic circadian rhythm of CONSTANS expression.

Short-Day Plants
The roles of circadian rhythms and light in short-day plants are not yet as well understood. Studies with rice, a short-day plant,
suggests that the mechanism described for Arabidopsis may work there as well but with CONSTANS acting as a suppressor of
FLOWERING LOCUS T and thus as an inhibitor of flowering under long days.

Trees
Photoperiodism not only controls flowering in some trees but also stops vegetative growth and promotes the setting of winter buds
as the days grow shorter in the autumn. In aspens (Populus sp.) this control is mediated by CONSTANS and FLOWERING
LOCUS T.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 16.4E: Photoperiodism and Phytochrome is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

16.4E.3 https://bio.libretexts.org/@go/page/5806
 SECTION OVERVIEW
16.5: Plant Development - Hormones
Topic hierarchy

16.5A: Abscisic acid (ABA)

16.5B: Auxin

16.5C: Cytokinins

16.5D: Ethylene

16.5E: Gibberellins

16.5F: Strigolactones

This page titled 16.5: Plant Development - Hormones is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.5.1 https://bio.libretexts.org/@go/page/5797
16.5A: Abscisic acid (ABA)
Unlike animals, plants cannot flee from potentially harmful conditions like drought, freezing, exposure to salt water or salinated
soil. They must adapt or die. The plant hormone abscisic acid (ABA) is the major player in mediating the adaptation of the plant to
stress.

Figure 16.4.3.1.1 ABA

Here are a few examples.

Closing of stomata
Some 90% of the water taken up by a plant is lost in transpiration. Most of this leaves the plant through the pores called stomata -
in the leaf. Each stoma is flanked by a pair of guard cells. When the guard cells are turgid, the stoma is open. When turgor is lost,
the stoma closes. In angiosperms and gymnosperms (but not in ferns and lycopsids), ABA is the hormone that triggers closing of
the stomata when soil water is insufficient to keep up with transpiration.
The mechanism:
ABA binds to receptors at the surface of the plasma membrane of the guard cells.
The receptors activate several interconnecting pathways which converge to produce
a rise in pH in the cytosol
transfer of Ca2+ from the vacuole to the cytosol.
These changes stimulate the loss of negatively-charged ions (anions), especially NO3− and Cl−, from the cell and also the loss
of K+ from the cell.
The loss of these solutes in the cytosol reduces the osmotic pressure of the cell and thus turgor.
The stomata close.

Protecting cells from dehydration

ABA signaling turns on the expression of genes encoding proteins that protect cells - in seeds as well as in vegetative tissues - from
damage when they become dehydrated.

Root growth
ABA can stimulate root growth in plants that need to increase their ability to extract water from the soil.

Bud dormancy
ABA mediates the conversion of the apical meristem into a dormant bud. The newly developing leaves growing above the
meristem become converted into stiff bud scales that wrap the meristem closely and will protect it from mechanical damage and
drying out during the winter. ABA in the bud also acts to enforce dormancy so if an unseasonably warm spell occurs before winter
is over, the buds will not sprout prematurely. Only after a prolonged period of cold or the lengthening days of spring
(photoperiodism) will bud dormancy be lifted.

Seed maturation and dormancy

Seeds are not only important agents of reproduction and dispersal, but they are also essential to the survival of annual and biennial
plants. These angiosperms die after flowering and seed formation is complete. ABA is essential for seed maturation and also
enforces a period of seed dormancy. As we saw for buds, it is important the seeds not germinate prematurely during unseasonably
mild conditions prior to the onset of winter or a dry season. ABA in the seed enforces this dormancy. Not until the seed has been
exposed to a prolonged cold spell and/or sufficient water to support germination is dormancy lifted.

16.5A.1 https://bio.libretexts.org/@go/page/5798
Abscission
ABA also promotes abscission of leaves and fruits (in contrast to auxin, which inhibits abscission). It is, in fact, this action that
gave rise to the name abscisic acid.
The dropping of leaves in the autumn is a vital response to the onset of winter when ground water is frozen - and thus cannot
support transpiration - and snow load would threaten to break any branches still in leaf.
Most nondeciduous species in cold climates (e.g., pines) have "needles" for leaves. These are very narrow and have a heavy
waterproof cuticle. The shape aids in shedding snow, and the cuticle cuts down on water loss.

Seedling growth
ABA inhibits stem elongation probably by its inhibitory effect on gibberellic acid.

Apical dominance
ABA - moving up from the roots to the stem - synergizes with auxin - moving down from the apical meristem to the stem - in
suppressing the development of lateral buds. The result is inhibition of branching or apical dominance.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 16.5A: Abscisic acid (ABA) is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.5A.2 https://bio.libretexts.org/@go/page/5798
16.5B: Auxin
Auxins are plant hormones. The most important auxin produced by plants is indole-3-acetic acid (IAA). It plays important roles in
a number of plant activities, including:
development of the embryo
leaf formation
phototropism
gravitropism
apical dominance
fruit development
abscission
root initiation and development
the shade-avoidance effect

Figure 16.4.3.2.1: indole-3-acetic acid (IAA)

Embryonic Development
From the very first mitotic division of the zygote, gradients of auxin guide the patterning of the embryo into the parts that will
become the organs of the plant:
shoot apex,
primary leaves,
cotyledon(s),
stem,
root.

Leaf Formation
The formation of new leaves in the apical meristem is initiated by the accumulation of auxin. Already-developing leaves deplete
the surrounding cells of auxin so that the new leaves do not form too close to them. In this way, the characteristic pattern of leaves
in the plant is established. Auxin also controls the precise patterning of the epidermal cells of the developing leaf.

Phototropism
Plant shoots display positive phototropism: when illuminated from one direction, the shoot proceeds to grow in that direction.
Proposed Mechanism for phototropism is a multiple process. The direction of light is detected at the tip of the shoot with (blue
light is most effective). It is absorbed by a flavoprotein called phototropin. Flavoproteins contain flavin as a prosthetic group.
Auxin moves from the tip down. An auxin transporter - one of the PIN proteins - is inserted in the plasma membrane at the lateral
face of cells of the shoot. Auxin is pumped out of these efflux transporters and accumulates in the cells on the shady side. This
stimulates elongation of the cells on the shady side causing the shoot to bend toward the light.

Gravitropism
Gravitropism is a plant growth response to gravity.
Plant shoots display negative gravitropism: when placed on its side, a plant shoot will grow up
Roots display positive gravitropism: they grow down.

16.5B.1 https://bio.libretexts.org/@go/page/5799
Possible Mechanism of Gravitropism in Roots
When a root is placed on its side,
Statoliths (organelles containing starch grains) settle by gravity to the bottom of cells in the root tip.
This causes PIN proteins to redistribute to the underside of the cell where they pump auxin out of the cell; that is, they are
efflux transporters.
The auxin then accumulates along the under side of the root.
This INHIBITS root cell elongation.
So the cells at the top surface of the root elongate, causing the root to grow down.

Apical Dominance
Growth of the shoot apex (terminal shoot) usually inhibits the development of the lateral buds on the stem beneath. This
phenomenon is called apical dominance. If the terminal shoot of a plant is removed, the inhibition is lifted, and lateral buds begin
growth. Gardeners exploit this principle by pruning the terminal shoot of ornamental shrubs, etc. The release of apical dominance
enables lateral branches to develop and the plant becomes bushier. The process usually must be repeated because one or two
laterals will eventually outstrip the others and reimpose apical dominance.

Figure 16.4.3.2.2 Apical dominance

Apical dominance seems to result from the downward transport of auxin produced in the apical meristem. In fact, if the apical
meristem is removed and IAA applied to the stump, inhibition of the lateral buds is maintained.

Figure 16.4.3.2.3 Potato eyes

The common white potato is really a portion of the underground stem of the potato plant. It has a terminal bud or "eye" and several
lateral buds. After a long period of storage, the terminal bud usually sprouts but the other buds do not. However, if the potato is
sliced into sections, one bud to a section, the lateral buds develop just as quickly as the terminal bud.

Fruit Development

16.5B.2 https://bio.libretexts.org/@go/page/5799
Pollination of the flowers of angiosperms initiates the formation of seeds. As the seeds mature, they release auxin to the
surrounding flower parts, which develop into the fruit that covers the seeds.
Some commercial growers deliberately initiate fruit development by applying auxin to the flowers. Not only does this ensure that
all the flowers will "set" fruit, but it also maximizes the likelihood that all the fruits will be ready for harvest at the same time.

Abscission
Auxin also plays a role in the abscission of leaves and fruits. Young leaves and fruits produce auxin and so long as they do so, they
remain attached to the stem. When the level of auxin declines, a special layer of cells — the abscission layer — forms at the base
of the petiole or fruit stalk. Soon the petiole or fruit stalk breaks free at this point and the leaf or fruit falls to the ground.

Figure 16.4.3.2.5 Abscission mimosa

The figure on the right shows a nice demonstration of the role of auxin in abscission. If the blade of the leaf is removed, as shown
in the figure, the petiole remains attached to the stem for a few more days. The removal of the blade seems to be the trigger as an
undamaged leaf at the same node of the stem remains on the plant much longer, in fact, the normal length of time. If, however,
auxin is applied to the cut end of the petiole, abscission of the petiole is greatly delayed.
Fruit growers often apply auxin sprays to cut down the loss of fruit from premature dropping.

Root Initiation and Development

The localized accumulation of auxin in epidermal cells of the root initiates the formation of lateral or secondary roots. Auxin also
stimulates the formation of adventitious roots in many species. Adventitious roots grow from stems or leaves rather than from the
regular root system of the plant.
Horticulturists may propagate desirable plants by cutting pieces of stem and placing them base down in moist soil. Eventually
adventitious roots grow out at the base of the cutting. The process can often be hastened by treating the cuttings with a solution or
powder containing a synthetic auxin.
Once a root is formed, a gradient of auxin concentration develops highest at the tip promoting the production of new cells at the
meristem, and lowest in the region of differentiation, thus promoting the elongation and differentiation of root cells. The drop in
auxin activity in the regions of elongation and differentiation is mediated by cytokinin — an auxin antagonist.

16.5B.3 https://bio.libretexts.org/@go/page/5799
Translocation of Auxin
Auxin moves through the plant by two mechanisms: It passes in the sap moving through the phloem from where it is synthesized
(its "source", usually the shoot) to a "sink" (e.g., the root). It also passes from cell to cell by the following mechanism.
Auxin can enter the cell by diffusion and also through influx transporters in the plasma membrane. It moves out through efflux
transporters - called PIN proteins. Eight different types of PIN proteins have been identified so far. These are transmembrane
proteins inserted in localized portions of the plasma membrane, e.g.,
at the top of the cell where they move auxin toward the top of the plant;
at the basal surface of the cell where they move auxin down the plant;
at the lateral surface of the cell where they move auxin laterally (e.g., to mediate phototropism and gravitropism).
Identifying the signals that direct the appropriate placement of the PIN proteins is an active area of research.
How does auxin achieve its many different effects in the plant? Auxin effects are mediated by two different pathways: immediate,
direct effects on the cell and turning on of new patterns of gene expression

Direct effects of auxin

The arrival of auxin in the cytosol initiates such immediate responses as
changes in the concentration of and movement of ions in and out of the cell
reduction in the redistribution of PIN proteins
Some of the direct effects of auxin may be mediated by its binding to a cell-surface receptor designated ABP1 ("Auxin-binding
protein 1").

Effects of auxin on gene expression

Many auxin effects are mediated by changes in the transcription of genes. Auxin enters the nucleus and binds to its receptor, a
protein called TIR1 ("transport inhibitor response protein 1") which now can bind to proteins responsible for attaching ubiquitin to
one or another of several Aux/IAA proteins. This triggers the destruction of the Aux/IAA proteins by proteasomes. Aux/IAA
proteins normally bind transcription factors called auxin response factors (ARF) preventing them from activating the promoters
and other control sequences of genes that are turned on (or off) by auxin. Destruction of the Aux/IAA proteins relieves this
inhibition, and gene transcription begins.
This mechanism is another of the many cases in biology where a pathway is turned on by inhibiting the inhibitor of that pathway (a
double-negative is a positive). For example, the gibberellins, another group of plant hormones, exert their effects using a similar
strategy. The presence in the cell of many different Aux/IAA proteins (29 in Arabidopsis), many different ARFs (23 in
Arabidopsis) and several (~4) TIR1-like proteins provides a logical basis for mediating the different auxin effects that I have
described. But how this is done remains to be discovered.

Synthetic auxins as weed killers

Figure 16.4.3.2.6 2,4-D

Some of the most widely-used weed killers are synthetic auxins. These include 2,4-dichlorophenoxy acetic acid (2,4-D) and 2,4,5-
trichlorophenoxy acetic acid (2,4,5-T). As the formulas show, 2,4,5-T is 2,4-D with a third chlorine atom, instead of a hydrogen
atom, at the #5 position in the benzene ring (blue circles).

16.5B.4 https://bio.libretexts.org/@go/page/5799
2,4-D and its many variants are popular because they are selective herbicides, killing broad-leaved plants but not grasses (no one
knows the basis of this selectivity).
Why should a synthetic auxin kill the plant? It turns out that the auxin influx transporter works fine for 2,4-D, but that 2,4-D
cannot leave the cell through the efflux transporters. Perhaps it is the resulting accumulation of 2,4-D within the cell that kills it.
A mixture of 2,4,-D and 2,4,5-T was the "agent orange" used by the U.S. military to defoliate the forest in parts of South Vietnam.
Because of health concerns, 2,4,5-T is no longer used in the U.S.

This page titled 16.5B: Auxin is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.5B.5 https://bio.libretexts.org/@go/page/5799
16.5C: Cytokinins
Cytokinins are plant hormones that are derivatives of the purine adenine. They are not to be confused with cytokines. They were
discovered as an absolutely essential ingredient in medium for growing plant cells in culture. Without cytokinins in the medium,
plant cells will not divide by mitosis. Cytokinins have been implicated in many plant activities; usually along with some other plant
hormone such as auxin or ethylene.
Among these:
mitosis
chloroplast development
differentiation of the shoot meristem
stimulating the development of lateral buds and therefore branching
differentiation of the tissues of the root
leaf formation
leaf senescence
One of the clearest examples of cytokinin activity occurs in the germination of seeds. The endosperm of monocot
seeds, such as corn (maize), contains large stores of the precursor to the cytokinin zeatin (right). When the corn
kernel germinates, zeatin moves from the endosperm to the root tip where it stimulates vigorous mitosis.

Steps in cytokinin signaling

The following are the steps in cytokinin signaling:
A cytokinin, like zeatin, binds to a receptor protein embedded in the plasma membrane of the cell.
The internal portion of the receptor then attaches a phosphate group to a protein in the cytosol.
This protein moves into the nucleus where
it activates one or more nuclear transcription factors.
These bind to the promoters of genes.
Transcription of these genes produces mRNAs that move out into the cytosol.
Translation of these mRNAs produces the proteins that enable the cell to carry out its cytokine-induced function.

This page titled 16.5C: Cytokinins is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.5C.1 https://bio.libretexts.org/@go/page/5800
16.5D: Ethylene

Ethylene is a plant hormone that differs from other plant hormones in being a gas.
It has the molecular structure:

H2C=CH2
As they approach maturity, many fruits (e.g., apples, oranges, avocados) release ethylene. Ethylene then promotes the ripening of
the fruit. Commercial fruit growers can buy equipment to generate ethylene so that their harvest ripens quickly and uniformly.
The presence of ethylene is detected by transmembrane receptors in the endoplasmic reticulum (ER) of the cells. Binding of
ethylene to these receptors unleashes a signaling cascade that leads to activation of transcription factors and the turning on of gene
transcription.
The ill-fated FlavrSavr tomato contains an antisense transgene that interferes with the synthesis of ethylene and hence slows
ripening.

Plant functions affected by Ethylene

Ethylene also affects many other plant functions such as:
abscission of leaves, fruits, and flower petals
drooping of leaves
sprouting of potato buds
seed germination
stem elongation in rice (by promoting the breakdown of abscisic acid (ABA) and thus relieving ABA's inhibition of gibberellic
acid)
flower formation in some species

This page titled 16.5D: Ethylene is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.5D.1 https://bio.libretexts.org/@go/page/5801
16.5E: Gibberellins
During the 1930s Japanese scientists isolated a growth-promoting substance from cultures of a fungus that parasitizes rice plants.
They called it gibberellin. After the delay caused by World War II, plant physiologists in other countries succeeded in isolating
more than 30 closely-related compounds. One of the most active of these - and one found as a natural hormone in the plants
themselves - is gibberellic acid (GA).

Figure 16.4.3.5.1 GA3

GA has a number of effects on plant growth, but the most dramatic is its effect on stem growth. When applied in low
concentrations to a bush or "dwarf" bean, the stem begins to grow rapidly. The length of the internodes becomes so great that the
plant becomes indistinguishable from climbing or "pole" beans. GA seems to overcome the genetic limitations in many dwarf
varieties.
Synthesis of gibberellins also helps grapevines climb up toward the light by causing meristems that would have developed into
flowers to develop into tendrils instead.

 Note

One of the 7 pairs of traits that Mendel studied in peas as he worked out the basic rules of inheritance was dwarf-tall. The
recessive gene - today called le - turns out to encode an enzyme that is defective in enabling the plant to synthesize GA. The
dominant gene, Le, encodes a functioning enzyme permitting normal GA synthesis and making the "tall" phenotype.

Effects of gibberellins on gene expression

Gibberellins exert their effects by altering gene transcription, the steps for which are described below.
Gibberellin enters the cell and binds to a soluble receptor protein called GID1 ("gibberellin-insensitive dwarf mutant 1") which
now can bind to a complex of proteins (SCF) responsible for attaching ubiquitin to one or another of several DELLA proteins.
This triggers the destruction of the DELLA proteins by proteasomes.
DELLA proteins normally bind gibberellin-dependent transcription factors, a prominent one is designated PIF3/4, preventing
them from binding to the DNA of control sequences of genes that are turned on by gibberellin.
Destruction of the DELLA proteins relieves this inhibition and gene transcription begins.
This mechanism is another of the many cases in biology where a pathway is turned on by inhibiting the inhibitor of that pathway (a
double-negative is a positive).
Another example: Auxin.
Although most of the specific proteins involved are quite different, both gibberellins and auxin affect gene expression by a similar
mechanism of relief of repression.

Ligand Gibberellins Auxin

Receptor GID1 TIR1

Proteasome activator SCF SCF

Transcription factor repressor DELLA Aux/IAA

Transcription factor PIF3/4 ARF1

The dwarf varieties of rice and wheat that have played such an important part in the "green revolution" carry mutant genes that
interfere with the synthesis of their gibberellins (in the case of rice)
for wheat, reduce their ability to respond to their own gibberellins (because of mutant genes for a DELLA protein).

16.5E.1 https://bio.libretexts.org/@go/page/5802
Dwarf varieties of sorghum and more recently maize (corn) also exist, but in these cases, the mutation interferes with auxin
transport, not gibberellin activity.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 16.5E: Gibberellins is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.5E.2 https://bio.libretexts.org/@go/page/5802
16.5F: Strigolactones

Figure 16.4.3.6.1 Strigolactones

Strigolactones are manufactured in, and secreted from, the roots and have been known for some time to
promote the germination of some plant seeds. Unfortunately these include seeds of the genus Striga (witchweed) whose
developing root invades the root of the strigolactone-secreting host plant (e.g., rice, corn, and sorghum) stealing nutrients from
it and causing serious crop losses.
signal mycorrhizal fungi to connect to the root system forming a mutualistic relationship.
However, these activities do not qualify them as plant hormones (both activities take place in the soil surrounding the roots). Only
if it can be demonstrated that strigolactones are translocated in the plant from the place of manufacture (roots) to another part of the
plant where they exert an effect, can they be called hormones.
Two reports in the 11 September 2008 issue of Nature come close to proving the case.
Strigolactones (or possibly molecules derived from them) suppress the development of lateral buds and thus inhibit branching of
the plant. Mutations in genes needed for the synthesis of strigolactones stimulate the development of lateral buds producing a more
highly-branched plant than normal. Application of a synthetic strigolactone near the base of these mutant plants inhibits
development of lateral buds above and thus restores normal branching.
Auxin and, in certain circumstances, abscisic acid also inhibit branching, that is, they promote apical dominance. But both auxin
and abscisic acid participate in a number of different plant functions while the effect of strigolactones on branching seems quite
specific.

This page titled 16.5F: Strigolactones is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

16.5F.1 https://bio.libretexts.org/@go/page/5803
 CHAPTER OVERVIEW
Unit 17: Ecology
Ecology studies the interactions among organisms and their environment. Objects of study include interactions of organisms with
each other and with abiotic components of their environment. Topics of interest include the biodiversity, distribution, biomass, and
populations of organisms, as well as cooperation and competition within and between species. Ecosystems are dynamically
interacting systems of organisms, the communities they make up, and the non-living components of their environment. Ecosystem
processes, such as primary production, pedogenesis, nutrient cycling, and niche construction, regulate the flux of energy and matter
through an environment.
17.1: Energy Flow through the Biosphere
17.1A: Ecosystem Productivity
17.1B: Food Chains and Food Webs
17.1C: Biomes
17.1D: Freshwater Ecosystems
17.1E: Marine Ecosystems
17.1F: Biomagnification of Pesticides
17.2: Cycles of Matter in the Biosphere
17.2A: Carbon Cycle
17.2B: Nitrogen Cycle
17.2C: Symbiotic Nitrogen Fixation
17.2D: Soil
17.2E: Sewage Treatment
17.2F: Chlorination and the Law of Unintended Consequences
17.2G: Air Pollution
17.2H: Acid Rain
17.2I: Ozone
17.3: The Growth of Populations
17.3A: The Human Population
17.3B: Principles of Population Growth
17.4: Interactions between Species
17.4A: Symbiosis
17.4B: Insecticides
17.4C: Biological Control of Pests

This page titled Unit 17: Ecology is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1
 SECTION OVERVIEW
17.1: Energy Flow through the Biosphere
Topic hierarchy

17.1A: Ecosystem Productivity

17.1B: Food Chains and Food Webs

17.1C: Biomes

17.1D: Freshwater Ecosystems

17.1E: Marine Ecosystems

17.1F: Biomagnification of Pesticides

This page titled 17.1: Energy Flow through the Biosphere is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

17.1.1 https://bio.libretexts.org/@go/page/5810
17.1A: Ecosystem Productivity

The Input of Energy

Tropical regions every day and temperate regions during the growing season receive some 8,000 to 10,000 kilocalories (kcal) of
energy each day on each square meter (1 m2) of surface. A kilocalorie is the amount of heat needed to warm 1 kg of water 1 degree
Celsius (°C). Because all of the light trapped in photosynthesis is ultimately released as heat, it makes sense to follow the flow of
energy through ecosystems in units of heat.
How efficient are plants at converting this energy into organic molecules?

Gross Productivity
Gross productivity is the amount of energy trapped in organic matter during a specified interval at a given trophic level.
The table shows the use of visible sunlight is a cattail marsh. The plants have trapped only 2.2% of the energy falling on them.

Photosynthesis 2.2%

Reflection 3.0

Evaporation
(including transpiration and 94.8
heating of the surroundings

Total 100.0%

However, at least half of this is lost by cellular respiration as the plants run their own metabolism.

Net Productivity
Net productivity is the amount of energy trapped in organic matter during a specified interval at a given trophic level less that lost
by the respiration of the organisms at that level. One way to determine this is to collect and weigh the plant material produced on 1
m2 of land over a given interval. One gram of plant material (e.g., stems and leaves), which is largely carbohydrate, yields about
4.25 kcal of energy when burned (or respired).
The table shows representative values for the net productivity of a variety of ecosystems — both natural and managed. These
values are only approximations and are subject to marked fluctuations because of variations in temperature, fertility, and
availability of water.

Estimated Net Productivity of Certain Ecosystems (in kilocalories/m2/year)

Temperate deciduous forest 5,000

Tropical rain forest 15,000

Tall-grass prairie 2,000

Desert 500

Coastal marsh 12,000

Ocean close to shore 2,500

Open ocean 800

Clear (oligotrophic) lake 800

Lake in advanced state of eutrophication 2,400

Silver Springs, Florida 8,800

Field of alfalfa (lucerne) 15,000

Corn (maize) field, U.S. 4,500

17.1A.1 https://bio.libretexts.org/@go/page/5814
 Rice paddies, Japan 5,500

Lawn, Washington, D.C. 6,800

Sugar cane, Hawaii 25,000

What happens to the net productivity of a plant community?

Some is harvested by plant-eating herbivores, e.g., insects, deer. Often this is only the start of a series of transformations as it
passes through a series of heterotrophs — that together make up a food chain.
Some is consumed by organisms of decay, e.g., fungi and bacteria.
Some may be stored, e.g., in a growing forest or as peat in a bog.

What about humans?

Humans, like all heterotrophs, depend upon net productivity for their food both directly as we consume plant material (e.g., rice,
wheat, corn) and indirectly when we eat animals that have, themselves, fed on plant material (poultry, cattle, sheep, etc.) and/or
animal products (e.g., milk, eggs).
We also use the earth's net productivty to meet other needs such as:
wood for fuel
wood and fiber (e.g., cotton, flax) to house and clothe us
Added together it is estimated that our species now appropriates some 20% of world's net productivity for our own use. However,
this figure obscures large regional variations with estimates running as high as 80% in South central Asia to as low as 6% in South
America.
We also reduce the net productivity of our planet by other activities such as
paving over land for buildings, roads, parking lots, etc.
burning forests to clear them for agriculture

This page titled 17.1A: Ecosystem Productivity is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

17.1A.2 https://bio.libretexts.org/@go/page/5814
17.1B: Food Chains and Food Webs
The source of all food is the activity of autotrophs, mainly photosynthesis by plants. They are called producers because only they
can manufacture food from inorganic raw materials. This food feeds herbivores, called primary consumers. Carnivores that feed
on herbivores are called secondary consumers. Carnivores that feed on other carnivores are tertiary (or higher) consumers. Such
a path of food consumption is called a food chain. Each level of consumption in a food chain is called a trophic level.
The table gives one example of a food chain and the trophic levels represented in it.

Grass Grasshopper Toad Snake Hawk

Bacteria of decay
→ → → → →
In general,

Autotrophs Herbivores Carnivores

(Producers) (Primary Consumers) (Secondary, tertiary, etc. consumers) Decomposers
→ → →

Food Webs
Most food chains are interconnected. Animals typically consume a varied diet and, in turn, serve as food for a variety of other
creatures that prey on them. These interconnections create food webs.

Energy Flow Through Food Chains

Figure 17.1.2.1 Silver Springs ecosystem

H. T. Odum analyzed the flow of energy through a river ecosystem in Silver Springs, Florida. His findings are shown here. The
figures are given in kilocalories per square meter per year (kcal/m2/yr).
At each trophic level,
Net production is only a fraction of gross production because the organisms must expend energy to stay alive. Note that the
difference between gross and net production is greater for animals than for the producers - reflecting their greater activity.
Much of the energy stored in net production was lost to the system by
decay
being carried downstream
Note the substantial losses in net production as energy passes from one trophic level to the next.
The ratio of net production at one level to net production at the next higher level is called the conversion efficiency. Here it
varied from
17% from producers to primary consumers (1478/8833) to
4.5% from primary to secondary consumers (67/1478).

17.1B.1 https://bio.libretexts.org/@go/page/5815
 From similar studies in other ecosystems, we can take 10% as the average conversion efficiency from producers to primary
consumers.
Animal husbandry often exceeds this 10% value. For example, broilers (young chickens) can gain half a pound (227 g) of
weight for every pound (454 g) of food they eat. (Since the water content of the two is not the same, the conversion efficiency is
somewhat less than the apparent 50%.) Nonetheless, the loss of energy as it passes from producers to primary consumers
explains, for example, why it costs more to buy a pound of beefsteak than a pound of corn.
Conversion efficiencies from primary consumers to secondary consumers (herbivores to carnivores) tend to be much lower,
averaging about 1%.
In this ecosystem, all the gross production of the producers (20,810) ultimately disappeared in respiration (14,198) and
downstream export and decay (6612). So there was no storage of energy from one year to the next. This is typical of mature
ecosystems, such as a mature forest.
Some ecosystems do store energy, for example,
The slow rate of decay in bogs causes peat to accumulate (the source of the world's coal)
A young forest accumulates organic matter as the trees grow.

The Pyramid of Energy

Figure 17.1.2.2 Silver Springs

Conversions efficiencies are always much less than 100%. At each link in a food chain, a substantial portion of the sun's energy —
originally trapped by a photosynthesizing autotroph - is dissipated back to the environment (ultimately as heat). Thus it follows that
the total amount of energy stored in the bodies of a given population is dependent on its trophic level. For example, the total
amount of energy in a population of toads must necessarily be far less than that in the insects on which they feed. The insects, in
turn, have only a fraction of the energy stored in the plants on which they feed. This decrease in the total available energy at each
higher trophic level is called the pyramid of energy.
Using Odum's data on net productivity at the various levels in Silver Springs, we get this pyramid. The figures represent net
production at each trophic level expressed in kcal/m2/yr.

The Pyramid of Biomass

Figure 17.1.2.3 Silver Springs

How does one measure the amount of energy in a population?
Since all organisms are made of roughly the same organic molecules in similar proportions, a measure of their dry weight is a
rough measure of the energy they contain. A census of the population, multiplied by the weight of an average individual in it, gives
an estimate of the weight of the population. This is called the biomass (or standing crop). This, too, diminishes with the distance
along the food chain from the autotrophs which make the organic molecules in the first place.
The graphic shows the pyramid of biomass for Silver Springs. (It, too, is based on the data obtained by Howard T. Odum.) The
figures represent the dry weight of organic matter (per square meter) at the time of sampling. Analysis of various ecosystems
indicates that those with squat biomass pyramids (with conversion efficiencies between one trophic level and the next averaging
10% or better) are less likely to be disrupted by physical or biotic changes than those with tall, skinny pyramids (having conversion
efficiencies less than 10%).

17.1B.2 https://bio.libretexts.org/@go/page/5815
The Pyramid of Numbers

Figure 17.1.2.4 Bluegrass pyramid

Small animals are more numerous than larger ones. This graph shows the pyramid of numbers resulting when a census of the
populations of autotrophs, herbivores, and two levels of carnivores was taken on an acre (0.4 hectare) of grassland. The figures
represent number of individuals counted at each trophic level. The pyramid is based on data acquired by Evans, Cain, and
Walcott, and has been redrawn by permission from E. P. Odum, Fundamentals of Ecology, 2nd. ed., © W. B. Saunders Co.,
Philadelphia, 1959.
The pyramid arises because:
Each species is limited in its total biomass by its trophic level.
So, if the size of the individuals at a given trophic level is small, their numbers can be large and vice versa.
Predators are usually larger than their prey.
Occupying a higher trophic level, their biomass must be smaller.
Hence, the number of individuals in the predator population is much smaller than that in the prey population.

This page titled 17.1B: Food Chains and Food Webs is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

17.1B.3 https://bio.libretexts.org/@go/page/5815
17.1C: Biomes
A biome is a large, distinctive complex of plant communities created and maintained by climate.
How many biomes are there?

Figure 17.1.3.1 Biomes

A study published in 1999 concluded that there are 150 different "ecoregions" in North America alone. But I shall cast my lot with
the "lumpers" rather than the "splitters" and lump these into 8 biomes:
tundra
taiga
temperate deciduous forest
scrub forest (called chaparral in California)
grassland
desert
tropical rain forest
temperate rain forest
The figure shows the distribution of these 8 biomes around the world. A number of climatic factors interact in the creation and
maintenance of a biome. Where precipitation is moderately abundant — 40 inches (about 1 m) or more per year — and distributed
fairly evenly throughout the year, the major determinant is temperature. It is not simply a matter of average temperature, but
includes such limiting factors as whether it ever freezes or length of the growing season. If there is ample rainfall, we find 4
characteristic biomes as we proceed from the tropics (high temperatures) to the extreme latitudes (low temperatures). In order, they
are:
tropical rain forest or jungle
temperate deciduous forest
taiga
tundra

Tropical Rain Forest

17.1C.1 https://bio.libretexts.org/@go/page/5816
 Figure 17.1.3.2 Rainforest
In the Western Hemisphere, the tropical rain forest reaches its fullest development in the jungles of Central and South America.
The trees are very tall and of a great variety of species.
One rarely finds two trees of the same species growing close to one another.
The vegetation is so dense that little light reaches the forest floor.
Most of the plants are evergreen, not deciduous.
The branches of the trees are festooned with vines and epiphytes (see the photo taken in the Luquillo National Forest of Puerto
Rico).

 Note

Epiphytes are plants that live perched on sturdier plants. They do not take nourishment from their host as parasitic plants do.
Because their roots do not reach the ground, they depend on the air to bring them moisture and inorganic nutrients. Many
orchids and many bromeliads (members of the pineapple family like "Spanish moss") are epiphytes.

The lushness of the tropical rain forest suggests a high net productivity, but this is illusory. Many of the frequent attempts to use the
tropical rain forest for conventional crops have been disappointing. Two problems:
The high rainfall leaches soil minerals below the reach of plant roots.
The warmth and moisture cause rapid decay so little humus is added to the soil.
The tropical rain forest exceeds all the other biomes in the diversity of its animals as well as plants. Most of the animals - mammals
and reptiles, as well as birds and insects live in the trees. The closest thing to a tropical rain forest in the continental United States
are the little wooded "islands" found scattered through the Everglades in the southern tip of Florida. Their existence depends on the
fact that it never freezes, and they often escape the fires that periodically sweep the Everglades.

Temperate Deciduous Forest

17.1C.2 https://bio.libretexts.org/@go/page/5816
 Figure 17.1.3.3 Temperate forest
This biome occupies the eastern half of the United States and a large portion of Europe. It is characterized by:
hardwood trees (e.g., beech, maple, oak, hickory) which
are deciduous; that is, shed their leaves in the autumn.
The number of different species is far more limited than in the jungle.
Large stands dominated by a single species are common.
Deer, raccoons, and salamanders are characteristic inhabitants.
During the growing season, this biome can be quite productive in both natural and agricultural ecosystems.
The photo (by Dick Morton) shows a view of this biome in Maine in the autumn.

Taiga

Fig.17.1.3.4 Taiga
The taiga is named after the biome in Russia.
It is a land dominated by conifers, especially spruces and firs.
It is dotted with lakes, bogs, and marshes.
It is populated by an even more limited variety of plants and animals than is the temperate deciduous forest.
In North America, the moose is such a typical member that it has led to the name: "spruce-moose" biome.
Before the long, snowy winter sets in, many of the mammals hibernate, and many of the birds migrate south.
Although the long days of summer permit plants to grow luxuriantly, net productivity is low.
The photo (courtesy of Dr. Benjamin Dane of Tufts University) shows the "spruce-moose" biome in British Columbia.

17.1C.3 https://bio.libretexts.org/@go/page/5816
Tundra
At extreme latitudes, the trees of the taiga become stunted by the harshness of the subarctic climate. Finally, they disappear leaving
a land of bogs and lakes.
The climate is so cold in winter that even the long days of summer are unable to thaw the permafrost beneath the surface layers
of soil.
Sphagnum moss, a wide variety of lichens, and some grasses and fast-growing annuals dominate the landscape during the short
growing season.
Caribou feed on this growth as do vast numbers of insects.
Swarms of migrating birds, especially waterfowl, invade the tundra in the summer to raise their young, feeding them on a large
variety of aquatic invertebrates and vertebrates.
As the brief arctic summer draws to a close, the birds fly south, and
all but a few of the permanent residents, in one way or another, prepare themselves to spend the winter in a dormant state.

Biomes established by altitude

Figure 17.1.3.5 Biomes Altitude vs Latitude

Temperature is the major influence on the biomes discussed above. Because temperatures decline with altitude as well as latitude,
similar biomes exist on mountains even when they are at low latitudes. As a rule of thumb, a climb of 1000 feet (about 300 m) is
equivalent in changed flora and fauna to a trip northward of some 600 miles (966 km).

Figure 17.1.3.6 Alpine tundra

The photo is of alpine tundra at 12,000 feet (3,658 m) in the Rocky Mountains.
Field studies in various parts of the Northern Hemisphere have shown that in recent decades many species of animals and plants
have
shifted their ranges farther north (averagiing 16.9 kilometers per decade)
shifted their ranges higher in the mountains (averaging 11.0 meters per decade)
These observations add to the growing body of evidence that global warming is affecting a broad assortment of living things.

Biomes established by rainfall

The other major biomes are controlled not so much by temperature but by the amount and seasonal distribution of rainfall.
The prevailing winds in the western half of North America blow in from the Pacific laden with moisture. Each time this air rises up
from the western slopes of, successively, the Coast Ranges, the Sierras and Cascades, and finally the Rockies, it expands and cools.
Its moisture condenses to rain or snow, which drenches the mountain slopes beneath. When the air reaches the eastern slopes, it is
relatively dry, and much less precipitation falls. How much falls and when determine whether the biome will be
temperate rain forest

17.1C.4 https://bio.libretexts.org/@go/page/5816
 grassland
desert or
chaparral

Temperate Rain Forest

The temperate rain forest combines high annual rainfall with a temperate climate. The Olympic Peninsular in North America is a
good example. An annual rainfall of as much as 150 inches (381 cm) produces a lush forest of conifers.

Grasslands

Figure 17.1.3.7 Grasslands

Grasslands are also known as prairie or plains. The annual precipitation in the grasslands averages 20 inches (~51 cm) per year. A
large proportion of this falls as rain early in the growing season. This promotes a vigorous growth of perennial grasses and herbs,
except along river valleys - is barely adequate for the growth of forests. The photo shows grassland in the Badlands National
Monument in South Dakota.
Fire is probably the factor that tips the balance from forest to grasslands. Fires set by lightning and by humans regularly swept the
plains in earlier times. Thanks to their underground stems and buds, perennial grasses and herbs are not harmed by fires that
destroy most shrubs and trees.
The abundance of grass for food, coupled with the lack of shelter from predators, produces similar animal populations in grasslands
throughout the world. The dominant vertebrates are swiftly-moving, herbivorous ungulates. In North America, bison and antelope
were conspicuous members of the grassland fauna before the coming of white settlers. Now the level grasslands supply corn,
wheat, and other grains, and the hillier areas support domesticated ungulates: cattle and sheep.
When cultivated carefully, the grassland biome is capable of high net productivity. A major reason: rainfall in this biome never
leaches soil minerals below the reach of the roots of crop plants.

Desert

Figure 17.1.3.8 Desert

Annual rainfall in the desert is less than 10 inches (25 cm) and, in some years, may be zero. Because of the extreme dryness of the
desert, its colonization is limited to
plants such as cacti, sagebrush, and mesquite that have a number of adaptations that conserve water over long periods
fast-growing annuals whose seeds can germinate, develop to maturity, flower, and produce a new crop of seeds all within a few
weeks following a rare, soaking rain.
The photo shows the desert in the Anza-Borego park in southern California.
Many of the animals in the desert (mammals, lizards and snakes, insects, and even some birds) are adapted for burrowing to escape
the scorching heat of the desert sun. Many of them limit their forays for food to the night. The net productivity of the desert is low.

17.1C.5 https://bio.libretexts.org/@go/page/5816
High productivity can sometimes be achieved with irrigation, but these gains are often only temporary. The high rates of
evaporation cause minerals to accumulate near the surface and soon their concentration may reach levels toxic to plants.

Chaparral

Figure 17.1.3.8 Chaparral

The annual rainfall in the chaparral biome may reach 20–30 inches (64–76 cm), but in contrast to the grasslands, almost all of this
falls in winter. Summers are very dry and all the plants - trees, shrubs, and grasses - are more or less dormant then.
The chaparral is found in California. (The photo shows the chaparral-clad foothills of the Sierra Nevada in California.) Similar
biomes (with other names, such as scrub forest), are found around much of the Mediterranean Sea and along the southern coast of
Australia.
The trees in the chaparral are mostly oaks, both deciduous and evergreen. Scrub oaks and shrubs like manzanita and the California
lilac (not a relative of the eastern lilac) form dense, evergreen thickets. All of these plants are adapted to drought by such
mechanisms as waxy, waterproof coatings on their leaves. The chaparral has many plants brought to it from similar biomes
elsewhere. Vineyards, olives, and figs flourish just as they do in their native Mediterranean biome. So, too, do eucalyptus trees
transplanted from the equivalent biome in Australia.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 17.1C: Biomes is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

17.1C.6 https://bio.libretexts.org/@go/page/5816
17.1D: Freshwater Ecosystems
Only 3% of the world's water is fresh. And 99% of this is either frozen in glaciers and pack ice or is buried in aquifers. The
remainder is found in lakes, ponds, rivers, and streams.

Figure 17.1.4.1 Littoral zone

The zone close to shore. Here light reaches all the way to the bottom. The producers are plants rooted to the bottom and algae
attached to the plants and to any other solid substrate. The consumers include
tiny crustaceans
flatworms
insect larvae
snails
frogs, fish, and turtles.

Limnetic zone
This is the layer of open water where photosynthesis can occur. As one descends deeper in the limnetic zone, the amount of light
decreases until a depth is reached where the rate of photosynthesis becomes equal to the rate of respiration. At this level, net
primary production no longer occurs.
The limnetic zone is shallower in turbid water than in clear and is a more prominent feature of lakes than of ponds.
Life in the limnetic zone is dominated by
floating microorganisms - called plankton
actively swimming animals - called nekton
The producers in this ecosystem are planktonic algae. The primary consumers include such animals as microscopic crustaceans
and rotifers - the so-called zooplankton. The secondary (and higher) consumers are swimming insects and fish. These nekton
usually move freely between the littoral and limnetic zones.

Profundal zone
Many lakes (but few ponds) are so deep that not enough light reaches here to support net primary productivity. Therefore, this zone
depends for its calories on the drifting down of organic matter from the littoral and limnetic zones. The profundal zone is chiefly
inhabited by primary consumers that are either attached to or crawl along the sediments at the bottom of the lake. Such bottom-
dwelling animals are called the benthos. The sediments underlying the profundal zone also support a large population of bacteria
and fungi. These decomposers break down the organic matter reaching them, releasing inorganic nutrients for recycling.

Fall overturn
Where there is a pronounced change of seasons, the warming of the surface of the lake in the summer prevents this water from
mixing with deeper water. This is because warm water is less dense than cold.
The surface water becomes enriched in oxygen some from the air above it and the rest - because it is in the limnetic zone - from
photosynthesis. But the water in the profundal zone - eing removed from both these sources - becomes stagnant. In the fall,
however, as the surface water cools, it becomes denser and sinks to the bottom — carrying oxygen with it.

Spring overturn
A similar phenomenon occurs when the ice melts in the spring.

17.1D.1 https://bio.libretexts.org/@go/page/5817
Rivers and Streams
The habitats available in rivers and streams differ in several ways from those in lakes and ponds.
Because of the current, the water is usually more oxygenated.
Photosynthesizers play a minor role in the food chains here; a large fraction of the energy available for consumers is brought
from the land; e.g., in falling leaves.
Oceans, like lakes, can be described in terms of zones. There are many parallels between the two but unfortunately a separate
vocabulary is used for each.

This page titled 17.1D: Freshwater Ecosystems is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

17.1D.2 https://bio.libretexts.org/@go/page/5817
17.1E: Marine Ecosystems
Intertidal zone
Examples:
sandy beaches
rocks
estuaries
mangrove swamps
coral reefs
coastal marshes
Some of these regions are quite productive. Many of their inhabitants have adaptations that enable them to survive periodic
exposure to the air and wave action.

Figure 17.1.5.1 Ocean

Neritic zone
This is the relatively shallow ocean that extends to the edge of the continental shelf. Net productivity here depends on planktonic
algae growing as deep as the light can reach.

Oceanic zone
Located over the ocean basins. Here, too, net productivity is pretty much limited to the depths that light can reach. The producers
are planktonic algae that support secondary and higher consumers (e.g., fish) in the nekton.
Despite its diversity of life, the net productivity of the open ocean is little better than that of a desert.

Abyssal plain
The bottom of the ocean basins: This dark, relatively unvarying region is largely inhabited by sparse populations of bottom-
dwelling organisms that make up the benthos. These are consumers and decomposers who depend on the organic matter drifting
down from the upper portions of the sea.
An exception: the communities around rifts. Rifts are spreading cracks in the sea floor where continental drift is taking place.
Although no light reaches here, net productivity does occur.
Chemoautotrophic bacteria and archaea manufacture food using energy secured by oxidizing the sulfur flowing out of the cracks
("black smokers"). These microbes support a large population of animals, e.g., tube worms. Some of these worms harbor
chemoautotrophic microbes within their tissues which probably supply them with the bulk of their calories.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 17.1E: Marine Ecosystems is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

17.1E.1 https://bio.libretexts.org/@go/page/5818
17.1F: Biomagnification of Pesticides
The figure shows how DDT becomes concentrated in the tissues of organisms representing four successive trophic levels in a food
chain. The concentration effect occurs because DDT is metabolized and excreted much more slowly than the nutrients that are
passed from one trophic level to the next. So DDT accumulates in the bodies (especially in fat). Thus most of the DDT ingested as
part of gross production is still present in the net production that remains at that trophic level.

Figure 17.1.6.1: In biomagnification the concentration of the persistent toxins (crosses) increase higher up the food chain. An
increase of toxin concentration as the food chain moves up to higher levels. Organisms at the top have a higher tissue concentration
of toxins and pollutants than lower levels. The concentration system is due to persistence of the toxins, food chain energetics, and
low rate of internal degradation or excretion of the substance.Trophic level I represents the primary producers. Trophic level II
represents the primary consumers. Trophic level III represents the secondary consumers. Trophic level IV represents the tertiary
consumers. (CC CC-SA 3.0).
This is why the hazard of DDT to nontarget animals is particularly acute for those species living at the top of food chains.
For example,
spraying a marsh to control mosquitoes will cause trace amounts of DDT to accumulate in the cells of microscopic aquatic
organisms, the plankton, in the marsh.
In feeding on the plankton, filter-feeders, like clams and some fish, harvest DDT as well as food. (Concentrations of DDT 10
times greater than those in the plankton have been measured in clams.)
The process of concentration goes right on up the food chain from one trophic level to the next. Gulls, which feed on clams,
may accumulate DDT to 40 or more times the concentration in their prey. This represents a 400-fold increase in concentration
along the length of this short food chain.
There is abundant evidence that some carnivores at the ends of longer food chains (e.g. ospreys, pelicans, falcons, and eagles)
suffered serious declines in fecundity and hence in population size because of this phenomenon in the years before use of DDT was
banned (1972) in the United States.

This page titled 17.1F: Biomagnification of Pesticides is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

17.1F.1 https://bio.libretexts.org/@go/page/5819
 SECTION OVERVIEW
17.2: Cycles of Matter in the Biosphere
Topic hierarchy

17.2A: Carbon Cycle

17.2B: Nitrogen Cycle

17.2C: Symbiotic Nitrogen Fixation

17.2D: Soil

17.2E: Sewage Treatment

17.2F: Chlorination and the Law of Unintended Consequences

17.2G: Air Pollution

17.2H: Acid Rain

17.2I: Ozone

This page titled 17.2: Cycles of Matter in the Biosphere is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

17.2.1 https://bio.libretexts.org/@go/page/5811
17.2A: Carbon Cycle
The concentration of carbon in living matter (18%) is almost 100 times greater than its concentration in the earth (0.19%). So living
things extract carbon from their nonliving environment. For life to continue, this carbon must be recycled. Carbon exists in the
nonliving environment as:
carbon dioxide (CO2) in the atmosphere and dissolved in water (forming HCO3−)
carbonate rocks (limestone and coral = CaCO3)
deposits of coal, petroleum, and natural gas derived from once-living things
dead organic matter, e.g., humus in the soil
Carbon enters the biotic world through the action of primarily photoautotrophs, like plants and algae, that use the energy of light
to convert carbon dioxide to organic matter and to a small extent, chemoautotrophs - bacteria and archaea that do the same but use
the energy derived from an oxidation of molecules in their substrate. Carbon returns to the atmosphere and water by respiration (as
CO2), burning, and decay (producing CO2 if oxygen is present, methane (CH4) if it is not.

Figure 17.2.1.1 Carbon cycle

The uptake and return of CO 2 are not in balance

Figure 17.2.1.2 Carbon dioxide concentration

The carbon dioxide content of the atmosphere is gradually and steadily increasing. The graph shows the CO2 concentration at the
summit of Mauna Loa in Hawaii from 1958 through 1999. The values are in parts per million (ppm). The seasonal fluctuation is
caused by the increased uptake of CO2 by plants in the summer. (In March 2015, its average worldwide concentration reached 400
ppm.)
The increase in CO2 probably began with the start of the industrial revolution. Samples of air trapped over the centuries in the
glacial ice of Greenland show no change in CO2 content until 300 years ago. Since measurements of atmospheric CO2 began late
in the nineteenth century, its concentration has risen over 20%. This increase is surely "anthropogenic"; that is, caused by human
activities:
burning fossil fuels (coal, oil, natural gas) which returns to the atmosphere carbon that has been locked within the earth for
millions of years.

17.2A.1 https://bio.libretexts.org/@go/page/5820
 clearing and burning of forests, especially in the tropics. In recent decades, large areas of the Amazon rain forest have been
cleared for agriculture and cattle grazing.

Where is the missing carbon?

Curiously, the increase in atmospheric CO2 is only about one-half of what would have been expected from the amount of fossil fuel
consumption and forest burning. Where has the rest gone? Research has shown that increased CO2 levels lead to increased net
production by photoautotrophs. There is evidence that at least some of the missing CO2 has been incorporated by: (1) increased
growth of forests, especially in North America, (2) increased amounts of photoautotrophic plankton in the oceans, and (3) uptake
by desert soils (mechanism as yet unknown)

The Greenhouse Effect and Global Warming

Despite these "sinks" for our greatly-increased CO2 production, the concentration of atmospheric CO2 continues to rise? Should
we be worried? Carbon dioxide is transparent to light but rather opaque to heat rays. Therefore, CO2 in the atmosphere retards the
radiation of heat from the earth back into space - the "greenhouse effect". Has the increase in carbon dioxide led to global
warming?

Figure 17.2.1.3 Green house

Some evidence:
Careful monitoring shows that the global air temperature in 2014 was 0.57°C higher than the average from 1961–1990, and that
14 of the 15 warmest years since records began being kept late in the 19th Century have occurred in this century (including
2005 and 2010 as well as 2014).
Many glaciers and ice sheets are receding.
Woody shrubs are now growing in areas of northern Alaska that 50 years ago were barren tundra.
Many angiosperms in temperate climates are flowering earlier in the spring than they used to.
Many species of birds and butterflies are moving north and breeding earlier in the spring.
Will continued increase in carbon dioxide lead to more global warming and, if so, how much? At this point, the answer depends on
what assumptions you plug into your computer models. But as the different models have been improved, they seem to be
converging on a consensus: a doubling of the CO2 concentration (expected by the end of this century) will cause the earth to warm
somewhere in the range of 1.1–6.4°C.

Other Greenhouse Gases

Although their levels in the atmosphere are much lower than that of CO2,
methane (CH4)
nitrous oxide (N2O)
hydrofluorocarbons (HFCs)
are also potent greenhouse gases.

Methane
Although methane ("marsh gas") is released by natural processes (e.g. from decay occurring in swamps), human activities now
account for some 60% of the total.

17.2A.2 https://bio.libretexts.org/@go/page/5820
 mining, processing, and use of coal, oil, and natural gas
release from landfills
growing rice in paddies
burning forests
raising cattle (fermentation in their rumens produces methane that is expelled from their GI tract)
So burning of the tropical rain forest adds to the atmospheric methane budget in two ways:
incomplete combustion during burning
release from the GI tract of the cattle that are later placed on the cleared land.
The methane concentration in Arctic air is presently some 1.9 parts per million, the highest level seen such measurements began.
Although this concentration is far less than that of CO2, methane is 28 times as potent a greenhouse gas. The marked warming of
the earth that occurred at the end of the Paleocene epoch is thought to have been caused by the release of large amounts of methane
from the sea floor.

This page titled 17.2A: Carbon Cycle is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

17.2A.3 https://bio.libretexts.org/@go/page/5820
17.2B: Nitrogen Cycle
All life requires nitrogen-compounds, e.g., proteins and nucleic acids. Air, which is 79% nitrogen gas (N2), is the major reservoir
of nitrogen. But most organisms cannot use nitrogen in this form. Plants must secure their nitrogen in "fixed" form, i.e.,
incorporated in compounds such as: nitrate ions (NO3−), ammonium ions (NH4+) and urea (NH2)2CO. Animals secure their
nitrogen (and all other) compounds from plants (or animals that have fed on plants).

Figure 17.2.2.1 Nitrogen cycle

Four processes participate in the cycling of nitrogen through the biosphere: (1) nitrogen fixation, (2) decay, (3) nitrification, and (4)
denitrification. Microorganisms play major roles in all four of these.

Nitrogen Fixation
The nitrogen molecule (N2) is quite inert. To break it apart so that its atoms can combine with other atoms requires the input of
substantial amounts of energy. Three processes are responsible for most of the nitrogen fixation in the biosphere:
atmospheric fixation by lightning
biological fixation by certain microbes alone or in a symbiotic relationship with some plants and animals
industrial fixation

Atmospheric Fixation
The enormous energy of lightning breaks nitrogen molecules and enables their atoms to combine with oxygen in the air forming
nitrogen oxides. These dissolve in rain, forming nitrates, that are carried to the earth. Atmospheric nitrogen fixation probably
contributes some 5– 8% of the total nitrogen fixed.

Industrial Fixation
Under great pressure, at a temperature of 600°C, and with the use of a catalyst, atmospheric nitrogen and hydrogen (usually derived
from natural gas or petroleum) can be combined to form ammonia (NH3). Ammonia can be used directly as fertilizer, but most of
its is further processed to urea and ammonium nitrate (NH4NO3).

Biological Fixation
The ability to fix nitrogen is found only in certain bacteria and archaea.
Some live in a symbiotic relationship with plants of the legume family (e.g., soybeans, alfalfa).
Some establish symbiotic relationships with plants other than legumes (e.g., alders).
Some establish symbiotic relationships with animals, e.g., termites and "shipworms" (wood-eating bivalves).
Some nitrogen-fixing bacteria live free in the soil.
Nitrogen-fixing cyanobacteria are essential to maintaining the fertility of semi-aquatic environments like rice paddies.
Biological nitrogen fixation requires a complex set of enzymes and a huge expenditure of ATP. Although the first stable product of
the process is ammonia, this is quickly incorporated into protein and other organic nitrogen compounds.

Decay
The proteins made by plants enter and pass through food webs just as carbohydrates do. At each trophic level, their metabolism
produces organic nitrogen compounds that return to the environment, chiefly in excretions. The final beneficiaries of these

17.2B.1 https://bio.libretexts.org/@go/page/5821
materials are microorganisms of decay. They break down the molecules in excretions and dead organisms into ammonia.

Nitrification
Ammonia can be taken up directly by plants — usually through their roots. However, most of the ammonia produced by decay is
converted into nitrates. Until recently this was thought always to be accomplished in two steps:
1. Bacteria of the genus Nitrosomonas oxidize NH to nitrites (NO ).
3
−

2. Bacteria of the genus Nitrobacter oxidize the nitrites to nitrates (NO ). −

These two groups of autotrophic bacteria are called nitrifying bacteria. Through their activities (which supply them with all their
energy needs), nitrogen is made available to the roots of plants. However, in 2015, two groups reported finding that bacteria in the
genus Nitrospira were able to carry out both steps: ammonia to nitrite and nitrite to nitrate. This ability is called "comammox" (for
complete ammonia oxidation).
In addition, both soil and the ocean contain archaeal microbes, assigned to the Crenarchaeota, that convert ammonia to nitrites.
They are more abundant than the nitrifying bacteria and may turn out to play an important role in the nitrogen cycle.
Many legumes, in addition to fixing atmospheric nitrogen, also perform nitrification - converting some of their organic nitrogen to
nitrites and nitrates. These reach the soil when they shed their leaves.

Denitrification
The three processes above remove nitrogen from the atmosphere and pass it through ecosystems. Denitrification reduces nitrates
and nitrites to nitrogen gas, thus replenishing the atmosphere. In the process several intermediates are formed:
nitric oxide (NO)
nitrous oxide (N2O)(a greenhouse gas 300 times as potent as CO2)
nitrous acid (HONO)
Once again, bacteria are the agents. They live deep in soil and in aquatic sediments where conditions are anaerobic. They use
nitrates as an alternative to oxygen for the final electron acceptor in their respiration.

Anammox (anaerobic ammonia oxidation)

Under anaerobic conditions in marine and freshwater sediments, other species of bacteria are able to oxidize ammonia (with NO ) −
2

forming nitrogen gas.

+ −
NH + NO → N +2 H O (17.2B.1)
4 2 2 2

The anammox reaction may account for as much as 50% of the denitrification occurring in the oceans. All of these processes
participate in closing the nitrogen cycle.

Are the denitrifiers keeping up?

Agriculture may now be responsible for one-half of the nitrogen fixation on earth through the use of fertilizers produced by
industrial fixation and the the growing of legumes like soybeans and alfalfa. This is a remarkable influence on a natural cycle. Are
the denitrifiers keeping up the nitrogen cycle in balance? Probably not. Certainly, there are examples of nitrogen enrichment in
ecosystems. One troubling example: the "blooms" of algae in lakes and rivers as nitrogen fertilizers leach from the soil of adjacent
farms (and lawns). The accumulation of dissolved nutrients in a body of water is called eutrophication.

This page titled 17.2B: Nitrogen Cycle is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

17.2B.2 https://bio.libretexts.org/@go/page/5821
17.2C: Symbiotic Nitrogen Fixation
Symbiotic nitrogen fixation occurs in plants that harbor nitrogen-fixing bacteria within their tissues. The best-studied example is
the association between legumes and bacteria in the genus Rhizobium. Each of these is able to survive independently (soil
nitrates must then be available to the legume), but life together is clearly beneficial to both. Only together can nitrogen fixation take
place. A symbiotic relationship in which both partners benefits is called mutualism.

Rhizobia
Rhizobia are Gram-negative bacilli that live freely in the soil (especially where legumes have been grown). However, they cannot
fix atmospheric nitrogen until they have invaded the roots of the appropriate legume.

The Infection Thread

The interaction between a particular strain of rhizobia and the "appropriate" legume is mediated by a "Nod factor" secreted by the
rhizobia and transmembrane receptors on the cells of the root hairs of the legume. Different strains of rhizobia produce different
Nod factors, and different legumes produce receptors of different specificity.

Figure 17.2.3.1 Infection thread

If the combination is correct, the bacteria enter an epithelial cell of the root; then migrate into the cortex. Their path runs within an
intracellular channel that grows through one cortex cell after another. This infection thread is constructed by the root cells, not the
bacteria, and is formed only in response to the infection. When the infection thread reaches a cell deep in the cortex, it bursts and
the rhizobia are engulfed by endocytosis into membrane-enclosed symbiosomes within the cytoplasm. At this time the cell goes
through several rounds of mitosis - without cytokinesis - so the cell becomes polyploid.
The above electron micrograph (courtesy of Dr. D. C. Jordan) shows a rhizobia-filled infection thread growing into the cell (from
the upper left to the lower right). Note how the wall of the infection thread is continuous with the wall of the cell. The dark ovals
are the symbiosomes.

Figure 17.2.3.2 Nitragin

The cortex cells then begin to divide rapidly forming a nodule. This response is driven by the translocation of cytokinins from
epidermal cells to the cells of the cortex. The above photo in fig. 17.2.3.2 (courtesy of The Nitragin Co. Milwaukee, Wisconsin)
shows nodules on the roots of the birdsfoot trefoil, a legume.

17.2C.1 https://bio.libretexts.org/@go/page/5822
 Figure 17.2.3.3 Bacteroids
The rhizobia also go through a period of rapid multiplication within the nodule cells. Then they begin to change shape and lose
their motility. The bacteroids, as they are now called, may almost fill the cell. Only now does nitrogen fixation begin. The electron
micrograph in fig. 17.2.3.3(courtesy of R. R. Hebert) shows bacteroid-filled cells from a soybean nodule. The horizontal line marks
the walls between two adjacent nodule cells.

Figure 17.2.3.4 Root nodules

Root nodules are not simply structureless masses of cells. Each becomes connected by the xylem and phloem to the vascular
system of the plant. The photo in fig. 17.2.3.4 on the left shows a developing lateral root on a pea root. On its right is a segment of
a pea root showing a developing nodule 12 days after the root was infected with rhizobia. Both structures are connected to the
nutrient transport system of the plant (dark area extending through the center of the root). (Photomicrographs courtesy of the late
John G. Torrey.) Thus the development of nodules, while dependent on rhizobia, is a well-coordinated developmental process of
the plant.
Although some soil bacteria (e.g., Azotobacter) can fix nitrogen by themselves, rhizobia cannot. Clearly rhizobia and legumes are
mutually dependent. The benefit to the legume host is clear. The rhizobia make it independent of soil nitrogen. But why is the
legume necessary? The legume is certainly helpful in that it supplies nutrients to the bacteroids with which they synthesize the
large amounts of ATP needed to convert nitrogen (N2) into ammonia (NH3). In addition, the legume host supplies one critical
component of nitrogenase - the key enzyme for fixing nitrogen.
The bacteroids need oxygen to make their ATP (by cellular respiration). However, nitrogenase is strongly inhibited by oxygen.
Thus the bacteroids must walk a fine line between too much and too little oxygen. Their job is made easier by another contribution
from their host: hemoglobin. Nodules are filled with hemoglobin. So much of it, in fact, that a freshly-cut nodule is red. The
hemoglobin of the legume (called leghemoglobin), like the hemoglobin of vertebrates, probably supplies just the right
concentration of oxygen to the bacteroids to satisfy their conflicting requirements.
The metal molybdenum is a critical component of nitrogenase and so is absolutely essential for nitrogen fixation. But the amounts
required are remarkably small. One ounce (28.3 g) of molybdenum broadcast over an acre (0.4 hectare) of cropland in Australia
was found to be sufficient to restore fertility for over ten years.

17.2C.2 https://bio.libretexts.org/@go/page/5822
 Figure 17.2.3.5 Molybdenum
The photo in fig. 17.2.3.5 shows that the legume clover grows normally only where the supply of molybdenum is adequate. The
soil shown here (in eastern Australia) is naturally deficient in molybdenum. Although the entire fenced-in plot was seeded to
clover, the plant was able to flourish and fix nitrogen only where molybdenum fertilizer had been added (foreground). (Photo
courtesy of A. J. Anderson.)
Because of the specificity of the interaction between the Nod factor and the receptor on the legume, some strains of rhizobia will
infect only peas, some only clover, some only alfalfa, etc. The treating of legume seeds with the proper strain of rhizobia is a
routine agricultural practice. (The Nitragin Company, that supplied one of the photos above specializes in producing rhizobial
strains appropriate to each leguminous crop.)
How did two such organisms ever work out such an intimate and complex living relationship? Assuming that the ancestors of the
rhizobia could carry out the entire process by themselves - as many other soil bacteria still do - they must have gained some real
advantage from evolving to share the duties with the legume. Perhaps the environment provided by their host, e.g., lots of food and
just the right amount of oxygen, enabled the rhizobia to do the job more efficiently than before.

This page titled 17.2C: Symbiotic Nitrogen Fixation is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

17.2C.3 https://bio.libretexts.org/@go/page/5822
17.2D: Soil
Soil is the entry point for most materials into terrestrial food webs. Through their roots, plants absorb water and minerals (e.g.,
nitrates, phosphates, potassium, copper, zinc). With these, they use photosynthesis to convert carbon dioxide (taken in through their
leaves) into carbohydrates, proteins, lipids, nucleic acids and the vitamins on which all heterotrophs depend. Along with
temperature and water, soil is a major determinant of productivity.

Figure 17.2.4.1 Soil profile

Topsoil
The very top layer consists of partially decayed organic debris like leaves. Beneath this is the topsoil. This horizon is usually dark
in color because of humus- partially decayed organic matter - which has been incorporated in it from above. Humus gives the soil
a loose texture that holds water and allows air to diffuse through it. Oxygen is essential to permit cellular respiration in plant roots,
decay organisms, and other inhabitants of the soil.

Subsoil
The subsoil is usually lighter in color that topsoil and often contains an accumulation of inorganic nutrients.

Weathered parent material

This represents the first steps in the chemical breakdown of rock into soil. Often the weathered parent material is underlain by the
parent material itself, although in some places it has been carried from another location by wind, water, or glaciers.

Parent material
The chemical nature of the parent material, whether granite, limestone, or sandstone, for example, has a great influence on the
fertility of the soil derived from it.

The Effect of Water on Soil

The Tropical Rain Forest
The lushness of the jungle biome is somewhat illusory. While productivity is high, the soils themselves tend to be of very poor
quality. Because of the high rainfall, nutrients are quickly washed out of the topsoil unless they are incorporated in the forest plants.
As plant and animal debris falls to the ground, it is quickly decomposed because of the warmth and moisture there. Thus minerals
are found mainly in the forest plants, not in the soil. When the plants are removed and cultivation attempted, the soils quickly lose
fertility. The situation is made worse by the lack of humus (the topsoil may be no thicker than 2 in. [= 5 cm]) and the high iron and
aluminum content of most of these soils. Once exposed to the sun, these lateritic soils soon bake into a bricklike material that
cannot be cultivated.
The most ancient (some might say primitive) way of working these soils is still the best:
clearing a small area of jungle
growing crops for only a year or two, and then
abandoning the area to jungle once again.

This page titled 17.2D: Soil is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

17.2D.1 https://bio.libretexts.org/@go/page/5823
17.2E: Sewage Treatment
The wastes generated by some 60% of the U.S. population are collected in sewer systems and carried along by some 14 billion
gallons (~53 billion liters) of water a day. Of this enormous volume, some 10% is allowed to pass untreated into rivers, streams,
and the ocean. The rest receives some form of treatment to improve the quality of the water (which makes up 99.9% of sewage)
before it is released for reuse.

Biochemical Oxygen Demand (BOD)

The BOD is an important measure of water quality. It is a measure of the amount of oxygen needed (in milligrams per liter or parts
per million) by bacteria and other microorganisms to oxidize the organic matter present in a water sample over a period of 5 days.
The BOD of drinking water should be less than 1. That of raw sewage may run to several hundred. It is also called the "biological"
oxygen demand.

Basic Sewage Treatment

Figure 17.2.5.1 Sewage treatment

Primary Treatment
The simplest, and least effective, method of treatment is to allow the undissolved solids in raw sewage to settle out of suspension
forming sludge. Such primary treatment removes only one-third of the BOD and virtually none of the dissolved minerals.
Attempts to use digested sludge as a fertilizer have been hampered by its frequent contamination by toxic chemicals derived from
industrial wastes.

Secondary Treatment
However, many treatment plants in North America then pass the effluent from primary treatment to secondary treatment. Here the
effluent is brought in contact with oxygen and aerobic microorganisms. They break down much of the organic matter to harmless
substances such as carbon dioxide. Primary and secondary treatment together can remove up to 90% of the BOD. After
chlorination to remove its content of bacteria, the effluent from secondary treatment is returned to the local surface water.

Advanced Waste Treatment

The combination of primary and secondary treatment removes most of the organic matter in sewage and thus lowers the BOD.
However, most of the nitrogen and phosphorus in sewage remains in the effluent from secondary treatment. These inorganic
nutrients can cause eutrophication of surface water receiving the effluent causing blooms of algae. To avoid this, a few
communities add a third stage of treatment called tertiary or advanced waste treatment.
Several techniques are available to remove dissolved salts from sewage effluent, but all are quite expensive.

This page titled 17.2E: Sewage Treatment is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

17.2E.1 https://bio.libretexts.org/@go/page/5824
17.2F: Chlorination and the Law of Unintended Consequences
Chlorination is the adding of chlorine to water in order to kill any dangerous bacteria that might be present. Most municipal water
supplies are chlorinated with chlorine gas, Cl2. Swimming pools, hot tubs, and the like are usually chlorinated with chlorine-
containing substances like
calcium hypochlorite, Ca(HClO)2
sodium hypochlorite, NaHClO (bleach)
trichloro-s-triazinetrione
In every case, the effectiveness of chlorination as a germicide is a result of chlorine's powerful oxidizing action. The widespread
chlorination of municipal water supplies has been one of the public health triumphs of the past century. However, chlorine also
reacts with any organic matter present in the water. Among the products formed are chloroform and a variety of other
trihalomethanes (THMs). Although these substances are normally present only in the range of parts per billion (ppb), they
nevertheless have caused considerable anxiety because several of them are known or suspected carcinogens.
The U.S. Environmental Protection Agency (EPA) sets a limit of <1 ppb of THMs in major water systems and an absolute limit of
100 ppb in any water system.
Assuming:
that laboratory animals respond the same as humans when fed these chemicals (they may not; when methylene chloride, a
THM, is fed to mice, it increases their incidence of cancer, but it is not carcinogenic when fed to rats),
that we know how to scale up from doses in rats and mice to the equivalent dose in humans (there is still controversy about how
best to do this),
that there is no threshold below which doses of THMs are safe and thus
that the concept of collective dose applies,
the EPA estimates that if everyone in the U.S. drank water containing 100 ppb of THMs for their entire lives, their chance of
developing cancer (currently about 25%, representing some 500,000 cancer deaths per year) would increase by some 700 cases per
year.

 Turn off the chlorinators?

Claiming that they were responding to the questions raised by the U.S. EPA over the safety of THMs, officials in Peru began,
in the late 80s, shutting down some of the chlorinators in the capital city, Lima, as well as in other cities and towns.
In January 1991, an outbreak of cholera began in several towns just north of Lima. Within weeks the epidemic of this
dangerous disease (the first epidemic of cholera in the Western hemisphere in a century) spread throughout Peru and eventually
through much of South and Central America. Once introduced into a city, town, or village, the disease spread rapidly through
contaminated, but now unchlorinated, water supplies.
By Dec. 31, 1992 — 23 months after the epidemic began, a total of 731,312 cases had been recorded with 6,323 deaths. Worst
hit was Peru itself. Barely 10 months into the epidemic (Nov. 13, 1991), 2,720 of its people had died of cholera. With a
population of 22 million, that works out to 140 deaths per million people. Even taking the EPA's gloomiest prediction, a
lifetime of drinking water containing 100 ppb of THMs would increase the rate of cancer deaths each year in Peru by less than
3 deaths per million.

What's to be done?
After the appalling devastation caused in Central and South America by misguided risk analysis, one might have hoped that the
choices would be clear.
Certainly don't suddenly stop disinfecting municipal water supplies!
Continue to explore alternatives to chlorination.
For example, many water systems in France and some in the U.S. use ozone as the disinfectant. However, this strong
oxidant also interacts with organic matter to produce undesirable contaminants.
Adding ammonia (NH3) as well as chlorine to water produces chloramine, which is an effective disinfectant but has the
disadvantage of producing carcinogenic nitrosamines and leaching lead from ancient water pipes.

17.2F.1 https://bio.libretexts.org/@go/page/5825
 Irradiation with ultraviolet light is least likely to produce unwanted contaminants.
Whatever method(s) used, treat the water to reduce the amount of organic matter in it.
Keep a cool head and try to evaluate the size of the risks involved before taking action.

This page titled 17.2F: Chlorination and the Law of Unintended Consequences is shared under a CC BY 3.0 license and was authored, remixed,
and/or curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history
is available upon request.

17.2F.2 https://bio.libretexts.org/@go/page/5825
17.2G: Air Pollution
Human activities add a number of ingredients to the air:
particles. In industrial areas and where there is heavy vehicular traffic, these contain carbon and hydrocarbons from the
incomplete combustion of fuels. The hydrocarbons include a variety of polycyclic aromatic hydrocarbons (PAHs) that have
been shown to cause mutations.
Inhaled particles smaller than 2.5 µm ("PM2.5") are taken deep into the lungs and may be deposited there. Chronic exposure to
these small particles has been linked to
reduced lung development and function in adolescents;
an increased risk of asthma;
increases in the incidence of heart disease and lung cancer later in life;
a significant increase in the frequency of germline mutations in the sperm of exposed mice.
The U.S. Environmental Protection Agency (EPA) has established an air quality standard of an annual average of no more than
15 µg of these particles in a cubic meter of air. (Los Angeles averaged 20 µg/m3 in 1999 and 2000.) A survey of 217 counties in
the U.S. showed an association between a reduction of 10 µg PM2.5 with an increase in life expectancy of almost 1 year.
Conversely, studies in Europe showed that an increase of 10 µg PM2.5 was associated with a decrease in life expectancy of
about 1 year.
sulfur dioxide (SO2). These are produced from the oxidation of fuels (e.g., coal and oil) containing sulfur compounds.
carbon monoxide (CO). Also produced from the incomplete combustion of fuels.
various volatile hydrocarbons including PAHs like benzopyrene, a notorious carcinogen). These are produced from the
incomplete combustion of gasoline.
nitrogen oxides ("NOX". These are produced by the chemical union of O2 and N2 in the cylinders of internal combustion
engines.

Photochemical smog
In bright sunlight nitrogen oxides, hydrocarbons and oxygen interact chemically to produce powerful oxidants like ozone (O3) and
peroxyacetyl nitrate (PAN). These secondary pollutants are damaging to plant life and lead to the formation of photochemical
smog. PAN is primarily responsible for the eye irritation so characteristic of this type of smog. The figure outlines representative
reactions leading to the formation of photochemical smog. Radicals are atoms or molecules with unpaired electrons. They are very
reactive chemically. The catalytic converter in automobile exhaust systems reduces air pollution by oxidizing hydrocarbons to CO2
and H2O and, to a lesser extent, converting nitrogen oxides to N2 and O2.

Figure 17.2.7.1 Photochemical smog

This page titled 17.2G: Air Pollution is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

17.2G.1 https://bio.libretexts.org/@go/page/5826
17.2H: Acid Rain
Is rain more acid than normal. Natural rain and snow is slightly acidic (pH 5.6) because of the carbon dioxide (CO2) dissolved in it.
But over recent decades, rain in North America and Europe downwind of industrial areas has had a pH close to 4.5 and sometimes
as low as 2.1 (equivalent to lemon juice).

Sulfur dioxide
The evidence is very strong that most of this acidity is caused by sulfur dioxide (SO2) released from the smokestacks of coal-
burning power plants and other industrial sources. The sulfur dioxide is converted into sulfuric acid (H2SO4). This may be carried
to the ground in rain or snow, but often particles containing sulfuric acid settle out of dry air. So the problem of acid rain is really
one of acid deposition in dry weather as well as wet.

Nitrogen oxides
Nitrogen oxides ("NOx"), which are converted into nitric acid, also contribute to acid deposition. Automobile exhaust accounts for
50% or more of the nitrogen oxides in polluted air.

Types of damage
Acid rain has been held responsible for damaging buildings and statues made of limestone, damaging aquatic life in lakes (true),
causing a decline in the vigor of U.S. and European forests (may be partially responsible), and harming human health (doubtful).

Sensitive areas
There is solid evidence that lakes in certain "sensitive" areas of North America and Europe have become more acid in recent
decades. Sensitive areas are downwind of major industrial areas and where the underlying rock is granite rather than limestone. In
North America, the Adirondacks of New York, the mountains of northern New England as well as large areas of southern Quebec
have been particularly hard-hit. Both the plant and animal life in a lake become altered as the pH drops. The productivity of the
lakes, and their content of desirable fish, decline.

The role of smokestacks

Coal burning by heavy industry was going on long before the lakes of northeastern North America began to show signs of damage.
Their acidification seems to have coincided with the trend to build very tall smokestacks - often more than 500 feet (152 m) high.
This was done to reduce local air pollution, but the result has been simply to transfer the problem further downwind.

Polluted air masses can cross political boundaries

Acid rain does not respect political boundaries. The lakes of Norway and Sweden suffer from the air pollution generated by the
industrial areas to their south and southwest. Canadians are distressed by the damage from the air pollution generated by the
industrial heartland of the U.S. The U.S. is not entirely to blame for their problems, however. Sensitive areas in Quebec are also
downwind of the smelters in Sudbury, Ontario, which have the dubious distinction of generating more sulfur dioxide pollution than
any other place in the entire world.

Current trends
Since the early 1980s, emissions of sulfur dioxide have been reduced in both Europe and North America. Even though nitrogen
oxides have not been reduced proportionally, the result has been a reduction in the amount of acid deposition. This seems to have
stopped the acidification of lakes but not yet reversed it. The technology exists to generate electricity from coal with greatly
reduced emissions and as this technology comes into use, that aspect of the problem should improve.

What about forests?

Not enough is yet known to be certain, but my guess is that sulfur dioxide will turn out to have only a supporting role to play and
that the major culprit will turn out to be ozone. Air pollution by ozone, like that by nitrogen oxides, is largely a matter of
automobile exhaust.

17.2H.1 https://bio.libretexts.org/@go/page/5828
This page titled 17.2H: Acid Rain is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

17.2H.2 https://bio.libretexts.org/@go/page/5828
17.2I: Ozone
Ozone is a highly active form of oxygen (O3 rather than O2). Ozone is made when a electric spark passes through air, and this
accounts for the characteristic odor give off by some electrical motors. Ozone presents two quite different biological problems: too
much at low levels of the atmosphere (the troposphere); too little at high altitudes (the stratosphere).

Ozone in the Troposphere

Ozone is produced by the reaction of sunlight, oxygen, and automobile exhaust (which contains hydrocarbons and nitrogen oxides).
Ozone is largely responsible for the discomfort associated with photochemical smog. This form of smog, long familiar to people
in the Los Angeles basin, is now common wherever sunlight and stagnant air occur in urban areas (Mexico City is a dramatic
example with ozone levels that often exceed 100 ppb and sometimes rise above 350 ppb). High levels of ozone during smog build-
up can cause difficulty to people with respiratory ailments like emphysema and asthma. Ozone also damages plants and may be an
important factor in the damage that is occurring to forests in Europe and North America.

Ozone in the Stratosphere

While we often have too much ozone around us, the concentration of ozone high in the stratosphere (which begins about 7 miles
[11 km] up — where airliners cruise) has declined over the past two decades. Satellite monitoring of the stratosphere, which began
in 1978, has revealed a marked decline. The most serious decline occurs over Antarctica in spring (October) when a precipitous
drop in ozone causes an ozone hole. The figure (courtesy of NASA) shows a map of the ozone hole measured over Antarctica on 5
October 1987 by a device carried on the Nimbus 7 satellite. The tips of South America (upper right quadrant ) and Africa (lower
right) are drawn in, as is the outline of Australia and New Zealand (lower left).

Figure 17.2I. 1: Scientists from NASA and NOAA work together to track the ozone layer throughout the year and determine when
the hole reaches its annual maximum extent. This year, unusually strong weather patterns caused warm temperatures in the upper
atmosphere above the South Pole region of Antarctic, which resulted in a small ozone hole. Credits: NASA Goddard/ Katy
Mersmann This video can be downloaded for free at NASA's Scientific Visualization Studio
The Dobson unit is a measure of the number of molecules of ozone in a vertical column of the atmosphere. You can see that the
concentration of ozone decreases in ever-smaller concentric circles with the lowest reading centered over the South Pole. Despite
an anomalous increase in October 2015 (attributed to a volcanic eruption in Chile), the hole has been steadily shrinking over the
last 14 years. This is probably the result of phasing out the manufacture and use of chlorofluorocarbons.

The Ozone Shield

The spreading of this ozone-depleted air may account for the more gradual and more protracted declines that are being seen at
midlatitudes. From 1978-1990, average ozone levels declined 8% over Europe and about 5% over the United States. This is
ominous because ozone shields the earth's surface from much of the ultraviolet radiation reaching the earth from the sun.
Ultraviolet rays can cause skin cancer, cataracts, and may depress the immune system.

17.2I.1 https://bio.libretexts.org/@go/page/5829
 Figure 17.2I. 2: O3_UVB
The graph (from C. R. Roy, et. al., in Nature 347:235, 1990) shows measurements of the intensity of ultraviolet light and the
concentration of ozone on several sunny days in Melbourne, Australia during December 1987 and January 1988. When ozone
levels were low, ultraviolet light was more intense and vice versa. The drop in ozone, which lasted about a month, was probably
caused by ozone-depleted air drifting in from the ozone hole over the South Pole. Most of the ultraviolet light that reaches the earth
is ultraviolet "B" (UV-B), which includes wavelengths from 280 to 320 nm.

Chlorofluorocarbons (CFCs)
Chlorofluorocarbons (CFCs) are synthetic gases in which the hydrogen atoms of methane are replaced by atoms of fluorine and
chlorine (e.g., CHF2Cl, CFCl3, CF2Cl2). These gases are noninflammable, nontoxic, and very stable. They were widely used in
industry as refrigerants (e.g., in refrigerators and air conditioners), solvents, propellants in aerosol cans (now banned in some
countries), and in the manufacture of plastic foams. CFCs escape to the air from all of these uses (e.g., from leaky and discarded
refrigeration units). Their chemical inertness, which makes CFCs so desirable for industry, also makes them a threat to the
atmosphere. Once in the atmosphere, it may take 60–100 years for them to decompose and disappear. In the meantime, they pose a
threat to the ozone shield.
Although some of the recent depletion of ozone in the stratosphere was probably due to natural causes (volcanic eruptions, fewer
sunspots), some is most likely caused by chlorofluorocarbons (CFCs). However, a multi-nation agreement drawn up in 1987 - the
Montreal Protocol - established a schedule for reducing the use of these materials. And, in fact, monitoring shows that the
concentration of CFCs in the stratosphere has been decreasing since the mid-90s.
CFCs have largely been replaced by hydrofluorocarbons (HFCs) in air conditioners and refrigerators. HFCs do not destroy ozone
but are potent greenhouse gases. While the ozone hole over the Antarctic still persists, there are signs of recovery of ozone levels at
mid-latitudes (where we live). Whether this trend continues may depend on the contribution to ozone-depletion by nitrous oxide.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 17.2I: Ozone is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

17.2I.2 https://bio.libretexts.org/@go/page/5829
 SECTION OVERVIEW
17.3: The Growth of Populations
17.3A: The Human Population

17.3B: Principles of Population Growth

This page titled 17.3: The Growth of Populations is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

17.3.1 https://bio.libretexts.org/@go/page/5812
17.3A: The Human Population
The Rate of Natural Increase ( r )
Birth rate (b) − death rate (d) = rate of natural increase (r)
birth rate expressed as number of births per 1000 per year (currently 13 in the U.S.)
death rate expressed as the number of deaths per 1000 per year (currently 8 in the U.S.)
So the rate of natural increase is 5 per thousand (0.005 or 0.5%).
Although the value of r is affected by both birth rate and death rate, the recent history of the human population has been affected
more by declines in death rates than by increases in birth rates.

Figure 12.3.1.1 Birth & death rates in Mexico

The graph shows birth and death rates in Mexico since 1930. The introduction of public health measures, such as better nutrition,
greater access to medical care, improved sanitation, and more widespread immunization has produced a rapid decline in death
rates, but until recently there was no corresponding decline in birth rates. In 2012, r is 1.5%. (Data from the Population Reference
Bureau.) Although death rates declined in all age groups, the reduction among infants and children had — and will continue to
have — the greatest impact on population growth. This is because they will soon be having children of their own. This situation,
resulting in a rapid rate of population growth, is characteristic of many of the poorer regions of the world.

The Demographic Transition

Slowly declining birth rates following an earlier sharp decline in death rates are today characteristic of most of the less-developed
regions of the world. The shift from high birth and death rates to low birth as well as death rates is called the demographic
transition.

Figure 17.3.1.2 Birth & death rates in Sweden

This graph (based on data from the Population Reference Bureau) shows that the demographic transition began much earlier in
Sweden than in Mexico and was, in fact, completed by the end of the nineteenth century. The spike in deaths in the interval
between 1901 and 1926 was caused by the worldwide influenza pandemic of 1918–1919. The birth rate in Sweden is now (2012)
12/1000; the death rate 10/1000, giving a rate of natural increase (r) of 0.2%.

The Story of Sri Lanka

Figure 17.3.1.3 Birth & death rates in Sri Lanka

17.3A.1 https://bio.libretexts.org/@go/page/5830
Prior to World War II, advances in public health has been largely limited to affluent, industrialized countries. But since then,
improvements in public health have been made in many of the poorer countries of the world - always with dramatic effect on death
rates.
In 1945, the death rate in Sri Lanka (then called Ceylon) was 22/1000.
In 1946, a large-scale program of mosquito control - using DDT - was started.
By eliminating its vector, the incidence of malaria dropped sharply.
After 9 years, the death rate dropped to 10/1000, and by 2012 was 6.
But a compensating decline in birth rates has come more slowly (18/1000 in 2012).
So by 2012 the population was increasing at an annual rate of 1.2% (12/1000/year).
At this rate the population would double in 57.5 years.
Let's see why.

Exponential Growth
The prediction that Sri Lanka will double its population in 57.5 years is based on:
the assumption that r will remain unchanged (which is surely false)
the mathematics of exponential growth.
The product of growth grows itself. So the growth of populations is a problem in "compound interest". At the end of each year (or
whatever period you choose to use), the base against which the rate is applied has grown. Whatever figures you pick, as long as r is
positive, a plot of population as time elapses will produce an exponential growth curve like this one.

Figure 17.3.1.4 Exponential growth

The rate of population growth at any instant is given by the equation
dN
= rN (17.3A.1)
dt

where
r is the rate of natural increase in
t — some stated interval of time, and
N is the number of individuals in the population at a given instant.
The algebraic solution of this differential equation is
rt
N = N0 e (17.3A.2)

where
N0 is the starting population
N is the population after
a certain time, t, has elapsed, and
e is the constant 2.71828... (the base of natural logarithms).
Plotting the results gives this exponential growth curve, so-called because it reflects the growth of a number raised to an exponent
(rt).

17.3A.2 https://bio.libretexts.org/@go/page/5830
Doubling Times
When a population has doubled,
N = N0 × 2. (17.3A.3)

Putting this in our exponential growth equation (Equation 17.3A.2)

rt
2 N0 = N0 e (17.3A.4)

ert = 2
rt = ln (natural logarithm) of 2 = 0.69
doubling time,
0.69
t = (17.3A.5)
r

So Sri Lanka with an r of 1.2% (0.012) has a doubling time

0.69
t = = 57.5. (17.3A.6)
0.012

(You can use the same equation to calculate how quickly an investment in, for example, a certificate of deposit will enable you to
double your money.)

The Population of the World

The solid line in this graph shows estimates of the size of the world's population over the last two millennia. The estimates from
1800 to 1991 are based on more accurate data than those before. The dotted line shows what would happen if exponential growth
continued to the year 2100. As you can see, the world's population has been growing exponentially (except during the years of the
black death). How long will it continue to do so? (Since the graph was drawn, the world's population has reached 7.1 billion; that
is, in 2012 we are still on course.) But can it continue indefinitely? Surely not.

Figure 17.3.1.5 World population

Predicting Future Population Size

With a 2012 rate of natural increase in Mexico of 1.5%, its population would be expected to double in 46 years (0.69/0.015 = 46)
from its 116.1 million people now to some 232 million in 2058. Will it? No one knows for certain. What actually happens to
population growth depends on a number of factors. Some of these can be estimated with some confidence, some cannot. Two that
can are:

17.3A.3 https://bio.libretexts.org/@go/page/5830
 the age structure of the population and
the total fertility rate (TFR).

Total Fertility Rate (TFR)

The total fertility rate is the average number of children that each woman will have during her lifetime. The TFR is an average
because, of course, some women will have more, some fewer, and some no children at all. Theoretically, when the TFR = 2, each
pair of parents just replaces itself. Actually it takes a TFR of 2.1 or 2.2 to replace each generation - this number is called the
replacement rate - because some children will die before they grow up to have their own two children. In countries with low life
expectancies, the replacement rate is even higher (2.2–3).

Age Structure of Populations

But even a TFR of 2.1 may not ensure zero population growth (ZPG). If at one period a population has an unusually large
number of children, they will — as they pass through their childbearing years — increase the r of the population even if their TFR
goes no higher than 2.
Most childbearing is done by women between the ages of 15 and 49. So if a population has a large number of young people just
entering their reproductive years, the rate of growth of that population is sure to rise.

Figure 17.3.1.6 France - India population

These pyramids compare the age structure of the populations of France and India in 1984. The relative number (%) of males and
females is shown in 5-year cohorts. Almost 20% of India's population were children — 15 years or less in age — who had yet to
begin reproduction. When the members of a large cohort like this begin reproducing, they add greatly to birth rates. In France, in
contrast, each cohort is about the size of the next until close to the top when old age begins to take its toll. Broad-based pyramids
like India's are characteristic of populations
with high birth rates
low life expectancies (where many people die before reaching old age)
advances in public health have recently reduced infant and childhood mortality
The age structure of a population also reflects the recent pattern of mortality. In countries where injuries, starvation, and disease,
etc. take a heavy toll throughout life, a plot of the age cohorts produces a broad based pyramid like that of India. In France (and
other countries in western Europe) almost everyone survives until old age, and a plot of the age cohorts is scarcely a pyramid at all.
So even if the TFRs were the same in both countries (they are not - in India it is 2.5, in France, 2.0), India is in for more years of
rapid population growth, France is not.

The U.S. Baby Boom

The TFR in the United States declined from more than 4 late in the nineteenth century to less than replacement in the early 1930s.
However, when the small numbers of children born in the depression years reached adulthood, they went on a childbearing spree
that produced the baby-boom generation. In 1957 more children were born in the United States than ever before (or since). These
population pyramids show the baby-boom generation in 1970 and again in 1985 (green ovals).

17.3A.4 https://bio.libretexts.org/@go/page/5830
 Figure 17.3.1.7 U. S Baby boom
Profound changes (e.g. enrollments in schools and colleges) have occurred — and continue to occur — in U.S. society as this bulge
passes into ever-older age brackets. The baby boomers seem not to be headed for the high TFRs of their parents. They are marrying
later and having smaller families than their parents. So it looks as though the TFR for the baby-boom generation will not exceed
replacement rate. But this is not the same as zero population growth. Even with the current TFR of 1.9, this large cohort of people
will keep the U.S. population growing during their reproductive years (current value for r = 0.5%).

Looking Ahead
Exponential growth cannot continue indefinitely. If the current world value for r (1.2%) remains unchanged, the world population
would grow from its current 7.1 billion to 9.6 billion over the next 38 years (2050).
Could the earth's resources sustain such a population?
If not, how large a human population can live decently on this planet?
Some demographers (students of population) say we have already exceeded the number. Others say the earth can hold billions
more.

Figure 17.3.1.8 Total fertility rates

Whatever the case, there are grounds for some optimism about future population growth.
The world value for r peaked around 1990 and has declined since. This is a reflection of the decline in total fertility rates (TFRs) in
undeveloped countries, presumably as the various factors involved in the demographic transition take hold, e.g.,
improved standard of living

17.3A.5 https://bio.libretexts.org/@go/page/5830
 increased confidence that your children will survive to maturity
improved status of women
increased use of birth control measures
The projection of future TFRs in the upper graph (from the Population Reference Bureau) predicts that the less developed countries
of the world will reach replacement fertility around the year 2020. In fact, they will probably reach it sooner because by 2012 the
world TFR has dropped to 2.4. Even so, will the world reach zero population growth (ZPG) then?
The right graph (based on data from the UN Long-Range World Population Projections, 1991) gives 5 estimates of the growth of
the world population from now until 2150, assuming that TFRs decline from the 1991 value of 3.4 to the values shown.
A value of 2.06 will produce a stable population of about 11.5 billion.
A value 5% below that (1.96) will cause the population to drop back to close to 6.1 billion while
a value of only 5% above (2.17) would produce a population of over 20 billion and still rising.

A consensus?
The several agencies that try to predict future population seem to be moving closer to a consensus that the world population will
continue to grow until after the middle of this century reaching a peak of some 9.6 billion (up from the current 7.1 billion) and then
perhaps declining in the waning years of this century.

This page titled 17.3A: The Human Population is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

17.3A.6 https://bio.libretexts.org/@go/page/5830
17.3B: Principles of Population Growth
Density-Independent Checks on Population Growth
The vagaries of the physical environment, for example drought, freezes, hurricane, floods, and forest fires are often check
population growth. Not only may they limit population growth but they often drive existing populations well below their previous
level. (And also make it unlikely that many animals will survive long enough to show signs of aging.)
These factors are described as density-independent because they exert their effect irrespective of the size of the population when
the catastrophe struck.

Fig.17.3.2.1 Population Density

This graph (from P. T. Boag and P.R. Grant in Science, 214:82, 1981) shows the decline in the population of one of Darwin's
finches (Geospiza fortis) on Daphne Major, a tiny (100 acres = 40 hectares) member of the Galapagos Islands. The decline (from
1400 to 200 individuals) occurred because of a severe drought that reduced the quantity of seeds on which this species feeds. The
drought ended in 1978, but even with ample food once again available the finch population recovered only slowly.
Catastrophic declines are particularly risky for populations living on islands. The smaller the island, the smaller the population of
each species on it, and the greater the risk that a catastrophe will so decimate the population that it becomes extinct. This appears to
be one reason for the clear relationship between size of island and the number of different species it contains.
The graph (redrawn from R. H. MacArthur and E. O. Wilson, The Theory of Island Biogeography, Princeton University Press)
shows the number of species of reptiles and amphibians on various islands in the West Indies. In general, if one island has 10 times
the area of another, it will contain approximately twice the number of species.
The same principle applies to many habitats. In a sense, most habitats are islands. A series of ponds, a range of mountain tops,
scattered groves of citrus trees, even individual trees within a grove, all are made up of patches of habitat separated by barriers to
the free migration of their inhabitants.
This has practical as well as theoretical importance. As the human population grows, jungles are cleared for agriculture, farms are
paved for shopping centers, rivers are dammed for hydroelectric power and irrigation, etc. Although wildlife sanctuaries are being
established, they must be made large enough so that they can support populations large enough to survive density-independent
checks when they strike.

 An example: Lake Guri

In 1986, the closing of a dam in Venezuela flooded over a thousand square miles (>2,500 km2) turning hundreds of hilltops
into islands. These ranged in size from less than 1 hectare (2.5 acres) to more than 150 hectares (370 acres).
Within 8 years:

17.3B.1 https://bio.libretexts.org/@go/page/5831
 The tiniest islands (<1 hectare) lost 75% of the species that had lived there.
The larger the island, the fewer species it lost.
But all the islands - even the largest - lost their top predators; that is carnivores like pumas, jaguars (image), and eagles at
the ends of food chains.
Those animal species that did remain - mostly herbivores and small carnivores - greatly increased their populations because
of
a reduction in competition for resources
no longer being eaten by predators
The intense grazing by the increased herbivore populations is degrading the variety of plant life on the smaller islands.

Density-Dependent Checks on Population Growth

Intra specific Competition
Intraspecific competition is competition between members of the same species.
In the summer of 1980, much of southern New England was struck by an infestation of the gypsy moth (Porthetria dispar). As the
summer wore on,
the larvae (caterpillars) pupated
the hatched adults mated
the females laid masses of eggs (each mass containing several hundred eggs) on virtually every tree in the region
In early May of 1981, the young caterpillars that hatched from these eggs began feeding and molting.
The results were dramatic:
In 72 hours, a 50-ft beech tree or a 25-ft white pine tree would be completely defoliated.
Large patches of forest began to take on a winter appearance with their skeletons of bare branches.
In fact the infestation was so heavy that many trees were completely defoliated before the caterpillars could complete their
larval development.
The result: a massive die-off of the animals; very few succeeded in completing metamorphosis.
Here, then, was a dramatic example of how competition among members of one species for a finite resource - in this case, food -
caused a sharp drop in population.

Figure 17.3.2.2 Population crash

The effect was clearly density-dependent. The lower population densities of the previous summer had permitted most of the
animals to complete their life cycle. The graph shows a similar population crash; in this case of reindeer on two islands in the
Bering Sea. Why the population on St. Paul Island went through so much more severe a boom-and-bust cycle than that on St.
George Island is unknown. Many rodent populations (e.g., lemmings in the Arctic) go through such boom-and-bust cycles.

Inter specific Competition

All the ecological requirements of a species constitutes its ecological niche. The dominant requirement is usually food, but others,
such as nesting sites and a place in the sun (for plants) may be important as well. When two species share overlapping ecological
niches, they may be forced into competition for the resource(s) of that niche. This interspecific competition is another density-
dependent check on the growth of one or both populations.

17.3B.2 https://bio.libretexts.org/@go/page/5831
 Figure 17.3.2.3 Interspecific competition
Like so many factors in ecology, interspecific competition is more easily studied in the laboratory than in the field. This graph
(based on the work of G. F. Gause) shows the effect of interspecific competition on the population size of two species of paramecia,
Paramecium aurelia and Paramecium caudatum.
When either species was cultured alone — with fresh food added regularly — the population grew exponentially at first and then
leveled off.
However, when the two species were cultured together, P. caudatum proved to be the weaker competitor. After a brief phase of
exponential growth, its population began to decline and ultimately it became extinct. The population of P. aurelia reached a
plateau, but so long as P. caudatum remained, this was below the population density it achieved when grown alone.
The habitat of most natural populations is far more complex than a culture vessel. In a natural habitat, the species at a competitive
advantage in one part of the habitat might be at a disadvantage in another. In addition, the presence of predators and parasites
would limit population growth of the more successful as well as the less successful species. So, in a natural setting, the less
effective competitor is usually not driven to extinction.

Character Displacement: an evolutionary response that lessens interspecific competition

When two closely-related species find themselves occupying the same geographic location (sympatric), their requirements for the
necessities of life are probably so similar that they are forced into intense interspecific competition. This can lead to one of two
possible outcomes.
1. The competition may be so intense that one species becomes eliminated entirely; that is, it is driven to extinction there.
2. Alternatively, the increased selection pressure may lead to character displacement — the evolutionary divergence of a trait
they both use to exploit the resources they both depend on. Such character displacement lessens the competition between them.
Over the past several years, the research teams led by Peter and Rosemary Grant have been able to observe character displacement
as it occurred between two species of Darwin's finches. This is their story.
For many years, G. fortis, the medium ground finch, lived on Daphne Major without its relatives, G. fulginosa, the small
ground finch, and G. magnirostris, the large one.
However, in 1982, G. magnirostris arrived and over the following years grew in population.
These were good years, with plenty of food, and the two species coexisted nicely.
However, a severe drought in 2003–2004, sharply reduced the available food including the large seeds that magnirostris and the
larger-beaked members of the fortis population competed intensely for.
The result was a massive die-off of both species with the larger-beaked members of the fortis population suffering greater
mortality than the smaller-beaked members of the species.
The offspring of the fortis survivors, born in 2005, had beaks that averaged over 5% smaller than the average of the parental
population. (After the drought of 1977, when G. magnirostris was not on the island to compete with fortis, their beak size
increased rather than decreased.)
This study of character displacement is described in the 14 July 2006 issue of Science.

Reproductive Competition
Declining birth rates also lead to reduced population growth.
We know that humans make deliberate family planning choices, but analogous behavior is found in other animals as well.
Fruit flies living under crowded conditions lay fewer eggs.
Laboratory rats in a confined area soon reach a stable population size even though abundant food is available. The main cause is
a sharp rise in infant mortality. Reduced maternal care and even cannibalism take a heavy toll of the newborn.

17.3B.3 https://bio.libretexts.org/@go/page/5831
 The honeybee queen regulates her rate of egg laying to the availability of food: reducing it during periods of poor flowering and
ceasing entirely in the late summer.
An alternative to limiting the number of offspring per pair of parents is to limit the number of parents. Some mammals and birds
achieve this by establishing breeding territories. Each mating pair occupies an area of a size sufficient to supply its needs including
those of its offspring. One or both members defend this territory against intrusion from other members of the same species. This
behavior not only ensures that the resources on which they depend will not be exceeded but may keep the population in check by
preventing breeding among its surplus members.
Social conventions among humans (e.g., attitudes about the proper age of marriage and desirable family size) also have a marked
influence on birth rates. However social conventions - and the birth control techniques that may supplement them — have been
most successful at reducing birth rates among just those people least in need of it. In the poorer countries, early marriage, a desire
for large families, and failure to employ birth control methods reliably are common.

Migration
Migration is often an important density-dependent factor in reducing populations. As the population increases, many of its
members emigrate.

Predation

Figure 17.3.2.4 Population changes

As a population increases, its predators are able to harvest it more easily. These graphs (based on data from Crombie, A. C.,
Journal of Animal Ecology, 16:44, 1947) show the population changes among flour beetles grown in plain flour (left) and in flour
containing pieces of glass tubing.
Each culture was started with four adults of each species. In plain medium, after an initial spurt of both populations, Tribolium
continued to expand its numbers while the Oryzaephilus population declined and was eventually driven to extinction (left). Several
factors were at work, but predation was by far the most important.
Tribolium adults feed voraciously on the eggs and pupae of Oryzaephilus.
But Oryzaephilus adults do not feed so vigorously on Tribolium eggs and do not eat their larvae at all.
Glass tubing provided a refuge for some Oryzaephilus larvae enabling them to complete their life cycle. This reduction in the
intensity of predation permitted the two populations to coexist indefinitely (right).

Parasitism
Parasites are able to pass from host to host more easily as the population density of the host increases. For this reason, epidemics
among humans are particularly severe in cities. In fact, for most of the period since humans began living in cities, city populations
have been maintained only through continual immigration from the countryside. Not until the development of community
sanitation, immunization, and other public health measures did cities avoid periodic sharp drops in population as a result of
epidemics.
The recurrent epidemics of the "black death" in Europe that began in the fourteenth century caused a sharp decline in population. In
just 3 years (1348–1350), at least one-quarter of the population of Europe died from the disease (probably plague). More recently,
the great influenza pandemic of 1918–1919 is thought to have killed over 20 million people worldwide.
The house finch, Carpodacus mexicanus, — native to western North America — is a recent immigrant to the eastern United States
where it is parasitized by a mycoplasma that reduces the lifespan and fecundity of the birds. Data collected by amateur bird
watchers show that the arrival of the disease (in the mid-90s) in areas with a high population of the birds drove their numbers down

17.3B.4 https://bio.libretexts.org/@go/page/5831
more than it did in regions of low finch populations. Whatever the starting value, all infected populations ended up with similar
populations. This is a clear example of the density-dependent effect of parasitism on a population.

Population Cycles
Some populations go through repeated and regular periods of boom followed by bust.

Figure 17.3.2.5 Population fluctuation

This graph shows the 10-year cyclical fluctuations in the populations (measured by counting the hides offered for sale at the
Hudson Bay trading posts in Canada) of the varying hare ("snowshoe rabbit") and its chief predator, the lynx, from 1850 to 1910.
The size of the lynx population was closely dependent on the size of its prey (hare) population. The factors causing the hare
population to go through its boom-and-bust cycles are still debated, but predation by lynxes was probably only one factor.
Recent field studies have provided clearer answers for three other cyclical populations, voles (a small rodent) in Finland, the red
grouse in Scotland, and lemmings (another small rodent) in Greenland.

Voles
The vole population in Finland regularly goes through 3-year cycles of boom-and-bust. When Korpimäki and Norrdahl removed all
their predators (both mammals and birds) from their test areas, the cycles ceased. Here, then, the cycles were driven by the density-
dependent check of predation.

Red grouse
The red grouse population in Scotland goes through cycles of 4–8 years. From peak to trough, the population may decline by a
factor of 1000. These cycles do not appear to be caused by the hunting of this popular game bird.
The birds are parasitized by a nematode, and infected birds have lower fecundity (birth rates down) and higher mortality (death
rates up) than uninfected birds.
P. J. Hudson and his colleagues treated large numbers of birds in several test areas with a drug to prevent or cure an infection. The
populations in the treatment areas ceased to cycle. It was not necessary to treat all the birds; 20% of them seem enough to prevent
epidemics (just as immunization of humans doesn't have to reach 100% to put an end to pathogen transmission).
Here, then, the cycles were driven by the density-dependent check of parasitism.

Lemmings
A 15-year study of the population of lemmings in northeast Greenland was reported by Gilg, O., et al., in Science, 31 October
2003. These workers showed that the lemming population rises and falls with a cycle of 4 years. The population of the shorttail
weasel (aka ermine, stoat), the principal predator of the lemming, does as well but with a 1-year lag behind the lemming
population.
Because of this lag, one might expect that the lemming population would continue to outstrip the weasel population until the
lemmings bumped into the carrying capacity of their environment (e.g., availability of food and nesting sites). But this does not
occur because as the lemming population grows, other predators (e.g., foxes and owls) shift their diet in favor of lemmings.
As the lemming population then begins to decline,
these flexible predators return to their former food sources while
the more "picky" weasels decline in numbers as their sole food source, the lemmings, have.

The Carrying Capacity of the Environment (K)

17.3B.5 https://bio.libretexts.org/@go/page/5831
 Figure 17.3.2.6 Yeast growth
This graph shows the growth of a yeast population in culture. After a period of exponential growth, the size of the population
begins to level off and soon reaches a stable value. This type of growth curve is called sigmoid or S-shaped. If we add fresh culture
medium to the container, exponential growth resumes until a new, higher plateau is reached. Evidently the growth rate (r) declines
as the density of the population approaches a certain limiting value.
When r = 0, dN/dt = 0 and the population ceases to grow. The yeasts have reached zero population growth or ZPG.
The causes:
running out of food
accumulation of ethanol. (When its concentration reaches 12–14%, the yeast die (which explains the maximum alcohol content
of natural alcoholic beverages like wine).
The limiting value of the population that can be supported in a particular environment is called its carrying capacity and is
designated K. When the population is far below K, its growth is exponential, but as the population approaches K, it begins to
encounter ever-stronger "environmental resistance". Let us use the expression
K−N
K
as a "growth realization factor", that is, a factor representing the degree to which the population can actually realize its maximum
possible rate of increase. Introducing this factor into our original (exponential) growth equation, we get

dN = rN K−N
( )
dt K

The equation tells us that

If the size of the population (N) is far below the carrying capacity of the environment (K), the growth realization factor will be
close to 1, and the population will show exponential growth.
But as N begins to approach K, the growth realization factor approaches zero, and the rate of population growth drops to zero:

dN = 0 = "ZPG" (zero population growth)

dt

Figure 17.3.2.7 Logistic curve

Plotting the growth of a population from an initial growth realization factor of 1 to a final factor of 0 produces a curve like this,
called the logistic growth curve or S-shaped curve of growth. Although actual populations are unlikely to follow the theoretical
logistic growth curve exactly, the curve can provide us with valuable guidance in managing populations.
Example 1: The logistic curve tells you that you are unlikely to rid your house of a large rat population by setting rat traps. No
matter how many you put out, the r for rats is so high (perhaps 0.0147 per day) that they will reproduce faster than you can catch
them. What you must do instead is to prevent them from getting food in and around your house. With a sharply-reduced K, their
population will decline.

17.3B.6 https://bio.libretexts.org/@go/page/5831
Example 2: The converse of the pest problem is how to keep endangered species from becoming extinct. But outlawing hunting
will have no appreciable impact if the habitat on which that species depends for its K — pasture or woods or whatever —
disappears under the parking lot of a shopping plaza.
Example 3: Modern intensive fishing methods have repeatedly produced ominous declines in the catch of many species as the
populations have been unable to maintain themselves. The logistic curve provides a goal to managing fisheries: harvest at only such
a rate that the population is maintained at K/2. At this size, the population is able to grow most rapidly. The value K/2 is known as
the maximum sustainable yield.

r -Strategists and K -Strategists

r-strategists
I once plowed up an old field and allowed it to lie fallow. In the first season it grew a large crop of ragweed.
Ragweed is well-adapted to exploiting its environment in a hurry - before competitors can become established. It grows rapidly and
produces a huge number of seeds (after releasing its pollen, the bane of many hay fever sufferers). Because ragweed's approach to
continued survival is through rapid reproduction, i.e., a high value of r, it is called an r-strategist. Other weeds, many insects, and
many rodents are also r-strategists. If fact, if we consider an organism a pest, it is probably an r-strategist.
In general r-strategists share a number of features:
1. They are usually found in disturbed and/or transitory habitats. In the second season of my field, perennial grasses and
wildflowers had produced a dense carpet of mixed vegetation and not a ragweed plant was to be found.
2. They have short life spans. The house mouse, with a maximum life span of 3 years, is an r-strategist.
3. They begin breeding early in life.
4. They usually have short generation times; that is, they have short gestation periods and are soon ready to produce another crop
of young. The housefly can produce 7 generations each year (each of about 120 young).
5. They produce large numbers of offspring. The American oyster, releasing a million eggs in one season, is an r-strategist. Most
of its offspring will die, but the sheer size of its output increases the likelihood that some offspring will disperse to new habitats.
6. They take little care of their offspring, and infant mortality is huge. If we plot a survivorship curve for an r-strategist, it is apt to
take the form of the curve labeled D. Although humans are not r-strategists, the higher birth rate in some countries may well be
a response to their higher rates of infant mortality (curve B).
7. They have efficient means of dispersal to new habitats.
For r-strategists, alleles that enhance any of the traits listed above will be favored by natural selection. Hence, r-strategists are said
to be the product of r-selection.

Figure 17.3.2.8 Survivorship curves

The graph shows 4 representative survivorship curves. The vertical axis gives the fraction of survivors at each age.
Curve A is characteristic of organisms that have low mortality until late in life when aging takes its toll.
Cure B is typical of populations in which such factors as starvation and disease obscure the effects of aging, and infant mortality
is high.
Curve C is a theoretical curve for organisms for which the chance of death is equal at all ages. This might be the case for
organisms that do not age (some fishes) or those that suffer severe random mortality throughout life (e.g., many songbirds). K-
strategists usually have survivorship curves somewhere between A and C.

17.3B.7 https://bio.libretexts.org/@go/page/5831
 Curve D is typical of organisms, oysters for example, that produce huge numbers of offspring accompanied by high rates of
infant mortality. Many r-strategists have such a curve.

K-strategists
When a habitat becomes filled with a diverse collection of creatures competing with one another for the necessities of life, the
advantage shifts to K-strategists. K-strategists have stable populations that are close to K. There is nothing to be gained from a high
r. The species will benefit most by a close adaptation to the conditions of its environment.
Typically, K-strategists share these qualities:
1. They are usually found in stable habitats. Most of the species in a mature forest will be K-strategists.
2. They have long life spans. The elephant and the tortoise are K-strategists.
3. They begin breeding later in life.
4. They usually have long generation times. It takes 9 months to produce a human baby.
5. Most produce small numbers of offspring. Birds are K-strategists, most species producing fewer than a dozen young each year.
6. They take good care of their young. Infant mortality tends to be low. If we plot a survivorship curve for a K-strategist, it usually
lies somewhere between curve A (above), where most of the population dies of old age, and curve C, where all ages are equally
at risk of being struck down by random hazards.
7. K-strategists typically have evolved in such a way that they become increasingly efficient at exploiting an ever-narrower slice of
their environment. Thus it is not surprising that many endangered species are K-strategists.
For K-strategists, alleles that enhance their ability to exploit the resources of their habitat; that is, to increase the carrying capacity,
K, of their environment, will be favored by natural selection. Hence, K-strategists are said to be the product of K-selection.

Population density can cause shifts in strategy

A team at the Santa Cruz campus of the University of California (Sinervo et al., in the 21 August 2001 issue of Nature) studied the
boom-and-bust cycles of the native side-blotched lizard. They found that the lizard population went through 2-year cycles of boom
and bust.
Year 1 = Boom
A low population of adults
living well below the carrying capacity (K) of their environment
produced large numbers of young (an r-strategy)
leading to rapid overcrowding and
Year 2 = Bust
A large population of adults
living close to or above the K of their environment
produced fewer surviving young
leading to a sharp decline in population and
Year 3 = another Boom year, and so on.
They also found that the population is polymorphic containing:
females with orange throats that produced as many as 5 clutches of eggs (averaging 6 eggs per clutch) a season. It takes lots of
food reserves to make eggs and the eggs of these highly-prolific orange-throated females tended to be smaller — and to hatch
into smaller lizards — than those of the
females with yellow throats. These females tend to lay fewer, but larger, eggs, and the young lizards that hatch from them are
larger than those produced by orange-throated mothers.
As they predicted, it turned out that:
Orange-throated lizards are r-strategists. In boom years, they were more successful than the yellow. The population explosion
of young lizards produced by them led to next year's bust.
Yellow-throated lizards are K-strategists. Producing smaller numbers of larger lizards, they were more successful at leaving
surviving offspring to lay the groundwork for the next boom year.

17.3B.8 https://bio.libretexts.org/@go/page/5831
Here, then, intraspecific competition has created a population cycle alternately favoring r-strategists and K-strategists.

This page titled 17.3B: Principles of Population Growth is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

17.3B.9 https://bio.libretexts.org/@go/page/5831
 SECTION OVERVIEW
17.4: Interactions between Species
Topic hierarchy

17.4A: Symbiosis

17.4B: Insecticides

17.4C: Biological Control of Pests

This page titled 17.4: Interactions between Species is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

17.4.1 https://bio.libretexts.org/@go/page/5813
17.4A: Symbiosis
Most of the interactions between species involve food, i.e., competing for the same food supply, eating (predation) and avoiding
being eaten (avoiding predation). These interactions are often brief. There are many cases, however, where two species live in close
association for long periods. Such associations are called symbiotic ("living together"). In symbiosis, at least one member of the
pair benefits from the relationship. The other member may be injured (parasitism), relatively unaffected (commensalism) or may
also benefit (mutualism). (Some people restrict the term symbiosis to only these mutually beneficial interactions, but we shall not.)

Mutualism
Symbiotic relationships in which each species benefits are mutualistic. There are hundreds of examples of mutualism between a
heterotroph and an alga.
Paramecium bursaria is a ciliate that engulfs unicellular green algae into vacuoles within its cell.
The paramecium certainly benefits from the food synthesized by the alga. It can be cultured apart from the alga but then
must be given extra food.
The alga presumably benefits from the carbon dioxide produced by its host as well as the host's ability to transport it to a
spot where there is ample light.
Many other aquatic heterotrophs
sponges
sea anemones
planarians
clams
also harbor algae within their cells.
Mutualistic relations between plants and fungi are very common. The fungus invades and lives in or among the cortex cells of the
secondary roots. The association is called a mycorrhiza. The fungus helps the host plant absorb inorganic nitrogen and phosphorus
from the soil. Some mycorrhizal fungi also secrete antibiotics which may help protect their host from invasion by parasitic fungi
and bacteria. Many mushrooms are the spore-forming bodies of mycorrhizal fungi. The truffle is often found in oak forests because
the fungus that produces it establishes mycorrhiza on oak roots.

Endosymbiosis
Endosymbiosis is a mutualistic relationship between a host and an organism living within its body or cells.
The pea aphid and its endosymbiont
The pea aphid, Acyrthosiphon pisum, is an insect pest that sucks the juices from its host plant. However, plant sap is deficient in
several essential amino acids. The pea aphid thrives nonetheless thanks to specialized cells within its body that contain the gamma
proteobacterium, Buchnera aphidicola, that can live nowhere else. The genome of this obligate intracellular Gram-negative
bacterium encodes a number of enzymes needed to complete the synthesis of the amino acids needed by its host. In return, the
aphid's genome encodes enzymes needed by Buchnera to synthesize its lipopolysaccharide cell wall and has lost genes that might
otherwise repel infection by Gram-negative bacteria.
Symbiotic nitrogen fixation
One of the most important examples of mutualism in the overall economy of the biosphere is the endosymbiotic relationship
between certain nitrogen-fixing bacteria and their legume hosts. A large body of evidence supports the view that intracellular
endosymbiotic relationships gave rise to eukaryotes with their mitochondria and chloroplasts.

 Cleaning Symbiosis

The drawing shows the Nile crocodile opening its mouth to permit the Egyptian plover to feed on any leeches attached to its
gums. Cleaning symbiosis is more common in fish.

17.4A.1 https://bio.libretexts.org/@go/page/5832
 Figure 17.4.1.1 Cleaning symbiosis. Herodotus asserted that the trochilus bird, possibly a sandpiper, was able to enter the
mouth of the Nile crocodile in what would now be called a cleaning symbiosis. Drawing by Henry Scherren, 1906

Commensalism
Commensalism means "at table together". It is used for symbiotic relationships in which one organism consumes the unused food
of another. Some examples:
the remora and the shark. The dorsal fin of the remora (a bony fish) is modified into a sucker with which it forms a temporary
attachment to the shark. When the shark feeds, the remora picks up scraps. The shark makes no attempt to prey on the remora.
Some species of barnacles are found only as commensals on the jaws of whales. And there are other species of barnacles found
only as commensals on those barnacles!
Many of the bacteria living in our large intestine. They feed on food which we cannot digest and do not harm us. And some help
us; that is, the relationship is mutualistic. Animals (e.g., mice) raised under germfree conditions are abnormal in several ways,
e.g.,
they have elevated levels of a subset of NKT cells
reduced levels of regulatory T cells (Treg) - both effects predisposing the animals to
asthma and inflammation of the intestine
So it is now standard practice to deliberately infect them with several species of microorganisms so that the animals develop
normally.

Epiphytes
Epiphytes are plants that live perched on sturdier plants. They do not take any nourishment from their host and simply benefit from
being better exposed to sunlight. Some examples include many orchids and many bromeliads (e.g., "Spanish moss" and other
members of the pineapple family).

Parasitism
A parasite is an organism that lives on or in the body of another organism (the host) from whose tissues it gets its nourishment, and
to whom it does some damage. Animals are parasitized by viruses, bacteria, fungi, protozoans, flatworms (tapeworms and flukes),
nematodes, insects (fleas, lice), and arachnids (mites). Plants are parasitized by viruses, bacteria, fungi, nematodes, and a few other
plants. Parasites damage their host in two major ways:
consuming its tissues, e.g., hookworms
liberating toxins, for example,
Tetanus bacilli secrete tetanus toxin which interferes with synaptic transmission.
Diphtheria bacilli secrete a toxin that inhibits protein synthesis by ribosomes.
The relationship between parasite and host varies along a spectrum that extends from "hit and run" parasites that live in their host
for a brief period and then move on to another with or without killing the first to parasites that establish chronic infections. Both
parasite and host must evolve to ensure the survival of both because if the parasite kills its host before it can move on, it destroys its
own meal ticket

17.4A.2 https://bio.libretexts.org/@go/page/5832
  Rabbits in Australia

In 1859, the European rabbit was introduced into Australia for sport. With no important predator there, it multiplied
explosively. The raising of sheep (another imported species) suffered badly as the rabbits competed with them for forage. This
picture (courtesy of Dunston from Black Star) gives you the idea. Having removed all forage plants, which ordinarily supply
them with water as well as food, the rabbits had to drink from a pool.

Figure 17.4.1.2 Australian rabbits. The mutual evolutionary adaptations of parasite and host may lead to the parasite becoming
less damaging at the same time as the host becomes more resistant.
In 1950, the myxoma virus was brought from Brazil and released. The epidemic that followed killed off millions of rabbits
(perhaps 99.5% of the population). Green grass returned and sheep raising once again became profitable. But the rabbits were
not eliminated. In fact, although small epidemics still occur, the rabbit population has recovered somewhat (although nowhere
near its pre-1950 levels). What happened? Thanks to careful planning, we know.
The rabbits today are more resistant to infection than their predecessors. This can be measured by infecting them with the
original strain that has been maintained in the laboratory.
At the same time, the virus circulating in the wild rabbits has become less virulent. This can be measured by determining
the % mortality of laboratory rabbits when they are infected with the current strain of virus.

Figure 17.4.1.3 Evolutionary adaptations

The graph (based on data of Sir Macfarlane Burnet and D. O. White) shows these mutual evolutionary adaptations over the
first six years after the introduction of the virus.

The "Degeneracy" of Parasites

During the course of adapting to conditions in their host, parasites often lose structures and functions that were essential for their
ancestors (and any free-living relatives). The tapeworm has no eyes, no digestive tract, and only vestiges of nervous, excretory, and
muscular systems. While you may call them degenerate, these losses represent a gain in efficiency and improved specialization.
What good would these structures be anyway in the human intestine? On the other hand, the tapeworm produces hundreds of
proglottids: egg-forming machines that improve the likelihood that the tapeworm will leave descendants that reach another host.
This emphasis on reproduction is also seen in
Rafflesia, a parasitic angiosperm found in Malaysia. It has no roots, stems, or leaves, although it does have tubes which
penetrate the tissues of its host. But it has a huge flower (~3 feet or 1 meter in diameter).
Sacculina, a barnacle that parasites crabs. The adult consists of little more than a sac (hence the name) containing reproductive
organs. Not until its larvae were discovered could it even be determined that Sacculina was a crustacean.

17.4A.3 https://bio.libretexts.org/@go/page/5832
  Mycobacterium leprae: pseudogenes
M. leprae causes leprosy (Hansen's disease). It is an intracellular parasite, taking up residence in Schwann cells where, in due
course, it triggers an autoimmune attack on them that leads to their destruction. The resulting loss of sensation makes it
difficult to avoid injury to the extremities. M. leprae is a mycobacterium and a close relative of M. tuberculosis, the cause of
TB.
M. leprae infection also occurs naturally in the wild armadillos living in a band of southern states extending from Alabama
through Texas. A survey of 39 human leprosy patients in that region revealed 25 of them infected with the identical strain
found in the local armadillos. Although it was the first bacterium to be identified as a cause of human disease (in 1873), no
bacteriologist has ever succeeded in cultivating it in vitro. It can, however, be propagated (slowly) in the nine-banded
armadillo, and this has provided enough material to sequence its entire genome.
Its sequence, which was published in the 22 February 2001 issue of Nature (Cole, S. T. et al.) — when compared to that of M.
tuberculosis — provides a vivid demonstration of degeneracy at the level of the genes. Although its genome is only about 25%
smaller than that of M. tuberculosis, it has only 40% of the genes of its cousin. Many of the missing genes are still detectible,
but they are now pseudogenes — genes that have mutated so that they can no longer be expressed in a protein product.

M. tuberculosis M. leprae

Size of genome (bp) 4,411,532 3,268,203

Protein-coding genes 3,959 1,604

citrate synthase genes (for citric acid cycle) 3 1

pyruvate dehydrogenase genes (for citric

6 2
acid cycle)

lactate dehydrogenase genes (cellular

2 1
respiration)

phosphofructokinase genes (glycolysis) 2 1

M. leprae is not an exception. The many bacterial genomes that have now been sequenced show that bacteria that are obligate
intracellular parasites express far fewer proteins than bacteria that can live on culture medium.

A collection of links to examples of parasites

Viruses
Retroviruses, incl HIV-1, the cause of AIDS
Influenza
an assortment of others
Bacteria, the agents of
tetanus, botulism, and anthrax
typhoid, cholera, and plague
staphylococcal and streptococcal infections
gonorrhea
tuberculosis, leprosy, and diphtheria
syphilis and Lyme disease
typhus fever and Rocky Mountain spotted fever
Protists
Plasmodium (agents of malaria)
Trypanosomes
Invertebrates
Tapeworms
Blood flukes
Games Parasites Play (some interesting interactions between host and parasite).

17.4A.4 https://bio.libretexts.org/@go/page/5832
The Evolution of Symbiosis
It seems plausible that what begins as a parasitic relationship might over the course of time evolve into a mutualistic one as the two
organisms evolve to minimize the damage to the host.
And there is some evidence for this. In 1966, K. W. Jeon discovered a culture of amoebas that had become infected with bacteria
(60,00 to 150,000 per cell). The infection slowed their rate of growth and made them much more fragile. But five years later, the
amoebas still were infected but now no ill effects could be seen. Most interesting for our question, the amoebas — or at least their
nuclei — had become dependent on the bacteria.
When the nucleus was removed from an infected amoeba and replaced with one from a uninfected strain, the combination
worked fine.
But when the nucleus from an uninfected cell was replaced with one from an infected cell, the combination usually failed to
survive.
Evidently, after 5 years, the nuclei had become dependent on a bacterial function (an enzyme produced by the bacteria but no
longer by the host). What started as parasitism had evolved into mutualism (the bacteria could not be grown outside their host). But
it doesn't always work like that. There are other examples where a mutualistic relationship seems to have evolved into a
commensalistic or even parasitic one. Some parasitic fungi seem to have evolved from ancestors living in the mutualistic
partnership of a lichen.
Some of the bacteria living in our large intestine supply us with vitamin K, thus evolving from commensalism to mutualism.
Mutually beneficial symbiotic relationships can lead to "degeneracy" also. Some marine annelid worms have completely lost the
digestive tract of their relatives (like the common earthworm). One species gets its nourishment from a large population of at least
5 different species of bacteria living underneath its outer skin. The most abundant of these are chemoautotrophs (but these
bacteria are gamma- and delta- proteobacteria not beta-proteobacteria) that manufacture food from carbon dioxide using the energy
provided by oxidizing inorganic substances (H2S, H2) in the sediments in which the worm lives.
The nature of a symbiotic relationship can also change as circumstances change. Some fungi, bacteria, and protozoans that live
harmlessly in most of us can cause opportunistic infections — that is become parasitic — in immunodeficient people, e.g., those
with AIDS.

This page titled 17.4A: Symbiosis is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

17.4A.5 https://bio.libretexts.org/@go/page/5832
17.4B: Insecticides
Inorganics
Inorganic compounds of arsenic, such as lead arsenate, have long been used against insect pests. However, these materials are
highly toxic to nontarget organisms and persist in the environment. (Years after apple growers stopped using lead arsenate, high
concentrations of lead can still be found in orchard soils.)

Botanicals
These are organic molecules (or mixtures) extracted from plants. Popular examples:
pyrethrins
rotenone
nicotine
azadirachtin. This extract from the neem tree affects insect growth and is discussed further under growth regulators.
Features:
very toxic to insects
relatively harmless to other organisms (except fish!)
decompose readily so residues do not accumulate on crops or in the soil
expensive, but you can get
more bang for the buck by adding a synergist like piperonyl butoxide. Synergists have little toxicity themselves but enhance
the effectiveness of the insecticide with which they are mixed.

Pyrethroids
Pyrethrins break down so rapidly in sunlight that they are of little use outdoors on crops. However, a number of synthetic pyrethrin-
like substances — called pyrethroids — do not have this defect and are effective.
Example:
permethrin (Ambush®, Pounce®)

Bacillus thuringiensis (B.t.)

This bacterium parasitizes many caterpillars. Its spores and/or mixtures of its protein toxins are now being used against a variety of
insect pests. Examples:
Dipel®
Javelin®
Agree®
These are all stomach poisons; that is, they must be ingested to work.

Chlorinated Hydrocarbons
DDT was the first of a long line of insecticides based on hydrocarbons with chlorine atoms
replacing some of the hydrogen atoms. Its chemical name is dichloro, diphenyl, trichloroethane
(see figure).
Some others:
methoxychlor
dieldrin (see figure)
dicofol (Kelthane®)
endosulfan (Thiodan®, Phaser®)
DDT was introduced during World War II and, along with penicillin and the sulfa drugs, was responsible for the fact that this was
the first war in history where trauma killed more people - combatants and noncombatants alike - than infectious disease.
DDT is effective against

17.4B.1 https://bio.libretexts.org/@go/page/5833
 vectors of human diseases such as
malaria and yellow fever (both transmitted by mosquitoes)
plague (transmitted by fleas)
many crop pests
Prior to the introduction of DDT, the number of cases of malaria in Ceylon (now Sri Lanka) was more than a
million a year. By 1963 the disease had been practically eliminated from the island. However, growing concern about the hazards
of DDT led to its abandonment there in the mid-1960s, and soon thereafter malaria became common once again.
DDT was especially effective against malarial mosquitoes because of its persistence and resistance to breakdown in the
environment. One or two sprays a year on the walls of homes kept them free of mosquitoes. But DDT has several serious
drawbacks.

Insecticide resistance
As early as 1946, Swedish workers discovered populations of houseflies resistant to DDT. This was quickly followed by many
other reports of developing resistance. Other chlorinated hydrocarbons (like dieldrin and methoxychlor) were developed as
substitutes, but in time insects developed resistance to these as well.

Persistence
DDT is stable and fat soluble. These properties cause it to accumulate in fat tissue. People who were heavily exposed to DDT
(during its manufacture or application) often showed concentrations of DDT in their fat 1000 times higher than that in their blood.
Even these high levels were probably of little harm to the workers. In the early stages of exposure, the blood levels of DDT (and its
metabolite DDE) rise rapidly at first and then reach a steady level. From that point on, the body excretes it as fast as it acquires it.

Biomagnification
Although no harmful effects from average exposures to DDT have been seen in humans, DDT and other chlorinated hydrocarbons
have been shown to harm other species, such as fishes, earthworms, and robins. The hazard of DDT to nontarget animals is
particularly acute for those species living at the top of food chains. Carnivores at the ends of long food chains (e.g., ospreys,
pelicans, falcons, and eagles) once suffered serious declines in fecundity and hence in population size because of this. High levels
of chlorinated hydrocarbons interfere with forming eggshells of normal thickness.
Correlation between DDE concentrations in the eggs of Alaskan falcons and hawks and reduction in the thickness of their eggshells
(compared with shells collected prior to 1947). DDE is a metabolite of DDT. Data from T. J. Cade, et. al., Science 172:955, 1971.
Average Concentration Reduction in
Species Location
of DDE in Eggs (ppm) Shell Thickness

Peregrine falcon Alaskan tundra (north slope) 889 -21.7%

Peregrine falcon Central Alaska 673 -16.8%

Peregrine falcon Aleutian Islands 167 -7.5%

Rough-legged hawk Alaskan tundra (north slope) 22.5 -3.3%

Gyrfalcon Seward Peninsular, Alaska 3.88 0

Another group of nontarget victims of DDT (and other pesticides) are insects that prey upon insect pests; that is, the natural
enemies of the pests. Killing these has serious ecological and economic effects. For example, once apple growers began controlling
pests with DDT, they quickly found their orchards being attacked by scale insects and mites. The reason: DDT had killed off their
natural enemies.

Organophosphates
The organophosphates, e.g., parathion (right), are related to the nerve gases developed during World War II.
They react irreversibly with the enzyme acetylcholinesterase, which is responsible for inactivating
acetylcholine (ACh) at neuromuscular junctions and at certain synapses in the central and peripheral nervous
systems.
Some other examples:

17.4B.2 https://bio.libretexts.org/@go/page/5833
 malathion
diazinon
phosmet (Imidan®)
chlorpyrifos (Lorsban®)
Some of the organophosphates are very toxic. Parathion, for example, is 30 times more toxic than DDT. Each year
organophosphates poison thousands of humans throughout the world, causing hundreds of deaths. Medical personnel caring for
poisoning victims are also at risk. They may be seriously poisoned by the excretions of, and even the vapors emanating from, their
patients.
This table gives the LD50 values for some insecticides. In each case, the chemical was fed to laboratory rats. Note that the lower the
LD50, the more toxic the chemical.

Oral LD50 in Rats

Chemical Category
(mg/kg)

Aldicarb ("Temik") Carbamate 1

Carbaryl ("Sevin") Carbamate 307

DDT Chlorinated hydrocarbon 87

Dieldrin Chlorinated hydrocarbon 40

Diflubenzuron ("Dimilin") Chitin inhibitor 10,000

Malathion Organophosphate 885

Methoprene JH mimic 34,600

Methoxychlor Chlorinated hydrocarbon 5,000

Parathion Organophosphate 3

Piperonyl butoxide Synergist 7,500

Pyrethrins Plant extract 200

Rotenone Plant extract 60

Unlike chlorinated hydrocarbons,

Organophosphates break down quickly in the environment, and thus residues on crops are less likely to be a problem.
They are not stored in animal tissue, so biomagnification has not been a problem either.
For these reasons, their use has greatly reduced the hazard to nontarget species like ospreys and eagles (at the price of a much
greater hazard to humans). Development of resistance is just as much a problem as it is with the chlorinated hydrocarbons. The
carbamates were introduced in an attempt to keep ahead.

Carbamates
Carbamate insecticides are also inhibitors of acetylcholinesterase, but their action is reversible.
Some examples:
carbaryl (Sevin®)
aldicarb (Temik®)
methomyl (Lannate®)
Features:
These compounds are rapidly detoxified and excreted so their risk to warm-blooded animals is less than the other agents we
have looked at.
They are degraded rapidly in the environment so persistence is not a problem.
They are, however, a danger to many useful insects, especially honeybees.

17.4B.3 https://bio.libretexts.org/@go/page/5833
Growth Regulators
The members of this diverse group interfere in one way or another with insect development. Although most insect growth
regulators do not affect adults, for many pests, it is the larval stages that are the most destructive.

Chitin Inhibitors
These substances, diflubenzuron (Dimilin®) is an example, interfere with the synthesis of chitin, the material that makes up the
insect exoskeleton. It seems to have very low toxicity for vertebrates, but is harmful to crustaceans as well as insects. Its effect on
fungi, which also synthesize chitin, needs to be studied.

Molting Disruptors
Insects must periodically shed their exoskeleton — called molting — in order to grow. Each molt
is triggered by a steroid hormone called ecdysone.
A few synthetic ecdysone
agonists, e.g.,
tebufenozide (Confirm®)
methoxyfenozide (Intrepid®)
inhibitors, e.g., azadirachtin (Neemix®)
are now used as insecticides.

Juvenile Hormone (JH)

In some insects, the final molt produces an adult that looks pretty much like the earlier larval stages. In others, like moths and
butterflies, the final molt of the larva (caterpillar) produces a pupa. After a period of metamorphosis, the adult moth emerges.
Ecdysone triggers larva-to-larva molts as long as another hormone, called juvenile hormone (JH), is present. In its absence,
ecdysone promotes the pupa-to-adult molt. Thus normal metamorphosis seems to occur when the output of JH diminishes
spontaneously in the mature caterpillar.
When solutions of JH are sprayed on mature caterpillars, or on the foliage upon which
they are feeding, their normal development is upset. This raises the possibility of using
JH as an insecticide (one that might avoid the problem of developing resistance).
As it turns out, JH is too unstable to be practical, but some synthetic JH mimics, e.g.,
methoprene (Altosid®)
pyriproxyfen (Esteem®, Knack®, Distance®)
diofenolan
are now being used.

Precocenes
These are substances, first discovered in plants, that damage the corpora allata thus preventing juvenile hormone (JH) from doing
its normal job. Applied to early larval stages, precocenes induce premature or precocious metamorphosis (like that induced by the
surgical removal of the corpora allata). Not only does precocious metamorphosis cut short the destructive larval phase of the insect,
but the adults are abnormal (besides being small). The females, for example, are sterile (because JH is needed for development of
the ovaries).

Summary
It is often said that the evolution of insecticide resistance requires the introduction of ever more powerful insecticides. But what is
really needed is a new substance that attacks some other chink in the insect's armor. Whether gram for gram the new substance is
more or less toxic to the insect (and whether its LD50 for mammals is lower or higher) is quite a separate issue.

This page titled 17.4B: Insecticides is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

17.4B.4 https://bio.libretexts.org/@go/page/5833
17.4C: Biological Control of Pests
The biological control of pests involves using natural enemies of the pest to control it — instead of chemical agents like
insecticides and herbicides. Not only should this be safer for the environment, but once established - the natural enemies might be
able to sustain their population avoiding the need for future treatments.
Most of the species that we consider pests are plants ("weeds") or animals (especially insects) that have invaded a new habitat
without being accompanied by the natural enemies that kept them in check in their original home. With increasing international
travel and trade, this problem becomes increasingly severe.

The Biological Control of Insects

Cottony Cushion Scale Insect
In 1887, this insect - an import from Australia, was devastating the citrus groves of California. A U.S. entomologist went to
Australia to find a natural enemy and came back with the vedalia beetle, a species of lady beetle. Released in California, the beetle
quickly brought the scale under control.
At least until 1946. In that year the pest made a dramatic comeback. This coincided with the first use of DDT in the groves. DDT
not only killed the target pest insects but the vedalia beetle as well. Only by altering spray procedures and reintroducing the beetle
was the scale insect again controlled.

The Sterile Male Technique

This technique was first applied against the screwworm fly, a serious pest of cattle. The female flies lay their eggs in sores or other
open wounds on the animals. After hatching, the larvae eat the tissues of their host. As they do so, they expose a still larger area to
egg laying, often finally killing the host.
Prior to its eradication from the southeastern United States, the screwworm was causing huge annual livestock losses. The sterile
male technique involves releasing factory-reared and sterilized flies into the natural population. Sterilization is done by exposing
the factory flies to just enough gamma radiation to make them sterile but not enough to reduce their general vigor.
Starting in early 1958, up to 50 million sterilized flies were released each week from aircraft flying over Florida and parts of the
adjoining states. Each time a fertile female in the natural population mated with a sterile male, the female layed sterile eggs. Since
the females mate only once, her reproductive career was at an end. By early 1959, the pest was totally eliminated east of the
Mississippi River. Success depended only on the sterile males. In fact, the presence of sterile females was a drawback (because
they competed with the intended target), but it was difficult to separate the sexes.
The southwestern states presented a harder problem because the fly winters in Mexico and with each new season could move
across the border. Even so, by expanding the program to include Mexico as well, the screwworm fly was finally eliminated from
both countries by 1991.
The sterile male technique has also been used with success against several other insect pests, including
The "medfly", a destructive fruit fly (not Drosophila) in California
The tsetse fly, the vector of African sleeping sickness.

Using Genetic Engineering to Improve the Sterile Male Technique

There are two problems with the sterile male technique
The factory produces both males and females in equal numbers. But if you release the females along with the males, many
males will mate with them rather than with wild females. For this reason, the sexes are now separated - an expensive operation -
and only males released.
Irradiation may harm the males in subtle ways - reducing their breeding effectiveness.
Genetic engineering may solve both these problems.
A group of British entomologists (see Thomas, D. D., et al., in the 31 March 2000 issue of Science) have engineered Drosophila so
that
Only males are produced.
When these mate with normal females, the females give birth only to males (thus ending the population).

17.4C.1 https://bio.libretexts.org/@go/page/5834
 Figure 17.4.3.1 Genetic engineering to improve male sterile techniques

The system works like this:

Transgenic flies are created containing a chromosome with an enhancer (En) for a gene (tet TA) that encodes a transcription
factor (green disk) that binds the response element (tet RE), which is part of the promoter for a gene (Toxin gene) encoding a
protein whose product is lethal to the insect.
Only females produce the transcription factor that binds En.
If the antibiotic tetracycline is given to the insects, it binds to the tet TA transcription factor, producing an allosteric change that
prevents the transcription factor from binding the tetracycline response element (tet RE).
The toxin gene is repressed and viable females are made.
In the absence of tetracycline, the tet TA transcription factor (green disk) turns on the toxin promoter and no females are
produced.
Because the tet TA enhancer (En) responds to a transcription factor made only by females, males are produced whether
tetracycline is present or not.
If this system could be applied to an insect pest (and most seem to produce the same female-specific transcription factor [red oval]),
removing tetracycline from the food of a batch of flies in the factory would produce a new generation containing only males.
Released into the wild, these would pass their transgenic chromosome on to the offspring of all the wild females they mated
with.
The genes are dominant so even though the next generation would be heterozygous, only males would be produced.
Thus the pest population would soon die out.
In 2010, release of male mosquitoes Aedes aegypti, the vector of dengue fever - genetically modified (GM) with a similar system
reduced the resident mosquito population in part of Grand Cayman (Caribbean) by 80%.

Gene Drive
Techniques have now been developed which greatly increase the frequency of any desired gene in a population. So far, the
uncertainties of quickly spreading an engineered gene through an entire wild population has kept the process strictly confined to the
laboratory. The process, called gene drive or the mutagenic chain reaction, is described on a separate page.

Male Confusion
Insect sex attractants have also been enlisted in the fight against harmful insects. Distributing a sex attractant throughout an area
masks the female's own attractant so the sexes fail to get together. This is called "communication disruption" or "male confusion".
In some cotton-growing areas, male confusion with the sex attractant of the pink bollworm reduced the need for conventional
chemical insecticides by 90%. It has been used successfully against pests that attack tomatoes, grapes, and peaches.

Parasites vs Insect Pests

Parasites, as well as predators, have been used to achieve control over destructive insects.
The bacterium Bacillus popilliae is supplied commercially to help control the Japanese beetle by infecting it with "milky
disease".

17.4C.2 https://bio.libretexts.org/@go/page/5834
 Bacillus thuringiensis ("Bt") is sold commercially to aid in controlling a number of harmful insects. In some cases, the
bacterium itself infects the pests and eventually kills them. But in most cases, it is the toxin manufactured by the bacterium
while it is growing in culture that does the job.

The Biological Control of Plants

Prickly-pear Cactus (Opuntia)
Introduced into Australia, this cactus soon spread over millions of hectares of range land driving out forage plants. In 1924, the
cactus moth, Cactoblastis cactorum, was introduced (from Argentina) into Australia. The caterpillars of the moth are voracious
feeders on prickly-pear cactus, and within a few years, the caterpillars had reclaimed the range land without harming a single native
species. However, its introduction into the Caribbean in 1957 did not produce such happy results. By 1989, the cactus moth had
reached Florida, and now threatens 5 species of native cacti there.

Klamath Weed

Figure 17.4.3.2
In 1946 two species of Chrysolina beetles were introduced into California to control the Klamath weed (also known as St.
Johnswort, and the same plant that yields the popular herbal concoction) that was ruining millions of acres of range land in
California and the Pacific Northwest. Before their release, the beetles were carefully tested to make certain that they would not turn
to valuable plants once they had eaten all the Klamath weed they could find.
The beetles succeeded beautifully, restoring about 99% of the endangered range land and earning them a commemorative plaque at
the Agricultural Center Building in Eureka, California. (Photo courtesy of John V. Lenz.)

Rules to Live By
Pick only candidates that have a very narrow target preference; i.e., eat only a sharply-limited range of hosts
Test each candidate carefully to be sure that once it has cleaned up the intended target, it doesn't turn to desirable species.
Don't use bio controls against native species.
Avoid introducing alien species into the environment.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 17.4C: Biological Control of Pests is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

17.4C.3 https://bio.libretexts.org/@go/page/5834
 CHAPTER OVERVIEW
Unit 18: Evolution
18.1: Evolution and Adaptation
18.2: Speciation
18.3: The Evolution of Body Form in Animals
18.4: Recapitulation
18.5: Mutation and Evolution
18.6: The Hardy-Weinberg Equilibrium
18.7: Polymorphisms
18.8: Kin Selection
18.9: The Origin of Life
18.10: Mars
18.11: Endosymbiosis
18.12: Geologic Eras

Thumbnail: A silhouette of human evolution. (CC BY SA 3.0 Unported; Tkgd2007).

This page titled Unit 18: Evolution is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1
18.1: Evolution and Adaptation
In 1859 the English naturalist Charles Darwin published The Origin of Species. The book contained two major arguments: First,
Darwin presented a wealth of evidence of evolution. He said that all living things on earth today are the descendants - with
modifications - of earlier species. Second, he proposed a mechanism - natural selection - to explain how evolution takes place.
Evolution involves two interrelated phenomena: adaptation and speciation. In adaptation, over the course of time, species modify
their phenotypes in ways that permit them to succeed in their environment. In speciation, over the course of time, the number of
species multiplies; that is, a single species can give rise to two or more descendant species. In fact, Darwin maintained that all
species are related; that is, any two species on earth today have shared a common ancestor at some point in their history.

Natural Selection
Living things produce more offspring than the finite resources available to them can support.
Thus living things face a constant struggle for existence.
The individuals in a population vary in their phenotypes.
Some of this variation is inheritable; that is, it is a reflection of variations in genotype.
Those variants best adapted to the conditions of their life are most likely to survive and reproduce themselves ("survival of the
fittest").
To the extent that their adaptations are inheritable, they will be passed on to their offspring.
The forces of natural selection act on phenotypes, but only if there is a change in the genotypes of a population has evolution
occurred.

The Measure of "Fitness"

Fitness is a measure of reproductive success. Those individuals who leave the largest number of mature offspring are the fittest.
This can be achieved in several ways:
Survival (mortality selection)
Mating success (sexual selection)
Family size (fecundity selection)

Survival
Any trait that promotes survival - at least until one's reproductive years are over - increases fitness. Such traits are adaptations.

Sexual Selection
In sexual selection, one sex - usually the female - chooses among the available males. Any inherited trait that improves the mating
success of certain individuals will become more pronounced in succeeding generations. Some examples:
When ready to mate, female three-spined sticklebacks (fish) choose males with many Class II MHC alleles over males with
fewer alleles. Class II alleles encode the proteins that present antigens to the immune system. Presumably, the more of them you
have, the greater the diversity of parasite antigens your immune system can recognize and defend against.The females
distinguish between the males by soluble molecules ("odors") the males release into the water. How these "odors" are controlled
by the MHC alleles is not known.
A culture of Drosophila set up with equal numbers of red-eyed and white-eyed flies of both sexes will, after 25 generations or
so, end up having only red-eyed (the "normal") flies in it. This despite the fact that white-eyed flies are just as healthy and live
just as long as red-eyed flies, i.e., they are equal in terms of survival. But, as it turns out, not only do red-eyed females prefer
red-eyed males, but white-eyed females do also.
In other cases of sexual selection, one phenotype prefers to mate with others of the same phenotype. This is called assortative
mating.

Fecundity Selection
The production of a large number of mature offspring is a measure of fitness. I stress mature because only they can pass these traits
on to another generation. Some ways to do this:
Earlier breeding. If some females become sexually mature earlier than others, their chances of leaving offspring are enhanced.

18.1.1 https://bio.libretexts.org/@go/page/5916
 For some species (e.g., fish, oysters), which provide little or no care for their young, fitness is measured by the number of
fertilized eggs they produce.
For species (such as ourselves) that take care of their young, selection acts to reduce family size (to a point). A large study in
Utah (U.S.A) showed that in the 19th century, families with fewer children had more surviving grandchildren.
All the forces of natural selection outlined above work on individuals. But there is an increasing body of evidence that natural
selection can also act on groups. Natural selection that appears to work counter to the benefit of some individuals while enhancing
the prospects of their relatives is called kin selection. It is discussed on a separate page.

Are Humans Exempt from Natural Selection?

It has been argued that advances in medicine, sanitation, etc. have removed humans from the rigors of natural selection. There is
probably some truth to this, but consider that of all the human eggs that are fertilized, fewer than half will ever reproduce
themselves. The others are eliminated as follows:
Mortality selection
Approximately 30% of pregnancies end by spontaneous abortion of embryos and fetuses or by stillbirth.
Death in infancy and childhood claims another 5% or more.
Sexual selection
Another 20% will survive to adulthood but never marry.
Fecundity selection
Of those that do marry, 10% will have no children.

Continuous Variation
Most traits in a population such as height and body weight vary in a continuous way from one extreme to the other.

Figure 18.1.1 Distribution of trait in population

A plot of the distribution of the trait in a population often produces a bell-shaped curve like this one that shows the distribution of
heights among a group of male secondary-school seniors. Such a distribution could arise from environmental factors - perhaps the
continuous height variation in the boys is simply a result of variation in their diet as they grew up or genetic factors - tall parents
tend to have tall children or - most likely - both.

Heritability
One can sort out the relative contribution of genetic and environmental factors by comparing the range of a trait in the offspring
compared with the average value of that trait in their parents. If the offspring of selected parents occupy the same range as the
entire population, environmental factors are working alone. The trait has a zero heritability. Example: The length of the seeds of a
pure strain of beans may vary over several millimeters. However, if extra-large beans are mated, the new crop shows no shift to a
larger size. So the heritability of length is zero. On the other hand, if the offspring of two extra-large mice are just as large as they
are, genes are probably at work. The trait is said to have a heritability of 1.

18.1.2 https://bio.libretexts.org/@go/page/5916
 Figure 18.1.2 Heritability

The Effects of Selection on Populations

The pressures of natural selection can affect the distribution of phenotypes in a population in several ways.

Figure 18.1.3 Effects of selection on population

Stabilizing Selection
Natural selection often works to weed out individuals at both extremes of a range of phenotypes resulting in the reproductive
success of those near the mean. In such cases, the result is to maintain the status quo. It is not always easy to see why both extremes
should be handicapped; perhaps sexual selection or liability to predation is at work. In any case, stabilizing selection is common. In
humans, for example, the incidence of infant mortality is higher for very heavy as well as for very light babies.

Directional Selection
A population may find itself in circumstances where individuals occupying one extreme in the range of phenotypes are favored
over the others. Since 1973, Peter and Rosemary Grant - aided by a succession of colleagues - have studied Darwin's finches in the
Galapagos Islands. When rainfall, and thus food, are plentiful, the ground finches tend to have a varied diet, e.g., eat seeds of a
range of sizes and show considerable variation in body and beak size (large beaks are better for large seeds but can handle small
seeds as well as small beaks).

Figure 18.1.4 Geo fortis

From 1976 through 1977, a severe drought struck the islands, with virtually no rainfall for over a year. This caused a precipitous
decline in the production of the seeds that are the dietary mainstay of Geospiza fortis, the medium ground finch. The graph (from P.
T. Boag and P. R. Grant in Science 214:82, 1981) shows how the population declined from 1400 to 200 on the island of Daphne
Major, a tiny (10-acre = 4 hectares) member of the Galapagos Islands.
One of the plants to make it through the drought produces seeds in large, tough fruits that are virtually impossible for birds with a
beak smaller than 10.5 mm to eat. Sampling the birds that died as well as those that survived showed that he larger birds were

18.1.3 https://bio.libretexts.org/@go/page/5916
favored over the smaller ones and Those with larger beaks were favored over those with smaller ones.

Beak length (mm) Beak depth (mm)

Dead birds 10.68 9.42

Survivors 11.07 9.96

Here, then was natural selection at work. But did it produce evolution? The answer turned out to be yes. As the population of G.
fortis recovered after the rains returned, the average body size and beak depth of their offspring was greater than before (an
increase of 4–5% for beak depth). The bell-shaped curve had been shifted to the right — directional selection.
More recently, the Grants and colleagues at Harvard Medical School have shown that
beak width and depth in the ground finches are correlated with the timing and intensity of expression of the gene, Bmp4, (that
encodes bone morphogenetic protein-4) in the tissue that will form the upper beak. Bmp4 expression appears earlier in
development and with greater intensity in the large-beaked Geospiza magnirostris (the large ground finch) than in its smaller-
beaked relatives, Geospiza fortis (the medium ground finch) and Geospiza fuliginosa (the small ground finch). See Abzhanov,
A., et al., Science, 3 September 2004.
However, beak length is correlated with the intensity of expression of the gene CaM that encodes the Ca2+-binding protein
calmodulin in the tissue that will form the upper beak. CaM expression is much higher in the embryonic tissue of the cactus
finches (G. scandens and G. conirostris - both with long beaks) than in their short-beaked relatives, the ground finches G. fortis
and G. magnirostris. (See Abzhanov, A., et al., Nature, 3 August 2006.)

Industrial Melanism
Many species of moths in the British Isles began to become darker in color in the 19th century. The best-studied example is the
peppered moth, Biston betularia. The moth gets its name from the scattered dark markings on its wings and body. In 1849, a coal-
black mutant was found near Manchester, England. Within a century, this black form had increased to 90% of the population in this
region. The moth flies at night and rests by day on tree trunks. In areas far from industrial activity, the trunks of trees are encrusted
with lichens. As the photos show, the light form (circled in red) is practically invisible against this background.

Figure 18.1.5 Peppered Moth

In areas where air pollution is severe, the combination of toxic gases and soot has killed the lichens and blackened the trunks.
Against such a background, the light form stands out sharply. The moth is preyed upon by birds that pluck it from its resting place
by day. In polluted woods, the dark form has a much better chance of surviving undetected. When the English geneticist H. B. D.
Kettlewell (who supplied the photos) released moths of both types in the woods, he observed that birds did, indeed, eat a much
higher fraction of the light moths he released than of the dark. Since pollution abatement programs were put in place after World
War II, the light form has been making a comeback in the Liverpool and Manchester areas.

Disruptive Selection
In some circumstances, individuals at both extremes of a range of phenotypes are favored over those in the middle. This is called
disruptive selection.
An example:
The residues ("tailings") of mines often contain such high concentrations of toxic metals (e.g., copper, lead) that most plants are
unable to grow on them. However, some hardy species (e.g. certain grasses) are able to spread from the surrounding

18.1.4 https://bio.libretexts.org/@go/page/5916
uncontaminated soil onto such waste heaps. These plants develop resistance to the toxic metals while their ability to grow on
uncontaminated soil decreases. Because grasses are wind pollinated, breeding between the resistant and nonresistant populations
goes on. But evidently, disruptive selection is at work. Higher death rates of both less resistant plants growing on contaminated soil
and more resistant plants growing on uncontaminated soil leads to increasing divergence of the populations into two
subpopulations with the extreme manifestations of this trait.
The evolutionary significance of disruptive selection lies in the possibility that the gene pool may become split into two distinct
gene pools. This may be a way in which new species are formed. The formation of one or more species from a single precursor
species is called speciation.

This page titled 18.1: Evolution and Adaptation is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

18.1.5 https://bio.libretexts.org/@go/page/5916
18.2: Speciation
One of the best definition os species is that of the evolutionary biologist Ernst Mayr: "A species is an actually or potentially
interbreeding population that does not interbreed with other such populations when there is opportunity to do so." However,
sometimes breeding may take place (as it can between a horse and a donkey) but if so, the offspring are not so fertile and/or well
adapted as the parents (the mule produced is sterile).

Allopatric Speciation: the Role of Isolation in Speciation

The formation of two or more species often (some workers think always!) requires geographical isolation of subpopulations of the
species. Only then can natural selection or perhaps genetic drift produce distinctive gene pools. It is no accident that the various
races (or "subspecies") of animals almost never occupy the same territory. Their distribution is allopatric ("other country").

Figure 18.2.1 Yellowthroat

The seven distinct subspecies or races of the yellowthroat Geothlypis trichas (a warbler) in the continental U.S. would soon merge
into a single homogeneous population if they occupied the same territory and bred with one another.

Darwin's Finches
As a young man of 26, Charles Darwin visited the Galapagos Islands off the coast of Ecuador. Among the animals he studied were
what appeared to be 13 species* of finches found nowhere else on earth.
Some have stout beaks for eating seeds of one size or another (#2, #3, #6).
Others have beaks adapted for eating insects or nectar.
One (#7) has a beak like a woodpecker's. It uses it to drill holes in wood, but lacking the long tongue of a true woodpecker, it
uses a cactus spine held in its beak to dig the insect out.
One (#12) looks more like a warbler than a finch, but its eggs, nest, and courtship behavior is like that of the other finches.

Figure 18.2.2 Darwin's finches

Darwin's finches. The finches numbered 1–7 are ground finches. They seek their food on the ground or in low shrubs. Those
numbered 8–13 are tree finches. They live primarily on insects.

1. Large cactus finch (Geospiza conirostris)

18.2.1 https://bio.libretexts.org/@go/page/5918
2. Large ground finch (Geospiza magnirostris)
3. Medium ground finch (Geospiza fortis)
4. Cactus finch (Geospiza scandens)
5. Sharp-beaked ground finch (Geospiza difficilis)
6. Small ground finch (Geospiza fuliginosa)
7. Woodpecker finch (Cactospiza pallida)
8. Vegetarian tree finch (Platyspiza crassirostris)
9. Medium tree finch (Camarhynchus pauper)
10. Large tree finch (Camarhynchus psittacula)
11. Small tree finch (Camarhynchus parvulus)
12. Warbler finch (Certhidia olivacea)
13. Mangrove finch (Cactospiza heliobates)

(From BSCS, Biological Science: Molecules to Man, Houghton Mifflin Co., 1963)
* Genetic analysis provides evidence that:
There are actually two species of warbler finch — Certhidia olivacea now called the green warbler finch and Certhidia fusca,
the gray warbler finch.
The various populations of Geospiza difficilis found on the different islands belong to one or another of three clades so
genetically distinct that they deserve full species status.
Whether the number is 13 or 17, since Darwin's time, these birds have provided a case study of how a single species reaching the
Galapagos from Central or South America could - over a few million years - give rise to the various species that live there today.
Several factors have been identified that may contribute to speciation.

Ecological opportunity
When the ancestor of Darwin's finches reached the Galapagos, it found no predators (There were no mammals and few reptiles on
the islands.) and few, if any, competitors. There were only a handful of other types of songbirds. In fact, if true warblers or
woodpeckers had been present, their efficiency at exploiting their niches would surely have prevented the evolution of warblerlike
and woodpeckerlike finches.

Geographical Isolation (allopatry)

The proximity of the various islands has permitted enough migration of Darwin's finches between them to enable distinct island
populations to arise. But the distances between the islands is great enough to limit interbreeding between populations on different
islands. This has made possible the formation of distinctive subspecies (= races) on the various islands.
The importance of geographical isolation is illuminated by a single, fourteenth, species of Darwin's finches that lives on Cocos
Island, some 500 miles (800 km) to the northeast of the Galapagos. The first immigrants there must also have found relaxed
selection pressures with few predators or competitors. How different the outcome, though. Where one immigrant species gave rise
to at least 13 on the scattered Galapagos Islands, no such divergence has occurred on the single, isolated Cocos Island.

Evolutionary Change
In isolation, changes in the gene pool can occur through some combination of natural selection, genetic drift, and founder effect.
These factors may produce distinct subpopulations on the different islands. So long as they remain separate (allopatric) we
consider them races or subspecies. In fact, they might not be able to interbreed with other races but so long as we don't know, we
assume that they could.
How much genetic change is needed to create a new species? Perhaps not as much as you might think. For example, changes at one
or just a few gene loci might do the trick. For example, a single mutation altering flower color or petal shape could immediately
prevent cross-pollination between the new and the parental types (a form of prezygotic isolating mechanism).

Reunion
The question of their status - subspecies or true species - is resolved if they ever do come to occupy the same territory again
(become sympatric). If successful interbreeding occurs, the differences will gradually disappear, and a single population will be

18.2.2 https://bio.libretexts.org/@go/page/5918
formed again. Speciation will not have occurred. If, on the other hand, two subspecies reunite but fail to resume breeding,
speciation has occurred and they have become separate species.
An example: The medium tree finch Camarhynchus pauper is found only on Floreana Island. Its close relative, the large tree
finch, Camarhynchus psittacula, is found on all the central islands including Floreana. Were it not for its presence on Floreana,
both forms would be considered subspecies of the same species. Because they do coexist and maintain their separate identity on
Floreana, we know that speciation has occurred.

Isolating Mechanisms
What might keep two subpopulations from interbreeding when reunited geographically? There are several mechanisms.
Prezygotic Isolating Mechanisms act before fertilization occurs. Sexual selection - a failure to elicit mating behavior. On Floreana,
Camarhynchus psittacula has a longer beak than Camarhynchus pauper, and the research teams led by Peter and Rosemary Grant
have demonstrated that beak size is an important criterion by which Darwin's finches choose their mates. Two subpopulations may
occupy different habitats in the same area and thus fail to meet at breeding time. In plants, a shift in the time of flowering can
prevent pollination between the two subpopulations. Structural differences in the sex organs may become an isolating mechanism.
The sperm may fail to reach or fuse with the egg.
Postzygotic Isolating Mechanisms act even if fertilization does occur. Even if a zygote is formed, genetic differences may have
become so great that the resulting hybrids are less viable or less fertile than the parental types. The sterile mule produced by mating
a horse with a donkey is an example. Sterility in the males produced by hybridization is more common than in females. In fact, it is
the most common postzygotic isolating mechanism. When Drosophila melanogaster attempts to mate with its relative Drosophila
simulans, no viable males are even produced. Mutations in a single gene (encoding a component of the nuclear pore complex) are
responsible.

Reinforcement
When two species that have separated in allopatry become reunited, their prezygotic and postzygotic isolating mechanisms may
become more stringent than those between the same species existing apart from each other. This phenomenon is called
reinforcement. It arises from natural selection working to favor individuals that avoid interspecific matings, which would produce
less-fit hybrids, when the two species are first reunited.

Speciation by Hybridization
Hybridization between related angiosperms is sometimes followed by a doubling of the chromosome number. The resulting
polyploids are now fully fertile with each other although unable to breed with either parental type - a new species has been created.
This appears to have been a frequent mechanism of speciation in angiosperms. Even without forming a polyploid, interspecific
hybridization can occasionally lead to a new species of angiosperm. Two species of sunflower, the "common sunflower",
Helianthus annuus, and the "prairie sunflower", H. petiolaris, grow widely over the western half of the United States. They can
interbreed, but only rarely are fertile offspring produced.
However, Rieseberg and colleagues have found evidence that successful hybridization between them has happened naturally in the
past. They have shown that three other species of sunflower (each growing in a habitat too harsh for either parental type) are each
the product of an ancient hybridization between Helianthus annuus and H. petiolaris. Although each of these species has the same
diploid number of chromosomes as the parents (2n = 34), they each have a pattern of chromosome segments that have been
derived, by genetic recombination, from both the parental genomes. They demonstrated this in several ways, notably by
combining RFLP analysis with the polymerase chain reaction (PCR).
They even went on to produce (at a low frequency) annuus x petiolaris hybrids in the greenhouse that mimicked the phenotypes
and genotypes of the natural hybrids. (These monumental studies were described in the 29 August 2003 issue of Science.)
Another example. In Pennsylvania, hybrids between a species of fruit fly (not Drosophila) that feeds on blueberries and another
species (again, not Drosophila) that feeds on snowberries feed on honeysuckle where they neither encounter competition from their
parental species nor have an opportunity to breed with them (no introgression). This study was published in the 28 July 2005 issue
of Nature. So speciation can occur as a result of hybridization between two related species, if the hybrid
receives a genome that enables it to breed with other such hybrids but not breed with either parental species,
can escape to a habitat where it does not have to compete with either parent,

18.2.3 https://bio.libretexts.org/@go/page/5918
 is adapted to live under those new conditions.

Adaptive Radiation
The processes described in this page can occur over and over. In the case of Darwin's finches, they must have been repeated a
number of times forming new species that gradually divided the available habitats between them. From the first arrival have come a
variety of ground-feeding and tree-feeding finches as well as the warblerlike finch and the tool-using woodpeckerlike finch. The
formation of a number of diverse species from a single ancestral one is called an adaptive radiation.

 Speciateion in theHouse mice on the island of Madeira

A report in the 13 January 2000 issue of Nature describes a study of house mouse populations on the island of Madeira off the
Northwest coast of Africa. These workers (Janice Britton-Davidian et al) examined the karyotypes of 143 house mice (Mus
musculus domesticus) from various locations along the coast of this mountainous island.

Figure 18.2.3 Madeira mice

Their findings:
There are 6 distinct populations (shown by different colors)
Each of these has a distinct karyotype, with a diploid number less than the "normal" (2n = 40).
The reduction in chromosome number has occurred through Robertsonian fusions. Mouse chromosomes tend to be
acrocentric; that is, the centromere connects one long and one very short arm. Acrocentric chromosomes are at risk of
translocations that fuse the long arms of two different chromosomes with the loss of the short arms.
The different populations are allopatric; isolated in different valleys leading down to the sea.
The distinct and uniform karyotype found in each population probably arose from genetic drift rather than natural selection.
The 6 different populations are technically described as races because there is no opportunity for them to attempt
interbreeding.
However, they surely meet the definition of true species. While hybrids would form easily (no prezygotic isolating
mechanisms), these would probably be infertile as proper synapsis and segregation of such different chromosomes would
be difficult when the hybrids attempted to form gametes by meiosis.

Sympatric Speciation
Sympatric speciation refers to the formation of two or more descendant species from a single ancestral species all occupying the
same geographic location. Some evolutionary biologists don't believe that it ever occurs. They feel that interbreeding would soon
eliminate any genetic differences that might appear. But there is some compelling (albeit indirect) evidence that sympatric
speciation can occur.

 Speciation in three-spined sticklebacks

The three-spined sticklebacks, freshwater fishes that have been studied by Dolph Schluter (who received his Ph.D. for his work
on Darwin's finches with Peter Grant) and his current colleagues in British Columbia, provide an intriguing example that is
best explained by sympatric speciation.
They have found:
Two different species of three-spined sticklebacks in each of five different lakes.
a large benthic species with a large mouth that feeds on large prey in the littoral zone
a smaller limnetic species with a smaller mouth that feeds on the small plankton in open water.
DNA analysis indicates that each lake was colonized independently, presumably by a marine ancestor, after the last ice age.

18.2.4 https://bio.libretexts.org/@go/page/5918
 DNA analysis also shows that the two species in each lake are more closely related to each other than they are to any of the
species in the other lakes.
Nevertheless, the two species in each lake are reproductively isolated; neither mates with the other.
However, aquarium tests showed that
The benthic species from one lake will spawn with the benthic species from the other lakes and likewise the limnetic
species from the different lakes will spawn with each other.
These benthic and limnetic species even display their mating preferences when presented with sticklebacks from
Japanese lakes; that is, a Canadian benthic prefers a Japanese benthic over its close limnetic cousin from its own lake.
Their conclusion: in each lake, what began as a single population faced such competition for limited resources that
disruptive selection — competition favoring fishes at either extreme of body size and mouth size over those nearer the
mean — coupled with
assortative mating — each size preferred mates like it
favored a divergence into two subpopulations exploiting different food in different parts of the lake.
The fact that this pattern of speciation occurred the same way on three separate occasions suggests strongly that ecological
factors in a sympatric population can cause speciation.

Sympatric speciation driven by ecological factors may also account for the extraordinary diversity of crustaceans living in the
depths of Siberia's Lake Baikal.

How many genes are needed to start down the path to sympatric speciation?
Perhaps not very many. The European corn borer, Ostrinia nubilalis, (which despite its common name is a major pest in the U.S. as
well) exists as two distinct races designated Z and E. Both can be found in the same area; that is, they are sympatric. But in the
field, they practice assortative mating - only breeding with mates of their own race.
The females of both races synthesize and release a pheromone that is a sex attractant for the males. Both races use the same
substance but different isomers of it. Which isomer is produced is under the control of a single enzyme-encoding gene locus. The
ability of the males to respond to one isomer or the other is controlled by 2 loci.

The Problem of Clines

There is another possible way for new species to arise in the absence of geographical barriers. If a population ranges over a large
area and if the individuals in that population can disperse over only a small portion of this range, then gene flow across these great
distances would be reduced. The occurrence of gradual phenotypic (and genotypic) differences in a population across a large
geographical area is called a cline. Successful interbreeding occurs freely at every point along the cline, but individuals at the ends
of the cline may not be able to interbreed. This can be tested in the laboratory.
And, on occasions, it is tested in nature. If a cline bends around so that the ends meet, and the populations reunited at the junction
cannot interbreed, then the definition of separate species has been met. Such species are called ring species and this type of
speciation is called parapatric speciation.
Two examples:

1. The Caribbean slipper spurge Euphorbia tithymaloides.

Genetic analysis shows that this wildflower originated in Central America where Mexico and Guatemala share a common
boundary. From there it spread in two directions
northeast through the Yucatan peninsula and then island-hopped through Jamaica, the Dominican Republic, Puerto Rico and
into the Virgin Islands;
south through Central America, on through Venezuela, and then north through Barbados and the other islands of the Lesser
Antilles finally also reaching the Virgin Islands.
Reunited in the Virgin Islands, the two populations have diverged sufficiently that they retain their distinctive genotypic and
phenotypic traits. Ongoing studies will determine to what degree they may be reproductively isolated.

2. The large-blotched salamander Ensatina eschscholtzii.

18.2.5 https://bio.libretexts.org/@go/page/5918
This animal is found in California where it occurs in a number of different subspecies or races. A single subspecies is found in
Northern California, and it is thought to be the founder of all the others. Over time that original population spread southward in two
directions:
down the Sierra Nevada mountains east of the great central San Joaquin Valley and
down the coast range of mountains west of the valley.
South of the valley, the eastern group has moved west and now meets the western group, closing the ring. Here the two populations
fail to interbreed successfully, maintaining their distinct identities. But each subspecies interbreeds in an unbroken chain up the two
paths their ancestors took.
Ring species present a difficult problem in assigning species designations. It is easy to say that the populations at the ends of the
cline represent separate species, but where did one give rise to the other? At every point along the cline, interbreeding goes on
successfully.
The same problem faces paleontologists examining the gradual phenotypic changes seen in an unbroken line of ever-younger
fossils from what one presumes to be a single line of descent. If one could resurrect the ancestral species (A) and the descendant
species (B) and they could not interbreed, then they meet the definition of separate species. But there was no moment in time when
one could say that A became B. So the clines of today are a model in space of Darwin's descent with modification occurring over
time.
Although clines present a problem for classifiers, they are a beautiful demonstration of Darwin's conviction that the accumulation
of small inherited differences can lead to the formation of new species.

This page titled 18.2: Speciation is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

18.2.6 https://bio.libretexts.org/@go/page/5918
18.3: The Evolution of Body Form in Animals
Advances in genetics - especially the sequencing of entire genomes from a wide variety of animals - has revealed an unexpected
paradox. While the animal kingdom contains an extraordinary diversity of body types, the great structural diversity of animals is
not reflected in their genetic makeup. Throughout the animal kingdom, one finds thousands of orthologous genes; that is, genes that
have similar sequences and encode similar products.

Advances in genetics - especially the sequencing of entire genomes from a wide variety of animals - has revealed an unexpected
paradox. While the animal kingdom contains an extraordinary diversity of body types:
with sizes ranging from the microscopic daphnia (a crustacean) to the great blue whale
with body plans as diverse as those of Drosophila and humans,
the great structural diversity of animals is not reflected in their genetic makeup. Throughout the animal kingdom, one finds
thousands of orthologous genes; that is, genes that have similar sequences and encode similar products.
At the level of the cell, and even of tissues, this perhaps should not be surprising. After all, most types of cells - from whatever
animal - are quite similar in their structure and function. Thus we would expect that their genes that encode ribosomal proteins,
cytochromes, histones, etc., etc. would be similar.
In trying to resolve the paradox that these findings present, it is useful to distinguish between
"housekeeping" genes - genes that encode proteins (e.g. cytochromes) and RNAs (e.g. ribosomal RNAs) that function in all
cells and
"toolkit" genes
genes that control the expression of other genes by encoding transcription factors
genes that encode cell-signaling proteins that signal the cell to turn on (or off) a genetic program.
Housekeeping genes generally
show modest sequence differences from animal to animal. Some of these are neutral in their effect on the gene's function while
others are the result of evolutionary adaptation. Both can be used to trace taxonomic relationships.
have simple control regions, i.e. promoters and enhancers.
are expressed in all types of cells in the body (almost half of our protein-encoding genes are expressed in every cell - liver,
neurons, muscle, etc.).
Toolkit genes generally
show very slight sequence differences between different animal species in their coding regions (exons) while
they have very elaborate control regions with many promoter and enhancer sites each of which has a binding site for one or
another different transcription factors.
The proteins (transcription factors and cell-signaling molecules) of toolkit genes are identical in whatever cells they are expressed
in. However, the function of that protein can vary greatly
in different tissues of the animal - a phenomenon called mosaic pleiotropy
at different times in the embryonic development of the animal - a phenomenon called heterochrony
Even such primitive animals as sponges and cnidarians have hundreds of toolkit genes that are clear orthologs to genes of humans.
Some examples are genes whose products are involved in cell signaling (e.g., Wnt and β-catenin, Hedgehog, Notch, Receptor
Tyrosine Kinases (RTKs), components of JAK/STAT pathways, and Transforming Growth Factor-beta TGF-β receptors).
In fact the sequences of many of these genes from different animal phyla are so similar that they can be interchanged. This
similarity can be tested in animals that can be made transgenic. Some examples:
The mouse gene Pax6 (also known as small eyes [Sey] for the mutant phenotype) can substitute for the mutant eyeless gene in
Drosophila while the human PAX6 gene can restore normal eye development in the mutant small eyes (Sey) mouse.
The mouse homeobox gene HoxB6 can substitute for the Drosophila homeobox gene Antennapedia (Antp) and when introduced
into Drosophila give rise to legs in place of antennae just as mutant Antp genes do.

18.3.1 https://bio.libretexts.org/@go/page/5920
Mosaic Pleiotropy
Pleiotropy is the production by a single gene of more than one effect on the phenotype. Mosaic refers to the patchy distribution of
cells and tissues expressing that phenotype.
An example:
Pitx1 is a
Homeobox gene (similar to bicoid in Drosophila) with orthologs found in all vertebrates.
It contains 3 exons that encode a protein of some 283 amino acids (varying slightly in different species) which is
A transcription factor that regulates the expression of other genes involved in the differentiation and function of
the anterior lobe of the pituitary gland (Pitx1 = "Pituitary homeobox1");
jaw development (mutations are associated with cleft palate in mammals);
development of the thymus and some types of mechanoreceptors;
development of the hind limbs.
Its activity in these regions is controlled by regulatory regions (promoters and/or enhancers) specific to each region (and
presumably turned on by other transcription factors in the cells of those regions).

Figure 18.3.1 Forelimbs

When we consider the dramatically-different activities that a given toolkit gene product can perform in different parts of the same
animal, it is easier to understand how easy it must be for these same genes to alter the structure of the same body part in different
species, e.g., the human arm and the wing of the bat.

Mutations in Regulatory Regions

Not all genes need to be expressed in all cells. In which cells and when a given gene will be expressed is controlled by the
interaction of:
extracellular signals turning on (or off)
transcription factors, which turn on (or off)
particular genes
A mutation that would be lethal in the protein coding region of a gene need not be if it occurs in a control region (e.g. promoters
and/or enhancers) of that gene. In fact, there is increasing evidence that mutations in control regions have played an important part
in evolution. Examples:
Humans have a gene (LCT) encoding lactase; the enzyme that digests lactose (e.g. in milk). In most of the world's people, LCT
is active in young children but is turned off in adults. However, northern Europeans and three different tribes of African
pastoralists, for whom milk remains a part of the adult diet, carry a mutation in the control region of their lactase gene that
permits it to be expressed in adults. The mutation is different in each of the 4 cases — examples of convergent evolution.
There are very few differences in the coding sequences between genes of humans and chimpanzees. However, many of their
shared genes differ in their control regions.
The story of Prx1. Prx1 encodes a transcription factor that is essential for forelimb growth in mammals. When mice have the
enhancer region of their Prx1 replaced with the enhancer region of Prx1 from a bat (whose front limbs are wings), the front
legs of resulting mice are 6% longer than normal. Here, then is a morphological change not driven by a change in the Prx1
protein but by a change in the expression of its gene.
The story of Pitx1.

Figure 18.3.2 Stickleback

18.3.2 https://bio.libretexts.org/@go/page/5920
In a remarkable study of three-spined sticklebacks published in the 15 April 2004 issue of Nature, Michael Shapiro, Melissa
Marks, Catherine Peichel, and their colleagues report that a mutation in a noncoding region of the Pitx1 gene accounts for most of
the difference in the structure of the pelvic bones of the marine stickleback and its close freshwater cousins.
The marine sticklebacks
have prominent spines jutting out in their pelvic region (red arrow) as well as the spines along the back (that give the fish its
name). These spines may help protect them from being eaten by predators. (Drawing courtesy of the Parks Administration in
the Emilia-Romagna region of Italy.)
express the Pitx1 gene in various tissues, including
thymus
mechanoreceptors
the pelvic region
The freshwater sticklebacks
have no or very much smaller spines in their pelvic region
express the identical Pitx1 gene in all the same tissues except those that develop into the pelvic structures
The reason: a deletion in an enhancer of Pitx1 responsible for turning on Pitx1 in the developing pelvic area. (Mice
homozygous for a mutation in this control region have deformed hind limbs.)
Here then is a remarkable demonstration of how a single gene mutation can not only be viable but can lead to a major change in
phenotype - adaptive evolution. (The changes seem not to have produce true speciation as yet. The marine and freshwater forms
can interbreed. In fact, that is how the differences in their hind limbs were found to be primarily due to the expression of Pitx1.)

Heterochrony
What toolkit proteins do is governed not only by what tissue they are being produced in but also by when they are produced - a
phenomenon called heterochrony.
Examples:
The transcription factor decapentaplegic (DPP) plays a wide variety of roles in the development of Drosophila from laying the
foundation for the future central nervous system in the early embryo to the elaboration of wings, legs, antennae, etc. in the
adult.
The formation of vertebrae. As their name implies, a key feature of all vertebrates is their backbone of vertebrae. However, the
number of these can vary greatly. Humans have 33 while snakes can have several hundred. However, the toolkit genes (e.g.,
Wnt, Notch, FGF-β) responsible for forming vertebrae appear to be the same for all. What makes the difference is the timing
(rate) at which pulses of these proteins are produced relative to the rate at which the embryo grows.

The Tc1 Mouse

So the evidence is increasing that what makes the difference between a human and a chimpanzee (or any other pair of animals) is in
large measure
not a matter of their inheritance of different genes and their encoded proteins and RNAs but
their inheritance of mutations in the control regions - promoters and enhancers - that regulate where and when these genes will
be expressed.
A vivid example of this is the work reported by Wilson et al. in the 17 October 2008 issue of Science. Their experimental material
was liver cells (hepatocytes) taken from
normal humans
normal mice
the Tc1 mouse
The Tc1 mouse is more than simply transgenic, it carries in most of its cells a human chromosome #21. This small chromosome is
the one that, when present in a triple dose (trisomy 21), produces Down syndrome in humans. Mice have a similar chromosome
that is designated #16.

18.3.3 https://bio.libretexts.org/@go/page/5920
The question that this remarkable animal could answer: will the genes on human chromosome #21 (105 of them) when present in a
mouse nucleus and surrounded by mouse transcription factors and signaling pathways respond as the mouse #16 does or as #21
does in human liver cells or something quite different from either?
The answer turned out that the #21 responded pretty much as it does in its normal human cellular environment.

One line of evidence

Several transcription factors turn on gene activity in liver cells. As seems to be the case with all transcription factors, the human
and mouse versions are close orthologs (95% identical in sequence). Using ChIP analysis, they found that the mouse transcription
factors bound to sites along the human chromosome much as the human transcription factors do. (Chromosome #21 does not
encode any transcription factors, so all those available in the mouse nucleus were of mouse origin.)

Transcription Factors A
Tissue Chromosome Sites Bound by TFs Gene Expression sec
(TFs)
on
human liver cells #21 human TFs human pattern human pattern d
#21 mouse TFs human pattern human pattern
line
Tc1 liver cells of
#16 mouse TFs mouse pattern mouse pattern evi
de
normal mouse liver cells #16 mouse TFs mouse pattern mouse pattern
nce
:
gene expression
These workers also examined the pattern of gene expression; that is, the production of messenger RNAs, in the various
combinations. They did this using microarrays. The human genes expressed on chromosome #21 by mouse transcription factors in
the Tc1 mouse cells were mostly the same as those turned on by human transcription factors in human cells.

The Bottom Line

All these lines of evidence point to the following:
Throughout the animal kingdom,
Genes encoding "housekeeping" proteins (histones, enzymes, etc., etc.) are remarkably conserved; that is, their products vary
only slightly - certainly not enough to account for the vast range of bodies seen in animals from sea anemones to humans.
Genes encoding "toolkit" proteins (transcription factors, cell signaling molecules) are also highly conserved (even more so).
So the key to the fabulous diversity in the animal kingdom must lie in what evolution has done to the DNA sequences that
control where and when genes are expressed in the developing animal.
So after years of looking for and sequencing open reading frames, the task now will be to analyze the sequence differences - arisen
by mutation and evolution - in the intergenic regions that serve as control regions of those genes. An early result of genome
analysis: during the radiation of the various mammalian orders, enhancers have diversified (evolved) much more rapidly than have
promoters and their associated protein-encoding genes.

This page titled 18.3: The Evolution of Body Form in Animals is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by
John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

18.3.4 https://bio.libretexts.org/@go/page/5920
18.4: Recapitulation
The embryonic development of all vertebrates shows remarkable similarities as you can see from these drawings (supplied by Open
Court Publishing Company). The drawings in the top row are of the embryonic stage called the pharyngula. At this stage ("I")
they all contain a notochord, dorsal hollow nerve cord, a tail extending behind the anus, and a series of paired branchial grooves.

Figure 18.4.1 George Romanes's 1892 copy of Ernst Haeckel's controversial embryo drawings. (Public Domain).
The branchial grooves are matched on the inside by a series of paired gill pouches. In fishes, the pouches and grooves eventually
meet and form the gill slits, which allow water to pass from the pharynx over the gills and out the body. In the other vertebrates
shown here, the grooves and pouches disappear. In humans, the chief trace of their existence is the eustachian tube and auditory
canal which (interrupted only by the eardrum) connect the pharynx with the outside of the head.

Anatomical Recapitulation
The idea that embryonic development repeats that of one's ancestors is called recapitulation. It is often expressed as "ontogeny
recapitulates phylogeny"; that is, embryonic development (ontogeny) repeats phylogeny (the genealogy of the species). This is a
distortion of the truth and implies that early in our embryonic development we go through a fishlike stage. We do not. Rather, we
pass through some (not all) of the embryonic stages that our ancestors passed through. Therefore, we find that the more distantly
related two vertebrates are, the shorter the period during which they pass through similar embryonic stages (fish and human) and
vice versa (fish and salamander).
We should also keep in mind that embryonic development prior to the pharyngula (stage I) may also be very different in the
different groups. For example, while the pharyngulas of the human and the salamander look quite similar, their earlier
development, starting with their fertilized eggs, are very different. The idea that "ontogeny recapitulates phylogeny" was proposed
over a century ago by the biologist Ernst Haeckel. He also made the drawings on which the drawings above are based. Periodically,
people rediscover that in making them, he altered certain details to emphasize his theory. Though they are schematic, the story they
illustrate here has stood the test of time.

Another Example
Fossil evidence suggests that the ancestors of the insects had a pair of legs on each of their body segments. In this, they resembled
today's millipedes (which may represent a second line of descent from these early forms). In any case, during embryonic
development of insects, limb buds appear on the abdomen just as they must have in their multilegged ancestors. But by the time the
larva hatches, only the six legs on the thorax (color) remain. The ones in the head become mouth parts. The ones in the abdomen
disappear. Both these changes appear to be controlled by the expression of HOX genes.

18.4.1 https://bio.libretexts.org/@go/page/5922
 Figure 18.4.2 Limb buds

Biochemical Recapitulation
Fish excrete a large part of their waste nitrogen as ammonia (NH3), while amphibians have the less toxic urea as their nitrogenous
waste. Actually, the fish-like tadpole excretes ammonia until it undergoes metamorphosis into the adult frog. Only then does its
chief nitrogenous waste become urea.

Figure 18.4.3 Biochem recapitulation

As for reptiles and birds, they convert their waste nitrogen compounds into the almost insoluble uric acid. During its development
within the egg, however, the chicken embryo first passes through a stage of ammonia excretion followed by a period in which it
excretes urea before finally turning to uric acid.

This page titled 18.4: Recapitulation is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

18.4.2 https://bio.libretexts.org/@go/page/5922
18.5: Mutation and Evolution
Mutations are the raw materials of evolution. Evolution absolutely depends on mutations because this is the only way that new
alleles and new regulatory regions are created. However, this seems paradoxical because most mutations that we observe are
harmful (e.g., many missense mutations) or, at best, neutral, For example, "silent" mutations encoding the same amino acid. Also,
many of the mutations in the vast amounts of DNA that lie between genes. Morevoer, most mutations in genes affect a single
protein product (or a small set of related proteins produced by alternative splicing of a single gene transcript) while much
evolutionary change involves myriad structural and functional changes in the phenotype.
So how can the small changes in genes caused by mutations, especially single-base substitutions ("point mutations"), lead to the
large changes that distinguish one species from another? These questions have, as yet, only tentative answers.

One Solution: Duplication of Genes and Genomes

Mutations that would be harmful in a single pair of genes can be tolerated if those genes have first been duplicated. Gene
duplication in a diploid organism provides a second pair of genes so that one pair can be safely mutated and tested in various
combinations while the essential functions of the parent pair are kept intact.
Possible benefits:
Over time, one of the duplicates can acquire a new function. This can provide the basis for adaptive evolution.
But even while two paralogous genes are still similar in sequence and function, their existence provides redundancy ("belt and
suspenders"). This may be a major reason why knocking out genes in yeast, "knockout mice", etc. so often has such a mild
effect on the phenotype. The function of the knocked out gene can be taken over by a paralog.
After gene duplication, random loss of these genes at a later time in one group of descendants different from the loss in another
group could provide a barrier (a "post-zygotic isolating mechanism") to their interbreeding. Such a barrier could cause
speciation: the evolution of two different species from a single ancestral species.
Evidence:
Paralogous genes. Genes in one species that have arisen by duplication of an ancestral gene. Example: genes encoding olfactory
receptors.
Duplication of the entire genome. Examples:
Polyploid angiosperms.
Genome analysis of three ascomycetes show that early in the evolution of the budding yeast, Saccharomyces cerevisiae, its
entire genome was duplicated. Each chromosome of the other ascomycetes contains stretches of genes whose orthologs are
distributed over two Saccharomyces cerevisiae chromosomes.
There is also evidence that vertebrate evolution has involved at least two duplications of the entire genome. Example: both
the invertebrate Drosophila and the invertebrate chordate Amphioxus contain a single HOX gene cluster while mice and
humans have four.

A Second Solution: Mutations in Regulatory Regions

Not all genes are expressed in all cells. In which cells and when a given gene will be expressed is controlled by the interaction of
(1) extracellular signals turning on (or off),(2) transcription factors, which turn on (or off), and (3) particular genes. A mutation that
would be lethal in the protein coding region of a gene need not be if it occurs in a control region (e.g. promoters and/or enhancers)
of that gene. In fact, there is increasing evidence that mutations in control regions have played an important part in evolution.
Examples:
Humans have a gene (LCT) encoding lactase; the enzyme that digests lactose (e.g. in milk). In most of the world's people, LCT
is active in young children but is turned off in adults. However, northern Europeans and three different tribes of African
pastoralists, for whom milk remains a part of the adult diet, carry a mutation in the control region of their lactase gene that
permits it to be expressed in adults. The mutation is different in each of the 4 cases examples of convergent evolution.
There are very few differences in the coding sequences between genes of humans and chimpanzees. However, many of their
shared genes differ in their control regions.
The story of Prx1. Prx1 encodes a transcription factor that is essential for forelimb growth in mammals. When mice have the
enhancer region of their Prx1 replaced with the enhancer region of Prx1 from a bat (whose front limbs are wings), the front

18.5.1 https://bio.libretexts.org/@go/page/5924
 legs of resulting mice are 6% longer than normal. Here, then is a morphological change not driven by a change in the Prx1
protein but by a change in the expression of its gene.
The story of Pitx1
The story of Style2.1 in the domestic tomato

A Third Solution?
Another theoretically-possible way by which a point mutation might give rise to a new gene is if the point mutation in a previously
noncoding section of DNA converts a triplet of nucleotides into ATG thus creating a new open reading frame (ORF). It is
increasingly evident that much of noncoding DNA is transcribed into a heterogeneous collection of RNAs. Transcription of DNA
with its newly-acquired ATG codon would produce an RNA molecule with a translation start codon (AUG). Translation of this
RNA would create a protein that most likely would be useless, perhaps even harmful but might, on rare occasions, provide the
starting point for the acquisition of a new useful gene.

Large Changes in Phenotype can come from small changes in Genotype

Selector Genes
The building of an organ requires the coordinated activity of many genes. However, these are often organized in hierarchies so that
"upstream genes" regulate the activity of "downstream genes". The closer you get to the top with a mutation, the greater the
changes affected downstream.
Follow these links to see examples of the influence of "master" (selector) genes on the phenotype.
Embryonic Development: Getting Started (especially the story of bicoid and nanos)
Organizing the Embryo: The Central Nervous System Organizing the Embryo: Segmentation (more on bicoid and nanos)
Embryonic Development: Putting on the finishing touches (especially the discussion of homeobox genes)

 The Story of Pitx1

Pitx1 is homeobox gene (similar to bicoid in Drosophila) with orthologs found in all vertebrates. It contains 3 exons that
encode a protein of some 283 amino acids (varying slightly in different species) which is a transcription factor that regulates
the expression of other genes involved in the differentiation and function of multiple features including:
1. the anterior lobe of the pituitary gland (Pitx1 = "Pituitary homeobox1");
2. jaw development (mutations are associated with cleft palate);
3. development of the thymus and some types of mechanoreceptors;
4. development of the hind limbs.
Its activity in these regions is controlled by regulatory regions (promoters and/or enhancers) specific to each region (and
presumably turned on by other transcription factors in the cells of those regions).
Pitx1 is an essential gene. Mutations in the coding regions are lethal when homozygous (shown in mice). However, mutations
in noncoding regions need not be. All vertebrates have a pelvic girdle with associated bones which make up the pelvic fins of
fishes and the hind legs of the tetrapods. Pitx1 is needed by them all for the proper development of these structures (as well as
the other functions of Pitx1).
In a remarkable study of three-spined sticklebacks published in the 15 April 2004 issue of Nature, Michael Shapiro, Melissa
Marks, Catherine Peichel, and their colleagues report that a mutation in a noncoding region of the Pitx1 gene accounts for most
of the difference in the structure of the pelvic bones of the marine stickleback and its close freshwater cousins.
The marine sticklebacks have prominent spines jutting out in their pelvic region (red arrow) as well as the spines along the
back (that give the fish its name). These spines may help protect them from being eaten by predators. (Drawing courtesy of the
Parks Administration in the Emilia-Romagna region of Italy.) The also express the Pitx1 gene in various tissues, including
thymus, mechanoreceptors, and the pelvic region.

18.5.2 https://bio.libretexts.org/@go/page/5924
 The four species of stickleback that inhabit the Atlantic coast of North America. These species are sympatric between
Newfoundland, Canada and Long Island, New York, United States. Image used iwth permission (CC BY-SA 3.0; Ghegeman).
The freshwater sticklebacks have no — or very much smaller — spines in their pelvic region. They express the identical Pitx1
gene in all the same tissues except those that develop into the pelvic structures. The reason: a mutation in an enhancer
upstream of the Pitx1 exons. The unmutated enhancer turns on Pitx1 in the developing pelvic area. (Mice homozygous for a
mutation in this control region have deformed hind limbs.)
Here then is a remarkable demonstration of how a single gene mutation can not only be viable but can lead to a major change
in phenotype - adaptive evolution. (The changes seem not to have produce true speciation as yet. The marine and freshwater
forms can interbreed. In fact, that is how the differences in their hind limbs were found to be primarily due to the expression of
Pitx1.)
A survey of 21 different populations of sticklebacks - both freshwater and marine - from different regions of North America,
Europe, and Japan has revealed a pattern of consistent genetic differences that distinguish the freshwater from the marine
forms. However, only 17% of the distinguishing mutations were found in exons that alter the amino acid sequence of the
encoded proteins. All the rest were "silent" and most, 41% or more, of these occurred in intergenic regions. These results
further demonstrate the importance of mutations in regulatory regions - promoters and enhancers - in the evolution of adaptive
phenotypes.

This page titled 18.5: Mutation and Evolution is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

18.5.3 https://bio.libretexts.org/@go/page/5924
18.6: The Hardy-Weinberg Equilibrium
If two individuals mate that are heterozygous (e.g., Bb) for a trait, we find that
25% of their offspring are homozygous for the dominant allele (BB)
50% are heterozygous like their parents (Bb)
25% are homozygous for the recessive allele (bb) and thus, unlike their parents, express the recessive phenotype.
This is what Mendel found when he crossed monohybrids. It occurs because meiosis separates the two alleles of each heterozygous
parent so that 50% of the gametes will carry one allele and 50% the other and when the gametes are brought together at random,
each B (or b)-carrying egg will have a 1 in 2 probability of being fertilized by a sperm carrying B (or b). (Left table)

Results of random union of the two gametes produced by two

individuals, each heterozygous for a given trait. As a result of meiosis, Results of random union of the gametes produced by an entire
half the gametes produced by each parent with carry allele B; the other population with a gene pool containing 80% B and 20% b.
half allele b.

0.5 B 0.5 b 0.8 B 0.2 b

0.5 B 0.25 BB 0.25 Bb 0.8 B 0.64 BB 0.16 Bb

0.5 b 0.25 Bb 0.25 bb 0.2 b 0.16 Bb 0.04 bb

However, the frequency of two alleles in an entire population of organisms is unlikely to be exactly the same. Let us take as a
hypothetical case, a population of hamsters in which 80% of all the gametes in the population carry a dominant allele for black coat
(B) and 20% carry the recessive allele for gray coat (b).
Random union of these gametes (right table) will produce a generation:
64% homozygous for BB (0.8 x 0.8 = 0.64)
32% Bb heterozygotes (0.8 x 0.2 x 2 = 0.32)
4% homozygous (bb) for gray coat (0.2 x 0.2 = 0.04)
So 96% of this generation will have black coats; only 4% gray coats.
Will gray coated hamsters eventually disappear? No. Let's see why not.
All the gametes formed by BB hamsters will contain allele B as will one-half the gametes formed by heterozygous (Bb)
hamsters.
So, 80% (0.64 + .5*0.32) of the pool of gametes formed by this generation with contain B.
All the gametes of the gray (bb) hamsters (4%) will contain b but one-half of the gametes of the heterozygous hamsters will as
well.
So 20% (0.04 + .5*0.32) of the gametes will contain b.
So we have duplicated the initial situation exactly. The proportion of allele b in the population has remained the same. The
heterozygous hamsters ensure that each generation will contain 4% gray hamsters. Now let us look at an algebraic analysis of the
same problem using the expansion of the binomial (p+q)2.
2 2 2
(p + q ) =p + 2pq + q (18.6.1)

The total number of genes in a population is its gene pool.

Let p represent the frequency of one gene in the pool and q the frequency of its single allele.
So, p + q = 1
p = the fraction of the population homozygous for p
2

q = the fraction homozygous for q

2

2pq = the fraction of heterozygotes

In our example, p = 0.8, q = 0.2, and thus

2 2 2
(0.8 + 0.2 ) = (0.8 ) + 2(0.8)(0.2) + (0.2 ) = 064 + 0.32 + 0.04 (18.6.2)

18.6.1 https://bio.libretexts.org/@go/page/5926
The algebraic method enables us to work backward as well as forward. In fact, because we chose to make B fully dominant, the
only way that the frequency of B and b in the gene pool could be known is by determining the frequency of the recessive
phenotype (gray) and computing from it the value of q.
q2 = 0.04, so q = 0.2, the frequency of the b allele in the gene pool. Since p + q = 1, p = 0.8 and allele B makes up 80% of the gene
pool. Because B is completely dominant over b, we cannot distinguish the Bb hamsters from the BB ones by their phenotype. But
substituting in the middle term (2pq) of the expansion gives the percentage of heterozygous hamsters. 2pq = (2)(0.8)(0.2) = 0.32
So, recessive genes do not tend to be lost from a population no matter how small their representation.

 Hardy-Weinberg law

So long as certain conditions are met (discussed below), gene frequencies and genotype ratios in a randomly-breeding
population remain constant from generation to generation. This is known as the Hardy-Weinberg law.

The Hardy-Weinberg law is named in honor of the two men who first realized the significance of the binomial expansion to
population genetics and hence to evolution. Evolution involves changes in the gene pool. A population in Hardy-Weinberg
equilibrium shows no change. What the law tells us is that populations are able to maintain a reservoir of variability so that if future
conditions require it, the gene pool can change. If recessive alleles were continually tending to disappear, the population would
soon become homozygous. Under Hardy-Weinberg conditions, genes that have no present selective value will nonetheless be
retained.

When the Hardy-Weinberg Law Fails

To see what forces lead to evolutionary change, we must examine the circumstances in which the Hardy-Weinberg law may fail to
apply. There are five:
1. mutation
2. gene flow
3. genetic drift
4. nonrandom mating
5. natural selection

Mutation
The frequency of gene B and its allele b will not remain in Hardy-Weinberg equilibrium if the rate of mutation of B -> b (or vice
versa) changes. By itself, this type of mutation probably plays only a minor role in evolution; the rates are simply too low.
However, gene (and whole genome) duplication - a form of mutation - probably has played a major role in evolution. In any case,
evolution absolutely depends on mutations because this is the only way that new alleles are created. After being shuffled in various
combinations with the rest of the gene pool, these provide the raw material on which natural selection can act.

Gene Flow
Many species are made up of local populations whose members tend to breed within the group. Each local population can develop
a gene pool distinct from that of other local populations. However, members of one population may breed with occasional
immigrants from an adjacent population of the same species. This can introduce new genes or alter existing gene frequencies in the
residents.
In many plants and some animals, gene flow can occur not only between subpopulations of the same species but also between
different (but still related) species. This is called hybridization. If the hybrids later breed with one of the parental types, new genes
are passed into the gene pool of that parent population. This process is called introgression. It is simply gene flow between species
rather than within them.
Comparison of the genomes of contemporary humans with the genome recovered from Neanderthal remains shows that from 1–3%
of our genes were acquired by introgression following mating between members of the two populations tens of thousands of years
ago.
Whether within a species or between species, gene flow increases the variability of the gene pool.

18.6.2 https://bio.libretexts.org/@go/page/5926
Genetic Drift
As we have seen, interbreeding often is limited to the members of local populations. If the population is small, Hardy-Weinberg
may be violated. Chance alone may eliminate certain members out of proportion to their numbers in the population. In such cases,
the frequency of an allele may begin to drift toward higher or lower values. Ultimately, the allele may represent 100% of the gene
pool or, just as likely, disappear from it.
Drift produces evolutionary change, but there is no guarantee that the new population will be more fit than the original one.
Evolution by drift is aimless, not adaptive.

Nonrandom Mating
One of the cornerstones of the Hardy-Weinberg equilibrium is that mating in the population must be random. If individuals (usually
females) are choosy in their selection of mates, the gene frequencies may become altered. Darwin called this sexual selection.
Nonrandom mating seems to be quite common. Breeding territories, courtship displays, "pecking orders" can all lead to it. In each
case certain individuals do not get to make their proportionate contribution to the next generation.
Assortative mating
Humans seldom mate at random preferring phenotypes like themselves (e.g., size, age, ethnicity). This is called assortative mating.
Marriage between close relatives is a special case of assortative mating. The closer the kinship, the more alleles shared and the
greater the degree of inbreeding. Inbreeding can alter the gene pool. This is because it predisposes to homozygosity. Potentially
harmful recessive alleles — invisible in the parents — become exposed to the forces of natural selection in the children.

Figure 18.6.1: Assortative mating. (Drawing by Koren © 1977 The New Yorker Magazine, Inc.)
It turns out that many species - plants as well as animals - have mechanisms be which they avoid inbreeding. Examples:
Link to discussion of self-incompatibility in plants.
Male mice use olfactory cues to discriminate against close relatives when selecting mates. The preference is learned in infancy -
an example of imprinting. The distinguishing odors are controlled by the MHC alleles of the mice and are detected by the
vomeronasal organ (VNO).

Natural Selection
If individuals having certain genes are better able to produce mature offspring than those without them, the frequency of those
genes will increase. This is simply expressing Darwin's natural selection in terms of alterations in the gene pool. (Darwin knew
nothing of genes.) Natural selection results from differential mortality and/or differential fecundity.
Mortality Selection
Certain genotypes are less successful than others in surviving through to the end of their reproductive period. The evolutionary
impact of mortality selection can be felt anytime from the formation of a new zygote to the end (if there is one) of the organism's
period of fertility. Mortality selection is simply another way of describing Darwin's criteria of fitness: survival.
Fecundity Selection
Certain phenotypes (thus genotypes) may make a disproportionate contribution to the gene pool of the next generation by
producing a disproportionate number of young. Such fecundity selection is another way of describing another criterion of fitness
described by Darwin: family size. In each of these examples of natural selection, certain phenotypes are better able than others to

18.6.3 https://bio.libretexts.org/@go/page/5926
contribute their genes to the next generation. Thus, by Darwin's standards, they are more fit. The outcome is a gradual change in
the gene frequencies in that population.

Calculating the Effect of Natural Selection on Gene Frequencies

The effect of natural selection on gene frequencies can be quantified. Let us assume a population containing
36% homozygous dominants (AA)
48% heterozygotes (Aa) and
16% homozygous recessives (aa)
The gene frequencies in this population are p = 0.6 and q = 0.4. The heterozygotes are just as successful at reproducing
themselves as the homozygous dominants, but the homozygous recessives are only 80% as successful. That is, for every 100 AA
(or Aa) individuals that reproduce successfully only 80 of the aa individuals succeed in doing so. The fitness (w) of the recessive
phenotype is thus 80% or 0.8.
Their relative disadvantage can also be expressed as a selection coefficient, s , where
s = 1 −w (18.6.3)

In this case,
s = 1 − 0.8 = 0.2. (18.6.4)

The change in frequency of the dominant allele (Δp) after one generation is expressed by the equation
2
sp0 q
0
Δp = (18.6.5)
2
1 − sq
0

where p and q are the initial frequencies of the dominant and recessive alleles respectively. Substituting, we get
0 0

2
(0.2)(0.6)(0.4)
Δp = (18.6.6)
2
1 − (0.2)(0.4)

0.019
= (18.6.7)
0.968

= 0.02 (18.6.8)

So, in one generation, the frequency of allele A rises from its initial value of 0.6 to 0.62 and that of allele a declines from 0.4 to
0.38 (q = 1 − p ).
The new equilibrium produces a population of
38.4% homozygous dominants (an increase of 2.4%) (p2 = 0.384)
47.1% heterozygotes (a decline of 0.9%)(2pq = 0.471) and
14.4% homozygous recessives (a decline of 1.6%)(q2 = 0.144)
If the fitness of the homozygous recessives continues unchanged, the calculations can be reiterated for any number of generations.
If you do so, you will find that although the frequency of the recessive genotype declines, the rate at which a is removed from the
gene pool declines; that is, the process becomes less efficient at purging allele a. This is because when present in the heterozygote,
a is protected from the effects of selection.

This page titled 18.6: The Hardy-Weinberg Equilibrium is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John
W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon
request.

18.6.4 https://bio.libretexts.org/@go/page/5926
18.7: Polymorphisms
A polymorphism is a genetic variant that appears in at least 1% of a population. (e.g., the human ABO blood groups, the human Rh
factor, and the human major histocompatibility complex). By setting the cutoff at 1%, it excludes spontaneous mutations that may
have occurred in - and spread through the descendants of - a single family.

Protein Polymorphisms
All the examples above are of the protein products of alleles. These can be identified by serology - that is, using antibodies to
detect the different versions of the protein. (Antibodies caused the clumping of the red blood cells in this test) and electrophoresis -
if amino acid changes in the protein alter its net electrical charge, it will migrate more or less rapidly in an electrical field. Enzymes
are frequently polymorphic. A population may contain two or more variants of an enzyme encoded by a single locus. The variants
differ slightly in their amino acid sequence and often this causes them to migrate differently under electrophoresis. By treating the
gel with the substrate for the enzyme, its presence can be visualized.

Figure 18.7.1 Electrophoresis of green treefog tissues. Courtesy of Susan McAlpine. The 4 alleles can be distinguished by the
speed with which their protein product migrates: Fast (F), moderately fast (E), medium (M), and slow (S)
Electrophoresis of tissue extracts from 15 different green treefrogs (Hyla cinerea) reveals 4 allelic versions of the enzyme
aconitase (one of the enzymes of the citric acid cycle). The results:
Eight frogs (#2, 3, 4, 6, 7, 9, 12, and 14) were homozygous for allele M.
Frog #8 was homozygous for allele E.
Three frogs (#1, 11, 15) are heterozygous for the M and S alleles.
Two (#5, 13) were heterozygous for M and E.
Frog #10 was heterozygous for M and F.
Electrophoretic variants of an enzyme occurring in a population are called allozymes.

Restriction Fragment Length Polymorphisms (RFLPs)

Proteins are gene products and so polymorphic versions are simply reflections of allelic differences in the gene; that is, allelic
differences in DNA. Often these changes create new - or abolish old - sites for restriction enzymes to cut the DNA. Digestion with
the enzyme then produces DNA fragments of a different length. These can be detected by electrophoresis. Most* RFLPs are
created by a change in a single nucleotide in the gene, and so these are called single nucleotide polymorphisms (SNPs).

Single Nucleotide Polymorphisms (SNPs)

Developments in DNA sequencing now make it easy to look for allelic versions of a gene by sequencing samples of the gene taken
from different members of a population (or from a heterozygous individual). Alleles whose sequence reveals only a single changed
nucleotide are called single nucleotide polymorphisms or SNPs. SNPs can occur in noncoding parts of the gene so they would not
be seen in the protein product. They might not alter the cutting site for any known restriction enzymes so they would not be seen by
RFLP analysis. As of October 2005, over one million SNPs had been identified across the human genome.

Copy Number Polymorphisms (CNPs)

Genetic analysis (using DNA chips and FISH) has revealed another class of human polymorphisms. These copy number
polymorphisms are large (thousands of base pairs) duplications or deletions that are found in some people but not in others. On
average, one person differs from another by 11 of these. One or more have been found on most chromosomes, and the list is
probably incomplete. While most of this DNA is non-coding, functional genes are embedded in some of it. Example: AMY1, the
gene encoding salivary amylase, an enzyme that digests starch. Humans vary in the number of copies of AMY1 in their genome.

18.7.1 https://bio.libretexts.org/@go/page/5928
 Populations whose diet is rich in starches (e.g., many Americans, Japanese) have an average of 7 copies of the gene.
Populations with low-starch diets (e.g., nomadic tribes in Siberia whose diet is dominated by dairy products and fish) average
only 5 copies.
In the case of AMY1, the more copies present, the more enzyme that is produced. How a person adapts to a change in gene number
for autosomal genes is unknown (in contrast to the way that human females adjust the activity of the genes on their two X
chromosomes to match that of males with their solitary X chromosome).

How are polymorphisms useful?

Polymorphism analysis is in widespread use. In tissue typing, it is use to find the best match between the donor, e.g., of a kidney,
and the recipient. It is used to find disease genes (e.g., the gene for Huntington's disease was located when the presence of the
disease was found to be linked to a RFLP whose location on the chromosome was known). In population studies, it is used to
assess the degree of genetic diversity in a population, including:
The McAlpine study, which produced the photo above, found that the heterozygous frogs were more successful breeders than
homozygous ones.
A search for polymorphisms in elephant seals and cheetahs has revealed that they have few or none.
Determining whether two populations represent separate species or races of the same species. This is often critical to applying
laws protecting endangered species.
Tracking migration patterns of a species (e.g., whales).

How do polymorphisms arise and persist?

They arise by mutation. But what keeps them in the population? Several factors may maintain polymorphism in a population.
Founder Effect: If a population began with a few individuals — one or more of whom carried a particular allele — that allele
may come to be represented in many of the descendants. In the 1680s Ariaantje and Gerrit Jansz emigrated from Holland to
South Africa, one of them bringing along an allele for the mild metabolic disease porphyria. Today more than 30000 South
Africans carry this allele and, in every case examined, can trace it back to this couple — a remarkable example of the founder
effect.
Genetic Drift: An allele may increase - or decrease - in frequency simply through chance. Not every member of the population
will become a parent and not every set of parents will produce the same number of offspring. The effect, called random genetic
drift, is particularly strong in small populations (e.g., 100 breeding pairs or fewer) and when the allele is neutral; that is, is
neither helpful nor deleterious
Eventually the entire population may become homozygous for the allele or - equally likely - the allele may disappear. Before either
of these fates occurs, the allele represents a polymorphism.
Two examples of reduced polymorphism because of genetic drift:
By 1900, hunting of the northern elephant seal off the Pacific coast had reduced its population to only 20 survivors. Since
hunting ended, the population has rebounded from this population bottleneck to some 100,000 animals today. However, these
animals are homozygous at every one of the gene loci that have been examined.
Cheetahs, the fastest of the land animals, seem to have passed through a similar period of small population size with its
accompanying genetic drift. Examination of 52 different loci has failed to reveal any polymorphisms; that is, these animals are
homozygous at all 52 loci. The lack of genetic variability is so profound that cheetahs will accept skin grafts from each other
just as identical twins (and inbred mouse strains) do. Whether a population with such little genetic diversity can continue to
adapt to a changing environment remains to be seen.

Natural Selection
Copy Number Polymorphisms
The varying number of copies of the AMY1 gene in different human populations appears to have arisen from the evolutionary
pressure of the differences in the starch content of their diet.
Balanced Polymorphism
In regions of the world (e.g., parts of Africa) where malaria caused by Plasmodium falciparum is common, the allele for sickle-cell
hemoglobin is also common. This is because children who inherit one gene for the "normal" beta chain of hemoglobin and one

18.7.2 https://bio.libretexts.org/@go/page/5928
sickle gene are more likely to survive than either homozygote. Children homozygous for the sickle allele die young from sickle-cell
disease but children homozygous for the "normal" beta chain are more susceptible to illness and death from falciparum malaria
than are heterozygotes. Hence the relatively high frequency of the allele in malarial regions. When natural selection favors
heterozygotes over both homozygotes, the result is balanced polymorphism. It accounts for the persistence of an allele even
though it is deleterious when homozygous.
Another example: prion proteins
All human populations are polymorphic for the prion protein PrPC. It is encoded by the prion protein gene (PRNP). Two of the
alleles have different codons at position 129 - one encoding methionine; the other valine. Homozygosity for either allele increases
the susceptibility to prion diseases. People who are heterozygous are more resistant. A study of elderly women who had survived
the kuru epidemic of the first half of the 20th century (eating the tissues of the deceased was banned in 1950) showed that 76.7% of
them were heterozygotes. This table compares the gene frequencies in this population as well as in a population that never
practiced mortuary feasts.
Table 1: M is the allele encoding the methionine; V the allele encoding valine.
MM MV VV

Survivors 0.133 0.767 0.100

Unexposed 0.221 0.514 0.264

A quick calculation will show that the gene pool of the exposed women deviates widely from what would be found if the
population were in Hardy-Weinberg equilibrium. In this case, strong mortality selection is the cause. The gene pool of the
unexposed population is close to being in Hardy-Weinberg equilibrium. Here, again, natural selection has favored heterozygotes
over both homozygotes (and led to the speculation that cannibalism may have been common earlier in human history).

 Natural vs. Sexual Selection: Balanced polymorphism in Soay sheep

Hirta is a tiny island in the North Atlantic 100 miles off the northwest coast of Scotland. In 1932 a small (107) population of
domestic sheep (Ovis aries) was introduced onto the island from the neighboring island of Soay. Since then these sheep have
been allowed to run wild and, since 1985, have been intensively studied. The sheep have horns and, in males, these play an
important role in competition for females. The size of the horns is strongly influenced by a single gene locus, RXFP2, with two
alleles: Ho+ and HoP.
Homozygous Ho+Ho+ males have the largest horns and sire more offspring but have reduced survival.
Homozygous HoPHoP males have smaller horns (sometime even vestigial horns called scurs). These males have less
success in mating but have increased survival.
Heterozygous Ho+HoP males are almost as successful at mating as Ho+Ho+ males and survive almost as well as HoPHoP
males. On balance, then, the heterozygotes have greater overall fitness than either homozygotes — another example of
balanced polymorphism. It arises as a trade-off between the opposing effects of natural selection (survival) and sexual
selection (reproductive success) on a single gene locus.
You can read about these findings in Johnston, Susan. E., et al., Nature 502, 93–95, 3 October 2013.

This page titled 18.7: Polymorphisms is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

18.7.3 https://bio.libretexts.org/@go/page/5928
18.8: Kin Selection
In the discussion of natural selection, the emphasis was on how natural selection works on individuals to favor the more fit and
disfavor the less fit in a population. The emphasis was on the survival (mortality selection), mating success (sexual selection), or
family size (fecundity selection) of individuals. But what of the worker honeybee who gives up her life when danger threatens her
hive? Or the mother bird who, feigning injury, flutters away from her nestful of young, thus risking death at the hands of a
predator? How can evolution produce genes for such instinctive patterns of behavior when the owner of these genes risk failing the
first test of fitness: survival?
A possible solution to this dilemma lies in the effect of such seemingly altruistic behavior on the overall ("inclusive") fitness of the
family of the altruistic individual. Linked together be a similar genetic endowment, the altruistic member of the family enhances
the chance that many of its own genes will be passed on to future generations by sacrificing itself for the welfare of its relatives. It
is interesting to note that most altruistic behavior is observed where the individuals are linked by fairly close family ties. Natural
selection working at the level of the family rather than the individual is called kin selection.
How good is the evidence for kin selection? Does the behavior of the mother bird really increase her chances of being killed? After
all, it may be advantageous to take the initiative in an encounter with a predator that wanders near. But even if she does increase her
risk, is this anything more than another example of maternal behavior? Her children are, indeed, her kin. But isn't natural selection
simply operating in one of the ways Darwin described: to produce larger mature families?
Perhaps clearer examples of altruism and kin selection are to be found in those species of birds that employ "helpers". One
example: Florida scrub jays (Aphelocoma coerulescens coerulescens). These birds occupy well-defined territories. When they
reach maturity, many of the young birds remain for a time (one to four years) in the territory and help their parents with the raising
of additional broods. How self-sacrificing! Should not natural selection have produced a genotype that leads its owners to seek
mates and start raising their own families (to receive those genes)?
But the idea of kin selection suggests that the genes guiding their seemingly altruistic behavior have been selected for because they
are more likely to be passed on to subsequent generations in the bodies of an increased number of younger brothers and sisters than
in the bodies of their own children. To demonstrate that this is so, it is necessary to show that
1. the "helping" behavior of these unmated birds is really a help and that
2. they have truly sacrificed opportunities to be successful parents themselves.
Thanks to the patient observations of Glen Woolfenden, the first point is established. He has shown that parents with helpers raise
larger broods than those without. But the second point remains unresolved. Perhaps by waiting until they have gained experience
with guarding nests and feeding young and until a suitable territory becomes available, these seemingly altruistic helpers are
actually improving their chances of eventually raising larger families than they would have if they started right at it. If so, then once
again we are simply seeing natural selection working through one of Darwin's criteria of individual fitness: ability to produce larger
mature families.
The evolutionary advantage of helping ceases if the young are not actually siblings of the helper. It is well-established (e.g., by
DNA analysis) that the females of many species of birds have "extramarital" affairs; that is, produce broods where the young have
been sired by more than one male. Interestingly, it turns out that the more promiscuous the females of a given species, the less
likely it is that they are assisted by helpers. Conversely, those species that employ helpers tend to be monogamous. (There are a few
exceptions.)

Kin Selection in Social Insects

The honeybee and other social insects provide the clearest example of kin selection. They are also particularly interesting examples
because of the peculiar genetic relationships among the family members.
Male honeybees (drones) develop from the queen's unfertilized eggs and are haploid. Thus all their sperm will contain exactly the
same set of genes. This means that all their daughters will share exactly the same set of paternal genes, although they will share —
on average — only one-half of their mother's genes. (Human sisters, in contrast, share one-half of their father's as well as one-half
of their mother's genes.) So any behavior that favors honeybee sisters (75% of genes shared) will be more favorable to their
genotype than behavior that favors their children (50% of genes shared).
Since that is the case, why bother with children at all? Why not have most of the sisters be sterile workers, caring for their mother
as she produces more and more younger sisters, a few of whom will someday be queens? As for their brothers, worker bees share

18.8.1 https://bio.libretexts.org/@go/page/5930
only 25% of their genes with them. Is it surprising, then, that as autumn draws near, the workers lose patience with the lazy
demanding ways of their brothers and finally drive them from the hive?

This page titled 18.8: Kin Selection is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

18.8.2 https://bio.libretexts.org/@go/page/5930
18.9: The Origin of Life
To account for the origin of life on our earth requires solving several problems:
How the organic molecules that define life, e.g. amino acids, nucleotides, were created.
How these were assembled into macromolecules, e.g. proteins and nucleic acids, - a process requiring catalysts.
How these were able to reproduce themselves.
How these were assembled into a system delimited from its surroundings (i.e., a cell).
A number of theories address each of these problems. As for the first problem, four scenarios have been proposed. Organic
molecules:
1. were synthesized from inorganic compounds in the atmosphere,
2. rained down on earth from outer space,
3. were synthesized at hydrothermal vents on the ocean floor,
4. were synthesized when comets or asteroids struck the early earth.

Scenario 1: Miller's Experiment

Stanley Miller, a graduate student in biochemistry, built the apparatus shown in Figure 18.9.1. He filled it with water (H2O),
methane (CH4), ammonia (NH3) and hydrogen (H2), but no oxygen. He hypothesized that this mixture resembled the atmosphere
of the early earth. The mixture was kept circulating by continuously boiling and then condensing the water. The gases passed
through a chamber containing two electrodes with a spark passing between them.

Figure 18.9.1 : Miller experiment. (CC BY-SA; Yassine Mrabet).

At the end of a week, Miller used paper chromatography to show that the flask now contained several amino acids as well as some
other organic molecules. However, it is now thought that the atmosphere of the early earth was not rich in methane and ammonia -
essential ingredients in Miller's experiments. In the years since Miller's work, many variants of his procedure have been tried.
Virtually all the small molecules that are associated with life have been formed:
17 of the 20 amino acids used in protein synthesis, and all the purines and pyrimidines used in nucleic acid synthesis.
But abiotic synthesis of ribose - and thus of nucleotides - has been much more difficult. However, success in synthesizing
pyrimidine ribonucleotides under conditions that might have existed in the early earth was reported in the 14 May 2009 issue of
Nature.

18.9.1 https://bio.libretexts.org/@go/page/5932
 And in 2015, chemists in Cambridge England led by John Sutherland reported that they had been able to synthesize precursors
of 12 of the 20 amino acids and two (of the four) ribonucleotides used by life as well as glycerol-1-phosphate, a precursor of
lipids. They created all of these molecules using only hydrogen cyanide (HCN) and hydrogen sulfide (H2S) irradiated with
ultraviolet light in the presence of mineral catalysts.

Scenario 2: Molecules from Outer Space

Astronomers, using infrared spectroscopy, have identified a variety of organic molecules in interstellar space, including methane
(CH4), methanol (CH3OH), formaldehyde (HCHO), cyanoacetylene (HC3N) (which in spark-discharge experiments is a precursor
to the pyrimidine cytosine), polycyclic aromatic hydrocarbonsas well as such inorganic building blocks as carbon dioxide (CO2),
carbon monoxide (CO), ammonia (NH3), hydrogen sulfide (H2S), and hydrogen cyanide (HCN).
There have been several reports of producing amino acids and other organic molecules in laboratories by taking a mixture of
molecules known to be present in interstellar space such as ammonia (NH3), carbon monoxide (CO), methanol (CH3OH) and water
(H2O), hydrogen cyanide (HCN) and exposing it to a temperature close to that of space (near absolute zero) and intense ultraviolet
(UV) radiation. Whether or not the molecules that formed terrestrial life arrived here from space, there is little doubt that organic
matter continuously rains down on the earth (estimated at 30 tons per day).
Alternatively, organic molecules can be transport to Earth via meteorites as demonstrated with the Murchison Meteorite that that
fell near Murchison, Australia on 28 September 1969. This meteorite turned out to contain a variety of organic molecules
including: purines and pyrimidines, polyols - compounds with hydroxyl groups on a backbone of 3 to 6 carbons such as glycerol
and glyceric acid (sugars are polyols) and the amino acids listed in Table 18.9.1. The amino acids and their relative proportions
were quite similar to the products formed in Miller's experiments.

Murchison meteorite at the The National Museum of Natural History (Washington). (CC SA-BY 3.0; :Basilicofresco).

 Table 18.9.1 : Representative amino acids found in the Murchison meteorite. Six of the amino acids (blue) are found in all living things, but
the others (yellow) are not normally found in living matter here on earth. The same amino acids are produced in discharge experiments like
C Miller's.
T Glycine Glutamic acid
h
Alanine Isovaline
e
q Valine Norvaline
u Proline N-methylalanine
e
Aspartic acid N-ethylglycine
st

18.9.2 https://bio.libretexts.org/@go/page/5932
 i
on is if these molecules identified in the Murchison meteorite were simply terrestrial contaminants that got into the meteorite
after it fell to earth? Probably not:
Some of the samples were collected on the same day it fell and subsequently handled with great care to avoid
contamination.
The polyols contained the isotopes carbon-13 and hydrogen-2 (deuterium) in greater amounts than found here on earth.
The samples lacked certain amino acids that are found in all earthly proteins.
Only L amino acids occur in earthly proteins, but the amino acids in the meteorite contain both D and L forms (although L
forms were slightly more prevalent).

Scenario 3: Deep-Sea Hydrothermal Vents

Some deep-sea hydrothermal vents discharge copious amounts of hydrogen, hydrogen sulfide, and carbon dioxide at temperatures
around 100°C. (These are not "black smokers".) These gases bubble up through chambers rich in iron sulfides (FeS, FeS2). These
can catalyze the formation of simple organic molecules like acetate. (And life today depends on enzymes that have Fe and S atoms
in their active sites.)

Scenario 4: Laboratory Synthesis of Nucleobases Under Conditions Mimicking the Impact of

Asteroids or Comets on the Early Earth
Researchers in the Czech Republic reported in 2014 that they had succeeded in the abiotic synthesis of adenine (A), guanine (G),
cytosine (C), and uracil (U) — the four bases found in RNA (an RNA beginning?) and three of the four found in DNA. They
achieved this by bombarding a mixture of formamide and clay with powerful laser pulses that mimicked the temperature and
pressure expected when a large meteorite strikes the earth. Formamide is a simple substance, CH3NO, thought to have been
abundant on the early earth and containing the four elements fundamental to all life.

Assembling Polymers
Another problem is how polymers - the basis of life itself - could be assembled.
In solution, hydrolysis of a growing polymer would soon limit the size it could reach.
Abiotic synthesis produces a mixture of L and D enantiomers. Each inhibits the polymerization of the other. (So, for example,
the presence of D amino acids inhibits the polymerization of L amino acids (the ones that make up proteins here on earth).
This has led to a theory that early polymers were assembled on solid, mineral surfaces that protected them from degradation, and in
the laboratory polypeptides and polynucleotides (RNA molecules) containing about ~50 units have been synthesized on mineral
(e.g., clay) surfaces.

An RNA Beginning?
All metabolism depends on enzymes and, until recently, every enzyme has turned out to be a protein. But proteins are synthesized
from information encoded in DNA and translated into mRNA. So here is a chicken-and-egg dilemma. The synthesis of DNA and
RNA requires proteins. So proteins cannot be made without nucleic acids and nucleic acids cannot be made without proteins. The
discovery that certain RNA molecules have enzymatic activity provides a possible solution. These RNA molecules — called
ribozymes — incorporate both the features required of life: storage of information and the ability to act as catalysts.

Figure 18.9.2 RNA. (The figure is based on the work of Green and Szostak, Science 258:1910, 1992.)
While no ribozyme in nature has yet been found that can replicate itself, ribozymes have been synthesized in the laboratory that can
catalyze the assembly of short oligonucleotides into exact complements of themselves. The ribozyme serves as both the template

18.9.3 https://bio.libretexts.org/@go/page/5932
on which short lengths of RNA ("oligonucleotides" are assembled following the rules of base pairing and the catalyst for
covalently linking these oligonucleotides.
In principal, the minimal functions of life might have begun with RNA and only later did proteins take over the catalytic machinery
of metabolism and DNA take over as the repository of the genetic code. Several other bits of evidence support this notion of an
original "RNA world":
Many of the cofactors that play so many roles in life are based on ribose; for example:
ATP
NAD
FAD
coenzyme A
cyclic AMP
GTP
In the cell, all deoxyribonucleotides are synthesized from ribonucleotide precursors.
Many bacteria control the transcription and/or translation of certain genes with RNA molecules, not protein molecules.

Reproduction?
Perhaps the earliest form of reproduction was a simple fission of the growing aggregate into two parts - each with identical
metabolic and genetic systems intact.

 The First Cell?

To function, the machinery of life must be separated from its surroundings - some form of extracellular fluid (ECF). This
function is provided by the plasma membrane. Today's plasma membranes are made of a double layer of phospholipids. They
are only permeable to small, uncharged molecules like H2O, CO2, and O2. Specialized transmembrane transporters are needed
for ions, hydrophilic, and charged organic molecules (e.g., amino acids and nucleotides) to pass into and out of the cell.
However, the same Szostak lab that produced the finding described above reported in the 3 July 2008 issue of Nature that fatty
acids, fatty alcohols, and monoglycerides - all molecules that can be synthesized under prebiotic conditions - can also form
lipid bilayers and these can spontaneously assemble into enclosed vesicles.
Unlike phospholipid vesicles, these
admit from the external medium charged molecules like nucleotides
admit from the external medium hydrophilic molecules like ribose
grow by self-assembly
are impermeable to, and thus retain, polymers like oligonucleotides.
These workers loaded their synthetic vesicles with a short single strand of deoxycytidine (dC) structured to provide a template
for its replication. When the vesicles were placed in a medium containing (chemically modified) dG, these nucleotides entered
the vesicles and assembled into a strand of Gs complementary to the template strand of Cs. Here, then, is a simple system that
is a plausible model for the creation of the first cells from the primeval "soup" of organic molecules.

From Unicellular to Multicellular Organisms

This transition is probably the easiest to understand.

18.9.4 https://bio.libretexts.org/@go/page/5932
 Figure 18.9.3 Unicellular to multicellular organisms
Several colonial flagellated green algae provide a clue. These species are called colonial because they are made up simply of
clusters of independent cells. If a single cell of Gonium, Pandorina, or Eudorina is isolated from the rest of the colony, it will
swim away looking quite like a Chlamydomonas cell. Then, as it undergoes mitosis, it will form a new colony with the
characteristic number of cells in that colony.
(The figures are not drawn to scale. Their sizes range from Chlamydomonas which is about 10 µm in diameter - little larger than a
human red blood cell - to Volvox whose sphere is some 350 µm in diameter - visible to the naked eye.)
The situation in Pleodorina and Volvox is different. In these organisms, some of the cells of the colony (most in Volvox) are not
able to live independently. If a nonreproductive cell is isolated from a Volvox colony, it will fail to reproduce itself by mitosis and
eventually will die. What has happened? In some way, as yet unclear, Volvox has crossed the line separating simple colonial
organisms from truly multicellular ones. Unlike Gonium, Volvox cannot be considered simply a colony of individual cells. It is a
single organism whose cells have lost their ability to live independently. If a sufficient number of them become damaged, the
entire sphere of cells will die.
What has Volvox gained? In giving up their independence, the cells of Volvox have become specialists. No longer does every cell
carry out all of life's functions (as in colonial forms); instead certain cells specialize to carry out certain functions while leaving
other functions to other specialists. In Volvox this process goes no further than having certain cells specialize for reproduction
while others, unable to reproduce themselves, fulfill the needs for photosynthesis and locomotion.
In more complex multicellular organisms, the degree of specialization is carried much further. Each cell has one or two precise
functions to carry out. It depends on other cells to carry out all the other functions needed to maintain the life of the organism and
thus its own.
The specialization and division of labor among cells is the outcome of their history of differentiation. One of the great problems in
biology is how differentiation arises among cells, all of which having arisen by mitosis, share the same genes.
The genomes of both Chlamydomonas and Volvox have been sequenced. Although one is unicellular, the other multicellular, they
have not only about the same number of protein-encoding genes (14,516 in Chlamydomonas, 14,520 in Volvox) but most of these
are homologous. Volvox has only 58 genes that have no relatives in Chlamydomonas and even fewer unique mRNAs.
At one time, many of us would have expected that a multicellular organism like Volvox with its differentiated cells and complex
life cycle would have had many more genes than a single-celled organism like Chlamydomonas. But that turns out not to be the
case.
How to explain this apparent paradox? My guess is that just as we have seen in the evolution of animals, we are seeing here that the
evolution of organismic complexity is not so much a matter of the evolution of new genes but rather the evolution of changes in the
control elements (promoters and enhancers) that dictate how and where the basic tool kit of eukaryotic genes will be expressed .
The evidence is compelling that all these organisms are close relatives; that is, belong to the same clade. They illustrate how
colonial forms could arise from unicellular ones and multicellular forms from colonial ones.

The Last Universal Common Ancestor (LUCA)?

The 3 kingdoms of contemporary life — archaea, bacteria, and eukaryotes — all share many similarities of
their metabolic and genetic systems . Presumably these were present in an organism that was ancestral to
these groups: the "LUCA". Although there are not enough data at present to describe LUCA, comparative

18.9.5 https://bio.libretexts.org/@go/page/5932
genomics and proteomics reveal a closer relationship between archaea and eukaryotes than either shares with the bacteria. Except,
of course, for the mitochondria and chloroplasts that eukaryotes gained from bacterial endosymbionts. Whether the endosymbionts
were acquired before or after a lineage of archaea had acquired a nucleus - and thus started the lineage of eukaryotes - is still
uncertain.

Creating Life?
When I headed off to college (in 1949), I wrote an essay speculating on the possibility that some day we would be able to create a
living organism from nonliving ingredients. By the time I finished my formal studies in biology — having learned of the incredible
complexity of even the simplest organism — I concluded that such a feat could never be accomplished.
Now I'm not so sure.
Several recent advances suggest that we may be getting close to creating life. (But note that these examples represent laboratory
manipulations that do not necessarily reflect what may have happened when life first appeared.)
Examples:
The ability to created membrane-enclosed vesicles that can take in small molecules and assemble them into polymers which
remain within the "cell".
The ability to assemble functional ribosomes — the structures that convert the information encoded in the genome into the
proteins that run life — from their components.
In 2008, scientists at the J. Craig Venter Institute (JCVI) reported (in Science 29 February 2008) that they had succeeded in
synthesizing a complete bacterial chromosome — containing 582,970 base pairs — starting from single deoxynucleotides. The
entire sequence of the genome of Mycoplasma genitalium was already known. Using this information, they synthesized some
10,000 short oligonucleotides (each about 50 bp long) representing the entire genitalium genome and then - step by step -
assembled these into longer and longer fragments until finally they had made the entire circular DNA molecule that is the
genome.
Could this be placed in the cytoplasm of a living cell and run it?
The same team showed in the previous year (see Science 3 August 2007) that they could insert an entire chromosome from one
species of mycoplasma into the cytoplasm of a related species and, in due course, the recipient lost its own chromosome
(perhaps destroyed by restriction enzymes encoded by the donor chromosome) and began expressing the phenotype of the
donor. In short, they had changed one species into another. But the donor chromosome was made by the donor bacterium, not
synthesized in the laboratory. However, there should be no serious obstacle to achieving the same genome transplantation with a
chemically-synthesized chromosome.
They've done it! The same team reported on 20 May 2010 in the online Science Express that they had successfully transplanted
a completely synthetic genome — based on that of Mycoplasma mycoides — into the related species Mycoplasma capricolum.
The recipient strain grew well and soon acquired the phenotype of the M. mycoides donor.
In the 4 April 2014 issue of Science (Annaluru, N. et al.), a large group of researchers - including many undergraduates at Johns
Hopkins University - reported that they had successfully replaced the natural chromosome 3 in Saccharomyces cerevisiae
(which has 16 chromosomes) with a totally-synthetic chromosome.
Their procedure:
1. Chemically synthesize 69- to 79-nt oligonucleotides representing all the stretches of the known chromosome 9 sequence
(which contains 316,617 base pairs) except for certain sequences such as transposons, many introns, and transfer RNA
genes. In addition new, non-native, sequences such as loxP sites were included to aid future manipulations of the genome.
2. Stitch these together into blocks of ~750 base pairs. This step was done in vitro by undergraduates enrolled in the "Build A
Genome" class at Johns Hopkins.
3. Introduce these into yeast cells which ligated them into stretches of DNA containing 2–4 thousand base pairs.
4. Introduce these stepwise into yeast cells so that they replace the equivalent portions of the native chromosome.
5. The result: a strain of yeast that grows just as well with its new artificial chromosome (now containing only 272,871 base
pairs) as it did before.

This page titled 18.9: The Origin of Life is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

18.9.6 https://bio.libretexts.org/@go/page/5932
18.10: Mars
In 1975, NASA launched two unmanned landers towards the planet Mars:
Viking 1 settled gently on Mars on July 20, 1976
Viking 2 landed on the opposite side of the planet on September 3, 1976.
Both Viking missions carried equipment designed to look for evidence of life. There were five different types of instruments:

Television cameras.
No images suggesting the presence of life were ever seen.

A gas chromatograph combined with a mass spectrometer

This apparatus examined the martian soil for the presence of organic molecules. Even though sensitive to concentrations in the
parts per billion (ppb) range, no organic matter was detected (except for traces of the solvents that had been used on earth to clean
the equipment). Even if organic molecules could be formed on Mars, the intensity of the ultraviolet light at the surface would soon
destroy them.

The Labeled-Release (LR) Experiment

Metabolism is a universal property of life on earth. The LR experiment was designed to look for evidence of catabolism by any
microorganisms that might have been present in the Martian soil. In this experiment, a soil sample was incubated with a dilute soup
of organic molecules (such as the amino acid glycine) which had been synthesized with the radioactive isotope 14C. Over a period
of 10 days, the atmosphere above the sample was monitored for the appearance of radioactive gases such as carbon dioxide (CO2).
The results:
a burst of gas production when the medium was first added
but not when the soil had been preheated to kill off any microorganisms it might have contained.
However, gas production did not increase as time went on (as would be expected if living organisms were growing in the
medium) and
later additions produced no additional gas.
Thus most scientists concluded that the gas was produced by nonliving chemistry (brought about by oxidizing agents in the soil).
This conclusion was strengthened by similar results using soils from a dry desert in northern Chile. (See Navarro-Gonzalez, R., et
al, Science, 7 November 2003)

The Pyrolytic-Release (PR) Experiment

The PR experiment was designed to look for evidence of anabolism.; specifically whether there were any microorganisms in the
martian soil that could synthesize complex organic molecules from carbon dioxide (CO2) and carbon monoxide (CO). In this
experiment, a mixture of radioactive CO2 and CO was introduced into a vessel containing a soil sample.
Because anabolism requires energy and the most important source of that energy here on earth is sunlight (for photosynthesis), the
incubation mixture was illuminated with a bright arc lamp.
After 5 days,
any unreacted CO2 and CO was flushed out of the system and then

18.10.1 https://bio.libretexts.org/@go/page/5934
 the soil sample was heated to drive off any radioactive organic molecules that might have been synthesized.
The result: organic matter was detected in 7 of 9 runs. However, some positive results were achieved even on runs where the soil
had first been heated to such a high temperature that any microorganisms present would have been killed (at least here on earth).

The Gas-Exchange (GEX) Experiment

In this experiment, a known mixture of gases was placed in the chamber along with the soil sample and then analyzed periodically
to see if any gases (e.g. CO2) had disappeared from - or been added to - the mixture.
In the first part of the experiment, nutrient broth was added to the chamber but not to the soil. There was a rapid release of
large amounts of O2 (which would not be expected from heterotrophic breakdown of organic substrates). This soon
subsided.
smaller amounts of CO2 (an expected product of catabolism).
One week later, more nutrient broth was added; this time directly to the soil. There was another, smaller, release of CO2 but no
release of O2. The conclusion: the gases were formed by nonbiological chemistry (oxidizing agents again).

So what can we conclude from these data?

The LR, PR, and GEX experiments all produced some positive results.

However:
All of these involved puzzling ambiguities, failing to behave as similar tests done on earthly soil samples would have.
All were later shown to be reproducible here on earth by nonbiological chemistry.
So the Viking studies probably did not reveal the presence of life on Mars. But this is not the same as saying that life does not now
nor ever did exist on Mars!

Perhaps:
The upper layers of soil are inhospitable to life.
Other places on Mars need to be sampled.

 The Curiosity Rover

On 6 August 2012, NASA's Curiosity rover landed on Mars. So far, its sampling has revealed evidence of short chains of
aliphatic hydrocarbons, chlorobenzene, an aromatic hydrocarbon and nitrates.

The Evidence from Martian Meteorites

Some meteorites are thought — because of their peculiar chemistry - to have reached earth from Mars. One of these ALH84001
(found in the Allan Hills of Antarctica in 1984) has been subjected to intensive analysis for ingredients suggestive of life processes.
In it have been found:
1. polycyclic aromatic hydrocarbons (PAHs). But in most of the Martian meteorites that have been examined, these and other
organic molecules have been trapped inside where no living thing could have deposited them, and PAHs and other organic
molecules are also found in meteorites arriving from elsewhere in the solar system.
2. minerals within the meteorite (e.g. carbonates, magnetite) that are formed by living organisms here on earth and appear to have
been deposited in the rock of the meteorite at some later time in its history;
3. objects that under the scanning electron microscope look like fossils of tiny microorganisms. However, even the largest of these
"nanofossils" have diameters of only 100 nanometers (nm) (0.1 µm, about the size of a ribosome). This is smaller than the
smallest microorganisms here on earth (the mycoplasmas, with diameters of about 300 nm) and is smaller than the estimates of
the minimum diameter (200 nm) needed to provide the volume necessary to build a living cell.
ALH84001 is thought to have landed in Antarctica some 13,000 years ago. But in July 2011, another Martian meteorite landed in
the Moroccan desert. With much less time for terrestrial contamination to occur, it may help settle some of the controversy over the
significance of the features found in ALH84001.

18.10.2 https://bio.libretexts.org/@go/page/5934
What would answer our question?
Organic matter is, despite its name, not the exclusive product of life. Many other meteorites contain organic matter and organic
molecules can, of course, be synthesized in the laboratory from inorganic precursors. What does distinguish the organic molecules
produced by life is the restriction to one enantiomer or the other. For example, all proteins synthesized by living things here on
earth use L-amino acids exclusively. Synthesis of amino acids in the chemistry laboratory produces a 50:50 mixture (called a
racemic mixture) of the L- and the D- forms. There is nothing to suggest that life couldn't work just as well with D-amino acids.
What is unlikely is the ability of proteins (e.g. enzymes) to be able to function if they are made from a mixture of L- and D-
enantiomers. So if martian soil should reveal the presence of all-L (or all-D) enantiomers, this would be powerful evidence that life
had produced them.
However,
Whether tested on Mars itself, or on samples returned to earth, rigorous care must be taken to ensure that there is no
contamination by terrestrial molecules.
There is some evidence that even nonbiological synthesis in space may favor one enantiomer over the other. Four amino acids
in the Murchison meteorite, which no one suggests have a biological origin, show a 7–9% excess of the L-form over the D-
form.
Over time, even in the cold, dry climate of Mars, a population of L- (or D-) enantiomers will spontaneously break down into a
racemic (50:50) mixture and thus obscure a biological origin.
The case for life on Mars - whether today or in the past - is neither proven nor disproven.

This page titled 18.10: Mars is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

18.10.3 https://bio.libretexts.org/@go/page/5934
18.11: Endosymbiosis
The endosymbiosis theory postulates that the mitochondria of eukaryotes evolved from an aerobic bacterium (probably related to
the rickettsias) living within an archaeal host cell and the chloroplasts of red algae, green algae, and plants evolved from an
endosymbiotic cyanobacterium living within a mitochondria-containing eukaryotic host cell.

The Evidence
Both mitochondria and chloroplasts can arise only from preexisting mitochondria and chloroplasts. They cannot be formed in a
cell that lacks them because nuclear genes encode only some of the proteins of which they are made.
Both mitochondria and chloroplasts have their own genome, and it resembles that of bacteria not that of the nuclear genome.
Both genomes consist of a single circular molecule of DNA.
There are no histones associated with the DNA.
Both mitochondria and chloroplasts have their own protein-synthesizing machinery, and it more closely resembles that of
bacteria than that found in the cytoplasm of eukaryotes.
The first amino acid of their transcripts is always fMet as it is in bacteria (not methionine [Met] that is the first amino acid
in eukaryotic proteins).
A number of antibiotics (e.g., streptomycin) that act by blocking protein synthesis in bacteria also block protein synthesis
within mitochondria and chloroplasts. They do not interfere with protein synthesis in the cytoplasm of the eukaryotes.
Conversely, inhibitors (e.g., diphtheria toxin) of protein synthesis by eukaryotic ribosomes do not - sensibly enough - have
any effect on bacterial protein synthesis nor on protein synthesis within mitochondria and chloroplasts.
The antibiotic rifampicin, which inhibits the RNA polymerase of bacteria, also inhibits the RNA polymerase within
mitochondria. It has no such effect on the RNA polymerase within the eukaryotic nucleus.

The Mitochondrial Genome

The genome of human mitochondria contains 16,569 base pairs of DNA organized in a closed circle (Figure 18.11.1). These
encode 2 ribosomal RNA (rRNA), molecules, 22 transfer RNA (tRNA) molecules, and 13 polypeptides. The 13 polypeptides
participate in building several protein complexes embedded in the inner mitochondrial membrane and include 7 subunits that make
up the mitochondrial NADH dehydrogenase, 3 subunits of cytochrome c oxidase, 2 subunits of ATP synthase, and cytochrome b.

18.11.1 https://bio.libretexts.org/@go/page/5935
 Control region
or "d-loop"
MT-TP
12S rRNA MT-TF Cytochrome b

16023
15956
7
1588
577
647
3' CYTB
5'
MT-TV
NADH

15953
15888
648
16 70

14 47
16

3
7
02
5'

67
3'
Dehydrogenase

14
RNR1
MT-TT ND6
16S rRNA

16 71
5' 5'
subunits

14 742
16
01

9
67
14

14
3'

14
MT-TE
3'
8
14
14
RNR2

ND5

3304 3'
MT-TL1 3229
3230
3307 site of A3243G mutation associated with MELAS & maternally transmitted diabetes mellitus & deafness
5' 5'
ND1 22 tRNA-encoding genes 12337 12336
MT-L2
4263 3' 4262 2 rRNA-encoding genes MT-TS2
12265
12207
12266
12206 MT-TH
MT-TI
NADH 4331
4402
4329 MT-TQ
4400 13 protein-encoding regions
12137
3'
12138
MT-TM
Dehydrogenase 4469
5'
4470
ND4
subunits
ND2
107 5'
60
1 3' 10766
3' 551 7MT-TA MT-TR 104
2 5 58 55
MT-TC
10 69
40 5' ND4L NADH
55
1 56 761 5
MT-TW 579 7 5 104
Dehydrogenase
59 826

5 5 MT-TG 3' 104 70

10
04
5

56 29 99

05
04
91
subunits

8
MT-TN 57 5' ND3
5'
26

91 10
58

MT-TY 58 COX1 3' 99 059

90
MT-TD MT-TK ATP6 5' COX3
3'
8527
7445

8295
8364
7518
7585

5'
92

3'
Cytochrome Oxidase
07

3'
5' 3'
857

subunits
8366
7446

8269
7514
7586

MT-TS1 COX2 ATP8

ATP Synthase
Cytochrome Oxidase subunits
subunits
Figure 18.11.1: Human mitochondrial genome, a 16,569-bp (base pair) circle of double-stranded DNA containing 37 genes,
specifing 2 ribosomal RNAs , 22 transfer RNAs and 13 polypeptides. Public Domain.
All these gene products are used within the mitochondrion, but the mitochondrion also needs >900 different proteins as well as
some mRNAs and tRNAs encoded by nuclear genes. The proteins (e.g., cytochrome c and the DNA polymerases used within the
mitochondrion) are synthesized in the cytosol and then imported into the mitochondrion.

The Chloroplast Genome

Figure 18.11.2 ChlDNA

The genome of the chloroplasts found in Marchantia polymorpha (a liverwort, one of the Bryophyta) contains 121,024 base pairs
in a closed circle. These make up some 128 genes which include:

18.11.2 https://bio.libretexts.org/@go/page/5935
 duplicate genes encoding each of the four subunits (23S, 16S, 4.5S, and 5S) of the ribosomal RNA (rRNA) used by the
chloroplast
37 genes encoding all the transfer RNA (tRNA) molecules used for translation within the chloroplast. Some of these are
represented in the figure by black bars (a few of which are labeled).
4 genes encoding some of the subunits of the RNA polymerase used for transcription within the chloroplast (3 of them shown in
blue)
a gene encoding the large subunit of the enzyme RUBISCO (ribulose bisphosphate carboxylase oxygenase)
9 genes for components of photosystems I and II
6 genes encoding parts of the chloroplast ATP synthase
genes for 19 of the ~60 proteins used to construct the chloroplast ribosome
All these gene products are used within the chloroplast, but all the chloroplast structures also depend on proteins RUBISCO,
for example, the enzyme that adds CO2 to ribulose bisphosphate to start the Calvin cycle, consists of multiple copies of two
subunits:
Encoded by nuclear genes translated in the cytosol, and imported into the chloroplast.
A large one encoded in the chloroplast genome and synthesized within the chloroplast, and a small subunit encoded in the
nuclear genome and synthesized by ribosomes in the cytosol. The small subunit must then be imported into the chloroplast.
The arrangement of genes shown in the figure is found not only in the Bryophytes (mosses and liverworts) but also in the
lycopsids (e.g., Lycopodium and Selaginella). In all other plants, however, the portion of DNA bracketed by the red arrows on
the left is inverted. The same genes are present but in inverted order. The figure is based on the work of Ohyama, K., et al.,
Nature, 322:572, 7 Aug 1986; and Linda A. Raubeson and R. K. Jansen, Science, 255:1697, 27 March 1992.
The evolution of the eukaryotic chloroplast by the endosymbiosis of a cyanobacterium in a mitochondria-containing eukaryotic
host cell led to the evolution of the green algae and plants as described above, red algae, and glaucophytes; a small group of
unicellular algae.

Secondary Endosymbiosis: Eukaryotes Engulfing Eukaryotes

The Nucleomorph
Once both heterotrophic and photosynthetic eukaryotes had evolved, the former repeatedly engulfed the latter to exploit their
autotrophic way of life. Many animals living today engulf algae for this purpose. Usually the partners in these mutualistic
relationships can be grown separately. However, a growing body of evidence indicates that the chloroplasts of some algae have not
been derived by engulfing cyanobacteria in a primary endosymbiosis like those discussed above, but by engulfing photosynthetic
eukaryotes (Figure 18.11.3). This is called secondary endosymbiosis. It occurred so long ago that these endosymbionts cannot be
cultured away from their host.

Figure 18.11.3: Secondary endosymbiosis

In two groups, the eukaryotic nature of the endosymbiont can be seen by its retention of a vestige of a nucleus (called its
nucleomorph). A group of unicellular, motile algae called cryptomonads appear to be the evolutionary outcome of a
nonphotosynthetic eukaryotic flagellate (i.e., a protozoan) engulfing a red alga by endocytosis. Another tiny group of unicellular
algae, called chlorarachniophytes, appear to be the outcome of a flagellated protozoan having engulfed a green alga.
The result in both cases: a motile, autotrophic cell containing its own nucleus, its own mitochondria, and its own endoplasmic
reticulum. The latter of which contains the endosymbiont with:
its own plasma membrane

18.11.3 https://bio.libretexts.org/@go/page/5935
 its own cytoplasm, the periplastid space
its own ribosomes
its own chloroplast, and
its nucleomorph - only a vestige of its original nucleus, but still surrounded by a nuclear envelope perforated with nuclear pore
complexes and containing a tiny but still-functioning genome.
The Four Genomes of Guillardia theta

The cryptomonad Guillardia theta contains four different genomes:

its own nuclear genome; by far the largest with 87.2x106 base pairs (bp) of DNA
the genome of its mitochondria (48,000 bp)
the genome of the chloroplast in its endosymbiont (121,000 bp)
the genome of the nucleomorph (551,264 bp)
Susan Douglas and her colleagues reported (in the 26 April 2001 issue of Nature) the completely-sequenced genome of the
nucleomorph.
It contains 3 small chromosomes with
47 genes for nonmessenger RNAs (rRNA, tRNA, snRNA)
464 genes for messenger RNA; that is, encoding proteins such as
65 proteins for its own ribosomes
30 for its chloroplast (a small fraction of the hundreds needed)
a variety of proteins needed within the nucleomorph, including
DNA licensing factors
histones
proteins needed for DNA replication (but no genes for DNA polymerases, which must be translated by and imported
from the host ribosomes)
The genes are crowded closely on the three chromosomes. In fact, 44 of them overlap each other. Only 17 genes contain introns,
and these are very small.
Genome Interactions in Guillardia theta
Millions of years of evolution have resulted in a complex but precisely-orchestrated array of interactions between the 4 genomes.
For example:
The chloroplast needs proteins synthesized by 3 different genomes: its own, the nucleomorph's, and the host's.
The nucleomorph genome has given up all (but one) of its genes encoding enzymes for general metabolic functions; the
endosymbiont now depends on those encoded by the host nucleus.
The nucleomorph itself also depends on genes (e.g., for DNA polymerases) residing in the host nucleus.

The Apicoplast
The apicoplast (short for "apicomplexan plastid") is a solitary organelle found in the apicomplexan protists: "sporozoans" like
Plasmodium falciparum (and the other agents of malaria) and Toxoplasma gondii.
Features:
Essential - the organisms cannot survive without it.
Encased by 4 membranes.
Contains its own genome, a circular molecule of DNA (35,000 base pairs) which encodes
~ 30 proteins
a full set of tRNAs plus some other RNAs
Only a few functions have been discovered, but these include
anabolic metabolism such as the synthesis of fatty acids
repair, replication, transcription, and translation of its genes
Clearly 30 proteins are not enough to accomplish so many functions so the apicoplast has to import from the cytosol ~500
nuclear-encoded proteins.

18.11.4 https://bio.libretexts.org/@go/page/5935
The apicoplast is the product of an ancient endosymbiosis in which the eukaryotic ancestor engulfed a unicellular alga - probably a
red alga - with a solitary chloroplast. Over time, the nucleus was lost (no residual nucleomorph) as well as many features of the
chloroplast (including its ability to perform photosynthesis).

 Secondary Symbiosis can Still Occur

Two Japanese scientists have discovered a heterotrophic flagellate that engulfs a unicellular green alga that lives freely in the
surrounding water. Once inside, the alga loses its flagella and cytoskeleton; the host loses its feeding apparatus. Moreover, the
host switches from heterotrophic to autotrophic nutrition (photosynthesis) and the host becomes capable of phototaxis. When
the host divides by mitosis, only one daughter cell gets the plastid. The other cell regrows the feeding apparatus and is ready to
engulf another alga.

This page titled 18.11: Endosymbiosis is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

18.11.5 https://bio.libretexts.org/@go/page/5935
18.12: Geologic Eras
History of life as revealed by the fossil record
With help from molecular phylogenies:

Eras Periods Epochs Aquatic Life Terrestrial Life

With approximate starting dates in millions of years ago in parentheses. Geologic features
in green
Humans in the
Holocene
new world

Quaternary Periodic
(2.6) glaciation
Pleistocene First humans
Continental
drift continues
Cenozoic (66)
The "Age of Pliocene Atmospheric Hominids
Mammals" oxygen reaches
Neogene (23)
today's level
Miocene Adaptive
(21%)
radiation of
Oligocene birds, continued
All modern
Paleogene (66) Eocene radiation of
groups present
mammals
Paleocene

Mesozoic (251) Still attached: N. America & N. Europe; Australia &

The "Age Antarctica; Mass extinction of both aquatic and
of Reptiles" terrestrial life at the end
Extinction of
Modern bony dinosaurs and
Cretaceous fishes pterosaurs; first
(146) snakes

Extinction of
ammonites, Rise of
plesiosaurs, angiosperms
ichthyosaurs

Africa & S. America begin to drift apart

Archaeopteryx;
Plesiosaurs, dinosaurs
ichthyosaurs dominant but
abundant; first mammals
diatoms (Eutheria) begin
to diversify

Jurassic (200) Ammonites

First lizards
again abundant

Skates, rays, Adaptive

and bony fishes radiation of
abundant dinosaurs

Pangaea splits into Laurasia and Gondwana;

atmospheric oxygen drops to ~13%

Triassic (251) Mass Mass

extinctions at extinctions at
the end. the end.
First mammals

18.12.1 https://bio.libretexts.org/@go/page/5936
 Eras Periods Epochs Aquatic Life Terrestrial Life

Ammonites Adaptive
abundant at first radiation of
reptiles:
thecodonts,
Rise of bony therapsids,
fishes turtles,
crocodiles, first
dinosaurs

Paleozoic (542) Periodic glaciation and arid climate; atmospheric

oxygen reaches ~30%. Volcanic eruptions killed off
90% of marine species at end.

Permian (299) Reptiles

abundant.
Extinction of
Cycads,
trilobites
conifers,
ginkgos

Pennsylvanian Ammonites, First reptiles

(320) Warm, humid bony fishes Coal swamps
climate
Forests of
Together
lycopsids,
the
sphenopsids,
Pennsylvanian
and seed ferns
and Adaptive
Amphibians
Mississippian radiation of
Mississippian abundant
make up the sharks
(359) Adaptive
"Carboniferous"
radiation of the
;
insects
also called the
(Hexapoda)
"Age of
Amphibians" Atmospheric oxygen begins to rise as organic matter
is buried, not respired
Ferns,
Cartilaginous lycopsids, and
and bony fishes sphenopsids
Devonian (416) abundant. First
Extensive
The "Age of Ammonites, gymnosperms
inland seas
Fishes" nautiloids, First amphibians
ostracoderms,
eurypterids Mild climate; First bony First myriapods
Silurian (443)
inland seas fishes and chelicerates

Fungi present
Ordovician Mild climate, Trilobites First plants
(485) inland seas abundant (liverworts?)
First insects

18.12.2 https://bio.libretexts.org/@go/page/5936
 Eras Periods Epochs Aquatic Life Terrestrial Life

First
vertebrates
(jawless
No fossils of
fishes).
terrestrial
Eurypterids,
eukaryotes, but
crustaceans
phylogenetic
mollusks,
trees suggest
echinoderms,
Cambrian (541) that lichens,
sponges,
mosses, perhaps
cnidarians,
even vascular
annelids, and
plants were
tunicates
present.
present.
Trilobites
dominant.

Periodic glaciation

Fossil evidence
of multicellular
Ediacaran
algae, fungi,
(635)
and bilaterian
Proterozoic invertebrates
(2500)
Evidence of
eukaryotes
~1.8 x109 years
ago

Evidence of
archaea and
Archaean
bacteria
(3600)
~3.5 x109
years ago

The Geologic and Evolutionary Record

A remarkable feature of the table above is how often evolutionary changes coincided with geologic changes on the earth. But
consider that changes in geology (e.g., mountain formation or lowering of the sea level) cause changes in climate, and together
these alter the habitats available for life. Two types of geologic change seem to have had especially dramatic effects on life:
continental drift and the impact of asteroids

Continental Drift

Figure 18.12.1 Pangaea

A body of evidence, both geological and biological, supports the conclusion that 200 million years ago, at the start of the Mesozoic
era, all the continents were attached to one another in a single land mass, which has been named Pangaea. This drawing of
Pangaea (adapted from data of R. S. Dietz and J. C. Holden) is based on a computer-generated fit of the continents as they would

18.12.3 https://bio.libretexts.org/@go/page/5936
look if the sea level were lowered by 6000 feet (~1800 meters). During the Triassic, Pangaea began to break up, first into two
major land masses:
Laurasia in the Northern Hemisphere
Gondwana in the Southern Hemisphere.
The present continents separated at intervals throughout the remainder of the Mesozoic and through the Cenozoic, eventually
reaching the positions they have today. Let us examine some of the evidence.

Shape of the Continents

The east coast of South America and the west coast of Africa and are strikingly complementary. This is even more dramatic when
one tries to fit the continents together using the boundaries of the continental slopes, e.g., 6000 feet (~1800 meters) down, rather
than the shorelines.

Geology
In both mineral content and age, the rocks in a region on the east coast of Brazil match precisely those found in Ghana on the
west coast of Africa.
The low mountain ranges and rock types in New England and eastern Canada appear to be continued in parts of Great Britain,
France, and Scandinavia.
India and the southern part of Africa both show evidence of periodic glaciation during Paleozoic times (even though both are
now close to the equator). The pattern of glacial deposits in the two regions not only match each other but also glacial deposits
found in South America, Australia, and Antarctica.

Fossils
Fossil reptiles found in South Africa are also found in Brazil and Argentina.
Fossil amphibians and reptiles found in Antarctica are also found in South Africa, India, and China.
Most of the marsupials alive today are confined to South America and Australia. But if these two continents were connected by
Antarctica in the Mesozoic, one might expect to find fossil marsupials there. In March 1982, this prediction was fulfilled with
the discovery in Antarctica of the remains of Polydolops, a 9-ft (2.7 m) marsupial.

The Impact Hypothesis

The Cretaceous period, the last period of the Mesozoic, marked the end of the Age of Reptiles. It was followed by the Cenozoic
era, the Age of Mammals. Although extinctions have occurred throughout the history of life, an extraordinary number of them
occurred in a relatively brief period at the end of the Cretaceous. Why?

The Alvarez Theory

Louis Alvarez, his son Walter, and their colleagues proposed that a giant asteroid or comet striking the earth some 66 million years
ago caused the massive die-off at the end of the Cretaceous. Presumably, the impact generated so much dust and gases that skies
were darkened all over the earth, photosynthesis declined, and worldwide temperatures dropped. The outcome was that as many as
75% of all species — including all dinosaurs — became extinct.
The key piece of evidence for the Alvarez hypothesis was the finding of thin deposits of clay containing the element iridium at the
interface between the rocks of the Cretaceous and those of the Paleogene period (called the K-Pg boundary after the German word
for Cretaceous). Iridium is a rare element on earth (although often discharged from volcanoes), but occurs in certain meteorites at
concentrations thousands of times greater than in the earth's crust.
After languishing for many years, the Alvarez theory gained strong support from the discovery in the 1990s of the remains of a
huge (180 km in diameter) crater in the Yucatan Peninsula that dated to 65 million years ago.
The abundance of sulfate-containing rock in the region suggests that the impact generated enormous amounts of sulfur dioxide
(SO2), which later returned to earth as a bath of acid rain. A smaller crater in Iowa, formed at the same time, many have
contributed to the devastation. Perhaps during this period the earth passed through a swarm of asteroids or a comet and the repeated
impacts made the earth uninhabitable for so many creatures of the Mesozoic.

18.12.4 https://bio.libretexts.org/@go/page/5936
Other Impacts
A mass extinction of non-dinosaur reptiles occurred earlier, at the end of the Triassic. It was followed by a great expansion in the
diversity of dinosaurs. The recent discovery of a layer enriched in iridium in rocks formed at the boundary between the Triassic and
Jurassic suggests that impact from an asteroid or comet may have been responsible then just as it was at the K-Pg boundary.
The largest extinction of all time occurred still earlier at the end of the Permian period. There is evidence off the coast of Australia
that a huge impact there may have contributed to the extinctions at the Permian-Triassic (P-T) boundary.

This page titled 18.12: Geologic Eras is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

18.12.5 https://bio.libretexts.org/@go/page/5936
 CHAPTER OVERVIEW
Unit 19: The Diversity of Life
19.1: Eukaryotic Life
19.1.1: Taxonomy
19.1.2: Protists
19.1.3: Ciliates
19.1.4: Volvox
19.1.5: Diversity and Evolutionary Relationships of the Plants
19.1.6: Arabidopsis Thaliana - A Model Organism
19.1.7: Fungi
19.1.8: Yeast
19.1.9: Barcoding
19.1.10: Invertebrates
19.1.11: Drosophila Melanogaster
19.1.12: Caenorhabditis Elegans
19.1.13: Vertebrates
19.1.14: Zebrafish
19.1.15: Monotremes
19.2: Microbes
19.2A: Bacteria
19.2B: Archaea
19.2C: Antibiotics
19.2D: E. coli
19.2E: Anthrax
19.2F: Bacillus Thuringiensis
19.2G: The Rapid Identification of Microorganisms
19.3: Viruses
19.3A: Viruses
19.3B: Influenza
19.3C: φX174
19.3D: Smallpox
19.3E: Retroviruses

This page titled Unit 19: The Diversity of Life is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1
 SECTION OVERVIEW
19.1: Eukaryotic Life
Topic hierarchy

19.1.1: Taxonomy

19.1.2: Protists

19.1.3: Ciliates

19.1.4: Volvox

19.1.5: Diversity and Evolutionary Relationships of the Plants

19.1.6: Arabidopsis Thaliana - A Model Organism

19.1.7: Fungi

19.1.8: Yeast

19.1.9: Barcoding

19.1.10: Invertebrates

19.1.11: Drosophila Melanogaster

19.1.12: Caenorhabditis Elegans

19.1.13: Vertebrates

19.1.14: Zebrafish

19.1.15: Monotremes

This page titled 19.1: Eukaryotic Life is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.1.1 https://bio.libretexts.org/@go/page/5938
19.1.1: Taxonomy
At least 1.7 million species of living organisms have been discovered, and the list grows longer every year (especially of insects in
the tropical rain forest). How are they to be classified? Ideally, classification should be based on homology; that is, shared
characteristics that have been inherited from a common ancestor. The more recently two species have shared a common
ancestor, the more homologies they share and the more similar these homologies are. Until recent decades, the study of homologies
was limited to anatomical structures and pattern of embryonic development. However, since the birth of molecular biology,
homologies can now also be studied at the level of proteins and DNA.

Anatomical homology: an example

Figure 19.1.1.1 Forelimbs

The figure shows the bones in the forelimbs of three mammals: human, whale, and bat (obviously not drawn to the same scale!).
Although used for such different functions as throwing, swimming, and flying, the same basic structural plan is evident in them all.
In each case, the bone shown in color is the radius. Body parts are considered homologous if they have
the same basic structure
the same relationship to other body parts
develop in a similar manner in the embryo
It seems unlikely that a single pattern of bones represents the best possible structure to accomplish the functions to which these
forelimbs are put. However, if we interpret the persistence of the basic pattern as evidence of inheritance from a common ancestor,
we see that the various modifications are adaptations of the plan to the special needs of the organism. It tells us that evolution is
opportunistic, working with materials that have been handed down by inheritance.

Protein Sequences
Protein sequencing provides a tool for establishing homologies from which genealogies can be constructed and phylogenetic trees
drawn. Here are two examples.

Hemoglobins
An example of molecular homology.

The numbers represent the number of amino acid differences between the beta chain of human hemoglobin and the hemoglobins of
the other species. In general, the number is inversely proportional to the closeness of kinship. All the values listed are for the beta
chain except for the last three, in which the distinction between alpha and beta chains does not occur. The human beta chain
contains 146 amino acid residues, as do most of the others.

19.1.1.1 https://bio.libretexts.org/@go/page/5941
Cytochrome c
Cytochrome c is part of the electron transport chain down which electrons are passed to oxygen during cellular respiration.
Cytochrome c is found in the mitochondria of every aerobic eukaryote - animal, plant, and protist. The amino acid sequences of
many of these have been determined, and comparing them shows that they are related. Human cytochrome c contains 104 amino
acids, and 37 of these have been found at equivalent positions in every cytochrome c that has been sequenced. We assume that each
of these molecules has descended from a precursor cytochrome in a primitive microbe that existed over 2 billion years ago. In other
words, these molecules are homologous.
The first step in comparing cytochrome c sequences is to align them to find the maximum number of positions that have the same
amino acid. Sometimes gaps are introduced to maximize the number of identities in the alignment (none was needed in this table).
Gaps correct for insertions and deletions that occurred during the evolution of the molecule.
This table shows the N-terminal 22 amino acid residues of human cytochrome c with the corresponding sequences from six other
organisms aligned beneath. A dash indicates that the amino acid is the same one found at that position in the human molecule. All
the vertebrate cytochromes (the first four) start with glycine (Gly). The Drosophila, wheat, and yeast cytochromes have several
amino acids that precede the sequence shown here (indicated by <<<). In every case, the heme group of the cytochrome is attached
to Cys-14. and Cys-17 (human numbering). In addition to the two Cys residues, Gly-1, Gly-6, Phe-10, and His-18 are found at the
equivalent positions in every cytochrome c that has been sequenced.
We assume that the more identities there are between two molecules, the more recently they have evolved from a common ancestral
molecule and thus the closer the kinship of their owners. Thus the cytochrome c of the rhesus monkey is identical to that of humans
except for one amino acid, whereas yeast cytochrome c differs from that of humans at 44 positions. (There are no differences
between the cytochrome c of humans and that of chimpanzees.)

Phylogenetic trees

Figure 19.1.1.2 Phylogenetic trees

With such information, one can reconstruct an evolutionary history of the molecule and thus of their respective owners. This
requires

19.1.1.2 https://bio.libretexts.org/@go/page/5941
 using the genetic code to determine the minimum number of nucleotide substitutions in the DNA of the gene needed to derive
one protein from another
a powerful computer program to search for the shortest paths linking the molecules together
The result is a phylogenetic tree. This one (the work of Walter M. Fitch and Emanuel Margoliash) shows the relationship between
20 species of eukaryotes. The numbers represent the minimum number of nucleotide substitutions in the gene for cytochrome c
needed to produce these 20 proteins from a series of hypothetical ancestral genes at the various branching points (nodes).
The tree corresponds quite well to what we have long believed to be the evolutionary relationships among the vertebrates. But there
are some anomalies. It indicates, for example, that the primates (humans and monkeys) split off before the split separating the
kangaroo, a marsupial, from the other placental mammals. This is certainly wrong. But sequence analysis of other proteins can
resolve such discrepancies.
Cytochrome c is an ancient molecule, and it has evolved very slowly. Even after more than 2 billion years, one-third of its amino
acids are unchanged. This conservatism is a great help in working out the evolutionary relationships between distantly-related
creatures like fish and humans.
But what of humans and the great apes? Their cytochrome c molecules are identical and can tell us nothing about evolutionary
relationships. However, some proteins have evolved much more rapidly than cytochrome c, and these can be used to decipher
recent evolutionary events. During blood clotting, short peptides are cut from fibrinogen converting it into insoluble fibrin. Once
removed, these fibrinopeptides have no further function. They have been pretty much free from the rigors of natural selection and
have, consequently, diverged rapidly during evolution. So they provide data useful in sorting out the twigs of phylogenetic trees of
mammals, for example.

DNA-DNA Hybridization
As we saw in the comparison of human and kangaroo cytochrome c, a single molecule provides only a narrow window for
glimpsing evolutionary relationships.

Figure 19.1.1.3 DNA-DNA hybridization

The technique of DNA-DNA hybridization provides a way of comparing the total genome of two species. Let us examine the
procedure as it might be used to assess the evolutionary relationship of species B to species A:
The total DNA is extracted from the cells of each species and purified.
For each, the DNA is heated so that it becomes denatured into single strands (ssDNA).
The temperature is lowered just enough to allow the multiple short sequences of repetitive DNA to rehybridize back into
double-stranded DNA (dsDNA).
The mixture of ssDNA (representing single genes) and dsDNA (representing repetitive DNA) is passed over a column packed
with hydroxyapatite. The dsDNA sticks to the hydroxyapatite; ssDNA does not and flows right through. The purpose of this
step is to be able to compare the information-encoding portions of the genome — mostly genes present in a single copy —
without having to worry about varying amounts of noninformative repetitive DNA.
The ssDNA of species A is made radioactive.
The radioactive ssDNA is then allowed to rehybridize with nonradioactive ssDNA of the same species (A) as well as — in a
separate tube — the ssDNA of species B.
After hybridization is complete, the mixtures (A/A) and (A/B) are individually heated in small (2°–3°C) increments. At each
higher temperature, an aliquot is passed over hydroxyapatite. Any radioactive strands (A) that have separated from the DNA
duplexes pass through the column, and the amount is measured from their radioactivity.
A graph showing the percentage of ssDNA at each temperature is drawn.
The temperature at which 50% of the DNA duplexes (dsDNA) have been denatured (T50H) is determined.
As the figure shows, the curve for A/B is to the left of A/A, i.e., duplexes of A/B separated at a lower temperature than those of
A/A. The sequences of A/A are precisely complementary so all the hydrogen bonds between complementary base pairs (A-T, C-G)

19.1.1.3 https://bio.libretexts.org/@go/page/5941
must be broken in order to separate the strands. But where the gene sequences in B differ from those in A, no base pairing will have
occurred and denaturation is easier.
Thus DNA-DNA hybridization provides genetic comparisons integrated over the entire genome. Its use has cleared up several
puzzling taxonomic relationships. DNA-DNA hybridization can also be used to compare genomes of mixed populations of
organisms. For example, when all the bacteria are extracted from 10 g of uncontaminated soil (there are about 1010 cells in it!), the
DNA extracted and purified from the bacteria and subjected to DNA-DNA hybridization analysis, the resulting curves indicate that
there are over a million different species in the soil sample, although the population is dominated by only a few of these.

Chromosome Painting
Another way to compare entire genomes is to attach a fluorescent label to the DNA of individual chromosomes of one species (e.g.,
human) and expose the chromosomes of another species to it. Regions of gene homology will hybridize taking up the fluorescent
label and the "painted" chromosomes can be examined under the microscope.
The method is a modification of fluorescence in situ hybridization (FISH) and is also called Zoo-FISH.
Chromosome painting has shown, for example, that large sections of human chromosome 6 (which includes hundreds of genes in
the major histocompatibility complex (MHC) have their counterpart; i.e. homologous genes, in
chromosome 5 of the chimpanzee
chromosome B2 of the domestic cat
chromosome 7 of the pig
chromosome 23 of the cow

Comparing DNA Sequences

Proteins are the expression of genes so why not compare the actual gene sequences? There are several advantages:
DNA is much easier to sequence than protein.
Genes contain sites that are much freer to change during evolution than protein sequences are. These include:
nucleotides that produce synonymous codons. For example, even if the amino acid at position 20 in two proteins is the
same, the codons for that amino acid might be different in the two species.
Introns and flanking sequences. These regions are relatively free to vary without hurting the final protein product. In other
words, these regions of the genome are under much less pressure from natural selection.
DNA is more stable than protein in the environment. This raises the possibility of doing DNA sequencing on the remains of
extinct organisms. Neaderthal remains over 38,000 years old have yielded samples of DNA that were successfully sequenced.
Some of the most informative studies using comparative DNA sequencing have been done with
rDNA genes; that is, the genes encoding the rRNA molecules (usually of the small subunit (18S in eukaryotes; 16S in bacteria)
of the ribosome.
genes on mitochondrial DNA (mtDNA).
In both cases, the genes are present in multiple copies making their isolation easier.

Cladistics
Ideally, a system of classification should reflect the genealogies of the organisms. Darwin realized this when he wrote: "our
classifications will come, as far as they can be so made, genealogies". A classification based strictly on the rule that all members of
a group must have shared a common ancestor more recently than they have with any species outside the group is called cladistics.
This phylogenetic tree or cladogram depicts the evolutionary relationships of 4 hypothetical species.

Figure 19.1.1.4 Lungfish - cow cladogram

19.1.1.4 https://bio.libretexts.org/@go/page/5941
 They are all descended from an ancestor with 5 traits (1,2,3,4,5) to be used in drawing the tree.
Over the course of time, 3 speciation events occurred producing the branches.
During this time, several of the ancestral traits evolved into a modified or derived form; each one indicated by a different color.
Taxonomists who use cladistic methods have created an extraordinary vocabulary to help them (not necessarily us).
Ancestral traits are called plesiomorphic (shown here as black numbers).
Derived traits are called apomorphic (shown here as colored numbers). All the members of a clade must share one or more
apomorphic traits not found in any other species.
Derived traits shared by two or more species are called synapomorphic. Here species A and B share the synapomorphic
trait designated with a blue 3.
Ancestral traits shared by two or more species are called symplesiomorphic. Here, the trait shown as black 1 is a
symplesiomorphic trait retained by all 4 species.
Note that in comparing the species, the more recent the common ancestor, the more apomorphic traits they share. Thus species
C and D share 4 of the 5 traits but only three (1, 2, and 5) with species A and only two (1 and 5) with species B.
Even if we reconstruct a precise genealogy and draw a phylogenetic tree to represent it, taxonomic problems may still remain.
1. The species is the only taxonomic category that exists in nature. All higher categories (e.g., genus, family, and order) are purely
arbitrary. They are created by taxonomists. For example,
Should species C and D be placed in a single genus with A and B in another?
Or are all four sufficiently closely related that they belong in a single genus?
Or are all four so distantly related that they should be placed in separate genera?
Note that none of these options (and others besides) violates the fundamental rule that all the members of any one group (or
"clade") must have had a common ancestor more recent than any they share with species in other groups.

Figure 19.1.1.5 Primate clades

Those taxonomists who are particularly impressed by the differences between species tend to increase the number of higher
categories. Those with this bias are known fondly as "splitters". "Lumpers", those taxonomists who marvel at the
uniformities they see among species, tend to create fewer higher categories. Thus, splitters might put each of the 4 species in
separate genera while lumpers would put them in a single genus.
2. Classifications based strictly on cladistics are too complex for convenience. In principle, a separate category has to be created
for all the branches derived from each node of the tree. The box shows the conventional classification of Homo sapiens (in the
order Primates of the class Mammalia). Compare it with the graphic above the box showing a classification of just the
primates based more closely on cladistics.

 Example

Scientific names. The Swedish naturalist Carolus Linnaeus - the "father of taxonomy" - created the system for naming species
that is used by biologists throughout the world. The scientific name of each species consists of two parts:
the name of the genus to which it is assigned and
the "specific epithet" which identifies the particular species within the genus.

19.1.1.5 https://bio.libretexts.org/@go/page/5941
 Latin names were used by Linnaeus, but so many species have been discovered since then that now taxonomists simply coin
new words and cast the genus name in the form of a Latin noun and the specific epithet as a Latin adjective. By tradition, both
names are printed in italics, and the genus name is capitalized, but not the specific epithet. Note, too, that the characters of the
Roman alphabet are always used even by biologists in countries where different characters are used for ordinary purposes.
Here is a description of a common jellyfish as it appears in a Japanese guide to marine life.

Reprinted with permission from Hoikusha Publishing Co., Ltd., Tokyo, Japan

3. A classification based strictly on evolutionary kinship (cladistics) also may often seem to violate common sense. Thus a
phylogenetic tree showing the evolutionary history that gave rise to the salmon (a fish), the lungfish, and the cow requires -
according to cladistics - that the lungfish and cow be placed in a clade separate from the salmon. Even though the lungfish is a
fish, the cow has shared a common ancestor with it more recently than its common ancestor with the salmon. Although it is
traditional to classify the lungfish and the salmon together in the class Pisces (fishes), and to assign the cow to the class
Mammalia, this violates the rule of cladistics (so Pisces is said to be a paraphyletic group). The lungfish and the cow with their
apomorphic traits of internal nostrils and epiglottis are descended from a common ancestor (red arrow) that is also the
ancestor of all land-living vertebrates (including ourselves!).
Even Darwin recognized that kinship alone was not always enough for a sound taxonomy so he added a second criterion - degree of
similarity - to be used in assigning species to a taxonomic category.
1. Deducing the evolutionary history of animals is particularly difficult because all the 24 or more phyla of animals appeared
within a short time before and during the Cambrian and have since evolved along separate lines. This means that all the
branches on the phylogenetic tree are long and bunched so closely at their base that it is difficult to determine their
relationships.
2. Computer power. More data would help, but as more data become available, the ability of computer programs to sort out the
most likely tree becomes overwhelmed.
3. Changing rate of evolution. There is considerable evidence that mutation rates are not steady from branch to branch in
phylogenetic trees. Thus a branch based on molecules that have evolved rapidly would seem longer than otherwise.
4. Back mutations. These mask the changes that preceded them and make branches look shorter than they should be.
5. Gene transfer between species. The recent availability of complete gene sequences for many bacteria have revealed genes that
appear to have passed from one group to another rather than having been descended from a common ancestor. Most of these
"horizontal" gene transfers are between two different species of bacteria, but the gene sequence of Mycobacterium tuberculosis
reveals 8 genes that it appears to have picked up from its human host! So many horizontal gene transfers have occurred that
some bacterial taxonomists despair that a proper phylogenetic tree can ever be deduced for them.
6. Convergent evolution. Evolution in which two species from different genealogies come to resemble each other is called
convergent evolution and structures that resemble each other superficially (and may serve the same function) are called
analogous.

19.1.1.6 https://bio.libretexts.org/@go/page/5941
 Figure 19.1.1.6 Wombat
There are many examples of marsupial mammals in Australia which bear a striking resemblance to placental mammals of Europe
and North America. The North American woodchuck or groundhog and the Australian wombat (photo courtesy of the Australian
News and Information Bureau), for examples, look superficially to be close relatives. But their similarities are analogous, not
homologous, and have arisen as a result of similar selection pressures in similar ecological niches. The wombat has no placenta,
cares for its young in a pouch as other marsupials do, and should be classified with them. In fact we are more closely related to the
North American woodchuck than the wombat is!
In the language of cladistics, the wombat is placed in a clade with all marsupials because they share the marsupial pouch (an
apomorphic trait) but are nonetheless mammals because they, too, have hair (a plesiomorphic trait).
Convergent evolution also occurs at the level of molecules.
Examples:
Cows and langur monkeys both synthesize a lysozyme that share the same activity, but comparison of their amino acid
sequences indicates that each has evolved from a different ancestral molecule.
Cows and the bacterium Yersinia both synthesize a tyrosine phosphatase with similar three-dimensional structures around their
active site and similar activity. However, each has evolved from a totally different ancestral molecule.
The bacterium Bacillus subtilis synthesizes a serine protease that acts just like those synthesized by mammals but not only has
an entirely different primary structure but its three-dimensional structure (tertiary) structure is different as well.
Representatives of four different orders of insects, orders that last shared a common ancestor 300 million years ago, have
independently evolved an identical point mutation in their Na+/K+ ATPase which protects it from inactivation by the cardiac
glycosides in the plants on which they feed. Link to an illustrated discussion of how this mutation can lead to aposematic
coloration and mimicry.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 19.1.1: Taxonomy is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.1.1.7 https://bio.libretexts.org/@go/page/5941
19.1.2: Protists
What are protists?
They are eukaryotes because they all have a nucleus.
Most have mitochondria although some have later lost theirs. Mitochondria were derived from aerobic alpha-proteobacteria
that once lived within their cells.
Many have chloroplasts with which they carry on photosynthesis. Chloroplasts were derived from photosynthetic
cyanobacteria living within their cells.
Many are unicellular and all groups (with one exception) contain some unicellular members.
The name Protista means "the very first", and some of the 80-odd groups of organisms that we classify as protists may well
have had long, independent evolutionary histories stretching as far back as 2 billion years. But genome analysis added to other
criteria show that others are derived from more complex ancestors; that is, are not "primitive" at all.
Genome analysis also shows that many of the groups placed in the Protista are not at all closely related to one another; that is,
the protists do not represent a single clade.
So we consider them here as a group more for our convenience than as a reflection of close kinship, and a better title for this
page would be "Eukaryotes that are neither Animals, Fungi, nor Plants".

The Euglenozoa
Most Euglenozoa are unicellular. Many swim by means of a single flagellum. They are not encased in a cell wall so they are
flexible as well as motile. Euglena is a typical member of the group (which numbers about 1600 species). Because some members
of the group (like Euglena) have chloroplasts, these organisms used to be called "Euglenophytes", but in fact they are neither plants
("phytes") nor animals ("zoa"). Rather — like the other organisms on this page — they are the living descendants of some of the
very earliest eukaryotes. Trypanosoma brucei, the cause of African sleeping sickness in humans, is a member of the group. The
electron micrograph shows T. brucei as it occurs in the salivary gland of the tsetse fly ready to be injected into the mammalian host
when the fly bites. The specimen is 12 µm long.

Figure 19.1.2.1 T. Brucei (by L. Tetley; courtesy of Keith Vickerman)

In Latin America, Trypanosoma cruzi, another member of the group, is the cause of Chagas disease in humans.

Ciliates, Sporozoans, and Dinoflagellates: the Alveolates

These three phyla are grouped in a clade called the alveolates because they all have a system of saclike structures ("alveoli") on the
inner surface of their plasma membrane as well as close homology in their gene sequences.

Ciliates
The ciliates move by the rhythmic beating of their cilia. Although single-celled, some are large enough to be seen with the naked
eye. In fact, the tiny parasitic wasp Megaphragma mymaripenne, with its tens of thousands of cells (4,600 neurons alone), is no
larger than Paramecium. They feed by sweeping a stream of particle-laden water through a "mouth" and "gullet" and into a food
vacuole. Undigested wastes are discharged at a permanent site. Fresh water ciliates cope with the continuous influx of water from
their hypotonic surroundings by pumping it out with one or more contractile vacuoles. Parasitic ciliates, which live in isotonic
surroundings, have no contractile vacuole. All of this rightly suggests that although they are unicellular, there is nothing
rudimentary about the ciliates. Their single cell is far more elaborate in its organization than any cell out of which multicellular
organisms are made. Examples: Paramecium, Stentor, Vorticella, Tetrahymena thermophila.

Sporozoans (Apicomplexa)
The members of this group share an "apical complex" of microtubules at one end of the cell (hence the name that many prefer to
the old name of sporozoans). All the members of the phylum are parasites. The genus Plasmodium causes malaria, one of the

19.1.2.1 https://bio.libretexts.org/@go/page/5943
greatest scourges of humans. There are 4 species that infect humans of which Plasmodium falciparum is the most dangerous.
Malaria has probably caused more human deaths than any other infectious disease; even today it is estimated to kill a million
people a year in the sub-Saharan Africa. The organism is transmitted from human to human through the bite of mosquitoes of the
genus Anopheles.

Figure 19.1.2.2 Plasmodium lifecycle

The diagram shows the Plasmodium life cycle.
The mosquito bite injects sporozoites into the human host.
These invade the liver where they develop into merozoites.
The merozoites invade red blood cells where they reproduce.
Periodically, they all break out of the red cells together bringing on the chills and fever characteristic of the disease.
Eventually some merozoites develop into either male or female gametocytes.
These will die unless they are sucked up by the bite of an anopheline mosquito.
Once in the stomach of the mosquito, the gametocytes form gametes: sperm and eggs.
These fuse to form zygotes.
The zygote invades the stomach wall of the mosquito forming thousands of sporozoites.
These migrate to the salivary gland, ready to be injected into a new human host.
Most forms of malaria are chronic. The organisms may coexist with their host for years (but cannot complete their life cycle
there).
Toxoplasma gondii is another parasitic member of this group. Plasmodium, Toxoplasma, and some of the other members of this
group contain a membrane-enclosed organelle called the apicoplast. They seem to have inherited it from a common ancestor that
acquired it by engulfing a chloroplast.

Dinoflagellates
There are about 1000 species of dinoflagellates. Most are unicellular. Most use chlorophylls a and c. Unlike most eukaryotes, they
lack histones on their chromosomes and have a simpler form of mitosis. They do have the eukaryotic type ("9 + 2") of flagellum
(two of them in fact). Occasionally they reproduce explosively, creating poisonous red tides that may cause extensive kills of
marine fish and make filter-feeding marine animals like clams unfit for human consumption.

The Stramenopiles
These organisms belong to a single clade, the stramenopiles (a/k/a heterokonts). There are four members in this group - diatoms,
golden algae, brown algae and water molds. The first three members share:
a yellow-brown pigment (which gives them their color). It is a carotenoid called fucoxanthin.
chlorophylls a and c
All four of them (plus a number of other groups not listed) share genes closely-homologous to those in both green and red
algae. This suggests that they are all descended from a heterotrophic eukaryotic ancestor that acquired both a green alga and a

19.1.2.2 https://bio.libretexts.org/@go/page/5943
 red alga by a secondary endosymbiosis. (While the water molds no longer are photosynthetic, they still retain both green and
red alga genes.)

Diatoms
Diatoms are unicellular. Their cell wall or shell is made of two overlapping halves. These are impregnated with silica and often
beautifully ornamented. The photo (courtesy of Turtox) is of Arachnoidiscus ehrenbergi magnified some 400 times. Diatoms are
major producers in aquatic environments; that is, they are responsible for as much as 40% of the photosynthesis that occurs in
fresh water and in the oceans. They serve as the main base of the food chains in these habitats, supplying calories to heterotrophic
protists and small animals. These, in turn, feed larger animals.

Figure 19.1.2.3 Arachnoidiscus ehrenbergi

Golden Algae (Chrysophyta)

Most are unicellular.
Found in fresh water.
Important producers in some aquatic food chains.
In low light conditions, may lose their chlorophyll and turn heterotrophic feeding on bacteria and/or diatoms.
Over 1000 species alive today; many more in the fossil record.

Brown Algae (Phaeophyta)

The rockweeds and kelps. Some kelps grow as long as 30 meters.
All are multicellular although without much specialization of cell types.
Most are found in salt water.
Used for food in some coastal areas of the world and harvested in the U. S. for fertilizer and as a source of iodine.

Water Molds (Oomycetes)

As their name suggests, water molds were once considered to be fungi. But unlike fungi, the cell wall of water molds is made of
cellulose, not chitin. Furthermore, their gene sequences are very different from those of fungi (and most closely related to those of
diatoms, golden and brown algae).
Some notable water molds:
Some species (e.g., Saprolegnia, Achyla) are parasites of fishes and can be a serious problem in fish hatcheries.
Downy mildews damage grapes and other crops.
Phytophthora infestans, the cause of the "late blight" of potatoes. In 1845 and again in 1846, it was responsible for the almost
total destruction of the potato crop in Ireland. This led to the great Irish famine of 1845–1860. During this period,
approximately 1 million people starved to death and many more emigrated to the New World. By the end of the period, death
and emigration had reduced the population of Ireland from 9 million to 4 million.
Phytophthora ramorum, which is currently killing several species of oaks in California.

Red Algae
The red algae are almost exclusively marine. Some are unicellular but most are multicellular. Approximately 6000 species have
been identified. They are photosynthetic using chlorophyll a. Their closest relatives are the green algae and land plants. Like the
cyanobacteria, they use as antenna pigments - phycoerythrin (which makes them red) and phycocyanin. They do not have the

19.1.2.3 https://bio.libretexts.org/@go/page/5943
eukaryotic "9+2" flagellum. Some are used as food in coastal regions of Asia. Agar, the base for culturing bacteria and other
microorganisms, is extracted from a red alga.

Slime Molds (Mycetozoa)

Cellular Slime Molds
The organisms in this group have a complex life cycle during the course of which they go through unicellular, multicellular,
funguslike (form spores) and protozoanlike (amoeboid) stages. Thousands of individual amoebalike cells aggregate into a slimy
mass - each cell retaining its identity (unlike plasmodial slime molds). The aggregating cells are attracted to each other by the
cyclic AMP (cAMP) that they release.
With the exception of one species that causes powdery scab on potatoes, these organisms are of little economic importance.
However, their combination of traits makes them of great scientific interest. Molecular phylogenies place them in the same clade as
animals (metazoa) and fungi.

Plasmodial (Acellular) Slime Molds (Myxomycetes)

Figure 19.1.2.4 Plasmodial stages of Stemonitis

At one stage in their life cycle, these organisms consist of a spreading, slimy, multinucleate mass called a plasmodium that moves
slowly over its substrate (e.g., a rotting log) engulfing food and growing as it does so. Eventually, the plasmodium develops stalks
that produce and release spores. If the spores land in a suitable location, they germinate forming single cells that move by both
flagella and pseudopodia. These fuse in pairs and start forming a new plasmodium.
The left photo (courtesy of Prof. I. K. Ross) shows the plasmodial stage of Stemonitis just before it formed sporangia. The right
photo (courtesy of Turtox) shows the fully developed sporangia of Stemonitis.
Physarum polycephalum, another member of this group, is the subject of many laboratory studies.

Protists without typical mitochondria

There are several groups of protists that were long thought to have no mitochondria. However, most (perhaps all) had them in the
past. Today, only remnants of their ancestor's mitochondria - called mitosomes remain.
Some examples are:
Microsporidia
All are unicellular obligate intracellular parasites.
Many are pathogenic in insects (one is even marketed commercially as a biocontrol agent).

19.1.2.4 https://bio.libretexts.org/@go/page/5943
 Some contaminate drinking water supplies and can cause gastrointestinal upsets in humans. Microsporidia, such as
Encephalitozoon cuniculi, are a common cause of diarrhea in AIDS patients. Encephalitozoon cuniculi has a tiny genome
with only 1,997 protein-encoding genes — fewer than many bacteria (e.g., E. coli has 4,290). Obliged to live within the cells
of its host, it has lost the genes for many important functions (e.g., the citric acid cycle) depending instead on its host.
Fungi are their closest relatives.
Entamoeba histolytica.
Causes amebic dysentery, the third most common parasitic disease of humans (after malaria and schistosomiasis). Its closest
relatives are the slime molds.
Giardia intestinalis (also known as Giardia lamblia)
Frequently encountered in public water supplies contaminated by animal feces. Causes diarrhea in humans. Avoids the host
immune response by periodically changing its surface protein coat.

Choanoflagellates

Figure 19.1.2.5 Choanoflagellates

These are single-celled (e.g., Monosiga), aquatic (both fresh water and marine) protists that have a single flagellum surrounded by
a collar ("choano" = collar) of microvilli. Some (e.g., Proterospongia) form simple colonies during part of their life. The flagellum
is used for swimming and also beats bacteria-containing water through the collar for feeding.
Sponges also use collar cells to filter food from the water. Not only does this suggest a close relationship between the two groups,
but other evidence indicates that choanoflagellates are the closest protistan relatives of all animals (metazoa). Although single cells,
they express genes for several proteins that are essential to cell-cell interactions in metazoans, such as
cadherins (attach cells to each other)
tyrosine kinases (used in many examples of cell-cell signaling)
What function these proteins have in the choanoflagellates is unknown.

This page titled 19.1.2: Protists is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.1.2.5 https://bio.libretexts.org/@go/page/5943
19.1.3: Ciliates
Although single-celled, there is nothing primitive or simple about these protists. Not only are they large for single cells (some can
be seen by the unaided eye), but they contain organelles that parallel in function the organs of multicellular creatures. In fact, some
biologists consider the ciliates to be acellular (not cellular) rather than unicellular in order to emphasize that their "body" is far
more elaborate in its organization than any cell out of which multicellular organisms are made.

Although single-celled, there is nothing primitive or simple about these protists. Not only are they large for single cells (some can
be seen by the unaided eye), but they contain organelles that parallel in function the organs of multicellular creatures. In fact, some
biologists consider the ciliates to be acellular (not cellular) rather than unicellular in order to emphasize that their "body" is far
more elaborate in its organization than any cell out of which multicellular organisms are made.
Ciliates have:
At least one small, diploid (2n) micronucleus. It contains the entire genome but is not active in gene transcription.
A large, polyploid macronucleus that contains the active genes that run the cell.

Sexual reproduction in Ciliates

Figure 19.1.3.1 Paramecium reproduction

Two parents come together and two parents separate. What kind of reproduction is that? you may well ask.
But the process they have been through is the very essence of sexual reproduction - genetic recombination. The "offspring" are
not the same as the parents. They are new individuals and their macronucleus will soon reflect that fact.
Ciliated protozoans have been the source of several important discoveries in biology, for example:
The first ribozymes were found in Tetrahymena thermophila.
Telomerase was also discovered in Tetrahymena thermophila.

This page titled 19.1.3: Ciliates is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.1.3.1 https://bio.libretexts.org/@go/page/5945
19.1.4: Volvox

Figure 19.1.4.1: Volvox is a genus of multicellular green algae. by http://www.mikro-foto.de (CC-SA-BY Frank Fox)

Volvox Reproduction
Volvox can reproduce both asexually and sexually. In asexual reproduction, the gonidia develop into new organisms that break out
of the parent (which then dies). In sexual reproduction, the presence of an inducing chemical causes
The gonidia of the males to develop into clusters of sperm.
The gonidia of the females to develop into new spheres each of whose own gonidia develops into a pair of eggs.
The sperm break out of the male parent and swim to the female where they fertilize her eggs.
The zygotes form a resting stage that enables Volvox to survive harsh conditions.
The genome of Volvox carteri consists of 14,560 protein-encoding genes - only 4 more genes than in the single-celled
Chlamydomonas reinhardtii! Most of its genes are also found in Chlamydomonas. The few that are not encode the proteins needed
to form the massive extracellular matrix of Volvox.

This page titled 19.1.4: Volvox is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.1.4.1 https://bio.libretexts.org/@go/page/5947
19.1.5: Diversity and Evolutionary Relationships of the Plants
Evolution and Classification
The organisms we call plants are assigned to a single clade; that is, a natural grouping based on the belief that they have all evolved
from a common ancestor more recent than any shared with other organisms. Among the criteria for doing this are:
their shared use of the photosynthetic pigments chlorophyll a and chlorophyll b
the similarities in the nucleotide sequences of the genes encoding both their small subunit (18S) and large subunit (25S)
ribosomal RNA
their shared cellulose cell wall

Figure 19.1.5.1 Plant clade

We shall examine here a selection of the most prominent groups.

Green Algae
The ancestors of these organisms were the most primitive members of the clade. In other words, organisms that we would put in
this division were probably the ancestors of all the other plants. There are some 7000 species living today. They include:
microscopic, unicellular forms like Chlamydomonas
colonial forms like the filamentous Spirogyra
multicellular forms like Volvox and Ulva, the sea lettuce
Although some of the multicellular forms are large, they never develop more than a few types of differentiated cells and their
fertilized eggs do not develop into an embryo.
Green algae are an important source of food for many aquatic animals. When lakes and ponds are "fertilized" with phosphates and
nitrates (e.g., from sewage and the runoff from fertilized fields and lawns), green algae often form extensive algal "blooms".

Liverworts and Mosses (Bryophytes)

These are fairly simple plants that do produce a number of differentiated cell types and whose fertilized egg develops into a distinct
embryo.
However, they have neither vascular tissue (xylem and phloem) nor woody tissue and thus never grow very large. Some 16,000
living species are known. Most grow in moist places.

Lycopsids (Lycophytes)
Prominent members of this group are often called club mosses. They are not mosses at all, but vascular plants with xylem and
phloem running through their roots, stems, and leaves. The leaves are quite simple and small with their vascular tissue in a single,
unbranched vein. The "club" of their name comes from the appearance of their spore-forming structures called strobili. Club
mosses are also sometimes called "ground pines", but they are not pines either. The photo shows Lycopodium obscurum.

19.1.5.1 https://bio.libretexts.org/@go/page/5949
 Figure 19.1.5.2 Club moss
About 1000 species of lycopsids exist today. All are small (those in the photo stand about 8 in. [20 cm] tall), but it was not always
so. Fossil lycopsids in the Mississippian and Pennsylvanian periods (the so-called Carboniferous era) reached heights of 100 feet
(30 meters). Their remains contributed to the formation of coal.

Chloroplast Genes
Chloroplasts (as well as mitochondria) have their own genome. The diagram (based on the work of Ohyama, K. et al., Nature
322:572, 1986 and Linda A. Raubeson and R. K. Jansen, Science 225:1697, 1992) shows the genome of the first chloroplast DNA
to be sequenced, that of the liverwort Marchantia polymorpha. It contains 121,024 base pairs encoding 128 genes. The short lines
indicate a few of the tRNA genes, some of which are labeled.

Figure 19.1.5.3 Chloroplast

The order of the genes between the arrows (~6:30 to ~10:00) is also found in the lycopsids. But in all other vascular plants, this
region is inverted and the order of the genes is precisely reversed. This provides further evidence that the other vascular plants we
shall examine below, the
horsetails
ferns
gymnosperms
angiosperms
belong to a separate clade.

Horsetails

19.1.5.2 https://bio.libretexts.org/@go/page/5949
 Figure 19.1.5.4 Horsetails
(Classified as Equisetopsida although many botanists prefer the older term Sphenopsida.)
The common name comes from the characteristic pattern of branching: whorls or rings of branchlets arising from an above-ground
shoot. The shoot develops each season from an underground stem (rhizome). Horsetails often grow in sandy places and incorporate
silica in their stems. This gives them an abrasive quality which caused them to once be used for cleaning pots and pans, which gave
rise to another common name: scouring rush.
Only one genus, Equisetum, containing about 25 species, survives today. However, many other, much larger, species were
dominant features of the Carboniferous and, like the early lycopsids, contributed to the formation of coal.
The drawing is of Equisetum palustre, a common horsetail. Spores are formed in the strobilus.

Ferns
(Assigned to the Pteridopsida although some botanisits prefer Filicopsida.)
Some 15,000 species of ferns live on earth today. Many of these are found in the tropics where some — the "tree ferns" — may
grow to heights of 40 ft (13 m) or more. The ferns of temperate regions are smaller. They are usually found in damp, shady
locations. Their stems — called rhizomes — as well as their roots grow underground and are perennial. Their leaves, called
fronds, grow up from the rhizome each spring.

Seed Plants (Spermatophytes)

Gymnosperms
Fossil from the Devonian period reveal fernlike plants that were heterosporous; that is, produced two kinds of spores: microspores
(male) and megaspores (female). The megaspores were not released from the parent sporophyte. Fertilization took place within the
tissue of the parent sporophyte thus freed from dependence on surface water. However, the necessity for the microspores to be
carried from one plant to another in order to reach the female gametophyte robbed them of their value as agents of dispersal. This
function was taken over by seeds - dormant, protected, embryo sporophytes.
The seed ferns, as these plants are called, were among the earliest gymnosperms. Although seed ferns are now extinct, some of
their living descendants, the cycads, resemble them closely. Cycads reveal their ancient lineage by the fact that after the microspore
reaches the ovule, it liberates a ciliated sperm which, swimming in moisture supplied by the parent sporophyte, reaches the egg.
Ginkgos are also gymnosperms that use motile sperm.

Conifers
These gymnosperms get their name from their cones: male cones in which the in which microspores develop and female cones in
which megaspores develop. The microspores develop into pollen grains that are carried by the wind to the female cones. Here each
germinates into a pollen tube which grows into the tissues of the female cone until it reaches the vicinity of the egg. (In pines, this
may take a year.) Then the tube ruptures and a sperm nucleus fuses with the egg to form the zygote.

19.1.5.3 https://bio.libretexts.org/@go/page/5949
 Figure 19.1.5.5 Pine lifecycle
After fertilization, the zygote develops into a tiny embryo sporophyte plant. There are approximately 630 species of living conifers.
They include the pines, spruces and firs. Conifers include the largest and the oldest of all living organisms. One redwood (genus
Sequoia) growing in California is almost 400 feet (122 meters) high. Bristlecone pines growing in the mountains of eastern
California are more than 4000 years old.
Although most conifers are evergreen, their leaves are modified as "needles", and these reduce snow load and transpiration during
the winter in the harsh high-latitude climates where conifers are the dominant species of plants. But by retaining their needles
during the winter, conifers are ready to begin photosynthesis immediately upon the return of spring.
Coniferous forests are of great economic importance producing lumber for building and pulp for paper making.

Angiosperms
Although angiosperms appear in the fossil record in Jurassic deposits, it was not until the end of the Mesozoic era that angiosperms
became the dominant plants of the landscape. That they dominate the earth's flora today is clear: there are some 260,000 species of
living angiosperms; the rest of the plant kingdom includes only some 47,700 species. Currently, the angiosperms are classified in
some 54 orders (The names of the orders end in ..ales, e.g., Arabidopsis is in the order Brassicales.). Each order contains from one
to several dozen families (Family names end in ..aceae, e.g., Arabidopsis is in the family Brassicaceae).

Monocots and Dicots

Of over 400 families of angiosperms, some 80 of them fall into a single clade, called monocots because their seeds have only a
single cotyledon. The remainder are the dicots whose seeds have two cotyledons. The large majority of these occupy a single clade
called the eudicots.

Figure 19.1.5.6 Monocot vs dicot

Monocot traits:
a single cotyledon in their seed
parallel venation in their leaves
petals and sepals in 3s or some multiple thereof

19.1.5.4 https://bio.libretexts.org/@go/page/5949
 vascular bundles scattered randomly throughout the stem
Monocots include:
palms (Arecaceae)
orchids (Orchidaceae)
yams, sweet potatoes (Dioscoreaceae)
lilies, onion, asparagus (Liliaceae)
bananas (Musaceae)
and all the grasses (Poaceae), which include many of our most important plants such as
corn (maize)
wheat
rice
and all the other cereal grains upon which we depend so heavily for food as well as
sugar cane and bamboo
Dicot traits:
two cotyledons in their seeds
netted venation in their leaves
petals and sepals in 4s, 5s, or some multiple thereof
vascular bundles in the stem arranged in a radial pattern like spokes of a wheel.
Here is a selection of eudicots.

Family Examples

Anacardiaceae poison ivy, cashews, pistachios

Asteraceae asters and all the other composite flowers

Brassicaceae cabbage, turnip; Arabidopsis, and other mustards

Cactaceae cacti

Cucurbitaceae squashes

Euphorbiaceae cassava (manioc)

Fabaceae beans and all the other legumes

Fagaceae oaks

Linaceae flax (source of linen)

Malvaceae cotton

Oleaceae olives, ashes, lilacs

Rosaceae roses, apples, peaches, strawberries, almonds

Rubiaceae coffee

Rutaceae oranges and other citrus fruits

Solanaceae potato, tomato, tobacco

Theaceae tea

Vitaceae grapes

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 19.1.5: Diversity and Evolutionary Relationships of the Plants is shared under a CC BY 3.0 license and was authored, remixed,
and/or curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history

19.1.5.5 https://bio.libretexts.org/@go/page/5949
is available upon request.

19.1.5.6 https://bio.libretexts.org/@go/page/5949
19.1.6: Arabidopsis Thaliana - A Model Organism
Arabidopsis Thaliana has become to plant biology what Drosophila melanogaster and Caenorhabditis elegans are to animal
biology. Arabidopsis is an angiosperm, a dicot from the mustard family (Brassicaceae). It is popularly known as thale cress or
mouse-ear cress. While it has no commercial value - in fact is considered a weed - it has proved to be an ideal organism for
studying plant development.

Figure 19.1.6.1: Arabidopsis Thaliana. Photo courtesy of Nicole Hanley Markelz of the Plant Genome Research Outreach Program
at Cornell University.
Some of its advantages as a model organism:
It has one of the smallest genomes in the plant kingdom: 135 x 106 base pairs of DNA distributed in 5 chromosomes (2n = 10)
and almost all of which encodes its 27,407 genes.
Transgenic plants can be made easily using Agrobacterium tumefaciens as the vector to introduce foreign genes.
The plant is small - a flat rosette of leaves from which grows a flower stalk 6–12 inches high.
It can be easily grown in the lab in a relatively small space.
Development is rapid. It only takes 5– 6 weeks from seed germination to the production of a new crop of seeds.
It is a prolific producer of seeds (up to 10,000 per plant) making genetics studies easier.
Mutations can be easily generated (e.g., by irradiating the seeds or treating them with mutagenic chemicals).
It is normally self-pollinated so recessive mutations quickly become homozygous and thus expressed.
Other members of its family cannot self-pollinate. They have an active system of self-incompatibility. Arabidopsis,
however, has inactivating mutations in the genes — SRK and SCR - that prevent self-pollination in other members of the
family.
However, Arabidopsis can easily be cross-pollinated to do genetic mapping and produce strains with multiple mutations.
Many of the findings about how plants work - described throughout these pages - were learned from studies with Arabidopsis.

This page titled 19.1.6: Arabidopsis Thaliana - A Model Organism is shared under a CC BY 3.0 license and was authored, remixed, and/or
curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is
available upon request.

19.1.6.1 https://bio.libretexts.org/@go/page/5951
19.1.7: Fungi
Some 100,000 species of fungi have been identified, but the true number is probably larger.

Characteristics of Fungi
Most fungi grow as tubular filaments called hyphae. An interwoven mass of hyphae is called a mycelium. The walls of hyphae are
often strengthened with chitin, a polymer of N-acetylglucosamine. The linkage between the sugars is like that of cellulose and
peptidoglycan and produces the same sort of structural rigidity.

Figure 19.1.7.1 Chitin

Fungi disperse themselves by releasing spores, usually windblown. Fungal spores are present almost everywhere (and are a
frequent cause of allergies). Spores of the wheat rust fungus have been found at 4000 m in the air and more than 1450 km (900
miles) from the place they were released. No wonder then that most fungi are worldwide in their distribution.
Fungi are heterotrophic. Some live as saprophytes, getting their nourishment from the surroundings (often having first digested it
by secreting enzymes). They perform a crucial role in nature by decomposing dead organisms and releasing their nutrients for reuse
by the living. Some live in a mutually beneficial symbiotic relationship with another organism, often a plant. The association of
fungus and plant root is called a mycorrhiza. Some 80% of land plants benefit from symbiotic mycorrhiza. The plant benefits by
more-efficient mineral (especially phosphorus) uptake and the fungus benefits by the sugars translocated to the root by the plant.

Figure 19.1.7.2 Indian pipe

Mycorrhizal fungi may also form conduits for nutrients between plant species. The colorless, and hence heterotrophic Indian pipe
(Monotropa uniflora - pictured on the right) is an angiosperm that must secure all its nourishment from mycorrhizal fungi that are
attached at the same time to the roots of some autotrophic plant such as a pine tree. Radioactive carbon administered to the pine (as
CO2) soon turns up in carbohydrates in nearby Indian pipes.
Some fungi are parasitic, causing serious damage to their host (a few examples are given below). Some fungi are both.
Metarhizium robertsii is a soil fungus that lives symbiotically with plants but parasitizes (and kills) soil insects. Its hyphae
penetrate both the roots of the plant and the corpse of the insect. It has been demonstrated that nitrogen released by the decaying
insect is transported by the fungus to the plant. (See S. W. Behie, P. M. Zelisko, M. J. Bidochka in Science, 22 June 2012.)
Metarhizium is an ascomycete.

Ascomycetes
Ascomycetes produce two kinds of spores: asexual spores called conidia and ascospores produced following sexual reproduction.
Four or eight ascospores develop inside a saclike ascus (the group is commonly called sac fungi). Some notable examples include:
Saccharomyces cerevisiae one of the budding yeasts. It ferments sugar to ethanol and carbon dioxide and thus is used to
make alcoholic beverages like beer and wine, to make ethanol for industrial use and in baking (it is often called baker's yeast).

19.1.7.1 https://bio.libretexts.org/@go/page/5953
 Here, it is the carbon dioxide that is wanted (to make bread and cakes "rise" and have a spongy texture). Yeast is also used in
the commercial production of some vitamins and in the production - using recombinant DNA technology - of some human
therapeutic proteins.
Neurospora crassa, another favorite "model" organism in the laboratory.
The fungal partner in most lichens is an ascomycete.
Powdery mildews that attack ornamental plants
The chestnut blight, which in a few decades killed almost all of the mature American chestnut trees in the Appalachians of
North America.
The Dutch elm disease, which has killed many of the American elms in the United States.
Pneumocystis jirovecii, which is a major cause of illness in immunosuppressed people, e.g., patients with AIDS.
The truffle and the morel, both highly-prized food delicacies. Truffles establish a symbiotic relationship with the roots of such
trees as oaks.

Figure 19.1.7.3 Truffles. (Public Domain).

Lichens
Lichens are fungi that live in a symbiotic association with an autotrophic green alga or cyanobacterium (the "photobiont") or - in
some cases - both. The fungal partner (the "mycobiont") in most lichens (98% of them) is an ascomycete. Zygomycetes make up
the remainder. The relationship is often characterized as mutualistic; that is, both partners benefit. But recent evidence (e.g. in
British soldier) suggests that while the fungus is dependent on its autotrophic partner, the photobiont is often perfectly content to
live alone. Recently many lichens have been found to harbor a third partner, a single-celled basidiomycete. Its function remains to
be discovered.

Figure 19.1.7.4 Lichens

Lichens secrete a variety of unusual chemicals; some of these probably assist in the breakdown of rock substrates like the one
shown here.

 The British Solder

The below image is of the colorful lichen called British soldier. The fungus is Cladonia cristatella, an ascomycete. Its name is
the name given to the lichen. The photobiont is Trebouxia erici, a green alga. It is found in many other lichens as well, and also
can be found growing independently. The algal cells eventually are killed by the fungus, but are continuously replaced by new
ones. So the relationship in this lichen is one of controlled parasitism rather than mutualism.

19.1.7.2 https://bio.libretexts.org/@go/page/5953
 Figure 19.1.7.5 British soldier
The red cap produces the spores of the fungus, but these alone cannot form new lichens. Other structures (e.g., soredia),
containing both partners, are needed to disperse the lichen to new locations. Some lichens release only fungal spores. These
mycobionts depend for their continued survival on finding an acceptable photobiont released from other lichens. Phylogenetic
trees, based on both ribosomal RNA genes and many protein-coding genes, as well as fossils indicate that lichens have been
present on the earth for at least 600 million years.

Today about 14,000 species of fungi form lichens. Lichens are extremely sensitive to air pollution. One of the best contemporary
examples of evolutionary adaptation is the change in coloration of the peppered moth as the lichens in its habitat declined because
of air pollution and then returned when air quality controls were put in place. Some modern fungi (e.g., Penicillium chrysogenum,
the source of the antibiotic penicillin) appear to have evolved from lichen-forming ancestors — abandoning their original symbiotic
way of life.

Basidiomycetes
Basidiomycetes include mushrooms, shelf fungi, puffballs, rusts, and smuts. They are dispersed by spores borne at the tips of
basidia (giving rise to the name for the group). Mushrooms are masses of interwoven hyphae growing up from the main mass of
the mycelium growing underground. The basidia develop on the undersides and release their spores (four from each basidium) into
the air.

Figure 19.1.7.6
A single mycelium may expand outward year after year as its hyphae grow into new terrain. In some species, mushrooms are sent
up once a year at the periphery producing a circle known since medieval times as a "fairy ring".
Some notable basidiomycetes:
Armillaria bulbosa. A single specimen in northern Michigan (USA) was found to have spread over 37 acres (15 hectares) of the
forest floor. RFLP analysis of samples taken from many different locations within this area showed that all the samples were
from a single clone. Assuming the normal rate of vegetative growth for this species, it must have taken 1500 years to spread to
that size.
the cultivated, edible mushroom that finds its way into pizza, soups, etc.
Amanita muscaria. Forms a beautiful mushroom but deadly when eaten.
Smuts. Parasites of important crops like wheat, oats, and rye.
Rusts. Some, such as

19.1.7.3 https://bio.libretexts.org/@go/page/5953
 wheat black stem rust (Puccinia graminis) and
white pine blister rust
are serious pests. Both have complicated life cycles during which they pass through a second plant host (barberry plants for
wheat black stem rust, gooseberries or wild currants for the white pine blister rust).

Zygomycetes
All the fungi assigned to this group (which probably does not represent a single clade) form spores in a sporangium. Some notable
examples:
the bread mold, Rhizopus stolonifera
Rhizopus oryzae, used to make sake, the rice wine of Asia. Can also infect humans, especially if they are immunosuppressed
(e.g., AIDS patients, transplant recipients).
Another species of Rhizopus is used in the commercial production of glucocorticoids.
Many mycorrhizal fungi belong to this group.

Chytrids
This small group (~1000 species) is thought to be the most primitive of the fungi. Unlike all the other fungi, its members produce
flagellated gametes (for sexual reproduction) and flagellated zoospores (for asexual reproduction). They are mostly aquatic.Two
species are responsible for the recent worldwide decline in amphibian populations (frogs, toads, and salamanders).

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 19.1.7: Fungi is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.1.7.4 https://bio.libretexts.org/@go/page/5953
19.1.8: Yeast

Figure 19.1.8.1 Yeast

This page titled 19.1.8: Yeast is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.1.8.1 https://bio.libretexts.org/@go/page/5955
19.1.9: Barcoding
Barcoding is the term applied to a technology that is being developed to speed the identification of specimens of living things. So
far, identification and classification of animals has progressed furthest. Although each individual in most species has a unique
genome sequence, the differences between individuals of one species are much smaller than the differences between individuals of
different species. Thus determining the genome sequence of a specimen should enable it to be positively classified if the sequences
of other members of its species are already in a database.
However, sequencing entire genomes of animals is an enormous undertaking. (Most mammals have some 3 billion base pairs of
DNA.) A more practical approach is to settle on the sequence of a single gene that is found in all animal life. The one that has been
chosen for animals is the gene, COI, encoding the largest subunit of cytochrome c oxidase.

Advantages
It is a mitochondrial gene and thus each cell has hundreds-to-thousands of copies of it as opposed to only two copies of each of
its nuclear genes.
It has no introns (in animals).
Thanks to the redundancy of the genetic code, it can mutate quite freely, especially in the third position of its codons.
Furthermore mitochondrial gene sequences vary more between related species than their nuclear genes do. For example, while
the sequence differences between the nuclear genes of humans and chimpanzee is only about 1%, the difference between their
mitochondrial gene sequences is some 9%.
Within a species, however, there is little variation from specimen to specimen in their mitochondrial gene sequences.

Procedure
The mitochondrial DNA is extracted.
A fragment from the 5' end of COI (~648 base pairs) is isolated (the entire gene has ~1500 base pairs).
The fragment is amplified by PCR using readily-available primers.
The sequence is determined and compared with those already in a database.

Early Results
Barcoding analysis of several hundred different birds has shown that barcode results usually reflect the species identification based
on more conventional criteria. However, a few cases have arisen where:
specimens thought to belong to the same species differ substantially in the COI sequence and thus probably represent
convergent evolution.
specimens thought to belong to different species have similar COI sequences and thus are probably local variants of what is
actually a single species.

Looking Ahead
Development of appropriate barcoding genes for plants (whose COI genes vary little) and fungi (whose COI genes are
interrupted by introns). One promising candidate for plants is the chloroplast gene rbcL which encodes the large subunit of
RUBISCO.
Development of hand-held sequencers that can barcode the DNA of a specimen in the field.
Promoting the development of barcoding is The Consortium for the Barcode of Life (CBOL). Their home page (link below)
provides other links describing goals, methods, achievements, etc. As of this writing, barcodes for over 112,000 species have been
entered in databases.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 19.1.9: Barcoding is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.1.9.1 https://bio.libretexts.org/@go/page/5956
19.1.10: Invertebrates
The Origin and Evolution of Animals (Metazoa)
We do not yet know from what group(s?) of eukaryotes the animals evolved. It occurred in Precambrian times. Before the
Cambrian was far along, most of the animal phyla had appeared. So each of the phyla described in this section has had a long,
independent history. The rapid (geologically speaking!) diversification of the animals has made it difficult to establish the
genealogical relationships between them — even using molecular data. Our best guesses are shown in the cladogram below..

Figure 19.1.10.1 Invertebrates

Sponges (Phylum Porifera)

Sponges are sessile, spending their lives anchored to a solid surface underwater. Most are marine although some live in fresh water.
Diploblastic; that is, the body wall is made of two layers of cells with a jellylike mesoglea between them. The body wall is
perforated with pores (hence the name Porifera) through which water containing food particles is filtered. The water is drawn in
through the pores by collar cells like those found in choanoflagellates. Some sponges can process a volume of water more than
100,000 times their own volume in the course of a day!

Figure 19.1.10.2 Sponge

Sponges are dispersed by small, free-swimming larvae. There are about 10,000 species known. Sponges are probably the most
ancient of today's invertebrates, their fossils appear in the geological record as far back as 635 million years. Despite their simple
body plan, sequencing shows that their genome (> 18,000 genes) contains many genes homologous to those found in much more
complex animals.

Cnidarians (Phylum Cnidaria)

19.1.10.1 https://bio.libretexts.org/@go/page/5958
 Figure 19.1.10.3 Obelia
Characteristics:
diploblastic; two layers of cells - ectoderm and endoderm - with a jellylike mesoglea between them;
predominantly radial symmetry: body parts (e.g., tentacles) arranged in whorls. However, in some sea anemones, there is only
one plane through the tubular body that divides it into two mirror-image halves; thus revealing bilateral symmetry.
cnidoblasts: specialized cells that secrete a stinging capsule called a nematocyst.
Food is taken through a mouth into the gastrovascular cavity. The cavity is also called a coelenteron and for many years the
name of this phylum was Coelenterata. There is no anus.
Sexual reproduction produces a free-swimming, ciliated larva called a planula.
The phylum contains about 10,000 species distributed in 3 classes:
Hydrozoa Although the freshwater hydra is a much-studied representative, it is not typical of the class.
Most members are
marine
colonial
produce two body forms: the sessile polyp (like the hydra) and the free-floating medusa (which disperses the species)
Scyphozoa Jellyfishes (the medusa stage is dominant). The jelly of the medusa is a much-enlarged mesoglea.
Anthozoa Sea anemones and corals. Have only the polyp stage.

Bilaterians
All the remaining groups of animals belong in a clade whose members share:
1. bilateral symmetry (hence the name); that is, dorsal-ventral and left-right axes
2. triploblastic (three tissue layers: ectoderm, mesoderm, endoderm)
3. HOX genes in one or more clusters with the genes within a cluster arranged in the same order as the body parts they affect.
The bilaterians contain two clades, the protostomia and the deuterostomia.

Protostomia vs. Deuterostomia

Long before the days of genome analysis, taxonomists were convinced of a fundamental division in the animal kingdom between
the protostomes ("first mouth") and the deuterostomes ("second mouth").

Protostomia Deuterostomia

Blastopore forms future mouth (in most groups). Blastopore forms future anus. Mouth forms later.

Few HOX genes for the posterior Multiple HOX genes for the posterior

Spiral cleavage of Lophotrochozoan embryos Perpendicular cleavage planes in embryo

Early cleavage cells committed; no identical twins Early cleavage cells totipotent; identical twins possible

19.1.10.2 https://bio.libretexts.org/@go/page/5958
 Protostomia Deuterostomia

Coelom arises by splitting of mesoderm Coelom arises between invaginating mesoderm during gastrulation

Lophotrochozoans and Ecdysozoans Echinoderms, Acorn worms, and Chordates

Let's first examine the protostomes. The deuterostomes are discussed below.

Lophotrochozoans vs. Ecdysozoans

Genome analysis, especially the analysis of 18S rRNA genes and HOX genes supports a major division of the Protostomia into
two superphyla: Lophotrochozoans and Ecdysozoans.

Lophotrochozoans
Their name was created from the names of formerly-separated groups that have now been joined in a single clade on the basis of
the similarities of their genomes. They all share a cluster of HOX genes quite different from those found in the ecdysozoans (and
deuterostomes). They share similar sequences in their 18S rRNA genes. The clade contains a number of phyla of which we shall
examine only 3.
flatworms (Platyhelminthes),
annelids (Annelida), and
mollusks (Mollusca).
Flatworms (Phylum Platyhelminthes)

Figure 19.1.10.4 Flatworm

This phylum contains some 20,000 species distributed among three classes. Turbellaria, free-living forms of which the planarian
is a commonly-studied example. Planaria share with the other members of the phylum (1) a flat, almost ribbonlike, shape and (2)
bilateral symmetry. The bilateral symmetry of planarians is associated with active locomotion by secreting a layer of mucus
underneath them and propelling themselves forward with the many cilia on their ventral surface and by swimming and a
concentration of sense organs in the head (called cephalization). Planarians feed through a mouth on their ventral surface. It leads
to an elaborate gastrovascular cavity. But there is no separate exit so undigested food has to leave by the mouth.
Trematoda, a group of parasitic
lung flukes
liver flukes
blood flukes (e.g., Schistosoma)
All of these have at least two different stages in their life cycle, each parasitic in a different host - one of which is usually a
snail.

19.1.10.3 https://bio.libretexts.org/@go/page/5958
 Figure 19.1.10.5 Lifecycle of Schistosoma
The diagram gives the life cycle of the blood fluke, Schistosoma mansoni. Once within the alternate host, a snail, a single
miracidium may produce as many as 200,000 infectious cercariae. Both sexes must infect the human if the cycle is to continue.
With the increasing use of irrigation in tropical regions, the incidence of human infection — known as schistosomiasis or bilharzia
— is rising alarmingly.
Cestoda; the parasitic tapeworms. They, too, alternate between an intermediate host (e.g., pig, fish) and a definitive host (e.g.,
us). The growing popularity of sushi and sashimi made of raw Pacific salmon has caused infections by the fish tapeworm to
become more common in the U.S.
Annelids (Phylum Annelida)

Figure 19.1.10.6 Trocophore larva

Characteristics:
segmented; that is, their body is made up of repeating units. Although some structures, e.g., the digestive tract, run straight
through, others like the excretory organs are repeated in each segment.
The major nerve trunk runs along the ventral side.
a large, fluid-filled coelom; It is lined with mesoderm and enables the internal organs to slide easily against one another making
for easy locomotion.
There are >15,000 species known. Some examples:
the common earthworm
leeches
marine forms such as the clam worm These animals produce a free-swimming trochophore larva (figure), which partly
accounts for the name Lophotrochozoan.
Mollusks (Phylum Mollusca)
With over 100,000 living species identified so far, the mollusks must be counted as among the most successful animals on earth
today. Most belong to the first 3 of the 6 classes shown here:
1. Bivalvia. Two shells encase the body. Includes the clams, mussels, oysters, and scallops.
2. Gastropoda. Snails and slugs. Snails have a single shell ("univalves') while slugs have none.
3. Cephalopoda. This marine group includes the various species of octopus, squid, as well as the chambered nautilus. A record
28-foot (8.5 m) octopus and 60-foot (18 m) squid make these the largest of all the invertebrates.
4. Scaphopoda. Marine, filter-feeding "tooth shells".
5. Monoplacophora. Until a live specimen was discovered in 1952, these animals were thought to have been extinct for millions
of years. It has a single shell (hence the name) and, unlike the other mollusks, is segmented (as are its relatives the annelids).

19.1.10.4 https://bio.libretexts.org/@go/page/5958
 6. Polyplacophora. The animals in this group, called chitons, have their dorsal surface protected by 8 overlapping plates or
"valves".
The trochophore larvae of mollusks is also evidence that they belong in the same clade with the annelids.

Ecdysozoans
All the members of this clade
grow by periodically molting - shedding their skin or exoskeleton
share a unique pattern of HOX genes, e.g. Ubx and Abd-B
The clade includes a number of phyla of which we shall examine 2:
nematodes
arthropods.

Roundworms (Phylum Nematoda)

Features:
A one-way digestive tract running from mouth to anus.
A cavity between the digestive tract and the body wall. It develops from the blastocoel and is called a pseudocoel.
Some 25,000 species have been identified but this may be less than 10% of the true number.
Most are free-living; found in soil where they are important decomposers.
One of these is Caenorhabditis elegans, a model laboratory animal.
Some are parasitic, including
hookworms (In 2003 the number of humans infected by hookworms was estimated at 740 million worldwide.)
pinworms and whipworms
filarial worms - threadlike worms that are transmitted to the definitive host from an intermediate host causing such human
ailments as
river blindness (Onchocerca volvulus) - acquired from the bite of infected black flies
elephantiasis (Wuchereria bancrofti) - acquired from infected mosquitoes
dracunculiasis (Guinea worm disease) (Dracunculus medinensis) - acquired from ingesting water containing infected
"water fleas" (Cyclops)
many parasites of commercially important plants like strawberries and oranges.
Most are small although one that parasitizes whales reached 30 feet (9 m)!

Arthropods (Phylum Arthropoda)

Some characteristics:
Incredible diversity. Over a million living species have been identified so far - more than all the other species of living things
put together - and this is probably only a fraction of them.
Live in every possible habitat: fresh water, salt water, soil, even in the most forbidding regions of Antarctica and high
mountains.
A jointed external skeleton made of chitin, a polymer of N-acetylglucosamine (NAG).
Segmented.
Pairs of jointed appendages; one pair to a segment - used for locomotion, feeding, sensation, weaponry.
Bilateral symmetry.
Main nerve cord runs along the ventral side.
We shall look at four groups (subphyla):
Crustacea
Hexapoda (the insects)
Myriapoda
Chelicerata

19.1.10.5 https://bio.libretexts.org/@go/page/5958
Crustacea

Figure 19.1.10.7 Crustacea

Head and thorax fused into a cephalothorax.
At least 40,000 species.
Most are aquatic, found in both fresh water and in the oceans.
Includes crayfish, lobsters, barnacles, crabs, shrimp.

Hexapoda - the insects

Body segments grouped into head, thorax, and abdomen.
Each of the 3 thoracic segments carries a pair of legs (hence the 6-legged "hexapoda")
Many have wings, usually 2 pairs (only one pair in flies - diptera).
Gas exchange through a tracheal system.
Nitrogenous waste is uric acid thus conserving water.
Some 950,000 species, and this may be only 10% of the number out there.
Dominate all habitats except for the oceans.
Most intensively-studied representative: Drosophila melanogaster.
Representative colonial insect: the honeybee, Apis mellifera

Myriapoda

Figure 19.1.10.8 Millipede

Some 13,000 species of
centipedes
millipedes
Neither group has the number of legs their name suggests, although one species of millipede does have 375 pairs.

Chelicerata

19.1.10.6 https://bio.libretexts.org/@go/page/5958
 Figure 19.1.10.9 Limulus
Anterior segments fused into a cephalothorax.
The first pair of appendages - the chelicerae - are used for feeding.
There are no antennae.
Includes:
Merostomata. The only member alive today is Limulus, the horseshoe "crab". It has existed in the sea virtually unchanged
for 200 million years.
Arachnids (some 75,000 species)
8-legged
scorpions, mites, ticks, spiders, daddy longlegs.

Evolutionary relationships of the arthropods

Figure 19.1.10.10 Anthropod sequence

An ever-increasing number of arthropod gene sequences appear to have answered some long-standing questions about the
evolutionary relationships of the various arthropod groups. A recent study (Regier, J. C., et al., Nature, 463:1079, 25 February
2010) examined 63 nuclear genes from 75 species of arthropods and concluded that
the crustacea are paraphyletic; that is, the single common ancestor from which all the animals we call crustaceans are descended
was also the ancestor of another group, the insects (Hexapoda). So insects are terrestrial crustaceans!
All these groups plus the millipedes and centipedes (Myriapoda) make up a clade designated Mandibulata.
So millipedes and centipedes are more closely related to the crustaceans than to, as once thought, the Chelicerata.

The Deuterostomes
In addition to the features listed above, the deuterostomes have (or had) gill slits. (The echinoderms have lost the gill slits of their
ancestors.)

Echinoderms (Phylum Echinodermata)

Figure 19.1.10.11 Starfish

Characteristics:
radial symmetry. HOWEVER, their larvae have bilateral symmetry so the echinoderms probably evolved from bilaterally
symmetrical ancestors and properly belong in the Bilateria.
water vascular system. Seawater is taken into a system of canals and is used to extend the many tube feet. These have suckers
on their tips and aid the animal in attaching itself to solid surfaces.

19.1.10.7 https://bio.libretexts.org/@go/page/5958
 no gill slits
About 6,000 species — all of them marine.
There are 5 classes of echinoderms:
Sea lilies (Crinoidea)
Sea Stars (aka "Starfish") (Asteroidea) The photo (courtesy of Dr. Charles Walcott) shows a sea star that lost an arm and is in
the process of regenerating a replacement.
Brittle stars (Ophiuroidea)
Sea cucumbers (Holothuroidea)
Sea urchins and sand dollars (Echinoidea)

Acorn Worms (Phylum Hemichordata)

The members of this small phylum (some 90 species have been identified) are marine forms most of whom live in burrows in ocean
sediments. Their closest living relatives are the echinoderms with which they share the clade Ambulacraria. However, they
possess a suite of features, both in their anatomy (e.g. gill slits) and their gene expression patterns, suggesting that their ancestors
also led to the evolution of the chordates.

Chordates (Phylum Chordata)

Figure 19.1.10.12 Larva of jawless vertebrate

During their embryonic development, all chordates pass through a stage called the pharyngula with these features:
a dorsal, tubular nerve cord ("1") running from anterior to posterior. At its anterior end, it becomes enlarged to form the
brain.
a flexible, rodlike notochord ("2") that runs dorsal to the digestive tract and provides internal support. In vertebrate chordates,
it is replaced by a vertebral column or backbone long before maturity.
pairs of gill pouches. These lateral outpocketings of the pharynx are matched on the exterior by paired grooves. In aquatic
chordates, one or more pairs of gill pouches break through to the exterior grooves, forming gill slits ("3"). These provide an exit
for water taken in through the mouth and passed over the gills.
a tail that extends behind the anus
The vast majority of chordates have a skull enclosing their brain (Craniata), and all but one of these (the hagfish) convert their
notochord into a vertebral column or backbone. These latter are the vertebrates.
Vertebrates also differ from all the other animals by having quadrupled their HOX gene cluster; that is, vertebrates have 4
clusters of HOX genes located on 4 different chromosomes.
Here we shall examine two groups of invertebrate chordates:
Urochordata and
Cephalochordata

Urochordata

19.1.10.8 https://bio.libretexts.org/@go/page/5958
 Figure 19.1.10.13 Tunicata
This group (also called Tunicata) includes animals known as ascidians (and commonly called sea squirts). They are
marine
sessile animals
feed by filtering food particles from seawater taken in through one opening, or siphon, and squirted out the other.
The one on the above is Halocynthia, the sea peach (photo courtesy of Ralph Buchsbaum). It is hard to see what makes these
animals chordates. The adults have neither notochord nor a dorsal tubular nervous system. However, these animals disperse
themselves with free-swimming larvae that have
dorsal tubular nervous system
notochord
gill slits
One of the most common species (Ciona intestinalis) has had its genome sequenced.
It has a very small genome: ~1.6 x 108 base pairs encoding ~16,000 genes. (Some 20% of these are organized in operons.)
Its larva is small (with ~2,600 cells) including only
36 muscle cells
40 notochord cells
100 neurons
These cells (as well as the others) develop along rigid pathways which can be easily observed because the larva is
transparent.
All these features are shared with C. elegans, but now we are talking about an animal far closer to the evolutionary line that
produced us. In fact, with 80% of Ciona's genes having homologs in us, tunicates are probably our closest invertebrate relatives.

Cephalochordata

Figure 19.1.10.14 Amphioxus

The representative member of this tiny subphylum of so-called lancelets is a small (5 cm), marine, fishlike creature called
amphioxus (above). For years its genus name was Amphioxus but that has now been replaced by the name Branchiostoma.
Amphioxus retains a dorsal nerve cord, notochord and gill slits throughout its life. There is a small cluster of neurons at the
anterior tip of the nerve cord with certain similarities of structure and gene expression to the vertebrate fore-, mid- and hindbrain.
Although able to swim, the lancelet spends most of its time partially buried in the sand while it filters microscopic food particles
from the water.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

19.1.10.9 https://bio.libretexts.org/@go/page/5958
This page titled 19.1.10: Invertebrates is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.1.10.10 https://bio.libretexts.org/@go/page/5958
19.1.11: Drosophila Melanogaster

Figure 19.1.11.1 Stages of Drosophila

Some of the reasons for its popularity:
The flies are small and easily reared in the laboratory.
They have a short life cycle The figure shows the various stages of the life cycle (not all drawn to the same scale). A new
generation of adult flies can be produced every two weeks.
They are fecund; a female may lay hundreds of fertilized eggs during her brief life span. The resulting large populations make
statistical analysis easy and reliable.
The giant ("polytene") chromosomes in the salivary (and other) glands of the mature larvae.
These chromosomes show far more structural detail than do normal chromosomes
They are present during interphase when chromosomes are normally invisible.
More recently, Drosophila has proven in other ways to have been a happy choice.
Its embryo grows outside the body and can easily be studied at every stage of development.
The blastoderm stage of the embryo is a syncytium (thousands of nuclei unconfined by cells) so that, for example,
macromolecules like DNA injected into the embryo have easy access to all the nuclei.
The genome is relatively small for an animal (less than a tenth that of humans and mice).
Mutations can targeted to specific genes.

This page titled 19.1.11: Drosophila Melanogaster is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.1.11.1 https://bio.libretexts.org/@go/page/5959
19.1.12: Caenorhabditis Elegans
Caenorhabditis elegans is a microscopic (~1 mm) nematode (roundworm) that normally lives in soil. It has become one of the
"model" organisms in biology. It is a true animal with at least rudiments of the physiological systems - feeding, nervous, muscle,
reproductive - found in "higher" animals like mice and humans. However, it is so small that large numbers can be raised in petri
dishes (where it is fed E. coli - another model organism). It reproduces rapidly.

Figure 1: A lateral (left side) anatomical diagram of an adult-stage nematode hermaphrodite Caenorhabditis elegans (C. elegans)
with emphasis on the digestive and reproductive systems. (CC BY-SA 3.0; K. D. Schroeder).
It is transparent so that every cell in the living animal can be seen under the microscope from the fertilized egg to the 556 cells of
the newly-hatched worm and, later, the 959 somatic cells, and a variable number of germ cells, of the adult worm. It can be easily
transformed with transgenes - DNA injected into the animal. It can also be treated with antisense RNA. Before it dies (after 2–3
weeks), it shows signs of aging and thus may provide general clues as to the aging process.
Its cells contain 5 pairs of autosomes and 2 X chromosomes. These animals are hermaphrodites, producing both sperm and eggs.
Most of the time they fertilize themselves, so that any recessive alleles quickly become homozygous and affect the phenotype. On
rare occasions, nondisjunction occurs during meiosis with the loss of one X chromosome. Animals with a single X are males and
are able to fertilize the eggs of the hermaphrodites (with more success than they have themselves).
C. elegans was the first multicellular eukaryote to have its entire genome sequenced. It contains some 19–20,000 protein-encoding
genes incorporated in 100,258,171 base pairs of DNA. In contrast to other eukaryotes, some 13–15% of its genes are grouped in
operons containing 2–8 genes each.

C. elegans Fertilization
Like all animals, C. elegans starts life as a fertilized egg (zygote) which then undergoes the mitotic divisions needed to produce the
adult. Because the worm is transparent and the pattern of differentiation is so rigid it has been possible to trace the lineage of every
single somatic cell in the animal. Just after hatching, the it contains 556 cells and is approximately 0.3 mm long. After reaching
maturity, it will contain 959 somatic cells and a variable number of germ cells in its gonad.
The diagrams below show the pathway by which each of the 556 cells in the larva of C. elegans has developed from the zygote.
The relative length of the vertical lines indicates the length of the interval before the next mitosis. Some pathways end in the
programmed death of the cell (apoptosis) even before the larva is complete.

19.1.12.1 https://bio.libretexts.org/@go/page/5960
 Figure 19.1.12.2 Pathway of 556 cells in larva of C.elegans. (Adapted, with permission, from J. Sulston, et al., in Monograph 17.
Copyright © Cold Spring Harbor Laboratory, NY.)
Several remarkable features have been found from these studies. The pattern of development is invariable from worm to worm.
Every one of the 556 cells that make up the newly-hatched larva develops from a rigid pattern of mitotic division leading back to

19.1.12.2 https://bio.libretexts.org/@go/page/5960
the zygote. 131 cells in the developing embryo die by apoptosis. This cell death is not random; which cells will die and at what
stage is completely predictable. Any failures in this programmed cell death can lead to serious abnormalities.
Each organ - skin, nerve, muscle, etc. - is made of cells derived from several different lineages. One might have expected that the
earliest cell divisions would produce daughter cells destined to go on to form a single structure in the embryo. But that is not
generally the case. Instead, most of the earliest cells will produce descendants that team up with other groups of cells to form the
various organs of the animal.
There is less flexibility of cell fate than occurs in mammals (or even amphibians). With a microscopic laser beam, a single cell can
be killed in the developing embryo. Often the result is that all the cells that would have descended from that cell fail to form.
Neighboring cells may not compensate for the loss as they do so freely in mammals. So it appears that the developmental controls
of C. elegans rely more on cell-intrinsic signals rather than inductive signals. But this distinction is relative, not absolute. Cells
originally destined to a different fate will in some cases switch their path of differentiation to replace the cells killed by the laser. In
these cases, the switch is clearly mediated by inductive signals liberated by nearby cells.

This page titled 19.1.12: Caenorhabditis Elegans is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.1.12.3 https://bio.libretexts.org/@go/page/5960
19.1.13: Vertebrates

Chordata

Figure 19.1.13.1Turnicate larva

During their embryonic development, all chordates pass through a stage called the pharyngula with these features:
The cephalochordates and tunicates never develop a vertebral column. They are thus "invertebrates" and are discussed with the
other invertebrates.
Craniata The vast majority of chordates have a skull enclosing their brain, eyes, inner ear, etc.). All but one group of these (the
hagfishes) also convert their notochord into a vertebral column or backbone thus qualifying as vertebrates.

Vertebrata

Figure 19.1.13.2 Vertebrate clade

Although hagfishes, never replace their notochord with a vertebral column, and thus might seem not to qualify as vertebrates, they
share a number of other features with other vertebrates and certainly should be classified with them. Still uncertain is whether they
represent the most primitive vertebrates or are simply degenerate vertebrates (probably the latter).
All the other members of the craniata convert their notochord into a vertebral column or "backbone" (even though in some it is
made of cartilage not bone). They also differ from all other animals in having quadrupled their HOX gene cluster; that is, they have
4 different clusters of HOX genes (on 4 separate chromosomes). Perhaps this acquisition played a key role in the evolutionary
diversity that so characterizes the vertebrates.
The vertebrates are subdivided into the
jawless vertebrates (Agnatha)
jawed vertebrates (Gnathostomata)

Agnatha

19.1.13.1 https://bio.libretexts.org/@go/page/5965
 Figure 19.1.13.3 Lamprey
Lampreys and hagfishes are the only jawless vertebrates to survive today. They both have a round mouth and for this reason are
often referred to as cyclostomes. They are the most primitive of the vertebrates. By "primitive", a biologist means that they are the
least changed from the first vertebrates. Besides lacking jaws,
They have no paired pectoral (shoulder) or pelvic (hip) fins.
Their notochord persists for life, never being completely replaced by a backbone even in the lampreys.
They have no scales.
The axons of their neurons are unmyelinated (like those of all invertebrates).
Lampreys have both an innate immune system and an adaptive immune system, but the latter is entirely different from that
found in the jawed vertebrates.
The photo (courtesy of the Carolina Biological Supply Company) is of the West Coast lamprey. Note the gill slits and the absence
of paired pectoral and pelvic fins.

Gnathostomata
As well as having jaws, all the members of this group have
Myelin sheaths around the axons of their neurons. This permits much more rapid transmission of nerve impulses - a trait
probably as important for active vertebrates as their jaws.
An adaptive immune system backing up their innate immune system.

Cartilaginous Fishes (Chondrichthyes)

Fossils of cartilaginous fishes become abundant in deposits dating to the Devonian period. They were very much like the sharks of
today. The group, which today is made up of some 1,188 species of sharks, skates and rays gets its name from the fact that their
skeleton is made of cartilage, not bone.
With their gills exposed to sea water, all marine fishes are faced with the problem of conserving body water in a strongly
hypertonic environment. Sea water is about 3.5% salt, over 3 times that of vertebrate blood. The cartilaginous fishes solve the
problem by maintaining such a high concentration of urea in their blood (2.5% — far higher than the ~0.02% of other vertebrates)
that it is in osmotic balance with - that is, is isotonic to - sea water.
This ability develops late in embryology, so the eggs of these species cannot simply be released in the sea. Two solutions are used:
Enclose the egg in an impervious case filled with isotonic fluid before depositing it in the sea.
Retain the eggs and embryos within the mother's body until they are capable of coping with the marine environment.
Both these solutions require internal fertilization, and the cartilaginous fishes were the first vertebrates to develop this. The pelvic
fins of the male are modified for depositing sperm in the reproductive tract of the female.

Bony Fishes (Osteichthyes)

As their name indicates, the skeleton in this group is made of bone. The group is subdivided into the
ray-finned fishes (Actinopterygii)
lobe-finned fishes (Sarcopterygii)

19.1.13.2 https://bio.libretexts.org/@go/page/5965
Ray-finned fishes
Their fins are thin and supported by spines.
There are over 30,000 species (representing more than half of all living vertebrates).
They are an important part of the human diet in many areas of the world and, in affluent nations, support a large sports fishing
industry.
Although the earliest bony fishes may have appeared late in the Silurian period, their fossils become abundant in freshwater
deposits of the Devonian period. In addition to gills, these fishes had a pair of pouched outgrowths from the pharynx which served
as lungs. They were inflated with air taken in through the mouth and may have provided a backup gas exchange organ when the
water became too warm and stagnant to carry enough dissolved oxygen. Their kidneys were adapted for the hypotonic environment
in which they lived.
These animals diversified through the remainder of the Devonian period (which is often called the "Age of Fishes"). Some
migrated to the oceans. In this more stable environment, their lungs became transformed into a swim bladder with which they
could alter buoyancy. Their kidneys became transformed as well adapting them to their new - hypertonic - surroundings.

Lobe-finned fishes
The only ones to survive today are:
two species of coelacanths. Coelacanths were long thought to have become extinct at the end of the Mesozoic era, some 70
million years ago. But in December 1938, a living coelacanth, Latimeria chalumnae, was pulled up from the depths of the
ocean off the east coast of Africa. Since then, over 200 additional specimens have been caught.
several species of lungfish found in Africa, South America, and Australia.
The nostrils of bony fishes open only to the outside and are used for smelling. Some of the lobe-finned fishes developed internal
openings to their nostrils. This made it possible to breath air with the mouth closed as modern lungfishes do.
Judging from present-day lungfishes, two other significant adaptations evolved in this group:
two atria and a partial septum in the ventricle of the heart (similar to the frog heart). This permitted a partial separation of
oxygenated blood returning from the lung(s) and the deoxygenated blood returning from the rest of the body.
an enzyme system to convert ammonia into the less toxic urea. This mechanism is highly-developed in the African and South
American lungfishes. While in the water, these fishes excrete their waste nitrogen as ammonia, just as most ray-finned fishes
do. In time of drought, these animals burrow in the mud and switch to urea production.

Figure 19.1.13.5 Frog

With their bony limbs and lungs inherited from their lobe-finned ancestors, amphibians were so successful during the
Carboniferous (Mississippian and Pennsylvanian periods) that these periods are known as the Age of Amphibians.
The Carboniferous was followed by the Permian, when the earth became colder and dryer. The fortunes of the amphibians began to
decline until only three groups - totaling about 6500 species - remain today:
frogs and toads (Anura) (The one pictured is Rana pipiens, the leopard frog.)
salamanders and newts (Urodela)
caecilians (Apoda), which are rare, limbless, tropical animals.
As the name suggests, amphibians are only semiterrestrial:
Their skin is soft and moist so they are at risk of desiccation in dry surroundings.
Their eggs have no waterproof covering so
they must be laid in water (which makes them useful animals for studying embryonic development) where they are fertilized
or

19.1.13.3 https://bio.libretexts.org/@go/page/5965
 placed within the mother's body (some use a pouch in the skin, some use their mouth, some even use their stomach — which
stops secreting acid and enzymes for the duration!) after external fertilization.

Amniotes (Amniota)

Figure 19.1.13.6 Amniotic egg

Some 310 million years ago (in the Pennsylvanian), some amphibians evolved the ability to lay shelled, yolk-filled eggs. The
embryo developing within the egg produces 4 extraembryonic membranes:
amnion, which surrounds the embryo with a fluid as watery as the pond water around a frog's egg (and accounts for the name
amniota)
chorion, which serves for gas exchange
allantois, which serves both for gas exchange and to store metabolic wastes
yolk sac, which supplies the embryo with food

Figure 19.1.13.7 Chameleon

With the arrival of the cold, dry Permian, reptiles were well-adapted to survive because of their development of a shelled, yolk-
filled egg which could be deposited on land without danger of drying out. The photo (courtesy of the Carolina Biological Supply
Company) shows an American chameleon emerging from its egg.
Other adaptations that enabled the reptiles to flourish for the next 220 million years were:
a dry, water-impermeable skin
lungs inflated by expansion of the rib cage
a partial septum in the ventricle reducing the mixing of oxygenated and deoxygenated blood
Beginning late in the Paleozoic era and exploding in the Triassic period, the reptiles underwent a remarkable adaptive radiation
producing the diapsids. This group developed the ability to convert their nitrogenous waste into uric acid. Uric acid is almost
insoluble in water so its excretion involves little loss of water. (It is the whitish paste that pigeons leave on statues.) This
modification largely freed the diapsids and their descendants from a dependence on drinking water; the water in their food is
usually sufficient.
Diapsid evolution soon produced:
lizards and snakes (Squamata - some 6,300 species survive today);
turtles
thecodonts.
Thecodonts were able to run fast by rising up on their hind legs, which became larger than their front legs, and using their long tail
for balance. The group diversified into:
crocodiles and alligators (Crocodilia — 22 species survive today)
an extraordinary array of dinosaurs from some of which evolved today's birds.

19.1.13.4 https://bio.libretexts.org/@go/page/5965
 Figure 19.1.13.8 Pigeon sternum
Feathers are the feature that most clearly distinguishes the birds from their dinosaur ancestors. These scaly skin outgrowths
provide a light, strong surface for the wings;
heat insulation, making it possible to be small but still warm-blooded.
Other adaptations are:All of these adaptations help birds to fly (to escape predators and find suitable food and nesting sites).
Almost 10,000 species are known today.

This page titled 19.1.13: Vertebrates is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.1.13.5 https://bio.libretexts.org/@go/page/5965
19.1.14: Zebrafish
The zebrafish, Danio rerio, has become another popular "model" organism with which to study fundamental biological questions.

Figure 19.1.14.1 Zebrafish This image is courtesy of Sarah Farrington of the Center for Cancer Research at MIT. It comes from the
home page of ZFIN ("Zebrafish Information Network").
The zebrfish is a small (1–1.5 inches)(2.5–3.8 cm) freshwater fish that grows easily in aquaria (it is available at many pet stores).
Some of its advantages for biologists:
It breeds early and often (daily).
It is a vertebrate, like us, and thus can provide clues to human biology that invertebrates like Drosophila and Caenorhabditis
elegans may not.
Its embryos, like those of most fishes, develop outside the body where they can be easily observed (unlike mice).
Its embryos are transparent so defects in development can be seen easily.
Individual cells in the embryo can be labeled with a fluorescent dye and their fate followed.
Embryonic development is quick (they hatch in two days).
They can absorb small molecules, such as mutagens, from the aquarium water.
Individual cells - or clusters of cells - can be transplanted to other locations in the embryo (as Mangold did with newt embryos).
They can be forced to develop by parthenogenesis to produce at will homozygous animals with either a male-derived or female-
derived genome.
They can be cloned from somatic cells.
They can be made transgenic (like mice and Drosophila)
Its genome (1.4 x 109 base pairs) has been sequenced revealing 26,606 protein-coding genes.

Forward and Reverse Genetics

Forward
Since Mendel's time, most genetics has involved
observing an interesting phenotype
tracking down the gene responsible for it.
So this "forward" genetics proceeds from phenotype -> genotype.
Some examples:
Mendel's work
RFLP analysis of large families
The one gene - one enzyme theory
These methods have been called "forward" genetics to distinguish them from a more recent approach, which has become an urgent
priority with the successes of genome sequencing.

Reverse
Rapid methods of DNA sequencing has generated a vast amount of data. Thousands of suspected genes have been revealed (e.g.,
finding open reading frames - ORFs), but the function of many of them is still unknown.
But now with a knowledge of the DNA sequence of a gene of unknown function, one can use methods for suppressing that
particular gene ("knockdown") and then observe the effect on the phenotype.
So this "reverse" genetics proceeds from genotype -> phenotype.

19.1.14.1 https://bio.libretexts.org/@go/page/5966
Reverse genetics has been applied successfully to
plants
mice
C. elegans
zebrafish
For example, the function of a mysterious gene sequence in Danio can be studied by
synthesizing a short antisense oligonucleotide complementary to a section of the gene.
The oligonucleotide is chemically-modified to make it more stable than a fragment of RNA.
Binding to its complementary sequence on the messenger RNA (mRNA) produced by transcription of the animal's gene, blocks
("knocks down") gene expression by
preventing translation or
disrupting normal splicing of the mRNA.
Because we share so many similar gene sequences (orthologous genes) with Danio, if one can discover the function of the gene in
Danio, then we have a better idea of the role of its ortholog in humans.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 19.1.14: Zebrafish is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.1.14.2 https://bio.libretexts.org/@go/page/5966
19.1.15: Monotremes

Monotremes are a small but remarkable group of mammals that consists of a single species of duckbill platypus
(Ornithorhynchus anatinus) found in Australia and three (perhaps four) species of spiny anteaters (echidnas) found in Australia
and New Guinea.

These animals retain several traits of their therapsid ancestors including

a cloaca - the final segment of the digestive tract into which both the urinary and reproductive tracts empty (monotreme = single
hole);
lay shelled eggs that undergo merobastic cleavage like that of reptiles (and birds) rather than the holoblastic cleavage of all
other mammals.
Despite these reptilian features, the monotremes meet all the criteria of true mammals:
milk secreted from mammary glands (but no nipples)
hair
teeth (only in the young; they are lost in adult montremes)
In the May 8 issue of Nature, a consortium of gene sequencers reported the results of sequencing the complete genome of the
platypus. They identified 18,527 protein-coding genes distributed on 52 chromosomes.
The mix of mammalian and reptilian phenotypic features turns out to be reflected in the genome as well. Examples:
The platypus has genes for egg yolk proteins that are also found in birds but not in therians.
The gene content of their X chromosomes resembles that of the Z chromosome in birds, not the X chromosome of other
mammals like us.
Other features of their genome reflect their unique biology:
The platypus produces a venom with genes which in other mammals encode for antimicrobial peptides called defensins.
The platypus has some 1000 genes for receptors in its vomeronasal organ — far more than found in other mammals. The
platypus hunts for food underwater and probably uses these receptors to detect prey (as well as using its electroreceptors for this
purpose).

This page titled 19.1.15: Monotremes is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.1.15.1 https://bio.libretexts.org/@go/page/5967
 SECTION OVERVIEW
19.2: Microbes
Topic hierarchy

19.2A: Bacteria

19.2B: Archaea

19.2C: Antibiotics

19.2D: E. coli

19.2E: Anthrax

19.2F: Bacillus Thuringiensis

19.2G: The Rapid Identification of Microorganisms

This page titled 19.2: Microbes is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.2.1 https://bio.libretexts.org/@go/page/5939
19.2A: Bacteria
Bacteria are microscopic organisms whose single cells have neither a membrane-enclosed nucleus nor other membrane-enclosed
organelles like mitochondria and chloroplasts. Another group of microbes, the archaea, meet these criteria but are so different from
the bacteria in other ways that they must have had a long, independent evolutionary history since close to the dawn of life. In fact,
there is considerable evidence that you are more closely related to the archaea than they are to the bacteria!

Properties of Bacteria
prokaryotic (no membrane-enclosed nucleus)
no mitochondria or chloroplasts
a single chromosome
a closed circle of double-stranded DNA
with no associated histones
If flagella are present, they are made of a single filament of the protein flagellin; there are none of the "9+2" tubulin-containing
microtubules of the eukaryotes.
Ribosomes differ in their structure from those of eukaryotes
Have a rigid cell wall made of peptidoglycan.
The plasma membrane (in Gram-positive bacteria) and both membranes in Gram-negative bacteria are phospholipid bilayers
but contain no cholesterol or other steroids.
No mitosis
Mostly asexual reproduction
Any sexual reproduction very different from that of eukaryotes; no meiosis
Many bacteria form a single spore when their food supply runs low. Most of the water is removed from the spore and
metabolism ceases. Spores are so resistant to adverse conditions of dryness and temperature that they may remain viable even
after 50 years of dormancy.

Classification of Bacteria
Until recently classification has done on the basis of such traits as:
shape
bacilli: rod-shaped
cocci: spherical
spirilla: curved walls
ability to form spores
method of energy production (glycolysis for anaerobes, cellular respiration for aerobes)
nutritional requirements
reaction to the Gram stain
Figure 19.2.1.1 Gram positive and negative
bacteria

Gram-positive bacteria are encased in a plasma membrane covered with a thick wall of peptidoglycan. Gram-negative bacteria are
encased in a triple-layer. The outermost layer contains lipopolysaccharide (LPS).
The bacterial cells are first stained with a purple dye called crystal violet.
Then the preparation is treated with alcohol or acetone.
This washes the stain out of Gram-negative cells.
To see them now requires the use of a counterstain of a different color (e.g., the pink of safranin).
Bacteria that are not decolorized by the alcohol/acetone wash are Gram-positive.
Although the Gram stain might seem an arbitrary criterion to use in bacterial taxonomy, it does, in fact, distinguish between two
fundamentally different kinds of bacterial cell walls and reflects a natural division among the bacteria. More recently, genome
sequencing, especially of their 16S ribosomal RNA (rRNA), has provided additional insights into the evolutionary relationships
among the bacteria.

19.2A.1 https://bio.libretexts.org/@go/page/5970
Gram-positive Bacteria
Firmicutes
Comparison of their sequenced genomes reveals that all the Gram-positive rods and cocci as well as the mycoplasmas belong to a
single clade that has been named the Firmicutes.
Gram-Positive Rods
Aerobic Gram-Positive Rods
Bacillus anthracis/cereus/thuringiensis. These organisms differ mainly in the plasmids they contain.
B. anthracis causes anthrax. Currently the biological agent favored by terrorists. Its 2 plasmids contain the genes needed to
synthesize
a capsule which (like those of pneumococci) makes it resistant to phagocytosis
the three components of the toxin that causes the disease symptoms
B. thuringiensis — the organism, its toxin, and even the gene (also plasmid-encoded) for the toxin are used as biocontrol agents
against a variety of insect pests.
Bacillus subtilis. A common soil bacterium. Its chromosome contains 4,214,814 bp of DNA encoding 4,100 genes.
Lactobacillus. Several species are used to convert milk into cheese, butter, and yogurt.
Anaerobic Gram-Positive Rods
Clostridium tetani. Clostridia are spore-forming obligate anaerobes. The spores of C. tetani are widespread in the soil and often
get into the body through wounds. Puncture wounds (e.g., by splinters or nails) are particularly dangerous because they provide
the anaerobic conditions needed for germination of the spores and growth of the bacteria.
C. tetani liberates a toxin that blocks transmitter release (by destroying the SNAREs needed) at inhibitory synapses in the
spinal cord and brain. This interferes with the reciprocal inhibition of antagonistic pairs of skeletal muscles so the victim suffers
violent muscle spasms. Fortunately, the disease - called tetanus - is now rare in developed countries, thanks to almost universal
immunization against the toxin. Chemical alteration of the toxin produces a toxoid that still retains the epitopes of the toxin.
Incorporated in a vaccine, the toxoid provides a relatively long-lasting (~10 years) immunity against tetanus.

Figure 19.2.1.2 Strep

The bacteria in this group grow in characteristic colonies.
Many cases of "food poisoning" are caused by staphylococci.
Most Streptococci grow in chains. The electron micrograph (courtesy of the Naval Dental Research Institute, Great Lakes, IL)
shows Streptococcus mutans, a common inhabitant of the mouth.
Streptococci cause
"strep throat"
impetigo
middle ear infections
scarlet fever (a result of a toxin produced by the organism)
rheumatic fever
a rare form of toxic shock syndrome
Pneumococci. The cells of these streptococci grow in pairs. Streptococcus pneumoniae causes bacterial pneumonia. This was
once a major killer — especially of the aged and infirm — but today there is an effective vaccine and any infections that do
occur usually respond quickly to antibiotics.

19.2A.2 https://bio.libretexts.org/@go/page/5970
Mycoplasmas
Mycoplasmas have the distinction of being the smallest living organisms. They are so small (0.1 µm) that they can be seen only
under the electron microscope. Mycoplasmas are obligate parasites; that is, they can live only within the cells of other organisms.
They are probably the descendants of Gram-positive bacteria who have lost their peptidoglycan wall as well as much of their
genome — now depending on the gene products of their host.
The DNA sequences of the complete genomes of seven mycoplasmas have been determined, including
Mycoplasma genitalium has 580,073 base pairs of DNA encoding 525 genes (485 for proteins; the rest for RNAs).
Mycoplasma urealyticum has 751,719 base pairs of DNA encoding 651 genes (613 for proteins; 39 for RNAs).
Mycoplasma pneumoniae has 816,394 base pairs of DNA encoding 679 genes.
How many genes does it take to make an organism?
The scientists at The Institute for Genomic Research (now known as the J. Craig Venter Institute - JCVI) who determined the
Mycoplasma genitalium sequence followed this work by systematically destroying its genes (by mutating them with insertions) to
see which ones are essential to life and which are dispensable. Of the 485 protein-encoding genes, they have concluded that only
381 of them are essential to life.
Workers at the JCVI have also succeeded in synthesizing the complete genome of one species of mycoplasma, inserted this into a
second species, which converted the second species into the first.

Actinobacteria
Most of these Gram-positive organisms grow as thin filaments - like a mold - rather than as single cells. In fact, they were long
thought to be fungi and were called actinomycetes. But fungi are eukaryotes and the actinobacteria are not.
Actinobacteria dominate the microbial life in soil where they play a major role in the decay of dead organic matter. Many of them
have turned out to be the source of valuable antibiotics, including streptomycin, erythromycin, and the tetracyclines.

Mycobacteria and Corynebacteria

These Gram-positive organisms are closely related to the actinobacteria and often classified with them. They include three
important human pathogens:
Mycobacterium tuberculosis is the agent of tuberculosis (TB). TB is estimated to have killed 2 million people in 2007. Under
ideal conditions, a single bacterium can cause infection. AIDS patients are especially at risk.
Its genome contains 4,411,532 bp of DNA encoding some 3,959 genes.
Mycobacterium leprae causes leprosy. Its genome contains 3,268,203 bp of DNA encoding only 1,604 genes.
Although a close relative of M. tuberculosis (they share 1,439 genes), much of its DNA encodes pseudogenes, genes that no
longer make a functional product. M. leprae is an obligate intracellular parasite; it has never been cultured in vitro. This is
probably because it has abandoned many of the genes needed for an independent existence choosing instead to depend on the
genes of its host cell.
Corynebacterium diphtheriae causes diphtheria. As in tetanus, it isn't the growth of the organism (in the throat) that is
dangerous but the toxin it liberates. The toxin is the product of a latent bacteriophage in the bacterium. It catalyzes the
inactivation of a factor necessary for amino acids to be added to the polypeptide chain being synthesized on the ribosome.
Sensibly enough, the toxin has no such effect on the translation machinery of bacteria (or of chloroplasts and mitochondria).
Treatment of the toxin with formaldehyde converts it into a harmless toxoid. Immunization with this toxoid — usually
incorporated along with tetanus toxoid and pertussis antigens in a "triple vaccine" (DTP) - protects against the disease.

Gram-negative Bacteria
The Proteobacteria
This large group of bacteria form a clade sharing related rRNA sequences. They are all Gram-negative but come in every shape
(rods, cocci, spirilla). They are further subdivided into 5 clades: alpha-, beta-, gamma-, delta-, and epsilon proteobacteria.

19.2A.3 https://bio.libretexts.org/@go/page/5970
Alpha (α) Proteobacteria.
Some examples:
Rickettsias. These bacteria are too small to be clearly seen under the light microscope. Almost all are obligate intracellular
parasites. This means that they can only grow and reproduce while within the living cells of their host - certain arthropods
(ticks, mites, lice, fleas) and mammals.
Rickettsia prowazekii causes typhus fever when it is transmitted to humans by lice.
Rocky Mountain spotted fever is a rickettsial disease transmitted by ticks.
The mitochondria of eukaryotes probably evolved from endosymbiotic bacteria. Because of the similarities of their genomes,
rickettsias may be the closest relatives to the ancestors of mitochondria.
Rhizobia. These bacteria live in a mutualistic relationship with the roots of legumes where they are able to "fix" nitrogen (N2)
in the air into compounds that can be used by living things.
Magnetospirillum magnetotacticum
Agrobacterium tumefaciens
Beta (β) Proteobacteria
Sulfur bacteria.
Certain colorless bacteria share the ability of chlorophyll-containing organisms to manufacture carbohydrates from inorganic
raw materials, but they do not use light energy for this. These so-called chemoautotrophic bacteria secure the necessary energy
by oxidizing some reduced substance present in their environment. The free energy released by the oxidation is harnessed to the
manufacture of food.
For example, some chemoautotrophic sulfur bacteria oxidize H2S in their surroundings (e.g., the water of sulfur springs) to
produce energy:
2H2S + O2 → 2S + 2H2O; ΔG = -100 kcal
They then use this energy to reduce carbon dioxide to carbohydrate (like the photosynthetic purple sulfur bacteria)
2H2S + CO2 → (CH2O) + H2O + 2S
This chemoautotroph oxidizes NH3 (produced from proteins by decay bacteria) to nitrites (NO2−). This provides the energy to
drive their anabolic reactions. The nitrites are then converted (by other nitrifying bacteria) into nitrates (NO3−), which supply
the nitrogen needs of plants.
Three important human pathogens among the β-proteobacteria.
Neisseria meningitidis.
Causes meningococcal meningitis, an extremely serious infection of the meninges that occasionally occurs in very young
children and in military camps. There is a vaccine that is effective against several strains but unfortunately not the most
dangerous one.
Neisseria gonorrhoeae. Causes gonorrhea, one of the most common sexually-transmitted diseases (STDs): over 300,000
cases were reported in the U.S. in 2009. In males, the bacterium invades the urethra causing a discharge of pus and often
establishes itself in the prostate gland and epididymis. In females, it spreads from the vagina to the cervix and fallopian
tubes. If the infection is untreated (penicillin is usually effective although strains resistant to it are now being encountered),
the resulting damage to the fallopian tubes may obstruct the passage of eggs and thus cause sterility.
Bordetella pertussis; the cause of "whooping cough".
Gamma (γ) Proteobacteria

The largest and most diverse subgroup of the proteobacteria.

Some examples
Escherichia coli. The most thoroughly-studied of all creatures (possibly excepting ourselves). Its entire genome has been
determined down to the last nucleotide: 4,639,221 base pairs of DNA encoding 4,377 genes. Lives in the human colon, usually
harmlessly. However, water or undercooked food contaminated with the O157:H7 strain has caused severe - occasionally fatal -
infections.
Salmonella enterica. Two major human pathogens:

19.2A.4 https://bio.libretexts.org/@go/page/5970
 Salmonella enterica var Typhi. Causes typhoid fever, a serious systemic infection occurring only in humans. This microbe
is also known as Salmonella typhi.
Salmonella enterica var Typhimurium. Confined to the intestine, it is a frequent cause of human gastrointestinal upsets but
is also found in many other animals (that are often the source of the human infection). Also known as Salmonella
typhimurium.
Vibrio cholerae. Causes cholera, one of the most devastating of the intestinal diseases. The bacteria liberate a toxin that causes
massive diarrhea (10–15 liters per day) and loss of salts. Unless the water and salts are replaced quickly, the victim may die (of
shock) in a few hours. Like other intestinal diseases, cholera is contracted by ingestion of food or, more often, water that is
contaminated with the bacteria.
Pseudomonas aeruginosa. A common inhabitant of soil and water, it can cause serious illness in humans with
defective immune systems
serious burns
cystic fibrosis
Frequently encountered in hospitals and resistant to most antibiotics and disinfectants.
Yersinia pestis. This bacillus causes bubonic plague. It is usually transmitted to humans by the bite of an infected flea. As it
spreads into the lymph nodes, it causes them to become greatly swollen, hence the name "bubonic" (bubo — swelling of a
lymph node) plague. Once in the lungs, however, the bacteria can spread through the air causing the rapidly lethal (2–3 days)
"pneumonic" plague. Untreated, ~30% of the cases of bubonic plague are fatal, and the figure for the pneumonic form reaches
100%. The recurrent epidemics of the "black death" in Europe from 1347–1351, which killed off at least 30% of the population,
was caused by this organism. DNA sequencing of samples retrieved from the bodies of plague victims of that era confirm this
diagnosis. Although no major epidemics have occurred in this century, the threat is not entirely over. Yersinia pestis still
flourishes in some rodent populations in the western U. S. and causes a dozen or so cases of human plague - primarily among
small game hunters -each year.
Francisella tularensis causes tularemia. This is primarily a disease of small mammals, but about 100 people become infected
each year in the United States. Most cases occur in south-central states (KS, MO, OK, AR). However, the import of infected
rabbits by game clubs has introduced the disease to Cape Cod and Martha's Vineyard in Massachusetts. In the summer of 2000,
15 people became ill (one died) on the island. All seem to have acquired their infection as they used lawn mowers and brush
cutters that presumably stirred up the organism from the carcasses of infected animals.
Haemophilus influenzae was once thought to cause influenza. It does not, but it can cause bacterial meningitis and middle ear
infections in children and pneumonia in adults — especially those whose resistance is lowered by other diseases (e.g., AIDS).
There is now an effective vaccine against the most dangerous strains. The complete genome of Haemophilus influenzae is
known: 1,830,138 bp of DNA encoding 1,743 genes.
Purple Sulfur Bacteria Like green plants, these bacteria are photosynthetic, using the energy of sunlight to reduce carbon
dioxide to carbohydrate. Unlike plants, however, they do not use water as a source of electrons.

Figure 19.2.1.3 Chromatium

In the process, they produce elemental sulfur (often - as seen in this photomicrograph of Chromatium - stored as granules within
the cell). [Image from H. G. Schlegel and N. Pfennig, Arch. Microbiol. 38[1], 1961.]
Photosynthetic bacteria contain special types of chlorophylls (called bacteriochlorophylls) incorporated into membranes. With this
machinery, they can run photosystem I but not photosystem II (which explains their inability to use water as a source of electrons).
Most photosynthetic bacteria are obligate anaerobes; they cannot tolerate free oxygen. Thus they are restricted to such habitats as
the surface of sediments at the bottom of shallow ponds and estuaries. Here they must make do with whatever radiant energy gets
through the green algae and aquatic plants growing above them. However, the absorption spectrum of their bacteriochlorophylls
lies mostly in the infrared region of the spectrum so they can trap energy missed by the green plants above them.

19.2A.5 https://bio.libretexts.org/@go/page/5970
Delta (δ) Proteobacteria
This group contains the myxobacteria. They are found in vast numbers in soil and are major players in the decay of organic matter.
Epsilon (ε) Proteobacteria
Two members of this small group that are human pathogens:
Helicobacter pylori, the main cause of stomach ulcers
Campylobacter jejuni; the bacterium most frequently implicated in gastrointestinal upsets.

Bacteroidetes

Figure 19.2.1.4 Spirochete

Two notorious examples:
Treponema pallidum (right), the cause of syphilis, one of the most dangerous of the sexually transmitted diseases (STDs).
(Image courtesy of Harry E. Morton.)
Borrelia burgdorferi is transmitted to humans through the bite of a deer tick causing Lyme disease (over 30,000 cases — the
largest number up to then — were reported in the U.S. in 2009).
Both these organisms have had their complete genomes sequenced.

Chlamydiae
Chlamydiae are also obligate intracellular parasites (they cannot make their own ATP).
Its genome contains 1,042,519 bp of DNA encoding 894 genes. In 2008, over 1.2 million cases were reported in the U. S., and
this is probably only half of the true total. The infection is usually spread by sexual intercourse making it the most common
sexually-transmitted disease (STD). It is easily cured if diagnosed, but many infections remain untreated and, in females, are a
major cause of pelvic inflammatory disease. This causes scarring of the uterus and fallopian tubes and often results in
infertility.
Mothers can pass the infection on to their newborn babies causing serious eye disease and pneumonia. To avoid this, pregnant
women are usually tested for chlamydia and treated with antibiotics if they are infected.
Chlamydia psittaci usually infects birds, but can infect their human contacts causing psittacosis (a.k.a. ornithosis).

Cyanobacteria (blue-green algae)

Figure 19.2.1.5 Oscillatoria

Unlike other photosynthetic bacteria, cyanobacteria
use chlorophyll a (as do plants)
use water as the source of electrons to reduce CO2 to carbohydrate (because they have photosystem II as well as photosystem
I).
CO2 + 2H2O → (CH2O) + H2O + O2
It is estimated that cyanobacteria are responsible for ~ 25% of the photosynthesis occurring on our planet.
The micrograph is of Oscillatoria, a filamentous cyanobacterium (magnified about 800 times). Each disk in the chains is one cell.
Cyanobacteria also contain two antenna pigments:

19.2A.6 https://bio.libretexts.org/@go/page/5970
 blue phycocyanin (making them "blue-green")
red phycoerythrin (The Red Sea gets its name from the periodic blooms of red-colored cyanobacteria.)
These two pigments also occur in red algae. Their chloroplasts (in fact probably all chloroplasts) evolved from an endosymbiotic
cyanobacterium.

This page titled 19.2A: Bacteria is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.2A.7 https://bio.libretexts.org/@go/page/5970
19.2B: Archaea
When these microscopic organisms were first discovered (in 1977), they were considered bacteria. However, when their ribosomal
RNA was sequenced, it became obvious that they bore no close relationship to the bacteria and were, in fact, more closely related
to the eukaryotes (including ourselves!) For a time they were referred to as archaebacteria, but now to emphasize their distinctness,
we call them Archaea. They have also been called Extremophiles in recognition of the extreme environments in which they have
been found:
thermophiles that live at high temperatures
hyperthermophiles that live at really high temperatures (present record is 121°C!)
psychrophiles that like it cold (one in the Antarctic grows best at 4°C)
halophiles that live in very saline environments (like the Dead Sea)
acidophiles that live at low pH (as low as pH 1 and who die at pH 7!)
alkaliphiles that thrive at a high pH.
Most of the >250 named species that have been discovered so far have been placed in two groups: Euryarchaeota
and Crenarchaeota

19.2B.1 Euryarchaeota
There are three main groups: Methanogens, Halophiles. and Thermoacidophiles.

19.2B.1.1 Methanogens
These are found living in such anaerobic environments as
the muck of swamps and marshes
the rumen of cattle (where they live on the hydrogen and CO produced by other microbes living along with them)
2

our colon (large intestine)

sewage sludge
the gut of termites
They are chemoautotrophs; using hydrogen as a source of electrons for reducing carbon dioxide to food and giving off methane
("marsh gas", CH ) as a byproduct.
4

4H + CO ⟶ CH +2 H O
2 2 4 2

Two methanogens that have had their complete genomes sequenced:

Methanocaldococcus jannaschii
Methanothermobacter thermoautotrophicus

19.2B.1.2 Halophiles
These are found in extremely saline environments such as the Great Salt Lake in the U.S. and the Dead Sea. They maintain osmotic
balance with their surroundings by building up the solute concentration within their cells.

19.2B.1.3 Thermoacidophiles
As their name suggests, these like it hot and acid (but not as hot as some of the Crenarchaeota!). They are found in such places as
acidic sulfur springs (e.g., in Yellowstone National Park) and undersea vents ("black smokers").

19.2B.2 Crenarchaeota
The first members of this group to be discovered like it really hot and so are called hyperthermophiles. One can grow at 121°C
(the same temperature in the autoclaves used to sterilize culture media, surgical instruments, etc.). Many like it acid as well as hot
and live in acidic sulfur springs at a pH as low as 1 (the equivalent of dilute sulfuric acid). These use hydrogen as a source of
electrons to reduce sulfur in order to get the energy they need to synthesize their food (from CO2).
Aeropyrum pernix is one member of the group that has had its genome completely sequenced. Other members of this group seem
to make up a large fraction of the plankton in cool, marine waters and the microbes in both soil and the ocean that convert ammonia
into nitrites (nitrification).

19.2B.1 https://bio.libretexts.org/@go/page/5971
19.2B.3 Evolutionary Position of the Archaea
The archaea have a curious mix of traits characteristic of bacteria as well as traits found in eukaryotes. The table summarizes some
of them.

Eukaryotic Traits Bacterial Traits

DNA replication machinery

histones
nucleosome-like structures single, circular chromosome
Transcription machinery operons
RNA polymerase no introns
TFIIB bacterial-type membrane transport channels
TATA-binding protein (TBP) Many metabolic processes
Translation machinery energy production
initiation factors nitrogen-fixation
ribosomal proteins polysaccharide synthesis
elongation factors
poisoned by diphtheria toxin

19.2B.4 What can we conclude from this collection of traits?

Many traits found in the bacteria first appeared in the ancestors of all the present-day groups. The split leading to the archaea and
the eukaryotes occurred after the bacteria had gone their own way. However, the acquisition by eukaryotes of mitochondria
(probably from an ancestor of today's rickettsias) and chloroplasts (from cyanobacteria) occurred after their line had diverged from
the archaea (i.e., the endosymbiosis hypothesis).
Bacteria Archaea Eukaryota

Entamoebae Slime
Spirochetes Chloroflexi Animals
molds
Gram- Methanosarcina Fungi
positives Methanobacterium Haloarchaea
Proteobacteria Methanococcus Plants
Cyanobacteria Thermococcus Ciliates
celer
Planctomyces Thermoproteus Flagellates
Pyrodicticum
Bacteroides Trichomonads
Cytophaga
Microsporidia
Thermotoga

Aquifex Diplomonads

Figure 19.2.2.1 Tree of life A speculatively rooted tree for rRNA genes, showing the three life domains Bacteria, Archaea, and
Eukaryota, and linking the three branches of living organisms to the LUCA (the black trunk at the bottom of the tree), 2009. (Public
Domain; NASA Astrobiology Institute via Wikipedia)
As more and more genes are sequenced, it appears that the line that eventually produced eukaryotes split off after the line leading
to the euryarchaeota. If that is the case, Archaea is a paraphyletic group, and we shared a common ancestor with the other archaea
more recently than they (and we) did with the euryarchaeota.

19.2B.5 Economic Importance of the Archaea

Because they have enzymes that can function at high temperatures, considerable effort is being made to exploit the archaea for
commercial processes such as providing enzymes to be added to detergents (maintain their activity at high temperatures and pH)
and an enzyme to covert corn starch into dextrins. Archaea may also be enlisted to aid in cleaning up contaminated sites, e.g.,
petroleum spills.

This page titled 19.2B: Archaea is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.2B.2 https://bio.libretexts.org/@go/page/5971
19.2C: Antibiotics
Humans, and our domestic animals, can serve as hosts to a wide variety of disease-causing organisms (pathogens)
including bacteria, viruses, fungi, protozoans, helminths (worms). This page will examine only those chemical agents that are used
to combat bacterial pathogens.

The Problem
There are many chemicals that are lethal to bacteria - cyanide does a good job — but they cannot be used to cure infections because
they are lethal to the host as well. The problem, then, is to find substances that attack a metabolic pathway found in the bacterium
but not in the host. This is not an insurmountable problem for bacterial pathogens because they differ in many respects from
eukaryotes.

The Solution
Natural products. A number of natural products, penicillin for example, have been discovered that are antibiotics suitable for
therapy. They were originally discovered as secretions of fungi or soil bacteria. Soils are complex ecosystems, and it is not
surprising that its inhabitants have evolved chemical defenses against each other.

Figure 19.2.3.1 Penicillium

The photo (courtesy of Merck & Co., Inc.) shows how the growth of bacteria on the agar in a culture dish has been inhibited by the
three circular colonies of the fungus Penicillium notatum. The antibiotic penicillin, diffusing outward from the colonies, is
responsible for this effect. Today, penicillin is made from cultures of Penicillium chrysogenum that has been specially adapted for
high yields.
Semi-synthetic products. These are natural products that have been chemically modified in the laboratory (and pharmaceutical
facility) to
improve the efficacy of the natural product
reduce its side effects
circumvent developing resistance by the targeted bacteria
expand the range of bacteria that can be treated with it
Completely synthetic products. The sulfa drugs are examples.

Sulfa Drugs and Folic Acid Analogs

Sulfa Drugs

Figure 19.2.3.2 PABA

Sulfanilamide was the first antibacterial agent. Many other sulfa drugs (such as sulfamethoxazole) have since come into use.

19.2C.1 https://bio.libretexts.org/@go/page/5972
 Both bacteria and their human hosts require folic acid for nucleic acid synthesis (it is converted into purines and thymidine) as
well as protein synthesis (precursor of the amino acids methionine and glycine). However, bacteria synthesize their folic acid
starting with para-aminobenzoic acid (PABA), while we must ingest our folic acid already formed; that is, for us it is a
vitamin.
Sulfanilamide, and the other sulfa drugs, are analogs of PABA; they compete with PABA and, when chosen, block the
synthesis of folic acid. Mammals ignore PABA and its analogs and thus can tolerate sulfa drugs.

Folic Acid Analogs

These synthetic molecules block the final step in the conversion of PABA to folic acid so they, too, block nucleotide and protein
synthesis in bacteria but not in mammals. Trimethoprim is one of several in current use. These folic acid analogs are often used in
combination with a sulfa drug.

The Beta-Lactams

Figure 19.2.3.3 Penicillin G. The beta-lactams get their name from the characteristic ring structure - shown here in blue - that they
all share. (The green arrow shows the bond that is broken by the beta-lactamases that are synthesized by many penicillin-resistant
bacteria.)
The beta-lactams include the
penicillins such as
penicillin G (a natural product) produced by the fungus Penicillium chrysogenum
ampicillin (a semi-synthetic)
amoxicillin (semi-synthetic)
cephalosporins There are over two dozen of them in current use. Most are semi-synthetics derived from the secretion of the
mold Cephalosporium. Some examples:
cephalexin (e.g., Keflex®)
cefaclor (e.g., Ceclor®)
cefixime (e.g., Suprax®)
carbapenems such as
meropenem (Merrem®)
ertapenem (Invanz®)

The beta-lactams all work by interfering with the synthesis of the bacterial cell wall — a structure that is not found in
eukaryotes. The walls of bacteria are made of a complex polymeric material called peptidoglycan.

Figure 19.2.3.4 NAG - NAM

Peptidoglycan contains both amino acids and amino sugars. The amino sugars are of two kinds

19.2C.2 https://bio.libretexts.org/@go/page/5972
 N-acetylglucosamine (NAG) and its close relative
N-acetylmuramic acid (NAM).
These two form a linear polymer of NAG alternating with NAM. They are linked by a glycosidic bond between the #1 and #4
carbons (this is the linkage attacked by lysozyme) and are oriented in the same way they are in cellulose. Side chains containing 4
or 5 amino acids are attached to each NAM. These form covalent bonds with amino acids in adjacent chains. The bonds may be
direct to the next chain or include additional peptide cross bridges (e.g., 5 glycine residues) which extend to chains in the same
plane (shown here) as well as to chains above and below.
This elaborate, covalently cross-linked structure provides the great strength of the cell wall. It also leads to the remarkable
conclusion that the bacterial cell wall meets the definition of a single molecule!
The beta-lactam antibiotics bind to and inhibit enzymes needed for the synthesis of the peptidoglycan wall. While they have little
effect on resting bacteria, they are lethal to dividing bacteria as defective walls cannot protect the organism form bursting in
hypotonic surroundings.

Aminoglycosides
These are products of actinomycetes (soil bacteria) or semi-synthetic derivatives of the natural products.
Examples are:
streptomycin
kanamycin
neomycin
gentamycin

The 70S bacterial ribosome differs in several ways from the 80S eukaryotic ribosome. The aminoglycosides bind to the 30S
subunit of the bacterial ribosome and interfere with the formation of the initiation complex. They also cause misreading of the
mRNA. Although the eukaryotic ribosome in the cytosol is relatively unaffected by these drugs, ribosomes in the mitochondria
are 70S and sensitive to their effects.

Tetracyclines
These are natural products derived from soil actinomycetes or their semi-synthetic derivatives. Examples:
chlortetracycline (aureomycin®)
oxytetracycline (terramycin®)
doxycycline
tigecycline (Tygacil®)
Tetracyclines bind to the 30S subunit of the bacterial ribosome. They prevent the transfer of activated amino acids to the ribosome
so protein synthesis is halted.

Macrolides, Lincosamides, Streptogramins, and Ketolides

The Chink in the Armor = the bacterial ribosome
These antibiotics bind to the large (50S) subunit of the bacterial ribosome where they block the growing peptide chain from exiting
the ribosome thus severely hindering protein synthesis. Because of their similar action, the development of antibiotic resistance to
one usually extends to all the others.

Macrolides
Macrolides are also products of actinomycetes (soil bacteria) or semi-synthetic derivatives of them. Erythromycin, azithromycin
(Zithromax®), and clarithromycin (Biaxin®) are a commonly-prescribed macrolides.

Lincosamides
The first member of this group was also isolated from a soil actinomycete (found near Lincoln, Nebraska). A semi-synthetic
derivative, called clindamycin (Cleocin®), is now widely used against Gram-positive bacteria.

19.2C.3 https://bio.libretexts.org/@go/page/5972
Streptogramins
Quinupristin and dalfopristin are examples. As of 1 October 1999, they will be sold as a mixture under the trade name Synercid.
Combined, they show great promise in treating certain infections resistant to vancomycin- currently the antibiotic of last resort for
some hospital-acquired infections.

Ketolides
Ketolides are derivatives of macrolides. Telithromycin (Ketek®) is an example. Ketolides also bind to the 50S subunit of the
bacterial ribosome. In so doing they cause it to induce frameshifts during translation. Bacteria that have become resistant to
macrolides, lincosamides, and streptogramins are still susceptible to ketolides.

Fluoroquinolones
Ciprofloxacin (Cipro®), levofloxacin and norfloxacin are examples. Cipro is the preferred antibiotic for people who have been
intentionally exposed to anthrax, although some other antibiotics appear to be equally effective.
The Chink in the Armor = DNA topoisomerases
The fluoroquinolones block the action of two bacterial topoisomerases - enzymes that relieve the coils that form in DNA when the
helix is being opened in preparation for replication or transcription or repair. The topoisomerases in eukaryotes are not affected.

Polypeptides
The most common of these is polymixin E (also known as colistin). It behaves as a detergent, increasing the permeability of the
membranes that encase bacteria and causing the contents of the bacterial cell to leak out.

Rifampin
This semi-synthetic antibiotic binds to the bacterial RNA polymerase and prevents it from carrying out its role in transcription. Its
affinity for the equivalent eukaryotic enzyme is much lower. Rifampin is also known as rifampicin.

Mupirocin
This antibiotic blocks the action of the bacterial isoleucine tRNA synthetase, the enzyme responsible for attaching the amino acid
isoleucine (Ile) to its tRNA in preparation for protein synthesis, so protein synthesis is inhibited. It spares the equivalent eukaryotic
enzyme.

Cycloserine
Cycloserine inhibits synthesis of the bacterial cell wall but by a different mechanism than the beta-lactam antibiotics discussed
above. Cycloserine is an analog of D-alanine and blocks the incorporation of D-alanine into the peptide bridges in the bacterial cell
wall. It is derived from an actinomycete.

Aminocyclitols
These products of another actinomycete achieve their effect by interfering with the 30S subunit of the bacterial ribosome.
Spectinomycin (trade name = Trobicin®) is an example. It is particularly effective against the gonococcus, the bacterium that
causes the sexually-transmitted disease (STD) gonorrhea.

Glycopeptides
Glycopeptides also interfere with the synthesis of the bacterial cell wall but by a different mechanism than the beta-lactams.
Vancomycin is a widely-used glycopeptide in the U.S. It binds to the D-alanines on the precursors of the peptidoglycan cross
bridges preventing their cross-linking. It has become the antibiotic of last resort as resistance to the other antibiotics has become
more and more common.

Oxazolidinones
The first of these new antibiotics, linezolid (Zyvox®), was approved by the U.S. Food and Drug Administration on 19 April 2000.
It is effective against many Gram-positive bacteria that have developed resistance to the older antibiotics.

19.2C.4 https://bio.libretexts.org/@go/page/5972
Linezolid attacks a previously-unexploited chink in the bacterium's armor: the proper assembly of the two ribosomal subunits (30S
and 50S). It does not affect eukaryotic ribosomes — and thus translation of mRNAs in the cytosol. However, it does affect the
bacterial-like mitochondrial ribosomes and can interfere with the synthesis of those mitochondrial proteins synthesized by them.

Lipopeptides
These are natural compounds derived from a species of Streptomyces. The one now in clinical use is daptomycin (Cubicin®). It is
effective against Gram-positive bacteria. It attacks another previously-unexploited chink in the bacterial armor — the integrity of
its cell membranes.
So far there is no evidence of bacteria developing resistance against it.

Resistance to Antibiotics
None of the antibiotics discussed above is effective against all bacterial pathogens.

Intrinsic resistance
Some bacteria are intrinsically resistant to certain of the antibiotics. Example: Gram-positive bacteria are much less susceptible to
polymixins than Gram-negative bacteria. [The "Gram" designations refer to the behavior of the bacteria when stained with the
Gram stain; this behavior is a reflection of the very different organization of their cell walls.]

Acquired resistance
Many bacteria acquire resistance to one or more of the antibiotics to which they were formerly susceptible.
Example: In the U.S. in the decade from 1985–1995, resistance of Shigella (which causes gastrointestinal illness) to ampicillin
grew from 32% to 67%. And, while only 7% of these isolates were resistant to the combination of sulfamethoxazole and
trimethoprim at the start of the decade, that figure had grown to 35% by the end of the decade.
Bacteria develop resistance by acquiring genes encoding proteins that protect them from the effects of the antibiotic. In some cases
the genes arise by mutation; in others, they are acquired from other bacteria that are already resistant to the antibiotic. The genes
are often found on plasmids which spread easily from one bacterium to another - even from one species of bacterium to another.
Examples:
Synthesis of the enzyme penicillinase - or other beta-lactamases - provides protection from the beta-lactam antibiotics. These
enzymes break the beta-lactam ring at the position shown with the green arrow in the diagram of penicillin G.
Likewise synthesis of cephalosporinases defeats the cephalosporins.
Defeating quinolones:
Some bacteria do this by modifying their DNA gyrase.
Others, e.g., Mycobacterium tuberculosis, develop quinolone resistance by synthesizing a protein that resembles a short
length of DNA. This protein binds the gyrase so it cannot form the DNA/gyrase complex that is the target of quinolone
action.
Some bacteria synthesize "pumps" in their plasma membrane through which they remove antibiotics like tetracyclines from the
interior of the cell.
Bacteria may methylate their ribosomes obscuring the target of antibiotics (e.g., erythromycin) that ordinarily bind to and
inactivate the ribosome — or conversely
they may enzymatically modify the antibiotic (e.g., kanamycin) so it can no longer "see" its ribosomal target.
Bacteria may modify the structure of their peptidoglycan wall and thus avoid the inhibitory effects of antibiotics like
cycloserine.
An alarming number of human pathogens have acquired genes to combat all the presently-used antibiotics except vancomycin and
recently vancomycin-resistant bacteria have appeared. These multidrug-resistant strains are particularly common in hospitals where
antibiotic use is heavy, and the patients often have weakened immune systems.

Measuring Antibiotic Resistance

19.2C.5 https://bio.libretexts.org/@go/page/5972
 Figure 19.2.3.5 Antibiotic disks
The figure illustrates the simplest method of the several available for measuring antibiotic resistance.
A suspension of the bacteria to be tested (e.g. cultured from the infected patient) is spread over the surface of a petri dish
containing a solid culture medium.
Disks of several different antibiotics are pressed on the surface of the agar. The concentration of antibiotic in each type of disk
is standardized.
Incubate overnight.
The bacteria will grown into a "lawn" except where an antibiotic to which they are sensitive has diffused out from its disk.
Measure the diameter of any zones of inhibition that are formed.

What can you do to delay the spread of antibiotic resistance?

Don't ask your doctor for an antibiotic to treat a viral disease (e.g., a cold) for which antibiotics are useless. (However, your
doctor may prescribe an antibiotic if you are infected by an influenza virus - not to fight the virus but to protect you against a
secondary bacterial infection of your damaged lungs.)
Stay the course. Use all doses prescribed even though you are feeling better. This will minimize the opportunity to select for
resistance among the bacteria that remain late in the infection.
Don't save unused antibiotics for later self-medication.
Farmers can help as well by avoiding the use of antibiotics in their livestock that are similar to those used in humans. Antibiotics
are widely used in healthy livestock to improve their growth rate (by an unknown mechanism).
An article in the 20 May 1999 issue of The New England Journal of Medicine documents the recent development of quinolone
resistance in Campylobacter jejuni, the most frequent bacterial cause of gastroenteritis in humans. The rise coincides with the
approval in 1995 of the use of quinolones by U. S. poultry farmers (chickens also become infected by C. jejuni). Similar recent
increases in fluoroquinolone-resistant C. jejuni have been reported in the Netherlands and also in Spain (where as many as 50% of
human infections are now caused by bacteria resistant to the antibiotic). In each country, the appearance of resistant strains
followed the widespread introduction of quinolone treatment for animals.

Future Prospects
Drug companies - after many years of complacency - are now responding to the threat of antibiotic-resistant bacteria. Over a dozen
new antibiotics are being developed and some have already reached clinical trials. Many of these are semi-synthetic modifications
of already-existing antibiotics, including new
beta-lactams
macrolides
glycopeptides
quinolones
modifications of vancomycin
Others are entirely new, attacking previously-unexploited chinks in the bacterial armor.
Urea hydroxamates, that block the enzyme (peptide deformylase) that removes fMet from the finished protein so it can begin its
work. (Eukaryotes do not begin translation with fMET.)
Heteroaromatic polycycles (HARP) that bind to bacterial promoters preventing gene transcription.

19.2C.6 https://bio.libretexts.org/@go/page/5972
This page titled 19.2C: Antibiotics is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.2C.7 https://bio.libretexts.org/@go/page/5972
19.2D: E. coli
Escherichia coli is a bacterium that is a common - but certainly not the most abundant - inhabitant of the human colon. It also lives
in the intestine of many other animals, wild as well as domestic.
Normally, E. coli does not cause disease although some strains frequently cause diarrhea in travelers, and it is the most common
cause of urinary tract infections. One strain, designated O157:H7, is particularly virulent and has been responsible for several
dangerous outbreaks in people eating contaminated food (usually undercooked hamburger).
Drinking water is tested for the presence of E. coli and related bacteria not because these bacteria are particularly dangerous but
because they are an indication of contamination by sewage, and sewage may contain organisms (e.g., Salmonella, hepatitis A virus)
that are dangerous.
E. coli is one of the most thoroughly studied of all living things. It is a favorite organism for genetic engineering as cultures of it
can be made to produce unlimited quantities of the product of an introduced gene. Several important drugs (insulin, for example)
are now manufactured in E. coli. However, E. coli cannot attach sugars to proteins so proteins requiring such sugars (e.g.,
glycoprotein hormones and clotting factors) have to be made in the cells of eukaryotes such as yeast cells and mammalian cells
grown in cell culture.
Because E. coli lives in the human intestine, this has raised fears that genetically-engineered versions might escape from the
laboratory (or factory) and take up residence in humans, producing a product that might be harmful. For this reason, genetic
engineering is done only on strains of E. coli that have been deliberately weakened so that they cannot survive for long in humans.
The complete sequence of the genome of a harmless laboratory strain of E. coli (K-12) was reported in the 5 September 1997 issue
of Science. The genome consists of a single molecule of DNA containing 4,639,221 base pairs. These encode 4288 proteins and 89
RNAs. Many of the genes were already known and the function of many others can be deduced from the similarity to known genes.
The complete sequence of the pathogenic strain O157:H7 was reported in the 25 January 2001 issue of Nature. It contains 5416
genes in 5.44 x 106 base pairs of DNA. Remarkably, these include 1,387 genes that are not present in its harmless laboratory
relative E. coli K-12 (and K-12 has 528 genes that are not found in O157:H7). So here are two strains of the same species that
differ in some 25% of their genes. Compare this with the difference between the genomes of humans and chimpanzees which
probably is no more than 1%!)

This page titled 19.2D: E. coli is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.2D.1 https://bio.libretexts.org/@go/page/5973
19.2E: Anthrax
Anthrax is a disease caused by the bacterium Bacillus anthracis. It normally affects cattle, sheep, goats, etc. It is acquired from
spores that remain viable in the environment (e.g. soil) for decades always able to germinate into active bacteria if they get into the
body of a susceptible host. Humans can be infected by Bacillus anthracis, and if the spores enter by way of the lungs, the disease
can be quickly fatal. These properties have made it one of the agents favored by bioterrorists.

Bacillus Anthracis. (CC BY-SA 4.0; BruceBlaus).

It is not the tissue-destructiveness of the active bacteria that is the problem but rather the toxin that they secrete. (This is like the
illnesses caused by the bacilli that cause diphtheria, tetanus, and botulism.) The bacteria are susceptible to antibiotics; for example,
Ciprofloxacin (Cipro®) is effective as are others such as doxycycline, but they must be given early before the toxin can produce
symptoms. Once the toxin is in the system, it can be neutralized by giving antitoxin antibodies (conferring passive immunity).
Presently these are harvested from donors who had received anthrax vaccine in the armed forces. But there is hope that monoclonal
antibodies can be manufactured that will be able to provide protection.
The anthrax toxin is composed of three different proteins (encoded by genes on one of the two plasmids in the organism):
PA ("protective antigen") It gets this name because it provides the epitopes that elicit protective antibodies in the anthrax
vaccine.
LF ("lethal factor")
EF ("edema factor")

Infection
PA molecules bind to receptors at the cell surface assembling in clusters of 7.
LF and/or EF molecules then bind to these clusters.
The complex is engulfed by receptor mediated endocytosis.
The drop in pH in the endosome (endocytic vesicle) produces a change in the structure of the PA cluster enabling it to release its
LF and EF into the cytosol.
EF is an adenylyl cyclase which raises the intracellular concentration of cAMP inhibiting phagocytosis by neutrophils.
As it name implies, LF in the cytosol so disturbs the machinery of the cell that it dies.

Future Prospects
In April of 2001, John Collier and his colleagues reported that several mutant versions of PA protected rats from death by the active
anthrax toxin. The mutant molecules coassembled with normal PA molecules, and the complex was still able to bind LF and EF.
However, the complex could not release LF or EF from the endosome, and the rats remained healthy. Perhaps one of these altered
PA molecules can be enlisted in the fight against bioterrorism as both a vaccine to protect people before exposure and a treatment
to block the lethal effects of the natural toxin after exposure.
Today's Anthrax Vaccine

19.2E.1 https://bio.libretexts.org/@go/page/5974
The vaccine is made from an extract of a weakened strain of B. anthracis (it makes no surface capsule). The extract contains large
amounts of PA, as well as some LF and EF.

Anthrax Strains
Scores of different strains of anthrax have been isolated from many parts of the world. While they share most of their harmful
traits, their genomes differ in the number of repeated sequences of noncoding DNA. These are called VNTRs (for variable number
of tandem repeats) and are simply longer versions of the short tandem repeats (STRs) now being used by law enforcement agencies
for DNA fingerprinting of humans. DNA fingerprinting of any strain of anthrax used by bioterrorists may help track down its
source.

This page titled 19.2E: Anthrax is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.2E.2 https://bio.libretexts.org/@go/page/5974
19.2F: Bacillus Thuringiensis
Bacillus thuringiensis is a bacterium that parasitizes the caterpillars of some harmful moths and butterflies. Spraying or dusting
plants with spores of this bacterium appear to be environmentally safe ways to attack such pests as the gypsy moth, the tent
caterpillar, and the tobacco hornworm (which also attacks tomatoes). The bacteria kill by a toxin which they secrete. The gene for
this toxin has been introduced into some crop plants in an effort to protect them from insect attack without the need for spraying.

Figure 19.2.6.1 Bollworm. Image courtesy of the Monsanto Corp.

On the left is a cotton boll being attacked by a cotton bollworm. The cotton plant that produced the boll on the right contains and
expresses the gene for the Bt toxin. The gene was introduced into the plant by genetic engineering. Transgenic cotton and corn
(maize) containing the gene for Bt toxin were widely planted for the first time in 1996. By 2009, these crops had been planted on
over 334 million acres (135x106 hectares) worldwide. In the United States over 70% of the cotton planted and 63% of the corn
planted is now with transgenic varieties. Crops transgenic for Bt toxin have shown improved yields with greatly-reduced need for
chemical insecticides. Not only does this reduce costs and possible health effects, but spares the natural enemies of other insect
pests.
B. thuringiensis appears to be the same organism as Bacillus cereus, a usually harmless soil organism, and Bacillus anthracis, the
cause of anthrax. What gives them their distinctive properties are the genes encoded by the plasmids they contain.

This page titled 19.2F: Bacillus Thuringiensis is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball
via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.2F.1 https://bio.libretexts.org/@go/page/5975
19.2G: The Rapid Identification of Microorganisms

The Need
diagnosis of infection so that the appropriate treatment (e.g., an antibiotic) can be started.
testing of food to ensure that it is not contaminated with infectious organisms like E. coli O157:H7 and Salmonella enterica
to identify the biological agent such as anthrax and smallpox in a possible terrorist attack so that appropriate measures can be
taken quickly

Methods
Culturing
The oldest and still most common.
For bacteria, spread samples on culture media and examine the resulting colonies for morphology and metabolic traits. For
viruses, inoculate cultures of living cells.
Disadvantage: it make take several days to learn the results.

Polymerase Chain Reaction (PCR)

Extract DNA from the sample and perform PCR.
Advantage: rapid (often less than an hour)
Disadvantage: overly sensitive to presence of contaminants

Immunoassays
Use a method that exploits the specificity and sensitivity of the reaction between antigen and antibodies. Takes 15 minutes or
longer.

Biosensors (CANARY)
In the 11 July 2003 issue of Science, a team of scientists at the Lincoln Laboratory in the U. S. reported a new method of rapid
identification that exploits living cells. They call their method CANARY (for Cellular Analysis and Notification of Antigen Risks
and Yields)
Their "biosensor" is a clone of B lymphocytes (B cells) that have been genetically engineered to express
a B cell receptor for antigen (BCR) selected to interact with an epitope on the suspected agent. The BCR on their clones is
surface IgM.
aequorin, a protein extracted from the same jellyfish that produces green fluorescent protein.
Aequorin emits light when it is exposed to calcium ions (Ca2+).
One of the first events (within seconds) when BCRs bind to antigen is a rise in the level of calcium ions in the cytosol.
Procedure:
Prepare the sample.
Mix - in separate wells - with B-cell clones each specific for a different suspected agent.
Place in a sensitive light detector.
If a clone has a BCR for an epitope present in the sample, that clone will emit light within a few seconds.
Results:
highly sensitive: can detect as few as 50 bacteria or 500 virions
highly specific: can detect the agent even in the presence of related contaminating agents.
fast: time elapsed from sample preparation to signal from the light detector is often less than 5 minutes.

This page titled 19.2G: The Rapid Identification of Microorganisms is shared under a CC BY 3.0 license and was authored, remixed, and/or
curated by John W. Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is
available upon request.

19.2G.1 https://bio.libretexts.org/@go/page/5976
 SECTION OVERVIEW
19.3: Viruses
19.3A: Viruses

19.3B: Influenza

19.3C: φX174

19.3D: Smallpox

19.3E: Retroviruses

This page titled 19.3: Viruses is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.3.1 https://bio.libretexts.org/@go/page/5940
19.3A: Viruses
Viruses are obligate intracellular parasites. Probably there are no cells in nature that escape infection by one or more kinds of
viruses. Viruses that infect bacteria are called bacteriophages. Outside the cell, they consist of particles called virions.

Figure 19.3.1.1 Poliovirus

Virions range in size from as small as the poliovirus shown above magnified some 450,000 times (courtesy of A. R. Taylor), which
is 30 nm in diameter (about the size of a ribosome) to as large as Pithovirus sibericum an amoeba-infecting virus which, at 1,500
nm, is larger than many bacteria.
The virion consists of
An outer shell, the capsid, made of protein. The capsid is responsible for
protecting the contents of the core
establishing what kind of cell the virion can attach to infecting that cell
Some capsids contain other ingredients (e.g., lipids, carbohydrates), but these are derived from their host cells.
an interior core containing
the genome; either DNA or RNA The genes are few in number (3–100 depending on the species). They encode those
proteins needed for viral reproduction that the host cell will not supply.
Often, one or more proteins (enzymes) needed to start the process of reproduction within the host cell.

Life Cycle
The virion attaches to the surface of the host cell - usually binding to a specific cell surface molecule that accounts for the
specificity of the infection. Example: HIV-1, the cause of AIDS, binds to the chemokine receptor CCR5 found on human
lymphocytes and macrophages.
Once inside the cell, the virions are uncoated.
Viral genes begin to be expressed leading to the synthesis of proteins needed for
replication of the genome
synthesis of new proteins to make new capsids and cores.
The details of these processes differ for different types of viruses and are described below for each type.

Viral Genomes
Either DNA or RNA, never both.
DNA viruses can be further divided into
those that have their genes on a double-stranded DNA molecule (dsDNA). Example: smallpox
those that have their genes on a molecule of single-stranded DNA (ssDNA). Example: Adeno-Associated Virus (AAV)
RNA viruses occur in four distinct groups:
1. Those with a genome that consists of single-stranded antisense RNA; that is, RNA that is the complement of the message
sense. This is also called negative-stranded RNA. Examples: measles, Ebola
2. Those with a genome that consists of single-stranded sense RNA; that is, the RNA has message sense (can act as a messenger
RNA - mRNA). This is also called positive-stranded RNA. Examples: poliovirus
3. Those with a genome made of several pieces of double-stranded RNA. Example: reovirus.

19.3A.1 https://bio.libretexts.org/@go/page/5977
 4. Retroviruses. Their RNA (also single-stranded) is copied by reverse transcriptase into a DNA genome within the host cell.
Example: HIV-1

DNA Viruses
Genome is a molecule of double-stranded DNA
Examples:
smallpox (variola)
vaccinia (used to immunize against smallpox until the disease was eliminated from the planet)
varicella-zoster (causes chicken pox the first time; shingles the second)
herpesviruses
herpes simplex viruses
HSV-1 - usually infects the trigeminal nerves periodically causing "cold sores" on the lips and face
HSV-2 - usually infects the genitals
KSHV; causes Kaposi's sarcoma in AIDS patients and other people with suppressed immune systems. Also called human
herpesvirus 8 (HHV-8).
human cytomegalovirus (HCMV); most of us have it; can cause blindness - even death - in people with suppressed
immune systems.
Epstein-Barr virus (EBV); causes mononucleosis and has been implicated in the development of Burkitt's lymphoma (a
cancer) and Hodgkin's disease. Its genome has been completely sequenced: 172,282 base pairs of DNA encoding 80 genes.
adenoviruses; some 50 different strains infect humans; responsible for some cases of the common "cold". Two strains have
been modified to serve as vectors in gene therapy trials.
papilloma viruses; several dozen types infect humans and two of these, HPV-16 and HPV-18, can cause cancer.
SV40; a virus that infects primate cells and causes tumors in rodent cells.
Some bacteriophages
T2 and T4; from which much early information about gene structure and expression was learned.
lambda; a popular vector

Figure 19.3.1.2 Infective cycle of DNA bacteriophages

The essential elements of the infective cycle of DNA bacteriophages consist of:
The virions attach to the surface of their host cell (a).
The proteins of the capsid inject the DNA core into the cell (b).
Once within the cell, some of the bacteriophage genes (the "early" genes) are transcribed (by the host's RNA polymerase) and
translated (by the host's ribosomes, tRNA, etc.) to produce enzymes that will make many copies of the phage DNA and will
turn off (even destroy) the host's DNA.
As fresh copies of phage DNA accumulate, other genes (the "late" genes) are transcribed and translated to form the proteins of
the capsid (c).
The stockpile of DNA cores and capsid proteins are assembled into complete virions (d).
Another "late" gene is transcribed and translated into molecules of lysozyme. The lysozyme attacks the peptidoglycan wall
(from the inside, of course).
Eventually the cell ruptures and releases its content of virions ready to spread the infection to new host cells (e).

19.3A.2 https://bio.libretexts.org/@go/page/5977
Hepatitis B
The genome of hepatitis B ("serum hepatitis") is also dsDNA, but its mode of replication is different from the other dsDNA
viruses.
Once inside its host cell (a liver cell), the virion core enters the nucleus.
The viral DNA is transcribed (by the host's Pol II) into molecules of mRNA.
These enter the cytoplasm where they are translated (again by host ribosomes, etc.) into the various proteins of the virus,
including a viral reverse transcriptase.
These components are assembled into new viral cores, and in each
one molecule of mRNA is reverse transcribed into a single strand of DNA, which then serves as the template for the synthesis
of the second strand.

Genome is single-stranded DNA

Examples:
φX174 (phiX174), another famous bacteriophage (infects E. coli) that helped usher in the modern era of molecular genetics. Its
single strand of DNA has 5,386 nucleotides and contains 11 protein-encoding genes.
Adeno-associated virus (AAV). This virus, which can only grow in cells infected with adenovirus, shows great promise as a
safe and effective vector for introducing therapeutic genes into human patients.

RNA Viruses
Negative-stranded RNA viruses:
Genome consists of one or more molecules of single-stranded "antisense" RNA.
Examples:
measles
mumps
respiratory syncytial virus (RSV), parainfluenza viruses (PIV), and human metapneumovirus. (In the U.S., these close
relatives account for hundreds of thousands of hospital visits each year, mostly by children.)
rabies
Ebola
influenza
Method of replication
In addition to its antisense RNA genome, the core of the virion contains an RNA replicase, which is an RNA-dependent RNA
polymerase.
Once released in the host cell, this polymerase makes many complementary copies of the genome, which are "sense" and serve
as messenger RNAs.
These are translated into the proteins needed to assemble fresh virions, e.g., capsid proteins and RNA polymerase.
Note that this strategy
provides many copies of mRNA
depends on the virion having its own RNA replicase (because the host cell does not) (So, naked RNA molecules of these
viruses are not infectious — in contrast to the next group: the positive-stranded RNA viruses)

Positive-stranded RNA
Genome is a molecule of single-stranded "sense" RNA.
Examples:
polioviruses
rhinoviruses (frequent cause of the common "cold"; 99 different strains are known)
noroviruses (frequent cause of outbreaks of gastrointestinal illness — especially in "closed" settings like cruise ships and
nursing homes)
coronaviruses (includes the agent of Severe Acute Respiratory Syndrome (SARS)

19.3A.3 https://bio.libretexts.org/@go/page/5977
 rubella (causes "German" measles)
yellow fever virus
West Nile virus
dengue fever viruses
equine encephalitis viruses
hepatitis A ("infectious hepatitis") and hepatitis C viruses
tobacco mosaic virus (TMV)
Method of replication
The "sense" RNA encodes an RNA replicase (an RNA-dependent RNA polymerase) that is translated by the host machinery
(ribosomes, etc.) into the enzyme, which catalyzes the synthesis of large numbers of "antisense" replicative intermediates.
These serve as templates for the synthesis of large numbers of mRNA molecules that
are translated by the host cell machinery into the proteins needed to make fresh virions
are incorporated into the new virions.

Double-stranded RNA
Examples:
reovirus
several plant viruses
Method of replication
The virus particle contains enzymatic machinery that transcribes each of the dsRNA molecules into a mRNA (complete with cap)
and exports these into the cytosol of the infected cell.

Retroviruses
These viruses contain a reverse transcriptase that copies their RNA genome into DNA.
Examples:
The Rous sarcoma virus (RSV)
HIV-1 and HIV-2, that cause AIDS
HTLV-1 and HTLV-2. 4–5% of the people infected with HTLV-1 develop adult T-cell leukemia/lymphoma (ATL).

Latent Viruses
Most of the infective cycles described for the various viruses end in the death of the host cell. Bacterial cells literally burst, a
process called lysis, and similar infective cycles are called lytic cycles.

Lysogeny
In some cases, though, the events of the lytic cycle are not completed. An E. coli cell infected by a DNA bacteriophage may
resume its normal existence, including reproducing itself.
Where has the virus gone?
It is still there and, in fact, is present in the descendants of the bacterium. That these cells still harbor the virus can be demonstrated
by irradiating the cells with ultraviolet rays or treating them with certain chemicals. Such treatment restores the normal lytic cycle.
The phage is said to have been "rescued" — hardly the case for its host!
The stable relationship between a bacteriophage and its host is called lysogeny. The viral DNA actually becomes replicated when
the host's DNA is replicated prior to each cell division. During lysogeny, the phage is called a prophage.

Transduction
In some cases, the prophage DNA becomes inserted into the chromosome of its host. In fact, when the phage is "rescued", the
released virions may contain some host genes as well as their own. When these virions infect new hosts, they insert these bacterial
genes into them. This process of genetic transfer, a virus-mediated transformation, is called transduction.

19.3A.4 https://bio.libretexts.org/@go/page/5977
What does the prophage do while it is a part of its host genome? It can express certain of its genes. For example, the gene that
encodes diphtheria toxin is the property of a prophage in the diphtheria bacillus, not of the bacillus itself.
Some animal viruses can also establish latent infections. Simian virus 40 (SV40) is a DNA virus that produces
a lytic infection in the kidney cells of the African green monkey (these cells are used to cultivate viruses in the lab)
but a latent infection in the cells of humans, mice, rats, and hamsters. Like lysogeny in bacteria, the SV40 genome becomes
incorporated as a provirus in the DNA of its host (in chromosome 7 in human cells).
Although a human cell with harboring SV40 shows no outward sign of the provirus, its presence can be detected by:
the appearance of viral-encoded antigens in the host cell
the ability of these cells to cause a lytic infection in African green monkey cells when fused with them.
Latent infections may also cause the cell to become cancerous. The cell has become transformed. In these cases, the word fulfills
both of its biological meanings:
"transformed" by the incorporation of new DNA
"transformed" as it becomes cancerous.
In humans,
lytic infections of plasma cells by the Epstein-Barr virus (EBV) occur in mononucleosis
latent infections of B cells by EBV predispose the person to lymphoma.
while
lytic infections by human papilloma virus (HPV) cause genital warts;
latent infections by some strains of HPV lead to cervical cancer.
and
while most CD4+ T cells infected by the retrovirus HIV-1 are killed (causing AIDS),
HIV-1 integrates as a provirus into the DNA of a few memory CD4+ T cells where it can persist for years with the potential of
creating active disease in the future.

This page titled 19.3A: Viruses is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.3A.5 https://bio.libretexts.org/@go/page/5977
19.3B: Influenza
Influenza is a viral infection of the lungs characterized by fever, cough, and severe muscle aches. In the elderly and infirm, it is a
major cause of disability and death (often as a result of secondary infection of the lungs by bacteria). Even in the young and
healthy, influenza produces a prostrating disease of a few days duration and one not soon forgotten. Influenza is not a case of low
fever and sniffles that keeps you home in bed for a day nor a gastrointestinal upset ("stomach flu").
Influenza was responsible for the most devastating plague in human history - the "Spanish" flu that swept around the world in 1918
killing 675,000 people in the U.S. and an estimated 20–50 million people worldwide. (A disease that attacks a large fraction of the
population in every region of the world is called a pandemic.) (It is uncertain where the flu first appeared, but it certainly wasn't in
Spain.)
No one at the time even knew what disease agent was causing the pandemic. Not until 1930 (in pigs) and 1933 (in humans) was it
established that influenza is caused by a virus.

Figure 19.3.2.1 Fluvirions

This electron micrograph (courtesy of Dr. K. G. Murti) shows several influenza virus particles (at a magnification of about
265,000x). The surface projections are molecules of hemagglutinin and neuraminidase (see below).
There are three types of influenza:
Common but seldom causes disease symptoms.
Often causes sporadic outbreaks of illness, especially in residential communities like nursing homes.
Responsible for regular outbreaks, including the one of 1918. Influenza A viruses also infect domestic animals (pigs, horses,
chickens, ducks) and some wild birds.

The Influenza A Virus

Figure 19.3.2.2 Flu virion

The influenza A virion is
a globular particle (about 100 nm in diameter)
sheathed in a lipid bilayer (derived from the plasma membrane of its host)
Studded in the lipid bilayer are three integral membrane proteins
some 500 molecules of hemagglutinin ("H")
some 100 molecules of neuraminidase ("N")

19.3B.1 https://bio.libretexts.org/@go/page/5978
 the M2 membrane protein (not shown).
Encased by the lipid bilayer are
some 3000 molecules of matrix protein
8 pieces or segments of RNA
Each of the 8 RNA molecules is associated with
many copies of a nucleoprotein
the three subunits of its RNA polymerase
some "non-structural" protein molecules of uncertain function

The Genes of Influenza A

The 8 RNA molecules (the number in brackets is the designated segment number):
The HA gene [4] encodes the hemagglutinin. 3 distinct hemagglutinins (H1, H2, and H3) are found in human infections; 15
others have been found in animal flu viruses.
The NA gene [6] encodes the neuraminidase. 2 different neuraminidases (N1 and N2) have been found in human viruses; 9
others in other animals.
The NP gene [5] encodes the nucleoprotein. Influenza A, B, and C viruses have different nucleoproteins.
The M gene [7] encodes two proteins (using different reading frames of the RNA): a matrix protein (M1 — shown in blue)
and an ion channel (M2) spanning the lipid bilayer (not shown).
The NS gene [8] encodes two different non-structural proteins (also by using different reading frames). These are found in the
cytosol of the infected cell but not within the virion itself.
One RNA molecule (PA [3], PB1 [2], PB2 [1]) encoding each of the 3 subunits of the RNA polymerase. Occasional
frameshifts during translation of PA produce a protein that reduces host gene expression.

The Disease
The influenza virus invades cells of the respiratory passages.
Its hemagglutinin molecules bind to sialic acid residues on the glycoproteins exposed at the surface of the epithelial cells of the
host respiratory system.
The virus is engulfed by receptor mediated endocytosis.
The drop in pH in the endosome (endocytic vesicle) produces a change in the structure of the viral hemagglutinin enabling it to
fuse the viral membrane with the vesicle membrane.
This exposes the contents of the virus to the cytosol.
The RNA enter the nucleus of the cell where fresh copies are made.
These return to the cytosol where some serve as messenger RNA (mRNA) molecules to be translated into the proteins of fresh
virus particles.
Fresh virus buds off from the plasma membrane of the cell (aided by the M2 protein) thus
spreading the infection to new cells.
The result is a viral pneumonia. It usually does not kill the patient (the 1918 pandemic was an exception; some victims died within
hours) but does expose the lungs to infection by various bacterial invaders that can be lethal. Before the discovery of the flu virus,
the bacterium Hemophilus influenzae was so often associated with the disease that it gave it its name.

Pandemics and Antigenic Shift

Three pandemics of influenza have swept the world since the "Spanish" flu of 1918.
The "Asian" flu pandemic of 1957;
the "Hong Kong" flu pandemic of 1968;
the "Swine" flu pandemic that began in April of 2009.
The pandemic of 1957 probably made more people sick than the one of 1918. But the availability of antibiotics to treat the
secondary infections that are the usual cause of death resulted in a much lower death rate. The hemagglutinin of the 1918 flu virus
was H1, its neuraminidase was N1, so it is designated as an H1N1 "subtype". Here are some others.
Some strains of influenza A

19.3B.2 https://bio.libretexts.org/@go/page/5978
 Date Strain Subtype Notes

1918 H1N1 pandemic of "Spanish" flu

1957 A/Singapore/57 H2N2 pandemic of "Asian" flu

1962 A/Japan/62 H2N2 epidemic

1964 A/Taiwan/64 H2N2 epidemic

1968 A/Aichi/68 H3N2 pandemic of "Hong Kong" flu

1976 A/New Jersey/76 H1N1 swine flu in recruits

1977 A/USSR/77 H1N1 "Russian" flu

pandemic of "swine" flu [now

2009 A/California/09 H1N1
designated A(H1N1)pdm09]

Until 2009, these data suggest that flu pandemics occur when the virus acquires a new hemagglutinin and/or neuraminidase. For
this reason, when an H1N1 virus appeared in a few recruits at Fort Dix in New Jersey in 1976, it triggered a massive immunization
program (which turned out not to be needed). However, an H1N1 virus appeared the following year (perhaps escaped from a
laboratory) causing the "Russian" flu. We now know that this virus was a direct descendant of the 1918 flu. While accumulating
mutations that made it less dangerous, it had been infecting humans until it was replaced by the H2N2 "Asian" flu of 1957. Because
most people born before the Asian flu pandemic of 1957 had been exposed to the H1N1 viruses circulating before, the Russian flu
primarily affected children and young adults. For the same reason, this pattern was also seen in the 2009-10 pandemic of "swine"
flu.
Where do the new H or N molecules come from?
Birds appear to be the source. Both the H2 that appeared in 1957 and the H3 that appeared in 1968 came from influenza viruses
circulating in birds. The encoding of H and N by separate RNA molecules probably facilitates the reassortment of these genes in
animals simultaneously infected by two different subtypes. For example, H3N1 virus has been recovered from pigs
simultaneously infected with swine flu virus (H1N1) and the Hong King virus (H3N2). Probably reassortment can also occur in
humans with dual infections.

Epidemics and Antigenic Drift

No antigenic shifts occurred between 1957 ("Asian") and 1968 ("Hong Kong"). So what accounts for the epidemics of 1962 and
1964? Missense mutations in the hemagglutinin (H) gene. Flu infections create a strong antibody response. After a pandemic or
major epidemic, most people will be immune to the virus strain that caused it. The flu virus has two options:
wait until a new crop of susceptible young people comes along
change the epitopes on the hemagglutinin molecule (and, to a lesser degree, the neuraminidase) so that they are no longer
recognized by the antibodies circulating in the bodies of previous victims.
By 1972, the H3 molecules of the circulating strains differed in 18 amino acids from the original "Hong Kong" strain
By 1975, the difference had increased to 29 amino acids.
The gradual accumulation of new epitopes on the H (and N) molecules of flu viruses is called antigenic drift. Spontaneous
mutations in the H (or N) gene give their owners a selective advantage as the host population becomes increasingly immune to the
earlier strains.

Flu Vaccines
Although a case of the flu elicits a strong immune response against the strain that caused it, the speed with which new strains arise
by antigenic drift soon leaves one susceptible to a new infection. Immunization with flu vaccines has proved moderately helpful in
reducing the size and severity of new epidemics.
Some vaccines incorporate inactivated virus particles; others use the purified hemagglutinin and neuraminidase. Both types
incorporate antigens from the three major strains in circulation, currently:
an A strain of the H1N1 subtype
an A strain of the H3N2 subtype and

19.3B.3 https://bio.libretexts.org/@go/page/5978
 a B strain.
Because of antigenic drift, the strains used must be changed periodically as new strains emerge that are no longer controlled by
people's residual immunity.
The process:
Chicken eggs are infected with the virus expressing the new H and/or N and simultaneously infected with a stock flu virus that
grows very well in eggs.
Genetic reassortment produces some viruses with both the new H and N genes along with the 8 other genes from the stock
strain.
This new virus is then grown in massive amounts and the H and N proteins purified for the new vaccine.
The whole process takes several weeks. A promising way to speed things up is to chemically synthesize the new H and N genes
and substitute them for the H and N genes in the stock virus. The new virus can be ready for vaccine production in a few days.
Strains used in vaccines for the flu seasons shown.
Season H1N1 H3N2 Type B

86–87 A/Chile/83* A/Mississippi/85 B/Ann Arbor/86

* As the 86–87 season got underway, it was found that A/Chile/83 no longer gave protection so A/Taiwan/86 was offered as a second shot late in
that season.

87–88 A/Taiwan/86 A/Leningrad/86 B/Ann Arbor/86

88–89 A/Taiwan/86 A/Sichuan/87 B/Victoria/87

89–90 A/Taiwan/86 A/Shanghai/87 B/Yamagata/88

90–91 A/Taiwan/86 A/Shanghai/89 B/Yamagata/88

91–92 A/Taiwan/86 A/Beijing/89 B/Panama/90

92–93 A/Texas/91 A/Beijing/89 B/Panama/90

93–94 unchanged unchanged unchanged

94–95 A/Texas/91 A/Shandong/93 B/Panama/90

95–96 A/Texas/91 A/Johannesburg/94 B/Harbin/94

96–97 A/Texas/91 A/Nanchang/95 B/Harbin/94

97–98 A/Johannesburg/96 A/Nanchang/95 B/Harbin/94

98–99 A/Beijing/95 A/Sydney/97 B/Beijing/93

99–00 A/Beijing/95 A/Sydney/97 B/Yamanashi/98

00–01 A/New Caledonia/99 A/Panama/99 B/Yamanashi/98

01–02 A/New Caledonia/99 A/Panama/99 B/Victoria/00 or similar

02–03 A/New Caledonia/99 A/Moscow/99 B/Hong Kong/2001

03–04 A/New Caledonia/99 A/Moscow/99 B/Hong Kong/2001

04–05 A/New Caledonia/99 A/Fujian/2002 B/Shanghai/2002

05–06 A/New Caledonia/99 A/California/2004 B/Shanghai/2002

06–07 A/New Caledonia/99 A/Wisconsin/2005 B/Malaysia/2004

07–08 A/Solomon Islands/06 A/Wisconsin/2005 B/Malaysia/2004

The B/Malasia component of the

vaccine provided no protection at
all. So all three components of the
08–09 vaccine were changed as
shown on the next line.

19.3B.4 https://bio.libretexts.org/@go/page/5978
 Season H1N1 H3N2 Type B

08–09 A/Brisbane/2007 A/Brisbane/2007 B/Florida/2006

09–10 A/Brisbane/2007 A/Brisbane/2007 B/Brisbane/2008

Because the 2009–2010 pandemic of the newly-emerged "swine flu" virus drove the "seasonal" H1N1 viruses (e.g., A/Brisbane/2007) to near
extinction,
the "swine flu" H1N1 – now called A(H1N1)pdm09 – replaced the "seasonal" H1N1 in the 10–11 vaccine.

10–11 A/California/2009 A/Perth/2009 B/Brisbane/2008

11–12 All three components were unchanged from the previous year

12–13 A/California/2009 A/Victoria/2011 B/Wisconsin/2010

13–14 A/California/2009 A/Victoria/2011 B/Massachusetts/2012

14–15 A/California/2009 A/Texas/2012 B/Massachusetts/2012

15–16 A/California/2009 A/Switzerland/2013 B/Phuket/2013

16–17 A/California/2009 A/HongKong/2014 B/Brisbane/2008

Several vaccines for the 2016-17 season will be quadrivalent; that is, contain a fourth component B/Phuket/2013.

FluMist®
On 17 June 2003, the U. S. Food and Drug Administration (FDA) approved FluMist® – a live-virus vaccine that is given as a spray
up the nose. The viruses have been weakened so that they do not cause illness, but are able to replicate in the relatively cool tissues
of the nasopharynx where they can induce an immune response. Presumably this is tilted towards IgA production, a better defense
against infection by inhaled viruses than blood-borne IgG antibodies. In any case, FluMist® induces a more rapid response than
inactivated vaccine and there is some evidence that it provides better protection against antigenic drift as well.
All three currently-circulating strains of flu (H1N1, H3N2, and B) are included. As new strains appear, they can be substituted.
At present, this new vaccine (technically known as LAIV "Live Attenuated Influenza Vaccine") is only approved for children older
than 24 months and adults younger than 50. People with immunodeficiency (e.g., AIDS) should also be cautious about taking it.
Update: For as yet unknown reasons, the nasal spray did not work during the 2015–2016 season, and it is not recommended for the
upcoming season.

Flublok®
On 16 January 2013, the U. S. FDA approved an entirely new type of vaccine. Flublok® is made in cell cultures transformed with
recombinant DNA encoding the hemagglutinins of the 3 currently circulating flu strains (H1N1, H3N2, and B). The final
concentration of antigens is three times that in the current vaccine. Cultures of insect cells are used so there is no problem with
possible egg allergies in those receiving the vaccine.

Other weapons against flu

It takes a while for the flu vaccine to build up a protective level of antibodies. What if you neglected to get your flu shot and now
an epidemic has arrived?

Amantadine and Rimantadine

These drugs inhibit the M2 matrix protein needed to get viral RNA into the cytosol. They work against A strains only, and
resistance to the drugs evolves quickly. By the 2009-2010 flu season, virtually all strains of both H3N2 and H1N1 had developed
resistance.

Zanamivir (Relenza®) and Oseltamivir (Tamiflu®)

These drugs block the neuraminidase and thus inhibit the release and spread of fresh virions. Spraying zanamivir into the nose or
inhaling it shortens the duration of disease symptoms by one to three days. Unfortunately, by the 2008-2009 flu season, all H1N1
strains circulating in the U.S. had become resistant to Tamiflu.

19.3B.5 https://bio.libretexts.org/@go/page/5978
Antibiotics
Antibiotics are of absolutely no value against the flu virus. However, they are often given to patients to combat the secondary
bacterial infections that occur and that are usually the main cause of serious illness and death.

Why so few drugs?

The mechanisms by which amantadine and zanamivir work provide a clue. There are far fewer anti-viral drugs than antibacterial
drugs because so much of the virus life cycle is dependent on the machinery of its host. There are many agents that could kill off
the virus, but they would kill off host cell as well. So the goal is to find drugs that target molecular machinery unique to the virus.
The more we learn about these molecular details, the better the chance for developing a successful new drug.

The "Spanish" Flu

Jeffery Taubenberger and his colleagues have sequenced the genes of the influenza virus that had been recovered from
preserved lung tissue of a U.S. soldier who died from influenza in 1918
lung tissue from a flu victim whose body had remained frozen in the permafrost of Alaska since she died in 1918
But even with all of its genes now completely sequenced, why the 1918 strain was so deadly is not fully understood. But deadly it
is. They have even been able to replace the 8 genes of a laboratory strain of flu virus with all 8 genes of the 1918 strain (using strict
biosafety containment procedures!). The resulting virus kills mice faster than any other human flu virus tested. (Reported in the 7
October 2005 issue of Science.)

The Swine Flu of 2009

A new H1N1 flu began infecting humans in North America in April 2009 and has now spread throughout much of the world.
Sequencing its genome revealed a novel virus - now called A(H1N1)pdm09 - that contained genes previously found in four
different strains of swine flu:
an HA gene (H1) derived from the swine flu of 1930 (and closely-related to the H1 of the great 1918 "Spanish" flu pandemic)
along with an NP and NS gene from that virus;
an NA gene (N1) from a virus that had been circulating in the pigs of Europe and Asia since 1979 along with the M gene from
that virus;
a PA and PB2 gene that entered pigs from birds around 1998;
a PB1 gene that passed from birds to humans around 1968 and from us to pigs around 1998.
Why this remarkable assortment of genes has enabled he virus to jump so successfully from pigs to humans remains to be
determined.
The amino acid sequence around the critical epitopes of its H1 molecules closely resemble those found in the resurrected 1918 flu
virus. This would explain why
Antibodies from elderly survivors of the 1918 pandemic neutralize the new swine flu virus.
Antibodies (raised in mice) to the new swine flu virus neutralize the resurrected 1918 flu virus.
The recent pandemic caused serious illness and death mostly in young adults and least in children and the elderly. As for the
elderly, this contrast to the usual pattern arose because people over 65, even if not old enough to have been exposed to the 1918
virus, had been exposed to H1 viruses that until 1957 had only drifted from the original 1918 virus, and thus they had developed
partial immunity. The antibodies in young adults were specific for seasonal flu strains circulating since 1957. These were unable
to protect them against the 2009 virus but may have formed damaging immune complexes with them. Youngsters had no anti-
flu antibodies and did not form such immune complexes.

"Bird Flu"
Many influenza A viruses are found in birds, both domestic and wild. Most of these cause little or no illness in these hosts.
However, some of their genes can enter viruses able to infect domestic animals, as was the case for the PA and PB2 genes of the
swine flu of 2009 (above).
On several occasions, bird flu viruses have also infected humans, often with alarmingly-high fatality rates. In 2003, human cases of
an H7N7 bird flu virus infection occurred in the Netherlands, and in the same year an H5N1 bird virus caused human cases in large

19.3B.6 https://bio.libretexts.org/@go/page/5978
areas of Asia. Most of the human cases seemed to have been acquired from contact with infected birds rather than from human-to-
human transmission.
And now in 2013, a new bird flu virus, H7N9, has appeared in humans in China. By the end of the summer of 2013, it had caused
135 observed cases (no one knows yet whether there may also be infected people who are not sick enough to show up at hospitals).
45 of the observed cases were fatal. The victims appear to have been infected through contact with infected poultry with little or no
evidence of human-to-human transmission.
As a glance at the tables above will show, humans have had long experience with infections and vaccines by both H1 and H3 flu
viruses. But the human population has absolutely no immunity against any H7 viruses. If this virus develops the capability to
spread efficiently from human to human, it could lead to another worldwide pandemic.

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 19.3B: Influenza is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.3B.7 https://bio.libretexts.org/@go/page/5978
19.3C: φX174
φX174 (phiX174) is a virus that infects the bacterium E. coli. Hence φX174 is a bacteriophage. Each complete infectious particle
(virion) of φX174 consists of a protein coat which envelopes a core that contains both protein and DNA. The coat of the virus
contains 60 molecules each of two proteins (F and G) and 12 molecules of another protein (H). The core of the virion contains one
molecule of DNA and 60 copies of a fourth protein, the J protein. The DNA molecule is single-stranded (ssDNA) and is in the form
of a closed circle. It contains 5386 nucleotides. This tiny genome was the first DNA genome ever to be sequenced (by Fred Sanger
in 1976).

Figure 19.3.3.1 PhiX

When φX174 attaches to its host, its ssDNA molecule is inserted into the cell. Here the DNA strand (+) serves as the template for
the synthesis of a complementary (−) strand. The two strands form a double helix which then replicates itself several times. The
minus strands of these DNA molecules then serve as templates for the synthesis of:
mRNA molecules.
some 200 complementary (+) strands of DNA, each of which will later be packaged into the core of a new virion.
The protein-synthesizing machinery of the host cell translates the viral mRNA molecules into 11 different kinds of proteins. Four of
these are the four (F, G, H, and J) that will be incorporated into new virions. As for the other 7 proteins
A, A*, and C play roles in the replication of viral DNA
B and D assist in the assembly of the virion proteins into new virions
E lyses the host cell so the newly-synthesized virions can escape
K boosts virion production
but none of these proteins become part of the virion.

19.3C.1 https://bio.libretexts.org/@go/page/5979
The 11 proteins encoded by φX174 DNA range in size from the A protein, which contains 513 amino acids, to the J protein, which
contains only 38. The 11 proteins together contain a total of 1986 amino acids (the A* protein is simply a shortened version of the
A protein). This raises a question. With 3 nucleotides needed to specify one amino acid, φX174 would need 5958 nucleotides to
encode 1986 amino acids (5958/3 = 1986). But its DNA molecule contains 5386 nucleotides, only enough to encode 1795 amino
acids. Furthermore, it turns out that 217 of the nucleotides do not encode anything, although some of them provide control signals.
So there are only 5169 coding nucleotides, and we would expect them to be able to encode only 1723 amino acids. How does
φX174 dictate the assembly of the remaining amino acids?

Overlapping Genes
It does so by using some stretches of nucleotides to encode two different sequences of amino acids. The principle is really quite
simple. It involves reading the codons it two different "reading frames", that is, grouping the nucleotides in shifted clusters of three.
For example, the sequence
. . . GAGCCGCAACTTC . . .
can be read in three different reading frames:
. . . GAG CCG CAA CTT C . . . which encodes . . Glu-Pro-Gln-Leu . .
or
. . . G AGC CGC AAC TTC . . . which encodes . . Ser-Arg-Asn-Phe . .
or
. . . GA GCC GCA ACT TC . . . which encodes . . Ala-Ala-Thr . .
φX174 actually uses two of these and, as you can see, each encodes a totally different sequence of amino acids.

There is even one spot where a single nucleotide (A) participates in three different codons:
It is the third nucleotide in the codon (AAA) for the final amino acid (Lys) in protein A;
the middle nucleotide in the codon AAT, which encodes Asn in the K protein; and
the first nucleotide in ATG, the codon that places methionine (Met) at the start position of protein C.
Why overlapping genes? φX174 is one of the tiniest viruses. Its use of overlapping genes enables it to increase the amount of
information it can store in a given amount of DNA. Not only was the φX174 genome the first to be sequenced, it was also the first
to be chemically synthesized in the laboratory. When introduced into E. coli, this synthetic molecule was fully infectious able to
produce intact viruses.

19.3C.2 https://bio.libretexts.org/@go/page/5979
 Figure 19.3.3.2 PhiX174
Above is an electron micrograph of the double-stranded φX174 DNA extracted from infected E. coli cells. The bar represents 0.5
µm. (Courtesy of David T. Denhardt.)

Contributors and Attributions

John W. Kimball. This content is distributed under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license and
made possible by funding from The Saylor Foundation.

This page titled 19.3C: φX174 is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.3C.3 https://bio.libretexts.org/@go/page/5979
19.3D: Smallpox
The threat of terrorism has raised the spectre of the use of biological agents as weapons. One of the possible agents is the variola
virus, the cause of smallpox. On October 26, 1977, Ali Maow Maalin came down with smallpox in the town of Merka in Somalia.
Within a few weeks he was fully recovered. Since that time, not a case of smallpox (except as a result of one laboratory accident)
has been discovered anywhere in the world. By May of 1980, the World Health Organization (WHO) felt that it could confidently
announce that smallpox had been completely eradicated. The WHO also asked that all countries with any stocks of variola virus in
their laboratories either destroy them or transfer them to one of two secure laboratories (at the Centers for Disease Control and
Prevention (CDC) in Atlanta, Georgia or a state lab in Koltsovo in Russia). Although 74 countries did so, the fear remains that
some countries may have retained stocks of the virus. Even before the complete eradication of smallpox, routine vaccination
against the disease was halted in most Western countries. So today anyone under 30 years of age is fully susceptible and even those
older may have lost protection against the disease.

 A Little History
Smallpox certainly qualified as one of the greatest scourges of humanity. It regularly killed 25% and sometimes as many as
50% of its victims. Introduced into Europe around the sixth century A.D., smallpox rivaled plague in its ability to decimate
entire populations. Introduced into the New World in the sixteenth century, smallpox devastated the native populations and
played a far greater role than weaponry in the Spanish Conquest.
How was such a pestilence eradicated? Four factors were decisive:
1. The variola virus, which causes the disease, attacks only humans; no animal reservoirs have been found (as they have for
the yellow fever virus, the rabies virus, and the plague bacillus).
2. If the victim recovers, the virus is completely eliminated from the body. There are no smallpox "carriers" as there are for
such diseases as typhoid fever and malaria.
3. An effective vaccine was available. The vaccine could quickly establish a strong (and reasonably long-lasting) immunity.
Thus the chain of contagion could be quickly broken by vaccinating all possible contacts associated with a new case.
4. The WHO and the countries involved provided personnel, money, and the determination to do the job. An effective vaccine
had, as we shall see, been available since 1796 and had already rendered many parts of the world free of the disease during
the first half of the 20th century. But still the disease smoldered in Asia, Indonesia, Brazil, and Africa. Only a heroic public
health effort — a campaign that began in 1967 — finally eliminated it worldwide.

Variolation
The first effective attempts to cope with smallpox were made in some of the same regions - Asia, India, Africa - that were the last
to be freed of the disease. The technique was deliberately to inoculate susceptible individuals (i.e., those with no pockmarks to
indicate that they had survived an earlier epidemic) with material taken from the pustules of people with a mild case of the disease.
This practice, called variolation, induced an active case in the recipient, but usually the case was less severe than if the disease had
been contracted in the normal way (by inhalation as it turned out).
Variolation was introduced into England and the American colonies early in the 18th century. The practice was often accompanied
by violent controversy. It was not entirely safe. The variolated person often became quite ill and the mortality rate, although only a
fraction of that for people who contracted the disease in the normal way, was nonetheless appreciable. But far more significant in
terms of public acceptance was the fact that variolated people were fully contagious to others during the period of their brief,
hopefully mild, illness. Thus a family electing variolation could start a fresh smallpox epidemic. Nonetheless, the practice
gradually gained favor until it was replaced by vaccination. This table (from J. B. Blake, Public Health in the Town of Boston,
1630-1832. Harvard University Press, 1959) shows the effect of variolation on the death rate from smallpox during three epidemics
in Boston.

Year 1721 1764 1792

Population 10,700 15,500 19,300

Natural Smallpox

Cases 5,759 699 232

19.3D.1 https://bio.libretexts.org/@go/page/5980
 Deaths 842 124 69

Deaths/1000 cases 146 177 298

Smallpox Caused by Variolation

Cases 130 4,977 9,152

Deaths 2 46 179

Deaths/1000 cases 15 9 20

Vaccination
Edward Jenner was a Gloucestershire physician who introduced the practice that led to the elimination of smallpox. Jenner's
success was grounded on two observations:
1. The regional folk belief that if a milkmaid had ever contracted cowpox, she would never contract smallpox.
2. The inability to variolate successfully those who had an earlier case of cowpox. Cowpox is a disease that produces pustules on
the teats and udders of cows. Persons in close contact with cows frequently contracted the disease and suffered a mild and
transient infection.
Jenner systematically exploited these observations.
First he deliberately induced cowpox in his human subjects by inoculating them with material from cowpox pustules.
Then he showed that these individuals could NOT be variolated.
Jenner's procedure, which we call vaccination, (L. vacca, cow) quickly replaced variolation as a public health measure because:
Any reaction it induced was far milder than the disease induced by variolation.
The vaccinated subject was not contagious to others.
Jenner's was the first safe and successful attempt to artificially induce an active immunity. Many successful attempts have followed
since Jenner's day, but the principles that guided him are still followed:
Develop a harmless (or as harmless as possible) preparation that will, upon introduction into the body,
induce a response that will protect the individual from a harmful pathogen.
Because of Jenner's priority and his success, the term vaccine is used today for all such preparations. The administration of a
vaccine is called immunization. The virus used in today's smallpox vaccine is called vaccinia virus. Possibly it is a relative of
cowpox virus, but when the switch occurred is lost in the obscurity of the years since Jenner's day.

What's Next?
Jenner himself was so confident of the efficacy of vaccination that he wrote:
"The annihilation of smallpox must be the final result of this practice".
In 1980, his prediction seemed to have been fulfilled. Today we are not so confident. What should we do now? Return to universal
vaccination or use the vaccine only for emergency and medical people who might be exposed as they responded to a terrorist attack
and those people in a "ring" around any person who comes down with the disease.
The argument against universal vaccination is that present vaccines are not 100% safe. There is a small, but definite, risk of serious
complications from the vaccine itself, especially in people who have an immunodeficiency (e.g., from AIDS or taking
immunosuppressant drugs). Such problems can be avoided by not giving the vaccine to people at risk. It can also be avoided by
having Vaccinia Immune Globulin (VIG) available to treat any cases of a bad response to the vaccine.

This page titled 19.3D: Smallpox is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.3D.2 https://bio.libretexts.org/@go/page/5980
19.3E: Retroviruses
The genome of retroviruses consists of RNA not DNA. HIV-1 and HIV-2, the agents that cause AIDS, are retroviruses. In
February 1997 it was reported that pig cells contain a retrovirus capable of infecting human cells (at least, in vitro). This is
troublesome because of the efforts that are being made to transplant pig tissue into humans (e.g., fetal pig cells into the brains of
patients with Parkinson's disease). Transplant recipients must have their immune systems suppressed if the transplant is to avoid
rejection. Could immunosuppressed patients be at risk from the retroviruses present in the transplanted cells? The probability that
the original hosts for HIV-1 and HIV-2 were some other primate suggests that retroviruses can move from one species to another.

Figure 19.3.5.1 Retrovirus

A typical, "minimal" retrovirus consists of:
an outer envelope which was derived from the plasma membrane of its host
many copies of an envelope protein embedded in the lipid bilayer of its envelope
a capsid; a protein shell containing
two molecules of RNA
molecules of the enzyme reverse transcriptase
Reverse transcriptase is a DNA polymerase that uses RNA as its template. Thus it is able to make genetic information flow in the
reverse (RNA ->DNA) of its normal direction
(DNA -> RNA).
Infection of a host cell requires that the cell have a surface protein that can serve as a receptor for the envelope protein of the
retrovirus. The envelope protein of HIV-1 binds to CD4 molecules (this property enables the virus to invade CD4+ T cells and
certain other cells that express CD4) and they bind to CCR5 (CC chemokine Receptor 5) - found on Th1 cells and macrophages.
All the proteins in the virus particle are encoded by its own genes.

Figure 19.3.5.2 Retrovirus lifecycle

When a retrovirus infects a cell
Its molecules of reverse transcriptase are carried into the cell attached to the viral RNA molecules.
The reverse transcriptase synthesizes DNA copies of the RNA.

19.3E.1 https://bio.libretexts.org/@go/page/5981
 These enter the nucleus and are inserted into the DNA of the host.
These inserts are transcribed by the host's enzymes into fresh RNA molecules which re-enter the cytosol where
some are translated by host ribosomes
the gag gene is translated into molecules of the capsid protein
the pol gene is transcribed into molecules of reverse transcriptase
the env gene is translated into molecules of the envelope protein
other RNA molecules become incorporated into fresh virus particles
The genome of retroviruses is flanked at each end by repeated sequences ("R") that enable the DNA copy of the genome to be
inserted into the DNA of the host and act as enhancers, causing the host nucleus to transcribe the DNA copies of the retroviral
genome at a rapid rate.

The retroviral genome also contains a packaging signal sequence ("P") which is needed for the newly-synthesized RNA molecules
to be incorporated in fresh virus particles. Most retroviruses also contain one or more additional genes. Some of these represent
RNA copies of genes that earlier were picked up from their eukaryotic host. Several cancers in animals are caused by retroviruses
that have, at some earlier time, picked up a proto-oncogene from their mammalian host and converted it into an oncogene.

This page titled 19.3E: Retroviruses is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

19.3E.2 https://bio.libretexts.org/@go/page/5981
 CHAPTER OVERVIEW
Unit 20: General Science
20.1: Epidemiology
20.2: Types of Clinical Studies
20.3: Scientific Methods
20.4: Scientific Papers
20.5: Statistical Methods
20.6: Drugs

Thumbnail: Original map by John Snow showing the clusters of cholera cases in the London epidemic of 1854. (Public Domain).

This page titled Unit 20: General Science is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

1
20.1: Epidemiology
A statistical correlation between two phenomena is simply that. It does not prove that one phenomenon caused the other. Just
because A is often associated with B, does not prove that A causes B. Example: the incidence of cirrhosis of the liver is associated
with cigarette smoking. Does smoking cause cirrhosis? Probably not. Excessive consumption of alcohol is a more likely cause.
However, as heavy drinkers tend to be heavy smokers, the statistical association is there, but in this case is probably a confounding
variable. How can one establish that A causes B? In the laboratory you could set up a controlled experiment treating one group of
animals with A and having a second control group without A but otherwise treated the same (thus avoiding confounding
variables). Such experimentation is rarely possible (or ethical) in humans so we must turn to the methods and criteria of
epidemiology.

John Snow - the First Epidemiologist

During an outbreak of cholera in London in 1854, John Snow plotted on a map the location of all the cases he learned of. Water in
that part of London was pumped from wells located in the various neighborhoods. Snow's map revealed a close association
between the density of cholera cases and a single well located on Broad Street. The Broad Street well is marked with an X (within
the red circle) in the above figure. Removing the pump handle of the Broad Street well put an end to the epidemic. This despite the
fact that the infectious agent that causes cholera was not clearly recognized until 1905.

Figure 20.1.1 : John Snow's map showing cholera deaths in London in 1854 (courtesy of The Geographical Journal)
Although an association between two phenomena is no more than that, one can apply several criteria to gauge the strength of the
association, and if it is strong, infer that one phenomenon causes the other.

 The five criteria to gauge the strength of the association

a high relative risk
consistency
a graded response to a graded dose
a temporal relationship
a plausible mechanism

Cigarette Smoking: A Case Study

In Table 20.1.1, the quotient of observed deaths divided by expected deaths (those in the control group) gives the relative death
rate. This value is a measure of risk. Although smoking is associated with many more cases of heart disease than of lung cancer,
lung cancer is the disease with the highest relative risk for smokers. The relative death rate from lung cancer is over 10 times
greater in smokers than in non-smokers. This is strong evidence that smoking causes lung cancer. Cigarette smoking is estimated to
be directly responsible for 80–90% of all lung cancer deaths (which totalled 160,390 in the U.S. in 2007).
This table gives the number of deaths from various causes in a prospective study of cigarette smokers ("observed deaths")
compared with the number to be expected among nonsmokers of the same ages ("expected deaths"). The differences between the

20.1.1 https://bio.libretexts.org/@go/page/6026
two represent "excess deaths". The contribution of each disease to the total of excess deaths is given as the "percentage of excess".
Note that coronary artery disease accounts for one half of the excess deaths in the smoking group.
Table 20.1.1 : Observed deaths, expected deaths, and relative death rates.
Cause of Death Observed Deaths Expected Deaths Excess Deaths Percentage of Excess Relative Death Rate

Total deaths (all

7316 4651 2665 100.0 1.57
causes)

Coronary artery
3361 1973 1388 52.1 1.70
disease

Other heart disease 503 425 78 2.9 1.18

Cerebrovascular
556 428 128 4.8 1.30
lesions

Aneurysm &
86 29 57 2.1 2.97
Buerger's disease

Other circulatory
87 68 19 0.7 1.28
diseases

Lung cancer 397 37 360 13.5 10.73

Cancer of mouth,
91 18 73 2.7 5.06
larynx, or esophagus

Cancer of the bladder 70 35 35 1.3 2.00

Other cancers 902 651 251 9.4 1.39

Gastric & duodenal

100 25 75 2.8 4.00
ulcer

Cirrhosis of the liver 83 43 40 1.5 1.93

Pulmonary disease
231 81 150 5.6 2.85
(except cancer)

All other diseases 486 453 33 1.2 1.07

Accident, violence,
363 385 -22 -0.8 0.94
suicide

Dividing the number of observed deaths by the number of expected deaths gives the "relative death rate" for each disease. This
shows that smokers die of lung cancer 10 times as often (10.73, above) as do nonsmokers, which is a very high relative risk.
However, in both groups lung cancer is rarer than coronary artery disease. (Data from E. C. Hammond and D. Dorn, 1966.)

Consistency
Our confidence that A causes B is strengthened when different studies using different populations all show the same association.
The earliest studies of smoking were retrospective; that is, after a disease was diagnosed, the patient's smoking habits were
determined. Later studies were prospective. A prospective study selects a population in good health and meeting any other desired
criteria (smoking habits in this case) and follows it over a period of years to see what happens to its members.

Figure 20.1.2 : Relationship between smoking and death

20.1.2 https://bio.libretexts.org/@go/page/6026
This graph shows essentially the same relationship between smoking and deaths from lung cancer in three different groups
(totalling over a million people) studied prospectively. Doll and Hill studied a group of British physicians. Dorn followed the health
of a group of U.S. veterans. Horn studied 187,783 U.S. male volunteers. In each case the relative death rates are graphed as a
function of number of cigarettes smoked each day (from zero at the left to over a pack at the right).

A Graded Response to a Graded Dose

All three studies graphed above show that the relative death rate from lung cancer increased with an increase in the average number
of cigarettes smoked each day. One goal of picking different groups to study is to avoid confounding variables. If, for example, all
the groups studied lived in cities, it would be difficult to distinguish between the effects of smoking and the effects of general air
pollution.

Figure 20.1.3 : Utah smokers

This graph compares the incidence of lung cancer among male Mormons and non-Mormons living in urban and rural areas of Utah.
Male non-Mormons living in the city have a higher risk of developing lung cancer than those living in the country. Is this because
of smoking or because of the pollution of urban air? It appears to be the former because Mormons show no such city vs. country
difference, and cigarette smoking is prohibited for Mormons. Studies like these help to eliminate the effect of confounding
variables. Probably less than 5% of lung cancer is caused by breathing polluted city air.

Temporal Relationship
If A causes B, then exposure to A must have preceded the onset of B. Establishing cause-effect relationships for possible
carcinogens has been particularly difficult because for cancers, the latency period between exposure and illness is often many
years. Nonetheless, data such as those shown in this graph, provide another strong link in the case against cigarettes.

Figure 20.1.4 : Cause - effect relationship for possible carcinogens

In recent decades, sales of cigarettes in the U.S. have dropped, both on a per capita basis and in absolute numbers. Whereas half of
adult males smoked in the mid-sixties, less than a third do today. This change has already caused the rate of lung cancer in males to
level off. Unfortunately, the rate is still rising for women (and in 1987 surpassed breast cancer as the leading cause of cancer deaths
in U.S. women).

Plausible Mechanism
Over 40 different chemicals found in cigarette smoke cause an increase in cancer when given over several years to laboratory rats.

20.1.3 https://bio.libretexts.org/@go/page/6026
So how strong is the case against cigarettes?
Defenders of the tobacco industry frequently claim that no one has proved that cigarette smoking causes lung cancer. In one sense
they are right. Proof from epidemiology differs from proof in a laboratory experiment. What we have seen here is that the more
closely we can meet the several criteria linking A and B, the more confident we can be that A causes B.
Few epidemiological studies have met these criteria better than those studying the statistical relationship between smoking and
health. Smoking is probably the greatest single cause of preventable illness in the United States.

 Rules to live by

Hardly a week goes by these days without a report in the press and on TV of another link between an environmental agent and
human disease. Does living near nuclear power stations increase one's risk of cancer? living near electric power lines? Does a
diet rich in saturated fats predispose U.S. males (but, for some reason, not French males) to early death from coronary artery
disease?
I hope that your ability to interpret the avalanche of reported associations - and any adjustments that you make in your life as a
result - will benefit from your applying to such reports the five criteria outlined here.

This page titled 20.1: Epidemiology is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

20.1.4 https://bio.libretexts.org/@go/page/6026
20.2: Types of Clinical Studies
Researchers in human (and veterinary) medicine are always on the lookout for new drugs, medical procedures, and life-style
changes that will improve their ability to bring better health to patients. For each one, they must establish whether it truly
represents an improvement from what was used before.

Retrospective Studies
In a typical retrospective study, the health profiles of the subjects in a particular "case" group (e.g. smokers) are compared with
those in a control group that has been selected to be as similar as possible to the "case" group (similar spread of ages, sex, etc.).
Retrospective studies are also called "case-control" studies. Retrospective studies run the risk of investigator bias; that is, the
investigator picks subjects that are most likely to show the effect that prompted the study in the first place.

Prospective Studies
A prospective study selects a population in good health and meeting any other desired criteria (e.g., smoking habits) and follows it
over a period of years to see what happens to its members. Prospective studies are also known as "cohort studies".

Clinical Trials
Where it is possible to do them, clinical trials represent the "gold standard" for evaluation. In performing a clinical trial (e.g. of a
new, and possibly better, drug), the investigator
assembles a group of subjects picked to be as similar as possible in their characteristics (to avoid "confounding variables")
assigns them randomly to the experimental group and a "control" group
performs the experiment on the first group. It is best to do this in a "double-blind" fashion; that is neither the subject nor the
experimenterknows who is getting the treatment and who is not.
Keeping
the subjects in the dark avoids the placebo effect; a response (often quite powerful) that is not due to the treatment but to the
expectations of the subject;
the experimenter in the dark avoids bias in the evaluation of the results. So, for example, a microscopist examining a slide of
tissue should not know whether it came from an experimental subject or a control.

Analyzing the Data

The data acquired in any type of clinical study must be evaluated to see if any effect seen is significant.

This page titled 20.2: Types of Clinical Studies is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W.
Kimball via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

20.2.1 https://bio.libretexts.org/@go/page/6027
20.3: Scientific Methods
There is nothing mysterious or even particularly unusual about the things that scientists do. There are many ways to work on
scientific problems. They all require common sense. Beyond that, they all display certain features that are especially - but not
uniquely - characteristic of science.
For example:
Skepticism. Good scientists use highly-critical standards in the judging of evidence. They approach data, claims, and theories
(ideally, even their own!) with healthy doses of skepticism.
Tolerance of uncertainty. Scientists often work for years - sometimes for an entire career - trying to understand one scientific
problem. This often involves finding facts that, for a time, fail to fit into any coherent pattern and that even may support
mutually contradictory explanations.
Sometimes, as one listens to scientists vigorously defending their views, their confidence seems absolute. But deep in their hearts,
they know that their views are based on probabilities and that a new piece of evidence may turn up at any time and force a major
shift in their views.
Although they certainly have no monopoly on hard work, their willingness to work long hours and years pursuing a problem is
the mark of all good scientists. For science is hard work.
Before undergoing the frustrations - tempered by occasional joys - of wresting more secrets from nature, you must learn the
foundations on which your subject is based.
Although scientific methods are as varied as science itself, there is a pattern to the way that scientists go about their work.
Scientific advances begin with observations.
A census of the members of a species in some habitat is an observation.
The readings on the display of a laboratory instrument are observations.
But science is more than a catalog of facts. The goal of science is to find an explanation for why the facts are as they are. Such
an explanation is a hypothesis.

Testing Hypotheses
A good hypothesis meets several standards:
1. It should provide an adequate explanation of the observed facts.
2. If two or more hypotheses meet this standard, the simpler one is preferred.
3. It should be able to predict new facts.
So if a generalization is valid, then certain specific consequences can be deduced from it. One of the most exciting events in
science is to predict the results of an experiment not yet performed if the hypothesis is valid and then to perform the experiment.

The Null Hypothesis

Experimental biology often involves setting up an experimental treatment and — at the same time — a control. Then one
compares the results of the experimental treatment with the results in the controls. If there is a difference, what is the probability
that it is due to chance alone; that is, the experimental treatment really had no effect?
The hypothesis that the experimental treatment had no effect is called the null hypothesis. Most workers feel that if the probability
(designated p) of the observed difference is less than 1 in 20 (p = <0.05), then the null hypothesis is disproved and the observed
difference is significant. But significance is not proof. In fact, hypotheses can never be proven to be absolutely "true" is the sense
that a theorem in geometry can. The most we can say is that there is a high probability that the hypothesis provides a valid
explanation of the phenomenon being studied.
Hypotheses that are supported by many observations come to be called theories. So, in contrast to some areas of human thought,
science can never prove that a theory is "true". But it can show that a theory is false. Lest the tentative nature of science cause you
to lose confidence in it, think of what science has produced. The many achievements of scientific methods, despite the absence of
absolute certainty, has been well-expressed in the sonnet "Paradox" by the late mathematician Clarence Wylie, Jr.

Not truth, nor certainty. These I foreswore

20.3.1 https://bio.libretexts.org/@go/page/6028
 In my novitiate, as young men called
To holy orders must abjure the world.
"If..., then...," this only I assert;
And my successes are but pretty chains
Linking twin doubts, for it is vain to ask
If what I postulate be justified,
Or what I prove possess the stamp of fact.
Yet bridges stand, and men no longer crawl
In two dimensions. And such triumphs stem
In no small measure from the power of this game,
Played with the thrice-attenuated shades
Of things, has over their originals.
How frail the wand, but how profound the spell!

Reproducibility of Scientific Work

The single feature that is most characteristic of science is its reproducibility. If scientists cannot duplicate their first results, they are
forced to conclude that these were invalid. This problem occurs often. Its cause is usually some unrecognized, and hence
uncontrolled, factor in the experiment (e.g., unrecognized variation in the properties of different batches of the materials used in the
experiment). With luck, the inability to reproduce experiments will be discovered by the same scientists who did the first
experiments. This is why scientists generally repeat their experiments several times before reporting them in a scientific paper.
On other occasions, workers in another laboratory fail to secure the same results when they repeat experiments that have been
published or, more often, perform experiments designed to carry the study into new areas, but these fail because of a flaw in the
original experiments. When this happens, all the parties concerned should get together to see if they can find out why their results
differ.
Often it is simply a matter of not using precisely the same materials and methods.
Sometimes, however, a serious flaw may be discovered in the design and/or execution of the original experiments.
And sometimes it proves impossible to find out why experiments that once seemed to work no longer do so.
In any of these cases, the failure to confirm the experiments must be reported. Although this is acutely embarrassing for the original
investigators, it represent one of the great strengths of science: its built-in system for self-correction.

Scientific Fraud
In the vast majority of cases, irreproducible results in science are caused by honest errors. On rare occasions, however, laboratory
reports cannot be confirmed because they are fraudulent. This is distressing to all concerned. If such a fraud becomes widely
known, it is also likely to cause a great deal of excitement among the general public. I believe, however, that rather than casting a
cloud over the scientific enterprise, these rare aberrations reveal its great strength.
There is probably no other area of human activity where error is detected and corrected more rapidly. I am confident that you can
think of a number of other fields of human study and activity where errors have been made that went uncorrected for years and
caused widespread harm. Dishonest scientists usually harm only themselves. They are disgraced; their careers often at an end. But
the progress of science usually moves forward as fast as (sometimes faster than) before.

20.3.2 https://bio.libretexts.org/@go/page/6028
Building on the Work of Others
Only rarely does a scientific discovery spring full-blown on the scene. When it does, it is likely to create a revolution in the way
scientists perceive the world around them and to open up new areas of scientific investigation. Darwin's theory of evolution and
Mendel's rules of inheritance are examples of such revolutionary developments.
Most science, however, consists of adding another brick to an edifice that has been slowly and painstakingly constructed by prior
work. In fact, it is possible to construct a genealogical tree that traces the historical development of any scientific discovery (even,
to a degree, Darwin's and Mendel's). The way in which science builds on the work of others is another illustration of what a
communal activity science is.
The development of a new technique often lays the foundation for rapid advances along many different scientific avenues. Just
consider the advances in biology that discovery of the light microscope and, later, the electron microscope have made possible.
Throughout these pages, there are many examples of experimental procedures. Each was developed to solve a particular problem.
However, each was then taken up by workers in other laboratories and applied to their problems.
In a similar way, the creation of a new explanation (hypothesis) in a scientific field often stimulates workers in related fields to
reexamine their own field in the light of the new ideas. Darwin's theory of evolution, for example, has had an enormous impact on
virtually every subspecialty in biology (and in other fields as well). To this very day, biologists in specialties as different as
biochemistry and animal behavior are guided in their work by evolutionary theory.

Basic Versus Applied Science

The distinction between basic and applied science is more one of goals than of methods. The same rules and standards apply to
each. However, the motivation behind the work is somewhat different. Researchers in applied science have before them a practical
problem to be solved. Much of the research that goes on in medicine and in agriculture is applied. The researcher in basic science,
on the other hand, is primarily driven by curiosity - the desire to find out more about how nature works. Both types of research are
not only honorable and demanding professions, but they are mutually dependent as well.
Applied science repeatedly loses momentum without periodic infusions of fresh ideas and discoveries from basic research. (The
light bulb would never have been discovered in the research and development (R and D) department of a candle manufacturer!)
On the other hand, much basic research has depended on the development of new tools and instruments and, more often than
not, these have been developed in laboratories devoted to applied research.

This page titled 20.3: Scientific Methods is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

20.3.3 https://bio.libretexts.org/@go/page/6028
20.4: Scientific Papers
Science is a communal activity. Only as new facts and hypotheses are taken up by the entire community of interested scientists do
these facts and hypotheses become part of science. Therefore, one of the major responsibilities of scientists is to see that their work
is reported to all those who might be interested.
Often this is done by word of mouth when scientists of similar interests gather together at meetings. But to be assured of a
permanent place in the scientific edifice, the work is reported in a paper submitted to a scientific journal. In most cases, the paper
will not be accepted for publication until it has been approved by several knowledgeable scientists from other laboratories who
serve as referees. Often they will suggest editorial changes in the paper or even additional experiments that should be done before
the paper is accepted for publication.
Papers in biology are usually divided into several sections (not necessarily in this order).

Summary or abstract
This section includes only the essence of the other sections. It should be as brief as possible, telling the reader what the goal of the
experiment was, what was found, and the significance of the findings. The abstract is often placed at the beginning of the paper
rather than at its end.

Introduction
This section of the paper describes the scientific question or problem that was the subject of the investigation. The introduction also
includes references to earlier reports of these and other scientists that have served as the foundation for the present work.

Results
Here the authors report what happened in their experiments. This report is usually supplemented with graphs, tables, and
photographs.

Discussion
Here the authors point out what they think is the significance of their findings. This is the place to show that the results are
compatible with certain hypotheses and less compatible, or even incompatible, with others. If the results contradict the results of
similar experiments in other laboratories, the discrepancies are noted here, and an attempt may be made to reconcile the
differences.

Materials and Methods

Here are precisely described the materials used (e.g., strains of organism, source of the reagents) and all the methods followed. The
goal of this section is to give all the details necessary for workers in other laboratories to be able to repeat the experiments
exactly. When many complex procedures are involved, it is acceptable to refer to earlier papers describing these methods in greater
detail.

Acknowledgments
In this brief but important section, the authors give credit to those who have assisted them in the work. These usually include
technicians (who may have actually performed most of the experiments!) and other scientists who donated materials for the
experiments and/or gave advice about them.

References
This section gives a careful listing of all earlier scientific work referred to in the main body of the paper. Most of the references are
to other scientific papers. Each reference should provide enough information so that another person can locate the document. This
means that each reference should include the name(s) of the author(s), the journal or book in which the report appears, and the year
of publication. In the case of scientific journals, the volume number in which the paper appears and the page number on which the
paper begins should be included. Sometimes the full title is given as well, although scientific papers often have such long titles that
this is omitted from the reference.

20.4.1 https://bio.libretexts.org/@go/page/6029
This page titled 20.4: Scientific Papers is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

20.4.2 https://bio.libretexts.org/@go/page/6029
20.5: Statistical Methods

What do the data tell us?

There are two kinds of numerical data acquired by biologists:
counting; e.g. the number of females in a population
measuring a continuous variable such as length or weight
In the first case, everyone can agree on the "true" value. In the second case, the measured values always reflect a range, the size of
which is determined by such factors as
precision of the measuring instrument and
individual variability among the objects being measured.
How are such data handled?

Calculating the Standard Deviation

The first step is to calculate a mean (average) for all the members of the set. This is the sum of all the readings divided by the
number of readings taken.
But consider the data sets:
46,42,44,45,43 and 52,80,22,30,36
Both give the same mean (44), but I'm sure that you can see intuitively that an experimenter would have much more confidence in
a mean derived from the first set of readings than one derived from the second.
One way to quantify the spread of values in a set of data is to calculate a standard deviation (S) using the equation
−−−−−−−−−
2
∑(x − x̄)
s =√ (20.5.1)
n−1

where ("x minus x-bar)2 is the square of the difference between each individual measurement (x) and the mean ("x-bar") of the
measurements. The symbol sigma indicates the sum of these, and n is the number of individual measurements.
Using the first data set, we calculate a standard deviation of 1.6.

The second data set produces a standard deviation of 22.9.

(Many inexpensive hand-held calculators are programmed to do this job for you when you simply enter the values for X.)

Standard Error of the Mean

In our two sets of 5 measurements, both data sets give a mean of 44. But both groups are very small. How confident can we be that
if we repeated the measurements thousands of times, both groups would continue to give a mean of 44? To estimate this, we
calculate the standard error of the mean (S.E.M. or Sx-bar) using the equation
S
Sx̄ = − (20.5.2)
√n

20.5.1 https://bio.libretexts.org/@go/page/6030
where S is the standard deviation and n is the number of measurements.
In our first data set, the S.E.M. is 0.7.
S 1.6
Sx̄ = = = 0.7 (20.5.3)
–
√5 2.23

In the second group it is 10.3.

S 22.9
Sx̄ = = = 10.3 (20.5.4)
–
√5 2.23

95%Confidence Limits
It turns out that there is a 68% probability that the "true" mean value of any effect being measured falls between +1 and −1 standard
error (S.E.M.). Since this is not a very strong probability, most workers prefer to extend the range to limits within which they can
be 95% confident that the "true" value lies. This range is roughly between −2 and +2 times the standard error.
So
for our first group, 0.7 x 2 = 1.4
for our second group, 10.3 x 2 = 20.6
So
if our first group is representative of the entire population, we are 95% confident that the "true" mean lies somewhere between
42.6 and 45.4 (44 ± 1.4 or 42.6 ≤ 44 ≤ 45.4).
for our second group, we are 95% confident that the "true" mean lies somewhere between 23.4 and 64.6 (44 ± 20.6 or 23.4 ≤ 44
≤ 64.6).
Put another way, when the mean is presented along with its 95% confidence limits, the workers are saying that there is only a 1 in
20 chance that the "true" mean value lies outside those limits.
Put still another way: the probability (p) that the mean value lies outside those limits is less than 1 in 20 (p = <0.05 ).

An example:
Assume that
the first data set ("A") (46,42,44,45,43) represents measurements of five animals that have been given a
particular treatment and
the second data set ("B") (52,80,22,30,36) measurements of five other animals given a different
treatment.
A third set ("C") of five animals was used as controls; they were given no treatment at all, and their measurements were
20,23,24,19,24. The mean of the control group is 22, and the standard error is 2.1.
Did treatment A have a significant effect? Did treatment B?
The graph shows the mean for each data set (red dots). The dark lines represent the 95% confidence limits (± 2 standard errors).
Although both experimental means (A and B) are twice as large as the control mean, only the results in A are significant. The
"true" value of B could even be simply that of the untreated animals, the controls (C).

Rejecting the null hypothesis

In principle, a scientist designs an experiment to disprove, or not, that an observed effect is due to chance alone. This is called
rejecting the null hypothesis.
The value p is the probability that there is no difference between the experimental and the controls; that is, that the null hypothesis
is correct. So if the probability that the experimental mean differs from the control mean is greater than 0.05, then the difference is
usually not considered significant. If p = <0.05, the difference is considered significant, and the null hypothesis is rejected.
In our hypothetical example, the difference between the experimental group A and the controls (C) appears to be significant; that
between B and the controls does not.

20.5.2 https://bio.libretexts.org/@go/page/6030
Narrowing the confidence limits
Two approaches can be taken to narrow the confidence limits.
enlarge the size of the sample being measured (increases n)
find ways to reduce the fluctuation of measurements about the mean.
The second goal is often much more difficult to achieve; if it proves impossible, perhaps the null hypothesis is right after all!

This page titled 20.5: Statistical Methods is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via
source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

20.5.3 https://bio.libretexts.org/@go/page/6030
20.6: Drugs

Testing New Drugs

Thousands of chemicals, both synthetic and extracted from "natural" sources, are being examined in the hope of finding new drugs
with which to combat human and veterinary diseases. The first step is to use laboratory tests to find if these substances have a
significant effect on, for example:
cells growing in tissue culture
laboratory animals such as rats and mice.
If the drug achieves the desired effect in laboratory animals, without killing them in the process, the drug developer applies to the
U. S. Food and Drug Administration for an IND, an investigational new drug application. Granting of an IND allows testing in
humans to begin. This occurs in three phases.

Phase I
A small group (20–100) of healthy volunteers is given the drug to see
if it is safe
how quickly it is absorbed, metabolized, and excreted from the body

Phase II
A group (up to several hundred) of volunteer patients with the disease are given the drug to see
how effective it is against the signs and symptoms of the disease
what doses are best
what side effects may occur
A control group of similar size is given a dummy drug (placebo). Ideally the trials are "blinded" with neither the subjects (nor the
investigator) knowing which pill a subject is receiving.

Phase III
Hundreds to thousands of patients with the disease are given the drug to get more reliable data on its
effectiveness
safety
best dose
rare side effects
all compared with the drug(s) that are currently used for the disease.
If all goes well, the drug manufacturer applies to the Food and Drug Administration for an NDA, a new drug application. If it is
granted, the generic name of the drug is replaced by a brand name chosen by the manufacturer. For example, one of the first drugs
used against AIDS was azidodideoxythymidine (AZT). When placed on the market, this name was replaced by the brand name
Retrovir®.

This page titled 20.6: Drugs is shared under a CC BY 3.0 license and was authored, remixed, and/or curated by John W. Kimball via source
content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

20.6.1 https://bio.libretexts.org/@go/page/6031
Index
A angiogenesis AZT
abscisic acid 12.8: Fighting Cancer with Inhibitors of 5.8: DNA Sequencing by the Dideoxy Method
Angiogenesis
16.5A: Abscisic acid (ABA)
angiosperms B
abscission
16.3D: Angiosperm Life Cycle
16.5A: Abscisic acid (ABA) B cell receptor (BCR)
Angiostatin
acid rain 15.4C: B Cells and T Cells
12.8: Fighting Cancer with Inhibitors of
17.2H: Acid Rain Angiogenesis
B cells
action potential anthrax 15.4C: B Cells and T Cells
15.8A: Neurons 19.2E: Anthrax
Bacillus anthracis
acute lymphoblastic leukemia Antigen 19.2E: Anthrax
12.14: Magnetic Fields and Cancer 15.4M: Antigen Presentation
Bacillus Thuringiensis
adaptation antigen presentation 19.2F: Bacillus Thuringiensis
15.9A: Mechanoreceptors 15.4M: Antigen Presentation
backcross
adenovirus vectors Antisense oligonucleotides 7.4: Polyploidy
11.3: Gene Therapy - Methods and Prospects 11.11: Antisense Oligodeoxynucleotides and their
bacteriophage
Adenoviruses Therapeutic Potential 19.3C: φX174
11.3: Gene Therapy - Methods and Prospects Antisense RNA Bacteriophages
adipocytes 11.10: Antisense RNA 5.2: The Hershey - Chase Experiments
3.13: Animal Tissues antisense strand barcoding
agent orange 11.10: Antisense RNA 19.1.9: Barcoding
12.13: Dioxin antiserum Base excision repair
aggressive mimicry 15.4P: Passive Immunity 5.13: DNA Repair
15.11.6: Avoiding Predation Apical Dominance Basidiomycetes
aging 16.5B: Auxin 19.1.7: Fungi
13.1: Aging Apicoplast Batesian mimicry
air pollution 18.11: Endosymbiosis 15.11.6: Avoiding Predation
17.2G: Air Pollution apomixis beta cells
Alarm Pheromone 15.7B: Asexual Reproduction in Animals 15.6.1.3: Hormones of the Pancreas
15.11.7: Pheromones apoptosis bile
Alcaptonuria 3.20: Apoptosis 15.1A: The Human Gastrointestinal Tract
11.9: Genetic Screening for Phenylketonuria Aposematic Coloration Biochemical Oxygen Demand (BOD)
allergy 15.11.6: Avoiding Predation 17.2E: Sewage Treatment
15.4.1: 15.4T Allergies Arabidopsis Thaliana bioluminescence
allografts 19.1.6: Arabidopsis Thaliana - A Model Organism 4.15: Bioluminescence
15.4K: Organ Transplants arteriosclerosis biomagnification
allopatric speciation 15.3A: Anatomy of Human Circulatory System 17.1B: Food Chains and Food Webs
17.1F: Biomagnification of Pesticides
18.2: Speciation Ascomycetes 17.4B: Insecticides
allopatry 19.1.7: Fungi
biome
18.2: Speciation assortative mating 17.1C: Biomes
allozymes 18.6: The Hardy-Weinberg Equilibrium
Birth Control
18.7: Polymorphisms Asthma 15.7C: Birth Control
alpha cells 15.4U: Asthma
blastocyst
15.6.1.3: Hormones of the Pancreas Atherosclerosis 15.6.1.7: Sex Hormones
alternation of generations 15.3A: Anatomy of Human Circulatory System
blastula
16.3C: Fern Life Cycle ATP 14.1: Embryonic Development
Alveolates 4.2: ATP
blind spot
19.1.2: Protists ATP synthase 15.9C: Vision
Amino acids 4.6: ATP Synthase
blodd
2.7: Amino Acids autocrine signals 15.3E: Blood
amniocentesis 15.6.1: Human Hormones
bone
15.7D: Prenatal Screening automictic thelytoky 15.10A: Bones
AMPA receptors 15.7B: Asexual Reproduction in Animals
Bone Marrow
15.11.4: Long-Term Potentiation (LTP) autophagosomes 15.4L: Bone Marrow Transplants
amphiphilic 3.8: Lysosomes and Peroxisomes
Bone Marrow Transplants
2.4: Phospholipids 3.10: The Proteasome
15.4L: Bone Marrow Transplants
Amylin autotrophs
4.11: Metabolism
Bowman's capsule
15.6.1.3: Hormones of the Pancreas
15.1B: Metabolism 15.5A: Human Kidneys
Anabolism Breathing
4.11: Metabolism
auxin
16.5B: Auxin 15.2B: Control of Breathing
15.1B: Metabolism

1 https://bio.libretexts.org/@go/page/27893
bryophytes Chemotaxis collective dose
16.3B: Moss Life Cycle 15.11.2: Taxis 12.11: Estimating Cancer Risks
chitin color blindness
C 19.1.7: Fungi 15.9C: Vision
C value Chlorination comammox
5.9: Genome Sizes 17.2F: Chlorination and the Law of Unintended 17.2B: Nitrogen Cycle
Consequences commensalism
C value paradox
5.9: Genome Sizes
chlorophyll 17.4A: Symbiosis
3.18: Chlorophylls and Carotenoids complement system
C. Elegans
19.1.12: Caenorhabditis Elegans
chloroplasts 15.4R: The Complement System
3.17: Chloroplasts complementarity determining region
C3 plants
16.2E: Photorespiration and C4 Plants
cholecystokinin 15.4B: Antibody-Antigen Binding
15.1A: The Human Gastrointestinal Tract complete metamorphosis
C4 plants
16.2E: Photorespiration and C4 Plants
Cholecystokinin (CCK) 15.6.2: Insect Hormones
15.6.1.2: Hormones of the Gut compound eyes
Calcitonin
15.6.1.1: Thyroid and Parathyroids
Cholesterol 15.9E: Vision in Arthropods
2.5: Cholesterol Conditioned Response
Calvin cycle
4.7: Photosynthesis - Pathway of Carbon Fixation
chorionic villus sampling (CVS) 15.11.3: Learned Behavior
15.7D: Prenatal Screening condom
CAM plants
16.2E: Photorespiration and C4 Plants
chromatin 15.7C: Birth Control
3.3: The Nucleus conjugation
camouflage
15.11.6: Avoiding Predation
chromatophores 5.1: Transformation in Bacteria
3.22: Chromatophores connexins
cAMP
4.14: Secondary Messengers
chromoplasts 3.15: Junctions between Cells
3.16: Plant Cells contig
carbon cycle
17.2A: Carbon Cycle
chronic myelogenous leukemia 11.13: Metagenomics
12.7: Chronic Myelogenous Leukemia (CML) control group
cardiac muscle
15.10B: Muscles
cilia 20.2: Types of Clinical Studies
3.12: Cilia Copy Number Polymorphisms (CNPs)
carotenoids
3.18: Chlorophylls and Carotenoids
ciliates 18.7: Polymorphisms
19.1.2: Protists corpus luteum
carpels 19.1.3: Ciliates
16.3D: Angiosperm Life Cycle 15.6.1.8: Progesterone
Circular Proteins crosslink mutation
carrying capacity 2.10: Proteins
17.3B: Principles of Population Growth 5.13: DNA Repair
circulatory system cryptochrome
case study 15.3A: Anatomy of Human Circulatory System
20.2: Types of Clinical Studies 15.9J: Magnetoreceptors
cisternae cytokinin
Casparian strip 3.6: Golgi Apparatus
16.2A: Xylem 16.5C: Cytokinins
Class I Histocompatibility Molecules cytoskeleton
catabolism 15.4E: Histocompatibility Molecules
4.11: Metabolism 3.11: The Cytoskeleton
15.1B: Metabolism
Class II Histocompatibility Molecules cytotoxic T cells
15.4E: Histocompatibility Molecules
catabolite activator protein (CAP) 15.4E: Histocompatibility Molecules
9.1: Regulation of Gene Expression in Bacteria
classical pathway cytotoxic T lymphocytes (CTLs)
15.4R: The Complement System
cellular respiration 15.4C: B Cells and T Cells
4.5: Cellular Respiration
clathrin 15.4I: Cytotoxic T lymphocytes (CTL)
3.24: Endocytosis
central nervous system
15.8C: The Human Central Nervous System
cleavage D
14.1: Embryonic Development
central vacuole 14.3: Cleavage
dalton (unit)
3.16: Plant Cells 1.7: Molecular Weight and the Mole
clines
centriole 18.2: Speciation
Darwin's Finches
3.7: Centrosomes and Centrioles 18.2: Speciation
Clinical Trials
centromere 20.2: Types of Clinical Studies
DDT
13.2: Telomeres 17.1F: Biomagnification of Pesticides
Clotting
centrosome 15.3H: Blood Clotting
deamination
3.7: Centrosomes and Centrioles 15.5C: Urea Cycle
Cocklebur chart
cGMP 16.4E: Photoperiodism and Phytochrome
delta cells
4.14: Secondary Messengers 15.6.1.3: Hormones of the Pancreas
cohesion theory
Chaperones 16.2A: Xylem
dendritic cells
2.10: Proteins 15.4O: Dendritic Cells
cohort studies
chemiosmosis 20.2: Types of Clinical Studies
dioxin
4.8: Photosynthesis - The Role of Light 12.13: Dioxin
4.10: Chemiosmosis
Collagen
3.21: Collagens
diploid
chemokines 5.9: Genome Sizes
15.11.2: Taxis

2 https://bio.libretexts.org/@go/page/27893
diploid number exocrine glands gene pool
7.1: Chromosomes 15.1A: The Human Gastrointestinal Tract 18.6: The Hardy-Weinberg Equilibrium
diversity Exocytosis gene therapy
11.13: Metagenomics 3.8: Lysosomes and Peroxisomes 11.3: Gene Therapy - Methods and Prospects
DNA 3.25: Exocytosis genetic drift
Unit 5: DNA experimental allergic encephalomyelitis 18.6: The Hardy-Weinberg Equilibrium
DNA typing 12.13: Dioxin genetic mosaic
11.7: Restriction Fragment Length Polymorphisms extracellular fluid 7.6: Sex Chromosomes
dolly 3.24: Endocytosis genome
15.3D: The Lymphatic System
13.2: Telomeres 2.14: Proteomics
dopamine extremophile Geologic Eras
19.2B: Archaea
15.6.1.5: Hormones of the Hypothalamus 18.12: Geologic Eras
double fertilization germination
16.3D: Angiosperm Life Cycle
F 16.4B: Germination of Seeds
dynein falciparum Ghrelin
3.12: Cilia 15.3I: Sickle-Cell Disease 15.6.1.2: Hormones of the Gut
dyneins fern gibberellins
3.12: Cilia 16.3C: Fern Life Cycle 16.5E: Gibberellins
Fibroblast Growth Factor 19 (FGF19) girdling
E 15.6.1.2: Hormones of the Gut 16.2B: Phloem
E. coli FISH global climate change
7.1: Chromosomes 17.2A: Carbon Cycle
19.2D: E. coli
ecdysone Flicker effect Glomerulus
15.9E: Vision in Arthropods 15.5A: Human Kidneys
15.6.2: Insect Hormones
15.11.5: Honeybee Navigation 15.5B: Vertebrate Kidneys
ecology florigen
Unit 17: Ecology
glucagon
16.4D: Flowering 15.6.1.3: Hormones of the Pancreas
ectoderm flower
3.13: Animal Tissues
glycolysis
16.3D: Angiosperm Life Cycle 4.4: Glycolysis
ectotherms flowering
15.3G: The Transport of Heat
glycophorin A
16.4D: Flowering 2.12: Glycoproteins
elastase fluorescence in situ hybridization
15.3J: Serine Proteases
glycosylation
7.1: Chromosomes 2.12: Glycoproteins
electrocytes Fragile X Syndrome 3.6: Golgi Apparatus
15.9I: Electric Organs and Electroreceptors 3.9: Protein Kinesis
10.1: Mutations - Causes and Significance
endocrine signals frameshift Golgi apparatus
15.6.1: Human Hormones 3.6: Golgi Apparatus
8.2: Crossing Over and Genetic Recombination in
Endocytosis Meiosis Graft rejection
3.24: Endocytosis Frog Embryology 15.4K: Organ Transplants
endometrium 14.2: Frog Embryology grana
15.6.1.7: Sex Hormones fronds 3.17: Chloroplasts
endoreplication 16.3C: Fern Life Cycle gravitropism
15.7B: Asexual Reproduction in Animals fruit 16.5B: Auxin
Endostatin 16.3D: Angiosperm Life Cycle gray matter
12.8: Fighting Cancer with Inhibitors of Fungi 15.8C: The Human Central Nervous System
Angiogenesis
19.1.7: Fungi greenhouse effect
endosymbiosis 17.2A: Carbon Cycle
18.9: The Origin of Life
18.11: Endosymbiosis
G guard cells
endotherms G proteins 16.2D: Gas Exchange in Plants
15.3G: The Transport of Heat 4.13: G Proteins
Epidemiology Gamma amino butyric acid (GABA) H
20.1: Epidemiology 15.8A: Neurons habituation
Epidermal Growth Factor gamma aminobutyric acid (GABA) 15.11.3: Learned Behavior
12.3: Oncogenes 15.8B: Synapses Hageman factor
epigenetics gamma cells 15.3H: Blood Clotting
9.5: Epigenetics 15.6.1.3: Hormones of the Pancreas halteres
epitope gastrin 14.6: Homeobox Genes
15.4B: Antibody-Antigen Binding 15.6.1.2: Hormones of the Gut hearing
estrogens Gastrointestinal Tract 15.9B: Hearing
15.6.1.7: Sex Hormones 15.1A: The Human Gastrointestinal Tract helper T cells
etiolation Gene cloning 15.4C: B Cells and T Cells
11.1: Recombinant DNA and Gene Cloning 15.4H: T Helper cells
16.4C: Etiolation
Euchromatin gene expression hematocrit
Unit 9: Regulation of Gene Expression 15.3E: Blood
3.3: The Nucleus

3 https://bio.libretexts.org/@go/page/27893
hematopoietic stem cell imprinting leaf
15.3E: Blood 15.11.3: Learned Behavior 16.2D: Gas Exchange in Plants
hemoglobin A inbreeding learned behavior
15.3I: Sickle-Cell Disease 18.6: The Hardy-Weinberg Equilibrium 15.11.3: Learned Behavior
hemoglobin S Incretins leucoplasts
15.3I: Sickle-Cell Disease 15.6.1.2: Hormones of the Gut 3.16: Plant Cells
hemophilia indel leukocytes
7.6: Sex Chromosomes 10.1: Mutations - Causes and Significance 15.4C: B Cells and T Cells
Hepatic Portal System induction Long interspersed elements (LINEs)
15.1A: The Human Gastrointestinal Tract 14.4: The Organizer 10.4: Transposons - "jumping genes"
hermaphrodite infection thread Loop of Henle
7.6: Sex Chromosomes 17.2C: Symbiotic Nitrogen Fixation 15.5A: Human Kidneys
heterochromatin inflammation luciferase
3.3: The Nucleus 15.4S: Inflammation 4.15: Bioluminescence
heteroduplex influenza luciferin
8.2: Crossing Over and Genetic Recombination in 19.3B: Influenza 4.15: Bioluminescence
Meiosis innate immunity Luteinizing Hormone (LH)
heteroplasmy 15.4Q: Innate Immunity 15.6.1.4: Hormones of the Pituitary
4.5: Cellular Respiration Insect Monitoring 15.7A: Sexual Reproduction
heterotrophs 15.11.7: Pheromones lymphocytes
4.11: Metabolism Insecticides 15.4C: B Cells and T Cells
Histocompatibility antigens 17.4B: Insecticides lysosomes
15.4E: Histocompatibility Molecules instincts 3.8: Lysosomes and Peroxisomes
Holoblastic Cleavage 3.10: The Proteasome
15.11.1: Innate Behavior
14.3: Cleavage interstitial fluid (ISF)
Homeobox Genes 15.3D: The Lymphatic System
M
14.6: Homeobox Genes intertidal zone Müllerian Mimicry
Honeybee Navigation 17.1E: Marine Ecosystems 15.11.6: Avoiding Predation
15.11.5: Honeybee Navigation Intrinsic factor Magnetoreceptors
hormesis 15.1A: The Human Gastrointestinal Tract 15.9J: Magnetoreceptors
12.11: Estimating Cancer Risks Invertebrates Magnetospirillum magnetotacticum
hormone response elements 19.1.10: Invertebrates 15.11.2: Taxis
15.6.1: Human Hormones Inverted Repeats magnetotaxis
Hox Cluster 9.10: Palindromes 15.11.2: Taxis
14.6: Homeobox Genes islets of Langerhans Major histocompatibility complex
Human pheromones 15.6.1.3: Hormones of the Pancreas 15.4E: Histocompatibility Molecules
15.11.7: Pheromones Male Confusion
hydrogen bonds J 15.11.7: Pheromones
1.5: Hydrogen Bonds
John Snow marasmus
hyperparathyroidism 20.1: Epidemiology
15.1C: Nutrition
15.6.1.1: Thyroid and Parathyroids mars
hyperpolarization K 18.10: Mars
15.8A: Neurons Masquerade
keratins
hyperthermophiles 15.11.6: Avoiding Predation
3.11: The Cytoskeleton
19.2B: Archaea Mechanoreceptors
Kidneys
hyphae 15.9A: Mechanoreceptors
15.5A: Human Kidneys
19.1.7: Fungi Meissner corpuscles
kin selection
hypoparathyroidism 15.9A: Mechanoreceptors
18.8: Kin Selection
15.6.1.1: Thyroid and Parathyroids melanin
kinetochore
hypothalamus 15.6.1.13: Melanocyte Stimulating Hormone (MSH)
7.1: Chromosomes
15.6.1.5: Hormones of the Hypothalamus melanophores
Knockout Mice 3.22: Chromatophores
11.5: Transgenic Animals
I 15.6.1.13: Melanocyte Stimulating Hormone (MSH)

Immune Globulin Membrane Fission

L 3.6: Golgi Apparatus
15.4P: Passive Immunity
lac operon Membrane Fusion
immunostimulants
9.1: Regulation of Gene Expression in Bacteria 3.6: Golgi Apparatus
12.9: Immunotherapy of Cancer
lac repressor Mendel
Immunosuppression
9.1: Regulation of Gene Expression in Bacteria 8.1: Mendel's Monohybrid Crosses
15.4K: Organ Transplants
Last Universal Common Ancestor Mendel’s Second Law
Impact Hypothesis
18.12: Geologic Eras (LUCA) 8.1: Mendel's Monohybrid Crosses

Imprinted Genes 18.9: The Origin of Life meninges

9.12: Imprinted Genes LD50 15.8C: The Human Central Nervous System
12.12: The LD50 test

4 https://bio.libretexts.org/@go/page/27893
menstruation myelin sheath oogenesis
15.6.1.7: Sex Hormones 15.8A: Neurons 15.7A: Sexual Reproduction
meristems myostatin operons
16.4A: Plant Growth 15.10B: Muscles 9.1: Regulation of Gene Expression in Bacteria
Merkel Cells Organ Transplants
15.9A: Mechanoreceptors N 15.4K: Organ Transplants
Meroblastic Cleavage nephric filtrate Organizer
14.3: Cleavage 15.5A: Human Kidneys 14.4: The Organizer
mesotherms nephrons osmosis
15.3G: The Transport of Heat 15.5A: Human Kidneys 3.23: Diffusion, Active Transport and Membrane
messenger RNA Channels
nervous system
3.4: Ribosomes 15.8: Nervous System
overpopulation
metabolism 17.3A: The Human Population
neurofilaments
Unit 4: Cell Metabolism 3.11: The Cytoskeleton
oxytocin
metabolome 15.6.1.5: Hormones of the Hypothalamus
Neuromuscular Junction
2.14: Proteomics 15.10B: Muscles
Ozone
Metagenomics 17.2I: Ozone
neurons
11.13: Metagenomics 15.8A: Neurons
Methanogens Neuropeptide Y (NPY) P
19.2B: Archaea 15.6.1.2: Hormones of the Gut p arm
microfilaments Nicotinamide adenine dinucleotide 7.1: Chromosomes
3.11: The Cytoskeleton
(NAD) p53
microglia 4.3: NAD and NADP
7.2: The Cell Cycle
3.13: Animal Tissues
nicotinamide adenine dinucleotide Pacinian corpuscle
mifepristone 15.9A: Mechanoreceptors
15.6.1.8: Progesterone
phosphate (NADP) packaging signal
4.3: NAD and NADP
migration 11.3: Gene Therapy - Methods and Prospects
17.3B: Principles of Population Growth
nitric oxide 19.3E: Retroviruses
Miller's Experiment 15.8F: Nitric Oxide (NO) Palindromes
18.9: The Origin of Life
nitrogen cycle 9.10: Palindromes
mimicry 17.2B: Nitrogen Cycle PAMP
15.11.6: Avoiding Predation
nitrogen fixation 15.4Q: Innate Immunity
mismatch mutation 17.2B: Nitrogen Cycle Pangaea
17.2C: Symbiotic Nitrogen Fixation
5.13: DNA Repair 18.12: Geologic Eras
notochord paracrine signals
Missense mutations 14.2: Frog Embryology
10.1: Mutations - Causes and Significance 15.6.1: Human Hormones
14.4: The Organizer
mole nuclear lamins Paralogous genes
1.7: Molecular Weight and the Mole 18.5: Mutation and Evolution
3.11: The Cytoskeleton
Molecular Weight Nucleomorph parapatric speciation
1.7: Molecular Weight and the Mole 18.2: Speciation
18.11: Endosymbiosis
molting nucleoplasm parasitism
15.6.2: Insect Hormones 17.4A: Symbiosis
3.3: The Nucleus
Monotremes nucleotide excision repair parathyroid hormone
19.1.15: Monotremes 15.6.1.7: Sex Hormones
5.13: DNA Repair
mosses nucleus Parathyroids
16.3B: Moss Life Cycle 15.6.1.1: Thyroid and Parathyroids
3.3: The Nucleus
Multipotent stem cells null hypothesis passive immunity
14.7: Stem Cells 15.4P: Passive Immunity
20.3: Scientific Methods
Murchison Meteorite nutrition Patterning
18.9: The Origin of Life 14.1: Embryonic Development
15.1C: Nutrition
muscle pavlov
15.11.3: Learned Behavior
3.13: Animal Tissues O
mutation pemphigoid
Oddity problems 3.15: Junctions between Cells
Unit 10: Mutation 15.11.3: Learned Behavior
mutation and Evolution Pemphigus
Okazaki fragments 3.15: Junctions between Cells
18.5: Mutation and Evolution 13.2: Telomeres
mutualism peptidoglycan
olfaction 19.2C: Antibiotics
17.2C: Symbiotic Nitrogen Fixation 15.9H: Olfaction - The Sense of Smell
17.4A: Symbiosis peristalsis
ommatidia
mycelium 15.8F: Nitric Oxide (NO)
15.9E: Vision in Arthropods
19.1.7: Fungi peroxisomal targeting signal
oncogene
mycorrhiza 3.8: Lysosomes and Peroxisomes
12.3: Oncogenes
19.1.7: Fungi peroxisomes
3.8: Lysosomes and Peroxisomes

5 https://bio.libretexts.org/@go/page/27893
petiole point mutations pseudoautosomal regions.
3.19: Plant Tissues 10.1: Mutations - Causes and Significance 7.6: Sex Chromosomes
phagocytosis pollen pseudogenes
3.24: Endocytosis 16.3D: Angiosperm Life Cycle 10.4: Transposons - "jumping genes"
pharyngula pollination 17.4A: Symbiosis
18.4: Recapitulation 16.3D: Angiosperm Life Cycle Psychedelics
Phenylalanine hydroxylase polygenic inheritance 15.8E: Drugs and the Nervous System
11.9: Genetic Screening for Phenylketonuria 8.6: Quantitative Trait Loci
Phenylalanine Tolerance Test polymerase chain reaction (PCR) Q
11.9: Genetic Screening for Phenylketonuria 11.2: Polymerase Chain Reaction q arm
Phenylketonuria Polymorphisms 7.1: Chromosomes
11.9: Genetic Screening for Phenylketonuria 11.7: Restriction Fragment Length Polymorphisms quantitative trait loci (QTL)
pheromone 18.7: Polymorphisms 8.6: Quantitative Trait Loci
15.11.7: Pheromones Polypeptides Queen Pheromone
Philadelphia chromosome 2.9: Polypeptides 15.11.7: Pheromones
12.7: Chronic Myelogenous Leukemia (CML) polyploidy
phloem 7.4: Polyploidy R
3.19: Plant Tissues population growth radiation damage
16.2B: Phloem 17.3B: Principles of Population Growth 10.3: Radiation and its effect on DNA
phosphoenolpyruvic acid (PEP) Positive Control of Transcription Recapitulation
16.2E: Photorespiration and C4 Plants 9.1: Regulation of Gene Expression in Bacteria 18.4: Recapitulation
Phospholipids primary cilium recombinant DNA
2.4: Phospholipids 3.12: Cilia 11.1: Recombinant DNA and Gene Cloning
Photochemical smog primer Recommended Dietary Allowances
17.2G: Air Pollution 11.2: Polymerase Chain Reaction 15.1D: Recommended Dietary Allowances
photoperiodism Primer Pheromones referees
16.4E: Photoperiodism and Phytochrome 15.11.7: Pheromones 20.4: Scientific Papers
Photophosphorylation prion reflex action
4.8: Photosynthesis - The Role of Light 15.8G: Prion Diseases 15.11.1: Innate Behavior
photosynthesis progestagens Regeneration
4.7: Photosynthesis - Pathway of Carbon Fixation 15.6.1.7: Sex Hormones 14.10: Regeneration
phototaxis progesterone Releaser Pheromones
15.11.2: Taxis 15.6.1.8: Progesterone 15.11.7: Pheromones
phototropism progesterone response element rem (unit)
16.5B: Auxin 15.6.1.8: Progesterone 10.3: Radiation and its effect on DNA
phylotype Progestins Resting Potential
11.13: Metagenomics 15.6.1.8: Progesterone 15.8A: Neurons
phytochrome programmed cell death restriction endonuclease
16.4C: Etiolation 3.20: Apoptosis 5.7: Restriction Enzymes
16.4E: Photoperiodism and Phytochrome prolactin 11.7: Restriction Fragment Length Polymorphisms
pinocytosis 15.6.1.4: Hormones of the Pituitary restriction enzymes
3.24: Endocytosis 15.6.1.5: Hormones of the Hypothalamus 5.7: Restriction Enzymes
Pitx1 Promoters Restriction Fragment Length
18.5: Mutation and Evolution 9.1: Regulation of Gene Expression in Bacteria
Polymorphisms (RFLPs)
placenta pronucleus
11.7: Restriction Fragment Length Polymorphisms
15.6.1.8: Progesterone 11.5: Transgenic Animals 18.7: Polymorphisms
15.7E: Extraembryonic Membranes and the Proopiomelanocortin
Physiology of the Placenta resveratrol
15.6.1.13: Melanocyte Stimulating Hormone (MSH) 13.1: Aging
plant hormones proprioception
16.5B: Auxin Retrospective Studies
15.9A: Mechanoreceptors 20.2: Types of Clinical Studies
plasma membrane Prospective Studies
3.2: Cell Membranes retrotransposons
20.2: Types of Clinical Studies 10.4: Transposons - "jumping genes"
plasmids proteasomes
11.1: Recombinant DNA and Gene Cloning Retroviruses
3.10: The Proteasome 19.3E: Retroviruses
plasminogen Protein Polymorphisms
15.3H: Blood Clotting reverse genetics
18.7: Polymorphisms 11.12: Forward and Reverse genetics
plasmodesmata proteome
3.15: Junctions between Cells Reverse transcriptase
2.14: Proteomics 19.3E: Retroviruses
16.2A: Xylem
platelets prothallus rhizome
16.3C: Fern Life Cycle 16.3C: Fern Life Cycle
15.3H: Blood Clotting
Pluripotent stem cells Prothoracicotropic Hormone (PTTH) ribosomes
15.6.2: Insect Hormones 3.4: Ribosomes
14.7: Stem Cells
Pneumograph protist riboswitches
19.1.2: Protists 9.1: Regulation of Gene Expression in Bacteria
15.2B: Control of Breathing

6 https://bio.libretexts.org/@go/page/27893
Root Pressure smooth endoplasmic reticulum testcross
16.2A: Xylem 3.5: Endoplasmic Reticulum 8.1: Mendel's Monohybrid Crosses
rough endoplasmic reticulum smooth muscle tetracyclines
3.5: Endoplasmic Reticulum 15.10B: Muscles 19.2C: Antibiotics
round dance Soil thrombin
15.11.5: Honeybee Navigation 17.2D: Soil 15.3H: Blood Clotting
Rubisco somatostatin thylakoid
16.2E: Photorespiration and C4 Plants 15.6.1.2: Hormones of the Gut 4.8: Photosynthesis - The Role of Light
15.6.1.5: Hormones of the Hypothalamus thyroid gland
S sori 15.6.1.1: Thyroid and Parathyroids
16.3C: Fern Life Cycle thyroxine
Sanger method
5.8: DNA Sequencing by the Dideoxy Method
Southern blotting 15.6.1.1: Thyroid and Parathyroids
11.8: Gel Blotting tissue factor
sarcomere
15.10B: Muscles
speciation 15.3H: Blood Clotting
15.10C: Testing the Sliding-Filament Hypothesis 18.2: Speciation tobacco mosaic virus
satiety signal Spemann Experiment 11.6: Transgenic Plants
15.6.1.2: Hormones of the Gut 14.4: The Organizer Total Fertility Rate
scientific fraud Spemann Organizer 17.3A: The Human Population
20.3: Scientific Methods 14.4: The Organizer Totipotent cells
secondary endosymbiosis spermatogenesis 14.7: Stem Cells
18.11: Endosymbiosis 15.7A: Sexual Reproduction Tracheal Breathing
Secondary Messengers spindle fibers 15.2D: Tracheal Breathing
4.14: Secondary Messengers 3.7: Centrosomes and Centrioles Trail Pheromone
secretin stamens 15.11.7: Pheromones
15.1A: The Human Gastrointestinal Tract 16.3D: Angiosperm Life Cycle transcriptome
15.6.1.2: Hormones of the Gut Stem Cells 2.14: Proteomics
Sedatives 14.7: Stem Cells transduction
15.8E: Drugs and the Nervous System Stem Growth 5.1: Transformation in Bacteria
Segmentation 16.4A: Plant Growth transformation
14.5: Segmentation - Organizing the Embryo Stimulants 5.1: Transformation in Bacteria
selector gene 15.8E: Drugs and the Nervous System Transgenic organism
14.6: Homeobox Genes stolons 11.5: Transgenic Animals
senescence 15.7B: Asexual Reproduction in Animals transgenic plant
13.1: Aging stomata 11.6: Transgenic Plants
Senses 16.2D: Gas Exchange in Plants transgenic plants
15.9: Senses stomatal index 16.3F: Transgenic Plants
sensitization 16.2D: Gas Exchange in Plants translation
15.11.3: Learned Behavior Strigolactones 6.4: The Translation of RNA into Proteins
serine proteases 16.5F: Strigolactones transmembrane glucose transporter
15.3J: Serine Proteases sulfa drugs (GLUT4)
Serpins 19.2C: Antibiotics
15.6.1.3: Hormones of the Pancreas
15.3J: Serine Proteases symbiosis transmissible spongiform
Sewage Treatment 17.4A: Symbiosis
17.2E: Sewage Treatment symplast encephalopathies
Sex Hormones 15.8G: Prion Diseases
16.2A: Xylem
15.6.1.7: Sex Hormones synapse transplantation antigens
shivering 15.4E: Histocompatibility Molecules
15.8A: Neurons
15.3G: The Transport of Heat 15.8B: Synapses transposase
sickle cell anemia 10.4: Transposons - "jumping genes"
10.1: Mutations - Causes and Significance T transposons
11.7: Restriction Fragment Length Polymorphisms T cell receptor (TCR) 10.4: Transposons - "jumping genes"
sievert (unit) 15.4C: B Cells and T Cells transversion
10.3: Radiation and its effect on DNA T Cells 10.1: Mutations - Causes and Significance
Silent mutations 15.4C: B Cells and T Cells triiodothyronine
10.1: Mutations - Causes and Significance taxes 15.6.1.1: Thyroid and Parathyroids
single nucleotide polymorphism 15.11.1: Innate Behavior tripeptide
11.7: Restriction Fragment Length Polymorphisms taxonomy 2.9: Polypeptides
skeletal muscle tissue 19.1.1: Taxonomy trisomy
15.10B: Muscles Tc1 mouse 7.1: Chromosomes
skepticism 18.3: The Evolution of Body Form in Animals Tropisms
20.3: Scientific Methods telomerase 16.2F: Tropisms
smallpox 13.2: Telomeres Trp operon
19.3D: Smallpox telomere 9.2: The Tryptophan Repressor
13.2: Telomeres

7 https://bio.libretexts.org/@go/page/27893
Trp repressor variola virus vomeronasal organ (VNO)
9.2: The Tryptophan Repressor 19.3D: Smallpox 15.11.7: Pheromones
Tryptophan Repressor vascular plant
9.1: Regulation of Gene Expression in Bacteria 3.19: Plant Tissues W
tuberculin test vasopressin waggle dance
15.4J: Cell-Mediated Immunity 15.6.1.4: Hormones of the Pituitary 15.11.5: Honeybee Navigation
vegetative growth white matter
U 16.4D: Flowering 15.8C: The Human Central Nervous System
Ultrabithorax (Ubx) vernalization
14.6: Homeobox Genes 16.4D: Flowering X
urea cycle Vertebrate Kidneys xylem
15.5C: Urea Cycle 15.5B: Vertebrate Kidneys 16.2A: Xylem
uric acid Vertebrate Lungs
15.5C: Urea Cycle 15.2C: Vertebrate Lungs Y
villi Y chromosome
V 15.1A: The Human Gastrointestinal Tract
7.6: Sex Chromosomes
vaccines vimentins
3.11: The Cytoskeleton
15.4W: Vaccines Z
vacuole Viruses
19.3: Viruses
Zebrafish
3.16: Plant Cells 11.12: Forward and Reverse genetics
19.3A: Viruses
19.1.14: Zebrafish

8 https://bio.libretexts.org/@go/page/27893
Glossary
Sample Word 1 | Sample Definition 1

1 https://bio.libretexts.org/@go/page/39888
Detailed Licensing
Overview
Title: Book: Biology (Kimball)
Webpages: 398
All licenses found:
CC BY 3.0: 99% (394 pages)
Undeclared: 1% (4 pages)

By Page
Book: Biology (Kimball) - CC BY 3.0 3.6: Golgi Apparatus - CC BY 3.0
Front Matter - CC BY 3.0 3.7: Centrosomes and Centrioles - CC BY 3.0
TitlePage - CC BY 3.0 3.8: Lysosomes and Peroxisomes - CC BY 3.0
InfoPage - CC BY 3.0 3.9: Protein Kinesis - CC BY 3.0
Table of Contents - Undeclared 3.10: The Proteasome - CC BY 3.0
About this Book - CC BY 3.0 3.11: The Cytoskeleton - CC BY 3.0
Licensing - Undeclared 3.12: Cilia - CC BY 3.0
3.13: Animal Tissues - CC BY 3.0
Unit 1: The Chemical Basis of Life - CC BY 3.0
3.14: Adipose Tissue - CC BY 3.0
1.1: Mixtures and Compounds - CC BY 3.0 3.15: Junctions between Cells - CC BY 3.0
1.2: Elements and Atoms - CC BY 3.0 3.16: Plant Cells - CC BY 3.0
1.3: Electronegativity and types of Chemical Bonds - 3.17: Chloroplasts - CC BY 3.0
CC BY 3.0 3.18: Chlorophylls and Carotenoids - CC BY 3.0
1.4: Noncovalent Bonding - CC BY 3.0 3.19: Plant Tissues - CC BY 3.0
1.5: Hydrogen Bonds - CC BY 3.0 3.20: Apoptosis - CC BY 3.0
1.6: Acids and Bases - CC BY 3.0 3.21: Collagens - CC BY 3.0
1.7: Molecular Weight and the Mole - CC BY 3.0 3.22: Chromatophores - CC BY 3.0
1.8: pH - CC BY 3.0 3.23: Diffusion, Active Transport and Membrane
Unit 2: The Molecules of Life - CC BY 3.0 Channels - CC BY 3.0
2.1: Organic Molecules - CC BY 3.0 3.24: Endocytosis - CC BY 3.0
2.2: Hydrocarbons - CC BY 3.0 3.25: Exocytosis - CC BY 3.0
2.3: Fats - CC BY 3.0 Unit 4: Cell Metabolism - CC BY 3.0
2.4: Phospholipids - CC BY 3.0 4.1: Enzymes - CC BY 3.0
2.5: Cholesterol - CC BY 3.0 4.2: ATP - CC BY 3.0
2.6: Carbohydrates - CC BY 3.0 4.3: NAD and NADP - CC BY 3.0
2.7: Amino Acids - CC BY 3.0 4.4: Glycolysis - CC BY 3.0
2.8: Enantiomers - CC BY 3.0 4.5: Cellular Respiration - CC BY 3.0
2.9: Polypeptides - CC BY 3.0 4.6: ATP Synthase - CC BY 3.0
2.10: Proteins - CC BY 3.0 4.7: Photosynthesis - Pathway of Carbon Fixation -
2.11: Rules of Protein Structure - CC BY 3.0 CC BY 3.0
2.12: Glycoproteins - CC BY 3.0 4.8: Photosynthesis - The Role of Light - CC BY 3.0
2.13: Nucleotides - CC BY 3.0 4.9: Photosynthesis - Dicovering the Secrets - CC BY
2.14: Proteomics - CC BY 3.0 3.0
Unit 3: The Cellular Basis of Life - CC BY 3.0 4.10: Chemiosmosis - CC BY 3.0
3.1: Animal Cells - CC BY 3.0 4.11: Metabolism - CC BY 3.0
3.2: Cell Membranes - CC BY 3.0 4.12: Intermediary Metabolism - CC BY 3.0
3.3: The Nucleus - CC BY 3.0 4.13: G Proteins - CC BY 3.0
3.4: Ribosomes - CC BY 3.0 4.14: Secondary Messengers - CC BY 3.0
3.5: Endoplasmic Reticulum - CC BY 3.0 4.15: Bioluminescence - CC BY 3.0

1 https://bio.libretexts.org/@go/page/97922
Unit 5: DNA - CC BY 3.0 Unit 9: Regulation of Gene Expression - CC BY 3.0
5.1: Transformation in Bacteria - CC BY 3.0 9.1: Regulation of Gene Expression in Bacteria - CC
5.2: The Hershey - Chase Experiments - CC BY 3.0 BY 3.0
5.3: The Double Helix of DNA - CC BY 3.0 9.2: The Tryptophan Repressor - CC BY 3.0
5.4: Base Pairing in DNA and RNA - CC BY 3.0 9.3: Regulation of Gene Expression in Eukaryotes -
5.5: DNA Replication - CC BY 3.0 CC BY 3.0
5.6: The Meselson - Stahl Experiment - CC BY 3.0 9.4: Steroid Response Elements - CC BY 3.0
5.7: Restriction Enzymes - CC BY 3.0 9.5: Epigenetics - CC BY 3.0
5.8: DNA Sequencing by the Dideoxy Method - CC 9.6: Visualization of Transcription and Translation in
BY 3.0 Bacteria - CC BY 3.0
5.9: Genome Sizes - CC BY 3.0 9.7: Footprinting - CC BY 3.0
5.10: The Human Genome Projects - CC BY 3.0 9.8: Chromatin Immunoprecipitation - CC BY 3.0
5.11: The Human and Chimpanzee Genomes - CC BY 9.9: Isolating Transcription Factors - CC BY 3.0
3.0 9.10: Palindromes - CC BY 3.0
5.12: Pyrosequencing - CC BY 3.0 9.11: Cell-specific gene expression - CC BY 3.0
5.13: DNA Repair - CC BY 3.0 9.12: Imprinted Genes - CC BY 3.0
5.14: Harlequin Chromosomes - CC BY 3.0 9.13: Ribozymes - CC BY 3.0
5.15: Metagenomics - Exploring the Microbial World Unit 10: Mutation - CC BY 3.0
- CC BY 3.0
10.1: Mutations - Causes and Significance - CC BY
Unit 6: Gene Expression - CC BY 3.0 3.0
6.1: One Gene - One Enzyme Theory - CC BY 3.0 10.2: Testing for Mutagenic Chemicals in Bacteria
6.2: The Transcription of DNA into RNA - CC BY and Mice - CC BY 3.0
3.0 10.3: Radiation and its effect on DNA - CC BY 3.0
6.3: Genetic Code - CC BY 3.0 10.4: Transposons - "jumping genes" - CC BY 3.0
6.4: The Translation of RNA into Proteins - CC BY Unit 11: Genomics - CC BY 3.0
3.0 11.1: Recombinant DNA and Gene Cloning - CC BY
6.5: RNA Editing - CC BY 3.0 3.0
6.6: Expressed Sequence Tags - CC BY 3.0 11.2: Polymerase Chain Reaction - CC BY 3.0
6.7: Ribosomal RNA (rRNA) Gene Cluster - CC BY 11.3: Gene Therapy - Methods and Prospects - CC BY
3.0 3.0
Unit 7: Cell Division - CC BY 3.0 11.4: Recent Advances in Gene Therapy - CC BY 3.0
7.1: Chromosomes - Undeclared 11.5: Transgenic Animals - CC BY 3.0
7.2: The Cell Cycle - CC BY 3.0 11.6: Transgenic Plants - CC BY 3.0
7.3: Mitosis - CC BY 3.0 11.7: Restriction Fragment Length Polymorphisms -
7.4: Polyploidy - CC BY 3.0 CC BY 3.0
7.5: Endoreplication - CC BY 3.0 11.8: Gel Blotting - CC BY 3.0
7.6: Sex Chromosomes - CC BY 3.0 11.9: Genetic Screening for Phenylketonuria - CC BY
7.7: Meiosis - CC BY 3.0 3.0
Unit 8: The Genetic Consequences of Meiosis - CC BY 11.10: Antisense RNA - CC BY 3.0
3.0 11.11: Antisense Oligodeoxynucleotides and their
8.1: Mendel's Monohybrid Crosses - CC BY 3.0 Therapeutic Potential - CC BY 3.0
8.2: Crossing Over and Genetic Recombination in 11.12: Forward and Reverse genetics - CC BY 3.0
Meiosis - CC BY 3.0 11.13: Metagenomics - CC BY 3.0
8.3: The Evidence of Creighton and McClintock - CC Unit 12: Cancer - CC BY 3.0
BY 3.0 12.1: Cancer in General - CC BY 3.0
8.4: Genetic linkage and Genetic Maps - CC BY 3.0 12.2: Cancer Cells in Culture - CC BY 3.0
8.5: Gene Mapping with Three-point Crosses - CC 12.3: Oncogenes - CC BY 3.0
BY 3.0 12.4: Tumor Suppressor Genes - CC BY 3.0
8.6: Quantitative Trait Loci - CC BY 3.0 12.5: BCL-2 - CC BY 3.0
8.7: Mapping the Genes of T2 - CC BY 3.0 12.6: Burkitt's Lymphoma - CC BY 3.0
8.8: rII Locus of T4 - CC BY 3.0

2 https://bio.libretexts.org/@go/page/97922
 12.7: Chronic Myelogenous Leukemia (CML) - CC 15.3G: The Transport of Heat - CC BY 3.0
BY 3.0 15.3H: Blood Clotting - CC BY 3.0
12.8: Fighting Cancer with Inhibitors of 15.3I: Sickle-Cell Disease - CC BY 3.0
Angiogenesis - CC BY 3.0 15.3J: Serine Proteases - CC BY 3.0
12.9: Immunotherapy of Cancer - CC BY 3.0 15.3K: Animal Circulatory Systems - CC BY 3.0
12.10: Cancer- The Causes and Prevention of Cancer 15.4: Immune System - CC BY 3.0
- CC BY 3.0 15.4.1: 15.4T Allergies - CC BY 3.0
12.11: Estimating Cancer Risks - CC BY 3.0 15.4A: Clonal Selection and Immunological
12.12: The LD50 test - CC BY 3.0 Memory - CC BY 3.0
12.13: Dioxin - CC BY 3.0 15.4B: Antibody-Antigen Binding - CC BY 3.0
12.14: Magnetic Fields and Cancer - CC BY 3.0 15.4C: B Cells and T Cells - CC BY 3.0
Unit 13: Aging - CC BY 3.0 15.4D: Antigen Receptors - CC BY 3.0
13.1: Aging - CC BY 3.0 15.4E: Histocompatibility Molecules - CC BY 3.0
13.2: Telomeres - CC BY 3.0 15.4F: Antigen Receptor Diversity - CC BY 3.0
Unit 14: Embryonic Development and its Regulation - 15.4G: Anatomy of the Immune System - CC BY
CC BY 3.0 3.0
15.4H: T Helper cells - CC BY 3.0
14.1: Embryonic Development - CC BY 3.0
15.4I: Cytotoxic T lymphocytes (CTL) - CC BY
14.2: Frog Embryology - CC BY 3.0
3.0
14.3: Cleavage - CC BY 3.0
15.4J: Cell-Mediated Immunity - CC BY 3.0
14.4: The Organizer - CC BY 3.0
15.4K: Organ Transplants - CC BY 3.0
14.5: Segmentation - Organizing the Embryo - CC BY
15.4L: Bone Marrow Transplants - CC BY 3.0
3.0
15.4M: Antigen Presentation - CC BY 3.0
14.6: Homeobox Genes - CC BY 3.0
15.4N: The Immunological Synapse - CC BY 3.0
14.7: Stem Cells - CC BY 3.0
15.4O: Dendritic Cells - CC BY 3.0
14.8: Embryonic Stem Cells - CC BY 3.0
15.4P: Passive Immunity - CC BY 3.0
14.9: Germline vs. Soma - CC BY 3.0
15.4Q: Innate Immunity - CC BY 3.0
14.10: Regeneration - CC BY 3.0
15.4R: The Complement System - CC BY 3.0
Unit 15: The Anatomy and Physiology of Animals - CC
15.4S: Inflammation - CC BY 3.0
BY 3.0
15.4U: Asthma - CC BY 3.0
15.1: Nutrition - CC BY 3.0 15.4V: AIDS - CC BY 3.0
15.1A: The Human Gastrointestinal Tract - CC BY 15.4W: Vaccines - CC BY 3.0
3.0 15.5: Excretion - CC BY 3.0
15.1B: Metabolism - CC BY 3.0
15.5A: Human Kidneys - CC BY 3.0
15.1C: Nutrition - CC BY 3.0
15.5B: Vertebrate Kidneys - CC BY 3.0
15.1D: Recommended Dietary Allowances - CC
15.5C: Urea Cycle - CC BY 3.0
BY 3.0
15.6: Hormones - CC BY 3.0
15.2: Gas Exchange - CC BY 3.0
15.6.1: Human Hormones - CC BY 3.0
15.2A: Human Respiratory System - CC BY 3.0
15.6.1.1: Thyroid and Parathyroids - CC BY
15.2B: Control of Breathing - CC BY 3.0
3.0
15.2C: Vertebrate Lungs - CC BY 3.0
15.6.1.2: Hormones of the Gut - CC BY 3.0
15.2D: Tracheal Breathing - CC BY 3.0
15.6.1.3: Hormones of the Pancreas - CC BY
15.3: Circulatory Systems - CC BY 3.0
3.0
15.3A: Anatomy of Human Circulatory System - 15.6.1.4: Hormones of the Pituitary - CC BY
CC BY 3.0 3.0
15.3B: How the Human Circulatory System 15.6.1.5: Hormones of the Hypothalamus - CC
Works - CC BY 3.0 BY 3.0
15.3C: The Heartbeat - CC BY 3.0 15.6.1.6: Adrenal Glands - CC BY 3.0
15.3D: The Lymphatic System - CC BY 3.0 15.6.1.7: Sex Hormones - CC BY 3.0
15.3E: Blood - CC BY 3.0 15.6.1.8: Progesterone - CC BY 3.0
15.3F: Blood Groups - CC BY 3.0

3 https://bio.libretexts.org/@go/page/97922
 15.6.1.9: Melatonin and the Pineal Gland - CC 15.11: Behavior - CC BY 3.0
BY 3.0 15.11.1: Innate Behavior - CC BY 3.0
15.6.1.10: Hormones of Kidney, Skin and 15.11.2: Taxis - CC BY 3.0
Heart - CC BY 3.0 15.11.3: Learned Behavior - CC BY 3.0
15.6.1.11: Leptin - the Fat Hormone - CC BY 15.11.4: Long-Term Potentiation (LTP) - CC BY
3.0 3.0
15.6.1.12: Hormones of the Liver - CC BY 3.0 15.11.5: Honeybee Navigation - CC BY 3.0
15.6.1.13: Melanocyte Stimulating Hormone 15.11.6: Avoiding Predation - CC BY 3.0
(MSH) - CC BY 3.0 15.11.7: Pheromones - CC BY 3.0
15.6.2: Insect Hormones - CC BY 3.0 15.11.8: Circadian Rhythms in Drosophila and
15.7: Sexual Reproduction - CC BY 3.0 Mammals - CC BY 3.0
15.7A: Sexual Reproduction - CC BY 3.0 Unit 16: The Anatomy and Physiology of Plants - CC BY
15.7B: Asexual Reproduction in Animals - CC BY 3.0
3.0 16.1: Plant Anatomy - CC BY 3.0
15.7C: Birth Control - CC BY 3.0 16.1.1: Plant Tissues - CC BY 3.0
15.7D: Prenatal Screening - CC BY 3.0 16.1.2: Roots - CC BY 3.0
15.7E: Extraembryonic Membranes and the 16.1.3: Stems - CC BY 3.0
Physiology of the Placenta - CC BY 3.0 16.1.4: The Leaf - CC BY 3.0
15.7F: Genetic Mosaics - CC BY 3.0 16.1.5: Arabidopsis Thaliana - CC BY 3.0
15.7G: Human Cloning - CC BY 3.0 16.2: Plant Physiology - CC BY 3.0
15.8: Nervous System - CC BY 3.0 16.2A: Xylem - CC BY 3.0
15.8A: Neurons - CC BY 3.0 16.2B: Phloem - CC BY 3.0
15.8B: Synapses - CC BY 3.0 16.2C: Transpiration - CC BY 3.0
15.8C: The Human Central Nervous System - CC 16.2D: Gas Exchange in Plants - CC BY 3.0
BY 3.0 16.2E: Photorespiration and C4 Plants - CC BY
15.8D: The Peripheral Nervous System - CC BY 3.0
3.0 16.2F: Tropisms - CC BY 3.0
15.8E: Drugs and the Nervous System - CC BY 16.3: Reproduction in Plants - CC BY 3.0
3.0
16.3A: Alternation of Generations in Plants - CC
15.8F: Nitric Oxide (NO) - CC BY 3.0
BY 3.0
15.8G: Prion Diseases - CC BY 3.0
16.3B: Moss Life Cycle - CC BY 3.0
15.9: Senses - CC BY 3.0
16.3C: Fern Life Cycle - CC BY 3.0
15.9A: Mechanoreceptors - CC BY 3.0 16.3D: Angiosperm Life Cycle - CC BY 3.0
15.9B: Hearing - CC BY 3.0 16.3E: Asexual Reproduction in Plants - CC BY
15.9C: Vision - CC BY 3.0 3.0
15.9D: Processing Visual Information - CC BY 3.0 16.3E: Self-incompatibility - How Plants Avoid
15.9E: Vision in Arthropods - CC BY 3.0 Inbreeding - CC BY 3.0
15.9F: Heat, Cold, and Pain Receptors - CC BY 16.3F: Transgenic Plants - CC BY 3.0
3.0
16.4: Plant Development - Fundamentals - CC BY 3.0
15.9G: Taste - CC BY 3.0
16.4A: Plant Growth - CC BY 3.0
15.9H: Olfaction - The Sense of Smell - CC BY
16.4B: Germination of Seeds - CC BY 3.0
3.0
16.4C: Etiolation - CC BY 3.0
15.9I: Electric Organs and Electroreceptors - CC
16.4D: Flowering - CC BY 3.0
BY 3.0
16.4E: Photoperiodism and Phytochrome - CC BY
15.9J: Magnetoreceptors - CC BY 3.0
3.0
15.10: Muscles - CC BY 3.0
16.5: Plant Development - Hormones - CC BY 3.0
15.10A: Bones - CC BY 3.0
16.5A: Abscisic acid (ABA) - CC BY 3.0
15.10B: Muscles - CC BY 3.0
16.5B: Auxin - CC BY 3.0
15.10C: Testing the Sliding-Filament Hypothesis -
16.5C: Cytokinins - CC BY 3.0
CC BY 3.0
16.5D: Ethylene - CC BY 3.0

4 https://bio.libretexts.org/@go/page/97922
 16.5E: Gibberellins - CC BY 3.0 19.1: Eukaryotic Life - CC BY 3.0
16.5F: Strigolactones - CC BY 3.0 19.1.1: Taxonomy - CC BY 3.0
Unit 17: Ecology - CC BY 3.0 19.1.2: Protists - CC BY 3.0
17.1: Energy Flow through the Biosphere - CC BY 3.0 19.1.3: Ciliates - CC BY 3.0
19.1.4: Volvox - CC BY 3.0
17.1A: Ecosystem Productivity - CC BY 3.0
19.1.5: Diversity and Evolutionary Relationships
17.1B: Food Chains and Food Webs - CC BY 3.0
of the Plants - CC BY 3.0
17.1C: Biomes - CC BY 3.0
19.1.6: Arabidopsis Thaliana - A Model Organism
17.1D: Freshwater Ecosystems - CC BY 3.0
- CC BY 3.0
17.1E: Marine Ecosystems - CC BY 3.0
19.1.7: Fungi - CC BY 3.0
17.1F: Biomagnification of Pesticides - CC BY 3.0
19.1.8: Yeast - CC BY 3.0
17.2: Cycles of Matter in the Biosphere - CC BY 3.0
19.1.9: Barcoding - CC BY 3.0
17.2A: Carbon Cycle - CC BY 3.0 19.1.10: Invertebrates - CC BY 3.0
17.2B: Nitrogen Cycle - CC BY 3.0 19.1.11: Drosophila Melanogaster - CC BY 3.0
17.2C: Symbiotic Nitrogen Fixation - CC BY 3.0 19.1.12: Caenorhabditis Elegans - CC BY 3.0
17.2D: Soil - CC BY 3.0 19.1.13: Vertebrates - CC BY 3.0
17.2E: Sewage Treatment - CC BY 3.0 19.1.14: Zebrafish - CC BY 3.0
17.2F: Chlorination and the Law of Unintended 19.1.15: Monotremes - CC BY 3.0
Consequences - CC BY 3.0
19.2: Microbes - CC BY 3.0
17.2G: Air Pollution - CC BY 3.0
17.2H: Acid Rain - CC BY 3.0 19.2A: Bacteria - CC BY 3.0
17.2I: Ozone - CC BY 3.0 19.2B: Archaea - CC BY 3.0
19.2C: Antibiotics - CC BY 3.0
17.3: The Growth of Populations - CC BY 3.0
19.2D: E. coli - CC BY 3.0
17.3A: The Human Population - CC BY 3.0 19.2E: Anthrax - CC BY 3.0
17.3B: Principles of Population Growth - CC BY 19.2F: Bacillus Thuringiensis - CC BY 3.0
3.0 19.2G: The Rapid Identification of
17.4: Interactions between Species - CC BY 3.0 Microorganisms - CC BY 3.0
17.4A: Symbiosis - CC BY 3.0 19.3: Viruses - CC BY 3.0
17.4B: Insecticides - CC BY 3.0 19.3A: Viruses - CC BY 3.0
17.4C: Biological Control of Pests - CC BY 3.0 19.3B: Influenza - CC BY 3.0
Unit 18: Evolution - CC BY 3.0 19.3C: φX174 - CC BY 3.0
18.1: Evolution and Adaptation - CC BY 3.0 19.3D: Smallpox - CC BY 3.0
18.2: Speciation - CC BY 3.0 19.3E: Retroviruses - CC BY 3.0
18.3: The Evolution of Body Form in Animals - CC Unit 20: General Science - CC BY 3.0
BY 3.0 20.1: Epidemiology - CC BY 3.0
18.4: Recapitulation - CC BY 3.0 20.2: Types of Clinical Studies - CC BY 3.0
18.5: Mutation and Evolution - CC BY 3.0 20.3: Scientific Methods - CC BY 3.0
18.6: The Hardy-Weinberg Equilibrium - CC BY 3.0 20.4: Scientific Papers - CC BY 3.0
18.7: Polymorphisms - CC BY 3.0 20.5: Statistical Methods - CC BY 3.0
18.8: Kin Selection - CC BY 3.0 20.6: Drugs - CC BY 3.0
18.9: The Origin of Life - CC BY 3.0
Back Matter - CC BY 3.0
18.10: Mars - CC BY 3.0
18.11: Endosymbiosis - CC BY 3.0 Index - CC BY 3.0
18.12: Geologic Eras - CC BY 3.0 Glossary - CC BY 3.0
Detailed Licensing - Undeclared
Unit 19: The Diversity of Life - CC BY 3.0

5 https://bio.libretexts.org/@go/page/97922