SCI 402

Learning Module
in

MODERN BIOLOGY

Consolidated by:
Ms. Evangeline Joyce D. Jungay
Introduction

This module is intended for BS Mechanical Engineering first year

undergraduate students of Batangas State University as their fundamental
course, enrolled in the midterm, AY 2020-2021. The lecture component of
Modern Biology provides students the opportunity to study the basic
foundation on biology and approaches to analyzing biological data. This
course is designed to convey the essentials of biology to provide a
framework for more specific understanding and contribution by engineering
students.

Modern Biology covers basic concepts and applications of the

principles of biology that are important in the engineering profession. The
topics include the cell, cellular energy transformations, cell reproduction
and genetics, biodiversity, biotechnology and special topics.

This course likewise offers an opportunity for students to relate and

apply the principles and theories of Biology in actual industrial processes,
operations and its implications to environment and to be aware of the
significance of biology in everyday life.

Students may own their learning by studying this material in their own
convenient time outside of class schedule as long as they comply with the
completion of all the learning tasks to be completed during the term.

This module is composed of 9 main topics, divided into areas relevant to

the course. Each main topic is divided into 4 sections:

● Objectives
● Lesson Proper
● Learning Tasks
● References
Intended Learning Outcomes

Upon completion of the course, students should be able to:

1. discuss basic organization of organisms and living being;

2. explain the machinery of the cell that is ultimately responsible for
various daily activities;
3. apply the concept of plant, animal and microbial systems and
growth
In real life situations;
4. explain the science behind biotechnology as the application of
biology; ii) discuss how advances in biotechnology affect our lives
presently and may do so in the future; iii) consider how
entrepreneurs actually convert scientific advances into concrete
commercial or social changes and;
5. present biological problems in relevant fields that require
engineering expertise to be solved.
 Topic I – Introduction to Biology

Learning Objectives:

1. Define biology.
2. Enumerate the characteristics of life and explain the significance of
each.
3. Explain the principles involved in the scientific inquiry.
4. Assess the importance of studying biology as applied to engineering
field.

Scope and Properties of Life

• Life is structured on a scale ranging from the molecular to the global.

• Biology is the scientific study of life.
• Biology covers the wide range diversity of life on earth.

What is Biology?

Biology is the study of life and living organisms. The word biology is derived
from the Greek word “bios”, which means life, and “logos”, which means
study. It is a study of the organism’s physical components and structure
and delves into their chemical processes and molecular interactions. It is a
natural science that studies the physiological mechanisms, development
and evolution of all life forms.
Biology: The scientific study of life

An animal or plant, or any living thing is called an organism.

Biology as a “unified science of life”

Biology is a vast subject that takes up a wide array of disciplines and

specializations. However, despite its many branches and broad scope,
unifying concepts serve as strong guiding principles and influences over all
recent study and research:

● the basic unit of life is cell

-All organisms are made up of cells and came from pre-existing cells.
● the basic unit of heredity are genes, composed of DNA or RNA
-All living organisms have genetic information that codes for a specific
structure or function of cells.
● a stable internal environment is found in all organisms
- All organisms must maintain a state of balance or homeostasis

● evolution is responsible for the unity and diversity among living

organisms
-It is the change over time that helps organisms adapt to their
environment and the driving force for biological diversity.
● all organisms survive by energy absorption and conversion
 -Energy is required for all living organisms to survive.

The Characteristics of Life

In studying biology, there is always a difference between living organisms

and non-living things. Defining life is not an easy matter, and scientists do
not always agree with each other. Below is the list of known and accepted
characteristics of life:

1. Organisms require energy and nutrients

All living things require energy and nutrients. Both are essential to
maintain life’s organization and functioning.
Energy is the capacity to do work. A nutrient is a substance that an
organism needs for growth and survival but cannot make for itself.
However, what type of energy and nutrients are acquired varies
considerably depending on the type of organism. The differences
allow us to classify all living things into two categories: producers
and consumers.
● Producers make their own food using energy and simple raw
materials they get directly from their environment.
● Plants are producers that use the energy of sunlight to make sugars
from water and carbon dioxide in a process called photosynthesis.
● Consumers cannot make their own food. They get their energy and
nutrients by feeding on other organisms. Animals are consumers.
● Decomposers are consumers that feed on the wastes and or
remains of other organisms.
● The leftover of consumer’s meals ends up in the environment, where
they serve as nutrients for producers. Said another way, nutrients
cycle between producers and consumers.
● Unlike nutrients, energy is not cycled. It flows in one direction: from
the environment, through organisms, and back to the environment. It
is a one-way flow because with each transfer, some energy escapes
as heat. Cells do not use heat to do work. Thus, all the energy that
enters the world of life eventually leaves it, permanently.

2. Organisms Sense and Respond to Change

 Every living thing has the ability to respond and sense to conditions
both inside and outside of itself.

For example, after you eat, the sugars from your meal enter your
bloodstream. The added sugars set in motion a series of events that
cause cells throughout the body to take up sugar faster, so the sugar
level in your body quickly falls. This response keeps your blood sugar
level within a certain range, which in turn helps keep your cells alive
and your body functioning. Unless that internal environment (fluid in
your blood) is kept within certain ranges of composition, temperature,
and other conditions, your body cells will die.
Homeostasis is the name for this process, which is a state of balance.

3. Organisms use DNA

• Information encoded in the organism’s DNA (deoxyribonucleic acid)

guides the ongoing metabolic activities that sustain the individual
through its lifetime. Such activities include:
⮚ Growth – increase in cell number, size, and volume
⮚ Development- the process by which the first cell of a new individual
becomes a multicelled adult
⮚ Reproduction- processes by which parents produce offspring.

DNA is the basis of similarities in form and function among

organisms.

The Scientific Method

Critical thinking is the deliberate process of judging the quality of

information before accepting it.
Scientific method is a systematic study used in the sciences to make
observations, hypotheses, predictions, testing, and draw results and
conclusions. From the results and conclusions, another hypothesis can be
made. Hypothesis is a tentative answer to a query which can lead to
predictions that can be tested by observation or experimentation.

Key Terms
hypothesis
inductive reasoning
deductive reasoning
variables
independent/dependent variable

Learning Task:

1. What are some of the important applications of biology in the

engineering field? Cite at least two (2) examples.
2. Discuss briefly the meaning of biology “as a unified science of life”.
 Topic II – The Cell

Learning Objectives:
1. Identify and illustrate the different parts of the cell and describe their
specific functions.
2. Differentiate prokaryotic from eukaryotic cells.
3. Name the different forms of biological molecules and give their
importance in living organisms.

The Cell

A cell is the smallest unit of life. All biological systems are based on the
same organic molecules. Simple organic building blocks bonded in different
numbers and arrangements form different versions of the molecules of life.

Cells maintain reserves of small organic molecules that they can

assemble into complex carbohydrates, lipids, proteins, and nucleic acids.
When used as subunits of larger molecules, the small organic molecules
(simple sugars, fatty acids, amino acids, and nucleotides) are called
monomers. Molecules that consist of multiple monomers are called
polymers.

Cells build polymers from monomers, and break down polymers to

release monomers. Metabolism refers to activities by which cells acquire
and use energy as they make and break apart organic compounds. These
activities help cells stay alive, grow, and reproduce.

All organisms consist of the same kinds of molecules, but small

differences in the way those molecules are put together can have big
effects in a living organism. With this concept, we introduce you to the
chemistry of life.
 The human cell

Cell Structure and Function

A cell is the smallest unit that shows the properties of life. Cells vary
dramatically in shape and in function. However, all cells share certain
organizational and functional features. Every cell has a plasma
membrane, an outer membrane that separates the cell’s contents from its
environment. A plasma membrane is selectively permeable, which means it
allows only certain materials to cross. Thus, it controls exchanges between
the cell and its environments. All cell membranes, including the plasma
membrane, consist mainly of lipids.

The plasma membrane encloses a fluid or jellylike mixture of waters,

sugars, ions, and proteins called cytoplasm. Some or all of a cell’s
metabolism occurs in the cytoplasm, and the cell’s internal components,
including organelles, are suspended in it. Organelles are structures that
carry out special metabolic functions inside a cell.

All cells start out life with DNA. We categorize cells based on whether
their DNA is housed in a nucleus or not. Only eukaryotic cells have a
nucleus (plural, nuclei), an organelle with a double membrane that
contains the cell’s DNA. In most bacteria and archeans, the DNA is
suspended directly in the cytoplasm.

Eukaryotic Cells

All protists, fungi, plants, and animals are eukaryotes. By definition, a

eukaryotic cell starts out life with a nucleus (eu- means true; karyon means
nut, or kernel).

The main components of eukaryotic cells

All eukaryotic cells start life with a nucleus and other

membrane-enclosed organelles.

Eukaryotic Cells

• Domain Eukarya
• Protists
• Fungi
• Plants
• Animals
• Cells contain:
• Membrane-bound nucleus
• Specialized organelles
• Plasma membrane
The functions of plasma membrane include:

• selectively permeable and surrounds the cellular contents.

• regulates the passage of materials into and out of the cell.
• participates in intercellular communications.

The cytoplasm (cytosol) is the gelatinous material inside the cell

membrane but outside the nucleus.
 • The cytoplasm contains organelles which are sub-cellular structures
that perform discrete functions. True organelles are bounded by a
phospholipid membrane.
Organelles of a Typical Cell

Ribosome - production of proteins – located attached to ER or free-floating

- responsible for protein synthesis

Endoplasmic

Reticulum (ER) - Passageway for materials

*Rough - produces proteins & processes molecules for secretion

*Smooth - produces lipids & detoxifies drugs & stores Ca++

Golgi Apparatus - packages material for export & processes

macromolecules

Lysosome - contains digestive enzymes. Each contains one specific

enzyme.

Mitochondria - Aerobic cellular respiration:

C6H12O6 + 6O2 6CO2 + 6H2O +ATP

• The mitochondrion (plural, mitochondria) is a type of organelle that

specializes in making ATP.
• Aerobic respiration, an oxygen-requiring series of reactions that
proceeds inside mitochondria, can extract more energy from organic
compounds than any other metabolic pathway.
• With each breath, you are taking in oxygen mainly for mitochondria in
your trillions of aerobically respiring cells.

Cilia, flagella, microvilli - surface projections – increase surface area &

produce movement

Nucleus - is a double-membrane organelle containing the nucleic acids

(DNA) and at least one nucleolus (contains ribosomal RNA).
 - This organelle stores the genetic information and contains the
blueprints for almost all protein syntheses.
DNA - RNA - protein

Lysosomes, Peroxisomes, Vacuoles are Vesicles

Vesicles – small, membrane-enclosed, saclike organelle: store transport,

or degrade their contents.

Vacuole – a fluid-filled organelle that isolates or disposes of waste, or toxic

materials.

Lysosome – take part in intracellular digestion

- contain powerful enzymes that can break down

carbohydrates, lipids, proteins, and nucleic acids.

- Vesicles inside white blood cells deliver ingested

bacteria, cell parts, and other

debris to lysosomes for destruction.

Peroxisome- is an enzyme- filled vesicle that breaks down amino acids,

fatty acids, and toxic substances.

Organelles without membranes

• Ribosomes – assembling polypeptide chains; responsible for protein

synthesis
• Centriole – anchor for cytoskeleton

Other Component: The Cytoskeleton

-cytoskeleton contributes to cell shape, internal organization,

movement

-elements of the cytoskeleton reinforce, organize, and move cell

structures, and often the whole cell.
Biomolecules

Organic molecules (Carbohydrates)

The molecules of life are organic, which means they consist mainly of
carbon and hydrogen atoms.

❑ Carbohydrates- consist of carbon, hydrogen, and oxygen.

Carbohydrates are the most plentiful biological molecules.
❑ Three main types are monosaccharides, oligosaccharides, and
polysaccharides.
- Cells use some carbohydrates as:
a. structural materials

b. for fuel

c. to store or transport energy

Lipids

❑ Lipids are hydrophobic organic compounds

❑ Common lipids include triglycerides, phospholipids, waxes, and
steroids.
❑ Lipids are fatty, oily, or waxy organic compounds.
❑ Fatty acids, the main component of soap, has a hydrophobic tail and
a hydrophilic head.
❑ Fatty acids can be saturated or unsaturated.
saturated- have only single bonds in their tails.

unsaturated – tails have one or more double bonds.

Proteins

❑ Proteins are the most diverse biological molecule. All cellular

processes involve them.
❑ Cells build thousands of different types of proteins by stringing
together amino acids in different orders.
 ❑ Proteins are chains of amino acids. The order of amino acids in a
polypeptide chain dictates the type of protein.
❑ Polypeptide chains twist and fold into coils, sheets, and loops, which
fold and pack further into functional domains.
❑ A protein’s shape is the source of its function, therefore, changes in a
protein’s structure may also alter its function.

Nucleic acids

❑ Nucleotides are subunits of DNA and RNA. Some have roles in

metabolism.
❑ Nucleotides are small organic molecules that function as energy
carriers, enzyme helpers, and chemical messengers.
❑ Nucleotides are monomers of DNA and RNA, which are nucleic
acids.
❑ DNA’s nucleotide sequence encodes heritable information.

Learning Task:

1. Differentiate a eukaryotic cell from a prokaryotic cell.

2. Make a chart of the different parts of the cell and their function/s.
 Topic III – Cellular Energy Transformations

Learning Objectives:

1. Describe the processes important in living organisms.

2. Discuss the transformation and production of energy during
photosynthesis and respiration.

Green Energy

Plants have stored energy in chemical bonds. Autotrophs harvest

energy directly from the environment, and obtain carbon from inorganic
molecules (auto – means self; troph refers to nourishment). Plants and
most other autotrophs make their own food by photosynthesis, a process
in which they use the energy of sunlight to assemble carbohydrates from
carbon dioxide and water. Photosynthesis feeds most other life on Earth.
Animals and other heterotrophs get energy and carbon by breaking down
organic molecules assembled by other organism (hetero- means other).

A lot of energy is locked up in the chemical bonds of molecules made

by plants. That energy can fuel heterotrophs, as when animal cell powers
ATP synthesis by breaking the bonds of sugars. Oxygen is used to break
bonds and, in the process, produce carbon dioxide.

Plants convert light energy to chemical energy to use in driving

cellular work. The first step is capturing light.

In plants and algae, photosynthesis takes place in chloroplasts

If you examine a section of leaf tissue in a microscope, you see that

the green pigment, chlorophyll, is not uniformly distributed in the cell but is
confined to organelles called chloroplasts. In plants, chlorophyll lies
mainly inside the leaf in the cells of mesophyll, a layer with many air spaces
and a high concentration of water vapor.

Photosynthesis
The principal raw materials for photosynthesis are water and carbon
dioxide.
CO2 is obtained from the air by a plant’s leaves.
H2O is obtained from the damp soil by a plant’s roots.
Chloroplasts rearrange the atoms of these ingredients to produce
sugars (glucose) and other organic molecules.
O2 is a by-product of photosynthesis.

Aerobic and Anaerobic Pathways

Every organism must extract energy from the organic fuel molecules
that it manufactures (for example, when plants photosynthesize). These
fuel molecules are transported to all the cells of a multicellular organism,
where they are broken down to provide the energy for cellular work.

Within each plant cell, glucose and other fuel molecules are broken
down during cellular respiration, a series of chemical reactions that break
apart fuel molecules and transfer the energy stored in their bonds to
adenosine triphosphate (ATP) for use in cellular work.

Cells use three different catabolic pathways to extract energy from

fuel molecules: aerobic respiration, anaerobic respiration, and fermentation
(another type of anaerobic pathway). Cells that live in environments where
oxygen is plentiful use an aerobic pathway, one that requires O2. Cells that
inhabit waterlogged soil or polluted water where oxygen is absent must use
anaerobic pathways (either anaerobic respiration or fermentation) that do
not require O2.

There are a few different pathways that breakdown carbohydrates,

but aerobic respiration is the one that typical eukaryotic cells use at least
most of the time. Aerobic respiration is the process by which cells use
oxygen to break down organic molecules, with the release of energy that
can be used for biological work. The chemical reactions of aerobic
respiration are grouped into four stages: (1) glycolysis (2) Acetyl coenzyme
A formation (transition reaction) (3) the citric acid cycle (Krebs cycle) (4)
electron transport.

Aerobic respiration begins with the same reactions in the cytoplasm.

Glycolysis is the first stage of cellular respiration, in which glucose is split
into two molecules of pyruvate for a net yield of two ATP. The term
glycolysis is derived from two Greek words that, taken together, mean
“splitting sugar.” The reactions of glycolysis occur in the cytoplasm.

Glycolysis ends with the formation of two three-carbon pyruvate

molecules. These products may now enter the second stage reactions of
aerobic respiration. Two ATP were invested to initiate the reactions of
glycolysis. A total of four ATP form, so the net yield is two ATP per
molecule of glucose that enters glycolysis.

Pyruvate is converted to acetyl CoA

Pyruvate, the end product of glycolysis, contains most of the energy

that was present in the original glucose molecule. Pyruvate molecules
move into the mitochondrion, where all subsequent reactions of aerobic
respiration take place.

Pyruvate molecules move into the matrix of the mitochondrion, the

pyruvate is converted in a multistep, enzyme-controlled reaction to the
two-carbon compound acetyl CoA. In the first reaction, an enzyme splits
each molecule of pyruvate into one molecule of CO2 and a two-carbon
acetyl group. CO2 diffuses out of the cell. Then, the two-carbon fragment
remaining is oxidized; the hydrogens removed during this oxidation are
accepted by NAD+, forming NADH, the reduced form. Finally, the oxidized
fragment, an acetyl group, is attached to coenzyme A. The product of this
reaction is acetyl-CoA.

The citric acid cycle oxidizes acetyl CoA

The citric acid cycle is also known as the Krebs cycle after sir Hans
Krebs, a British biochemist who worked out the details of the pathway in
the 1930’s.

The citric acid cycle is the common pathway for the final oxidation
reactions of the cell’s fuel molecules with the carbons being released as
CO2. The citric acid cycle also takes place in the mitochondrion.

The first reaction of the citric acid cycle occurs when acetyl CoA
transfers its two-carbon acetyl group to the four-carbon compound
oxaloacetate, forming citrate, a six-carbon compound. In later reactions,
two CO2 form and depart the cell. Two NAD+ are reduced when they accept
hydrogen ions and electrons, so two NADH form. ATP forms by
substrate-level phosphorylation, and FAD and another NAD+ are reduced.
The final steps of the pathway regenerate oxaloacetate.

Electron Transfer Phosphorylation

The third and last stage of aerobic respiration, electron transfer

phosphorylation, also occurs in the mitochondria. Remember that electron
transfer phosphorylation is a process in which the flow of electrons through
electron transfer chains ultimately results in the attachment of phosphate to
ADP (adenosine diphosphate).

The third stage reactions take place at the inner mitochondrial

membrane. They begin with the coenzymes NADH and FADH2, which
became reduced in the in the first two stages of aerobic respiration. These
coenzymes donate their cargo of electrons and hydrogen ions to electron
transfer chains embedded in the inner mitochondrial membrane. As the
electrons pass through the chains, they give up energy little by little. Some
molecules of the transfer chains harness that energy to actively transport
hydrogen ions across the inner membrane, from the matrix to the
intermembrane space. The ions that accumulate in the intermembrane
space set up a hydrogen ion gradient across the inner mitochondrial
membrane.

H+ can cross the inner mitochondrial membrane by flowing through

the interior of ATP synthases. The flow causes these membrane transport
proteins to attach phosphate groups to ADP, so ATP forms. The coenzymes
that were reduced in the first two stages can drive the synthesis of about
thirty-two ATP in the third stage.

Oxygen accepts electrons at the end of the mitochondrial electron

transfer chains. Aerobic respiration, which literally means “taking a breath
of air,” refers to oxygen as the final electron acceptor in this pathway. When
oxygen accepts electrons, it combines with H+ to form water, which is one
product of the third stage. A typical net yield of aerobic respiration is 36
ATP per glucose.

Anaerobic Pathways

Prokaryotes and some other organisms that inhabit waterlogged soil

or stagnant ponds where oxygen is absent must engage in anaerobic
respiration. In anaerobic respiration, energy is released from glucose and
other fuel molecules without O2; that is, oxygen is not the final electron
acceptor in the electron transport chain.

Fermentation, another anaerobic pathway, also degrades glucose

and other organic molecules without oxygen. Like aerobic respiration,
fermentation depends on the reactions of glycolysis. The final acceptor of
hydrogen in fermentation is an organic molecule. Two common types of
fermentation are alcohol fermentation and lactate fermentation.

Yeasts (unicellular fungi) and certain plant cells carry out a type of
fermentation known as alcohol fermentation. First, they degrade glucose to
pyruvate through the process of glycolysis. When deprived of O2, these
cells split CO2 off from pyruvate, eventually forming ethyl alcohol.
Learning Task:
1. What are the products of Glycolysis?
2. What are the products of Krebs cycle?
3. What is the end product of Electron Transport System (Chain)?
Topic IV – Cell Reproduction and Genetics

Objectives:
1. Define the cell cycle and mitosis
2. Explain how cells divide
3. Describe the stages of mitosis and meiosis
4. Define homozygous and heterozygous
5. Describe dominant and recessive alleles

The Cell Cycle

The cell cycle is the period from the beginning of one division to the
beginning of the next division. It consists of two main phases, interphase
and M phase. Timing of the cell cycle varies widely from one cell type to
another and from one species to another, but in actively growing plant and
animal cells, it is usually about 8 to 20 hours.

M phase involves two main processes, mitosis and cytokinesis.

Mitosis is the division of the nucleus, and cytokinesis is the division of the
cytoplasm to form two cells. Mitosis is the division of the cell nucleus
resulting in two daughter nuclei, each with the same number of
chromosomes as the parent nucleus. Cytokinesis is the stage of cell
division in which the cytoplasm divides to form two daughter cells. Before a
eukaryotic cell divides by cytokinesis, its nucleus must undergo mitosis, a
process that precisely distributes complete sets of chromosomes to each
daughter nucleus. As a result of mitosis, each new cell contains the
identical number and types of chromosomes present in the original parent
cell.
 Interphase is the stage of the cell cycle between successive cell
divisions. A meristematic cell spends most of its life in interphase, a period
of active growth and maintenance that precedes mitosis. Interphase
(“between phases”) is so named because it occurs between the phases of
successive cell divisions. During interphase, the cell synthesizes needed
materials and grows. Chromosomes undergo duplication during interphase,
although the process is not readily visible. Then, during mitosis, they
condense into visibly separate structures and are distributed to the two
daughter nuclei.

Interphase is subdivided into three periods; G1, S, and G2. The first
period, G1, or the first gap phase, is the time between the end of the
previous cell division and the beginning of DNA replication. The cell grows
during the G1 phase, which is typically the longest phase. Cells that are not
actually dividing usually remain in this part of the cell cycle. Toward the end
of G1, the cell synthesizes certain enzymes used in DNA replication. These
activities make it possible for the cell to enter the S phase.

The second period of interphase, called the S phase or synthesis

phase, involves the replication of DNA. Other materials, such as proteins
that are components of chromosomes, are also synthesized at this time so
that the cell can make duplicate copies of its chromosomes.

Following the completion of the S phase, the cell enters a second

gap phase, or G2. At this time, increased protein synthesis occurs as the
cell prepares to divide. For many cells, the G2 phase is short relative to the
G1 and s phases. The beginning of mitosis marks the completion of the G2
phase. To summarize, here is the sequence of interphase and M phase in
the eukaryotic cell cycle:
 G1 phase – S phase – G2 phase (interphase) mitosis and
cytokinesis(M phase)

The completion of interphase is signaled by the beginning of mitosis,

in which visible changes associated with the division of the nucleus take
place. Most other cellular activities, such as protein synthesis, are
suspended during mitosis, which is a relatively brief period of the cell’s life.
Mitosis is a continuous process, but for descriptive purposes, it is divided
into four stages: Prophase, metaphase, anaphase, telophase.

● Duplicated chromosomes condense and become visible during

prophase
● During metaphase, duplicated chromosomes line up on the midplane
● Chromosomes move toward the poles during anaphase
● During telophase, two separate nuclei form
● Cytokinesis forms two daughter cells

Meiosis

Sexual reproduction mixes up the genes of two parents, so only

about half of each parent’s genetic information is passed to offspring. An
individual’s genes collectively contain the information necessary to make a
new individual.

The somatic (body) cells of multicelled organisms that reproduce

sexually contain pairs of chromosomes. Typically, one chromosome of each
pair is maternal and the other is paternal. The two chromosomes of every
pair carry the same set of genes. Different forms of the same gene are
called alleles.

What Meiosis Does

Sexual reproduction involves the fusion of reproductive cells from two

parents. It requires meiosis, a nuclear division mechanism that halves the
chromosome number. The process of sexual reproduction begins with
meiosis in germ cells, which are immature reproductive cells. Meiosis in
germ cells produces mature reproductive cells called gametes. A sperm is
an example of a male gamete. An egg is a female gamete.

Gametes have a single set of chromosomes, so they are haploid (n):

their chromosome number is half of the diploid (2n) number. Human body
cells are diploid, with 23 pairs of homologous chromosomes. Meiosis of a
human germ cell (2n) normally produces gametes with 23 chromosomes:
one of each pair (n). the diploid chromosome number is restored at
fertilization, when two haploid gametes (one egg and one sperm) fuse to
form a zygote, the first cell of a new individual.

The first part of meiosis is similar to mitosis. A cell duplicates its DNA
before either nuclear division process starts. As in mitosis, the microtubules
of a spindle move the duplicated chromosomes to opposite spindle poles.
However, meiosis sorts the chromosomes into new nuclei not once, but
twice, so it results in the formation of four haploid nuclei. The two
consecutive nuclear divisions are called meiosis I and meiosis II. In some
cells, no resting period occurs between these two stages. In others,
interphase with no DNA replication separates meiosis I and II.
 DNA replications occurs prior to meiosis, so a cell’s chromosomes
are duplicated by the time meiosis I begins: Each chromosome consists of
two sister chromatids. The nucleus is diploid (2n): It contains two sets of
chromosomes, one from each parent.

Meiosis I

The first stage of meiosis I is prophase I. During this phase, the

chromosomes condense, and homologous chromosomes align tightly and
swap segments. The centrosome gets duplicated along with its two
centrioles. One centriole pair moves to the opposite side of the cell as the
nuclear envelope breaks up. Spindle microtubules begin to extend from the
centrosomes.

By the end of prophase I, microtubules of the spindle connect the

chromosomes to the spindle poles. Each chromosome is now attached to
one spindle pole, and its homologous partner is attached to the other. The
microtubules lengthen and shorten, pushing and pulling the chromosomes
as they do. At metaphase I, all of the microtubules are the same length,
and the chromosomes are aligned midway between the poles of the
spindle.

In anaphase I, the spindle microtubules separate the homologous

chromosomes and pull them toward opposite spindle poles. During
telophase I, the chromosomes reach the spindle poles. New nuclear
envelopes form around the two clusters of chromosomes as the DNA
loosens up. Each of the two haploid (n) nuclei that form contains one set of
(duplicated) chromosomes. The cytoplasm may divide at this point to form
two haploid cells. Interphase occurs in some cells at the end of meiosis I,
but the DNA is not replicated before meiosis II begins.
Meiosis II

During prophase II, the chromosomes condense as a new spindle

forms. One centriole moves to the opposite side of each nucleus, and the
nuclear envelopes break up. By the end of prophase II, microtubules
connect the chromosomes to the spindle poles. Each chromatid is now
attached to one spindle pole, and its sister is attached to the other. The
microtubules lengthen and shorten, pushing and pulling the chromosomes
as they do. At metaphase II, all of the microtubules are the same length,
and the chromosomes are aligned midway between the spindle poles.

In anaphase II, the spindle microtubules pull the sister chromatids

apart. Each chromosome now consists of one molecule of DNA. During
telophase II, the chromosomes, (now unduplicated) reach the spindle
poles. New nuclear envelopes form around the four clusters of
chromosomes as the DNA loosens up. Each of the four haploid (n) nuclei
that form contains one set of unduplicated chromosomes. The cytoplasm
may divide, so four haploid cells form.

How Meiosis Introduces Variations in Traits

Duplicated chromosomes swap segments with their homologous

partners during prophase I. It also showed how each chromosome aligns
with and then separates from its homologous partner during anaphase I.
Both events introduce novel combinations of alleles into gametes. Along
with fertilization, these events contribute to the variation in combinations of
traits among the offspring of sexually reproducing species.

Crossing over in Prophase I

 Early in prophase I of meiosis, all chromosomes in a germ cell
condense. When they do, each is drawn close to its homologue. The
chromatids of one homologous chromosome become tightly aligned with
the chromatids of the other along their length. This tight, parallel orientation
favors crossing over, a process in which a chromosome and its
homologous partner exchange corresponding pieces of DNA. Homologous
chromosomes may swap any segment or segments of DNA along their
length, although crossovers tend to occur more frequently in certain
regions.

Swapping segments of DNA shuffles alleles between homologous

chromosomes. It breaks up the particular combinations of alleles that
occurred on the parental chromosomes and makes new ones on the
chromosomes that end up in gametes. Thus, crossing over introduces
novel combinations of traits among offspring.

Segregation of Chromosomes Into Gametes

Normally, all of the new nuclei that form in meiosis I receive the same
number of chromosomes. However, whether a new nucleus ends up with
the maternal and paternal version of a chromosome is entirely random. The
chance that the maternal or the paternal version of any chromosome will
end up in a particular nucleus is 50%.

The process of chromosome segregation begins in prophase I.

imagine one of your own germ cells undergoing meiosis. Just call the
twenty-three chromosomes you inherited from your mother the maternal
ones, and the twenty-three from your father the paternal ones.
 During prophase I, microtubules fasten your cell’s chromosomes to
the spindle poles. Chances are fairly slim that all of the maternal
chromosomes get attached to one pole and all of the paternal
chromosomes get attached to the other. Microtubules extending from a
spindle pole bind to the centromere of the first chromosome they contact,
regardless of whether it is maternal or paternal. Each homologous partner
gets attached to the opposite spindle pole. Thus, there is no pattern to the
attachment of the maternal or paternal chromosomes to a particular pole.

Inheritance in Modern Terms

DNA was not proven to be hereditary material until the 1950’s, but
Mendel discovered its units, which we now call genes, almost a century
before then. Today, we know that individuals of a species share certain
traits because their chromosomes carry the same genes. Offspring tend to
look like their parents because they inherited their parent’s genes.

The DNA sequence of each gene occurs at a specific location, or

locus (plural, loci), on a particular chromosome. The somatic cells of
humans and other animals are diploid, so they have pairs of genes, on
pairs of homologous chromosomes. In most cases, both genes of a pair are
expressed.

The two genes of a pair may be identical, or they may be slightly

different. Alternative forms of a gene are called alleles. An individual with
identical alleles of a gene is said to be homozygous for the allele. The
particular set of alleles that an individual carries is called genotype.
 Alleles are the major source of variation in a trait. New alleles arise by
mutation. A mutation may cause a trait to change, as when a gene that
causes flowers to be purple mutates so the resulting flowers are white.
Flower color is an example of phenotype, which refers to an individual’s
observable traits. Any mutated gene is an allele, whether or not it affects
phenotype.

The offspring of a cross, or mating, between individuals that breed for

different forms of a trait are hybrids. Hybrids carry different alleles of a
gene, so they are said to be heterozygous for the alleles. An allele is
dominant when its effect masks that of a recessive allele paired with it.
Usually, italic capital letters signify dominant alleles, and lowercase italic
letters signify recessive ones. Thus, a homozygous dominant individual
carries a pair of dominant alleles. A homozygous recessive individual
carries a pair of recessive alleles. A heterozygous, or hybrid, individual
carries a pair of nonidentical alleles.

Learning Task:

1. What is the difference between mitosis and meiosis?

2. Distinguish homozygous and heterozygous.

3. Differentiate a dominant and recessive allele.

 Topic V- Central Dogma of Molecular Biology

Learning Objectives:

1. Describe the flow of information involving the genetic material.

2. Explain how the genetic code is translated into a specific sequence of
amino acids
3. Enumerate the different structures of the protein
4. Enumerate the functions of proteins
5. Explain protein folding and misfolding

Control of gene expression is essential to all organisms. In bacteria, it

allows the cell to take advantage of changing environmental conditions. In
multicellular organisms, it is critical for directing development and
maintaining homeostasis.

One way to control transcription is to regulate the initiation of

transcription. In order for a gene to be transcribed, RNA polymerase must
have access to the DNA helix and must be capable of binding to the gene’s
promoter, a specific sequence of nucleotides at one end of the gene that
tells the polymerase where to begin transcribing. How is the initiation of
transcription regulated? Protein-binding nucleotide sequences on the DNA
regulate the initiation of transcription by modulating the ability of RNA
polymerase to bind to the promoter. These protein-binding sites are usually
only 10 to 15 nucleotides in length (even a large regulatory protein has a
“footprint,” or binding area, of only about 20 nucleotides). Hundreds of
these regulatory sequences have been characterized, and each provides a
binding site for a specific protein able to recognize the sequence. Binding
the protein to the regulatory sequence either blocks transcription by getting
in the way of RNA polymerase or stimulates transcription by facilitating the
binding of RNA polymerase to the promoter.
 The process by which a gene’s information is converted into the
structures and functions of a cell by a process of producing biologically
functional molecule of either protein or RNA is made is called gene
expression. Gene expression is assumed to be controlled at various points
in the sequence leading to protein synthesis. DNA in genes specify
information, but information is not structure and function. Genetic info is
expressed into structure & function through protein synthesis. DNA in gene
controls the sequence of nucleotides in an RNA molecule. RNA controls
the primary structure of a protein.

The process of gene expression involves two main stages:

Transcription: the production of messenger RNA (mRNA) by the

enzyme RNA polymerase, and the processing of the resulting mRNA
molecule.

Translation: the use of mRNA to direct protein synthesis, and the

subsequent posttranslational processing of the protein molecule.

Some genes are responsible for the production of other forms of RNA that
play a role in translation, including transfer RNA (tRNA) and ribosomal RNA
(rRNA).

A structural gene involves a number of different components:

Exons. Exons code for amino acids and collectively determine the amino
acid sequence of the protein product. It is these portions of the gene that
are represented in final mature mRNA molecule.

Introns. Introns are portions of the gene that do not code for amino acids
and are removed (spliced) from the mRNA molecule before translation.

Control regions Start site.

A start site for transcription.

 A promoter. A region a few hundred nucleotides 'upstream' of the gene
(toward the 5' end). It is not transcribed into mRNA but plays a role in
controlling the transcription of the gene. Transcription factors bind to
specific nucleotide sequences in the promoter region and assist in the
binding of RNA polymerases.

Enhancers. Some transcription factors (called activators) bind to regions

called 'enhancers' that increase the rate of transcription. These sites may
be thousands of nucleotides from the coding sequences or within an intron.
Some enhancers are conditional and only work in the presence of other
factors as well as transcription factors.

Silencers. Some transcription factors (called repressors) bind to regions

called 'silencers' that depress the rate of transcription.

Transcription

Transcription is the process of RNA synthesis, controlled by the

interaction of promoters and enhancers. Several different types of RNA are
produced, including messenger RNA (mRNA), which specifies the
sequence of amino acids in the protein product, plus transfer RNA (tRNA)
and ribosomal RNA (rRNA), which play a role in the translation process.

Transcription involves four steps:

Initiation. The DNA molecule unwinds and separates to form a small open
complex. RNA polymerase binds to the promoter of the template strand
(also known as the 'sense strand' or 'coding strand'). The synthesis of RNA
proceeds in a 5' to 3' direction, so the template strand must be 3' to 5'.

Elongation. RNA polymerase moves along the template strand,

synthesizing an mRNA molecule. In prokaryotes RNA polymerase is a
holoenzyme consisting of a number of subunits, including a sigma factor
(transcription factor) that recognizes the promoter. In eukaryotes there are
three RNA polymerases: I, II and III. The process includes a proofreading
mechanism.
Termination. In prokaryotes there are two ways in which transcription is
terminated. In dependent termination, a protein is responsible for disrupting
the complex involving the template strand, RNA polymerase and RNA
molecule. In independent termination, a loop forms at the end of the RNA
molecule, causing it to detach itself. Termination in eukaryotes is more
complicated, involving the addition of additional adenine nucleotides at the
3' of the RNA transcript (a process referred to as polyadenylation).

Processing. After transcription the RNA molecule is processed in a number

of ways: introns are removed, and the exons are spliced together to form a
mature mRNA molecule consisting of a single protein-coding sequence.
RNA synthesis involves the normal base pairing rules, but the base
thymine is replaced with the base uracil.

Translation

In translation the mature mRNA molecule is used as a template to

assemble a series of amino acids to produce a polypeptide with a specific
amino acid sequence. The complex in the cytoplasm at which this occurs is
called a ribosome. Ribosomes are a mixture of ribosomal proteins and
ribosomal RNA (rRNA) and consist of a large subunit and a small subunit.

Transcription involves four steps:

Initiation. The small subunit of the ribosome binds at the 5' end of the
mRNA molecule and moves in a 3' direction until it meets a start codon
(AUG). It then forms a complex with the large unit of the ribosome complex
and an initiation tRNA molecule.

Elongation. Subsequent codons on the mRNA molecule determine which

tRNA molecule linked to an amino acid binds to the mRNA. An enzyme
peptidyl transferase links the amino acids together using peptide bonds.
The process continues, producing a chain of amino acids as the ribosome
moves along the mRNA molecule.
Termination. Translation in terminated when the ribosomal complex
reached one or more stop codons (UAA, UAG, UGA).

The ribosomal complex in eukaryotes is larger and more complicated than

in prokaryotes. In addition, the processes of transcription and translation
are divided in eukaryotes between the nucleus (transcription) and the
cytoplasm (translation), which provides more opportunities for the
regulation of gene expression.

Proteins

Proteins are large, complex molecules that play many critical roles in the
body. They do most of the work in cells and are required for the structure,
function, and regulation of the body’s tissues and organs.

Proteins are made up of hundreds or thousands of smaller units called

amino acids, which are attached to one another in long chains.

There are 20 different types of amino acids that can be combined to make
a protein. The sequence of amino acids determines each protein’s unique
3-dimensional structure and its specific function. Amino acids are coded by
combinations of three DNA building blocks (nucleotides), determined by the
sequence of genes.
Protein Structure

Each successive level of protein folding ultimately contributes to its shape

and therefore its function.

The shape of a protein is critical to its function because it determines

whether the protein can interact with other molecules. Protein structures
are very complex, and researchers have only very recently been able to
easily and quickly determine the structure of complete proteins down to the
atomic level. (The techniques used date back to the 1950s, but until
recently they were very slow and laborious to use, so complete protein
structures were very slow to be solved.) Early structural biochemists
conceptually divided protein structures into four “levels” to make it easier to
get a handle on the complexity of the overall structures. To determine how
the protein gets its final shape or conformation, we need to understand
these four levels of protein structure: primary, secondary, tertiary, and
quaternary.

Primary Structure
A protein’s primary structure is the unique sequence of amino acids in each
polypeptide chain that makes up the protein. Really, this is just a list of
which amino acids appear in which order in a polypeptide chain, not really
a structure. But, because the final protein structure ultimately depends on
this sequence, this was called the primary structure of the polypeptide
chain. For example, the pancreatic hormone insulin has two polypeptide
chains, A and B.

The gene, or sequence of DNA, ultimately determines the unique sequence

of amino acids in each peptide chain. A change in nucleotide sequence of
the gene’s coding region may lead to a different amino acid being added to
the growing polypeptide chain, causing a change in protein structure and
therefore function.

Secondary Structure

A protein’s secondary structure is whatever regular structures arise from

interactions between neighboring or near-by amino acids as the
polypeptide starts to fold into its functional three-dimensional form.
Secondary structures arise as H bonds form between local groups of amino
acids in a region of the polypeptide chain. Rarely does a single secondary
structure extend throughout the polypeptide chain. It is usually just in a
section of the chain. The most common forms of secondary structure are
the α-helix and β-pleated sheet structures and they play an important
structural role in most globular and fibrous proteins.

Tertiary Structure

The tertiary structure of a polypeptide chain is its overall three-dimensional

shape, once all the secondary structure elements have folded together
among each other. Interactions between polar, nonpolar, acidic, and basic
R group within the polypeptide chain create the complex three-dimensional
tertiary structure of a protein. When protein folding takes place in the
aqueous environment of the body, the hydrophobic R groups of nonpolar
amino acids mostly lie in the interior of the protein, while the hydrophilic R
groups lie mostly on the outside. Cysteine side chains form disulfide
linkages in the presence of oxygen, the only covalent bond forming during
protein folding. All of these interactions, weak and strong, determine the
final three-dimensional shape of the protein. When a protein loses its
three-dimensional shape, it will no longer be functional.
Quaternary Structure

The quaternary structure of a protein is how its subunits are oriented and
arranged with respect to one another. As a result, quaternary structure only
applies to multi-subunit proteins; that is, proteins made from more than one
polypeptide chain. Proteins made from a single polypeptide will not have a
quaternary structure.

In proteins with more than one subunit, weak interactions between the
subunits help to stabilize the overall structure. Enzymes often play key
roles in bonding subunits to form the final, functioning protein.

Protein Folding

Each protein has its own unique sequence of amino acids and the
interactions between these amino acids create a specify shape. This shape
determines the protein’s function, from digesting protein in the stomach to
carrying oxygen in the blood.

Changing the Shape of a Protein

If the protein is subject to changes in temperature, pH, or exposure to
chemicals, the internal interactions between the protein’s amino acids can
be altered, which in turn may alter the shape of the protein. Although the
amino acid sequence (also known as the protein’s primary structure) does
not change, the protein’s shape may change so much that it becomes
dysfunctional, in which case the protein is considered denatured. Pepsin,
the enzyme that breaks down protein in the stomach, only operates at a
very low pH. At higher pHs pepsin’s conformation, the way its polypeptide
chain is folded up in three dimensions, begins to change. The stomach
maintains a very low pH to ensure that pepsin continues to digest protein
and does not denature.
Enzymes
Because almost all biochemical reactions require enzymes, and because
almost all enzymes only work optimally within relatively narrow temperature
and pH ranges, many homeostatic mechanisms regulate appropriate
temperatures and pH so that the enzymes can maintain the shape of their
active site.
Reversing Denaturation
It is often possible to reverse denaturation because the primary structure of
the polypeptide, the covalent bonds holding the amino acids in their correct
sequence, is intact. Once the denaturing agent is removed, the original
interactions between amino acids return the protein to its original
conformation and it can resume its function.
However, denaturation can be irreversible in extreme situations, like frying
an egg. The heat from a pan denatures the albumin protein in the liquid egg
white and it becomes insoluble. The protein in meat also denatures and
becomes firm when cooked.
Chaperone proteins (or chaperonins ) are helper proteins that provide
favorable conditions for protein folding to take place. The chaperonins
clump around the forming protein and prevent other polypeptide chains
from aggregating. Once the target protein folds, the chaperonins
disassociate.

Learning Task:

1. Answer the Central Dogma worksheet provided.

 Topic VI – DNA Repair, Recombination and Transposition

Learning Objectives:

1. Understand the different type of DNA repair mechanisms

2. Explain why DNA repair is critical for cells.
3. Understand the process by which cells undergo recombination
4. Discuss the concepts of transposition and movement of specific
species of DNA in the genome.

DNA Repair

DNA repair, any of several mechanisms by which a cell maintains

the integrity of its genetic code. DNA repair ensures the survival of a
species by enabling parental DNA to be inherited as faithfully as
possible by offspring. It also preserves the health of an
individual. Mutations in the genetic code can lead to cancer and other
genetic diseases.
There are three types of repair mechanisms: direct reversal of the
damage, excision repair, and postreplication repair. Direct reversal repair
is specific to the damage. For example, in a process called
photoreactivation, pyrimidine bases fused by UV light are separated by
DNA photolyase (a light-driven enzyme). For direct reversal of alkylation
events, a DNA methyltransferase or DNA glycosylase detects and
removes the alkyl group. Excision repair can be specific or nonspecific.
In base excision repair, DNA glycosylases specifically identify and
remove the mismatched base. In nucleotide excision repair, the repair
machinery recognizes a wide array of distortions in the double helix
caused by mismatched bases; in this form of repair, the entire distorted
region is excised. Postreplication repair occurs downstream of the
lesion, because replication is blocked at the actual site of damage. In
order for replication to occur, short segments of DNA called Okazaki
fragments are synthesized. The gap left at the damaged site is filled in
through recombination repair, which uses the sequence from an
undamaged sister chromosome to repair the damaged one, or through
error-prone repair, which uses the damaged strand as a sequence
template. Error-prone repair tends to be inaccurate and subject to
mutation.

Often when DNA is damaged, the cell chooses to replicate over the
lesion instead of waiting for repair. Although this may lead to mutations,
it is preferable to a complete halt in DNA replication, which leads to cell
death.

DNA Recombination

DNA recombination involves the exchange of genetic material either

between multiple chromosomes or between different regions of the
same chromosome. This process is generally mediated by homology;
that is, homologous regions of chromosomes line up in preparation for
exchange, and some degree of sequence identity is required. Various
cases of nonhomologous recombination do exist, however.
One important instance of recombination in diploid eukaryotic organisms
is the exchange of genetic information between newly duplicated
chromosomes during the process of meiosis. In this instance, the
outcome of recombination is to ensure that each gamete includes both
maternally and paternally derived genetic information, such that the
resulting offspring will inherit genes from all four of its grandparents,
thereby acquiring a maximum amount of genetic diversity.
Recombination is also used in DNA repair (particularly in the repair of
double-stranded breaks), as well as during DNA replication to assist in
filling gaps and preventing stalling of the replication fork. In these cases,
a sister chromatid serves as the donor of missing material via
recombination followed by DNA synthesis.

DNA Transposition

Genomes are highly stable in a global sense. That is the relative

organization or order of genes of a bacterium (E. coli, for example) or
that within a eukaryotic chromosome remains the same whether one
maps them today or tomorrow or a few months from now. However,
within this background of global stability, there are local DNA changes
going on constantly. Some of these changes have evolutionary
advantages and can ultimately get fixed in the genome.

DNA transposition is carried out by elements that can move from one
locale to another within a genome or between genomes. Such elements
are called transposons. Their movement is mediated by enzymes called
transposases. Transposases recognize the specific end sequences that
define the limits of a transposable element and facilitate its movements
by cutting DNA these DNA ends (donor sites) and joining them to a
target (or recipient) DNA site. Although the donor sites are specific,
recognized by a particular transposase, the target sites are quite
non‐specific (except in a few rare instances). Thus, these elements can
end up in a variety of locations on the genome.

DNA transposons move from one genomic location to another by a

cut-and-paste mechanism. They are powerful forces of genetic change
and have played a significant role in the evolution of many genomes. As
genetic tools, DNA transposons can be used to introduce a piece of
foreign DNA into a genome. Thus, DNA transposons are useful tools to
analyze the regulatory genome, study embryonic development, identify
 genes and pathways implicated in disease or pathogenesis of
pathogens, and even contribute to gene therapy.

Learning Task:

1. What is the importance of DNA repair to cells?

2. What is the significance of DNA recombination?

Topic VII – Biodiversity

Learning objectives:

1. Describe plant growth and how plants obtain nutrition.

2. Discuss the processes of photosynthesis and nitrogen fixation.
3. Correlate the different composition of the biological systems to their
corresponding functions.
4. Enumerate the different types of microorganisms of medical and
economic importance.
5. Discuss control of microorganisms.

Plant Systems
For billions of years, almost all life in the biosphere has run on solar energy.
Of all organisms, however, only plants, algae, and certain prokaryotes are
capable of absorbing and converting light energy from the sun to chemical
energy through the process of photosynthesis. The end products of
photosynthesis are carbohydrates (formed from the simple raw materials
water and carbon dioxide and oxygen O2).

Plants are of central importance to life. Animals, humans, depend on

plants for food, which provides energy, and for oxygen.

Visible light is the energy that drives photosynthesis. Light makes up

a small portion of the electromagnetic spectrum, which is a vast,
continuous range of electromagnetic radiations propagated through space
and matter. All radiations in the electromagnetic spectrum behave as
though they travel in waves. A wavelength is the distance from one wave
peak to the next. At one end of the spectrum are gamma rays with
extremely short wavelengths, measured in nanometers. At the other end of
the spectrum are radio waves with wavelengths so long that they are
measured in full meters.

The portion of the electromagnetic spectrum from 380 and 760

nanometers is called the visible spectrum because humans can see it. The
visible spectrum includes all the colors of the rainbow. Ultraviolet radiation
(UV), which is invisible to the human eye, has a shorter range of
wavelengths than visible light, and infrared (IR) radiation, also invisible, has
a longer range.

Light is composed of small particles, or packets, of energy called

photons. The amount of energy in a photon depends on the wavelength of
light. The shorter the wavelength is, the more energy there is per photon;
the longer the wavelength, the less energy per photon. Thus, the energy of
a photon is inversely proportional to its wavelength.

Photosynthesis depends on visible light rather than some other

wavelength of radiation. The reason may be that most of the radiation
reaching our planet from the sun is within this portion of the
electromagnetic spectrum. Only radiation in the visible-light portion of the
spectrum excites certain types of biological molecules, causing their
reaction to jump into higher energy levels. Wavelengths of radiation that are
longer than visible light (microwaves, television waves, and radio waves)
do not possess enough energy to excite biological molecules. Wavelengths
shorter than visible light (ultraviolet radiation, X-rays, gamma rays) possess
so much energy that they disrupt biological molecules by breaking chemical
bonds.

In plants and algae, photosynthesis takes place in chloroplasts

If you examine a section of leaf tissue in a microscope, you see that

the green pigment, chlorophyll, is not uniformly distributed in the cell but is
confined to organelles called chloroplasts. In plants, chlorophyll lies
mainly inside the leaf in the cells of mesophyll, a layer with many air spaces
and a high concentration of water vapor. The interior of the leaf exchanges
gases with the outside through microscopic pores called stomata (sing.,
stoma). Each mesophyll cell has 20 to 100 chloroplasts.

The chloroplast is enclosed by outer and inner membranes. The inner

membrane encloses a fluid-filled region, the stroma, which contains most
of the enzymes required to produce carbohydrate molecules. Suspended in
the stroma is a third system of membranes that forms an interconnected
set of flat, disclike sacs called thylakoids. The thylakoid membrane
encloses a fluid-filled interior space, the thylakoid lumen. In some regions
of the chloroplast, thylakoid sacs are arranged in stacks called grana (sin.,
granum). Each granum looks something like a stack of coins, with each
“coin” being a thylakoid.

Thylakoid membranes contain several kinds of pigments, which are

substances that absorb visible light. Different pigments absorb different
wavelengths. Chlorophyll, the main pigment of photosynthesis, absorbs
light primarily in the blue and red regions of the visible spectrum. Green
light is not appreciably absorbed by chlorophyll. Plants usually appear
green because some of the green light that strikes them is scattered or
reflected to your eyes.

There are several kinds of chlorophyll. The most important is

chlorophyll a, the pigment that initiates photosynthesis. Chlorophyll b is an
accessory pigment that also participates in photosynthesis. It differs slightly
from the structure of the chlorophyll a molecule. This difference shifts the
wavelengths of light absorbed and reflected by chlorophyll b, making it
appear yellow-green, whereas chlorophyll a appears bright green.

Plants and algae also have accessory photosynthetic pigments, such

as carotenoids, which are yellow and orange. Carotenoids absorb
wavelengths of light different from those absorbed by chlorophyll, thereby
expanding the spectrum of light that provides energy for photosynthesis.
The large quantity of chlorophyll in most leaves usually masks the
presence of carotenoids in spring and summer; in autumn, when the
chlorophyll breaks down, other pigments, including carotenoids, become
visible.

Chlorophyll may be energized by light directly (by energy from the

light source) or indirectly (by energy passed by the accessory pigments that
have become energized by light). When a carotenoid molecule is
energized, its energy can be transferred to chlorophyll a. Carotenoids also
protect chlorophyll and other parts of the thylakoid membrane from excess
light energy that could easily damage the photosynthetic components.

The principal raw materials for photosynthesis are water and carbon
dioxide. The reactions of photosynthesis occur in two stages: the
light-dependent reactions (the photo part of photosynthesis) and the carbon
fixation reactions (the synthesis part of photosynthesis). Each set of the
reactions occur in the different part of the chloroplast.

Nitrogen fixation

Certain nitrogen-fixing bacteria, collectively called rhizobia, form

associations with the roots of leguminous plants – clover, peas, and
soybeans, for example. Swellings called nodules develop on the roots and
house millions of the rhizobia. The association between nitrogen-fixing
bacteria and the root of plants is mutually beneficial. The bacteria receive
the products of photosynthesis from the plants while helping the plant meet
its nitrogen requirements by producing ammonia from atmospheric
nitrogen. Because nitrogen is an essential part of biologically important
molecules such as proteins and nucleic acids, organisms – plants included
– must have nitrogen to survive.

Animal Systems

Organs and systems of the body

The body is made up of many, many millions of cells which you can not see
unless you use a microscope. Special cells come together to make an
organ.
An organ is a complex structure within the body. It has a special job or jobs
to do.
A body system consists of a number of organs which work together to carry
out a special job.
The animal body is made of 9 systems:
Musculo-skeletal system
Digestive system
Circulatory system
Respiratory system
Urinary system
Nervous system
Sensory system
Reproductive system
Lympho-reticular system
The organs of the body
An organ is a complex structure with a special job or a number of jobs to
do. For example:
· The eye is the organ of sight.
· The kidneys are organs which get rid of water and poisonous materials
from the body as urine.
· The liver has many jobs and is involved in more than one system.

Various organs are grouped together to form a body system which carries
out a special job.
System of the Organs in the Body Job or function
Body
Musculo-skeletal muscle (meat) bones Support and move the body
Digestive stomach, liver, intestine, Digest and absorb feed
pancreas
Circulatory heart, blood vessels The blood carries substances
around the body
Respiratory muzzle, windpipe, lungs Breathing
Urinary kidneys, bladder Get rid of poisons and waste
(urine)
Nervous brain, nerves spinal cord Pass messages around the
body, control the body
Sensory eyes, ears, nose skin Sense and detect things
outside the body
Reproductive testes, penis ovaries, To produce and feed young
uterus, vagina, vulva, udder
Lympho-reticular lymph nodes, spleen Protect against infectious
diseases, produce blood
The musculo-skeletal system
This system consists of the bones and the muscles (meat).The bones form
the skeleton which is the framework within the body. It carries weight and
supports the body.
Bones are connected together so they can move. The places where this
happens are called joints. The bones are held together at the joints by
elastic strands called ligaments. Between the bones is a softer material
called cartilage (gristle) which cushions the bones at the joints when the
body moves. Bones are very hard and contain minerals. Each bone has a
name such as the scapula (shoulder blade) and skull (head). There are
about 200 bones in the body.
Muscles are joined at both ends to the bones. The muscles are the meat of
the body and when they contract (shorten) or relax (lengthen) they make
the bones move.
If you bend your arm you can see and feel the muscles in your arm
working.
The digestive system
The digestive system consists of the teeth, mouth, gullet (oesophagus),
stomach, liver, intestine, pancreas, and rectum.
Digestion begins in the mouth where feed is broken down into small pieces
by the teeth and mixed with saliva before being swallowed.
In the stomach feed is mixed with the juices to form a soft paste. This then
passes into the intestine where bile from the liver and juices from the
pancreas are added. The action of these juices is to break down the feed
and allow the nourishment it contains to be absorbed by the blood in the
walls of the intestine. Waste matter collects in the rectum and passes out of
the body through the anus (or cloaca in birds).
The circulatory system and blood
The organs of the circulatory system are the heart and the blood vessels
(tubes). The heart is found in the chest cavity. It is a muscular pump which
sends blood around the body.
The blood vessels which carry blood away from the heart are called
arteries. Blood returns to the heart in veins. Joining the arteries and veins is
a fine network of small tubes called capillaries. The capillaries pass through
every part of the body.
When the heart beats its muscles contract and sends blood out through the
arteries. When the heart relaxes blood flows into it from the veins.
Every time the heart beats it sends a pulse along the arteries. You can feel
it at certain points on the body. By feeling the pulse we can count the rate
at which the heart beats. You can feel your pulse on your wrist.
The respiratory system
Respiration (breathing) consists of inspiration (breathing in) and expiration
(breathing out).
There are two lungs which are found in the chest protected by the bony
cage of the ribs. The windpipe carries air from the nostrils to the lungs
which are spongy because of air spaces in them. As the animal breathes,
air moves in and out of the lungs. Inside the lungs oxygen needed by the
body passes into the blood in the walls of the lungs and water and carbon
dioxide pass out of the blood into the air which is then breathed out.

The respiratory system

The urinary system

The main organs are the two kidneys, which lie against the backbone, and
the bladder.
Waste materials and water are taken out of the blood in the kidneys. This
forms urine. Urine collects in the bladder then passes out of the body.
Nervous system and sensory system
The bones of the skull and backbone protect the soft brain and spinal cord.
Fibres called nerves pass from the brain and spinal cord to all parts of the
body.
Messages pass from the various parts of the body along the nerves to the
brain. The brain sends a message back telling the different parts of the
body what to do.
The brain controls the body.

Nervous system

The brain also controls the senses, the sense organs are:
· the eyes for sight
· the ears for hearing
· the nose for smell
· the tongue for taste
· the skin for touch

Reproductive system (breeding)

The male reproductive organs, the testicles, lie in the scrotum behind the
penis. The testicles produce sperm which are contained in the fluid semen.
A tube passes from each testicle and joins to form a tube which runs down
the centre of the penis.
In the bird the testicles are inside the body.

Reproductive and urinary organs of the male

The female reproductive organ consist of two ovaries, one in each side of
the lower abdomen. The ovaries produce eggs which pass into the uterus
(or womb). Below the uterus is the vagina which opens to the outside
surrounded by the vulva. After birth the young are fed on milk produced by
the udder.

Female reproductive and urinary system

During mating (mounting) sperm passes from the male into the uterus and
joins with the eggs there. When the sperm joins the egg it forms the
embryo which develops into the young animal inside the uterus.
Reproduction is controlled by hormones (chemical messengers) which are
carried in the blood to the different organs.
These hormones control:
· Puberty of the animal
· Production of eggs
· Birth
· Production of semen
· Development of the embryo
· Milk production
Lympho-reticular system
Lymph is a colorless fluid which passes out of the blood into a network of
fine tubes called the lymphatic system. It passes through the lymph nodes,
where germs are filtered out and killed before it is returned to the veins.
The lymph nodes and spleen also produce special blood cells which protect
the body against disease. Sometimes when an animal is infected the lymph
nodes become swollen and can be felt beneath the skin.
Microbial Systems

Economic uses and benefits of microorganisms

 Microorganisms have been used as tools for the production of
products for millennia. Even in ancient times, the ability to produce vinegar
by allowing water to percolate through wood shavings was known and
widely practiced. Likewise, the transformation of a yeast suspension into
beer or a suspension of crushed grapes into wine was common knowledge.
The basis of these events may not have been known, but that did not
impede the sale or trade of such products.

These economic uses of microorganisms are the earliest examples

of biotechnology. As the knowledge of bacteria and yeast-chemical
behaviors grew, other biotechnological uses for the microbes were found. A
few examples include the use of the bacterium Lactobacillus acidophilus to
produce yogurt, the exploitation of a number of different bacteria to produce
a variety of cheeses, and the fermentation of cabbage to produce
sauerkraut. In the agricultural sector, the discovery of the ability
of Rhizobium spp. to convert elemental nitrogen to a form that was useable
by a growing plant, led to the use of the microorganism as a living fertilizer
that grew in association with the plant species.

In more modern times, the use of microorganisms as biotechnological

agents of profit has not only continued but has explosively increased.
Indeed the biotechnology sector as it is recognized today, is already a
multi-billion dollar sector worldwide.

The unraveling of the structure of DNA (deoxyribonucleic acid),

various species of ribonucleic acid (RNA), and the various processes
whereby the manufacture of protein from the nucleic acid templates occurs
was pivotal in advancing the use of microorganisms as factories. As
important was the discovery of how to remove DNA from one region of the
genome and move the DNA in a controlled way to another region of the
same DNA, or DNA in a completely different organism (prokaryotic or
eukaryotic). These gene splicing technologies, which can be accomplished
by various splicing and reannealing enzymes, or by the use of viruses or
mobile regions of viral DNA (such as transposons) as vectors have
allowed biotechnologists to create what are termed "designer genes,"
which are designed for a specific purpose. This ability has fueled the use of
microorganisms for economic gain and/or benefit.

The gene for the production of human insulin has been transferred
into the genome of the common intestinal tract bacterium Escherichia
coli . Successful expression and excretion of human insulin by the bacteria
allows the production of a large amount of insulin. Additionally, because the
insulin is identical to that produced in a human being, the chance of
immune reaction against the protein is virtually nonexistent. The example of
insulin reflects both the health benefit of the use of microbes and the
economic benefit to be realized, since the mass production of insulin that is
possible using bacteria lowers the cost of the product.

Other medical uses of microorganisms, particularly in the production

of antibiotics, have been the greatest boon to humans and other animals.
The list of maladies that can now be treated using microbiologically derived
compounds is lengthy, and includes cystic fibrosis, hemophilia, hepatitis B,
Karposi's sarcoma, rejection of transplanted organs, growth
hormone deficiency, and cancer. The worldwide sales of medical and
pharmaceutical drugs of microbial origin now exceeds U.S. $13 billion
annually.

Microorganisms have also been harnessed as factories to produce

compounds that are used in areas as divers as textile manufacture,
agriculture, and nutrition. Enzymes discovered in bacteria that can exist at
very elevated temperatures (thermophilic, or "heat loving" bacteria) can be
used to age denim to produce a "pre-washed" look. Similar enzymes are
being exploited in laundry detergent that operates in hot water.
Microorganisms are used to enhance the nutritional content of plants and
other food sources. The growing nutraceutical sector relies in part on the
nutritional enhancements afforded by microbes. Bacteria are also useful in
providing a degree of resistance to plants. An example is the use
of Bacillus thuringensis to supply a protein that is lethal to insect when they
consume it. The use of bacterial insecticides has reduced the use of
chemical insecticides, which is both a cost savings to the producer and less
stressful on the environment. Other bacterial enzymes and constituents of
the organisms are utilized to produce materials such as plastic.

A process known as DNA fingerprinting, which relies upon enzymes

that are produced and operate in bacteria, has enabled the tracing of the
fate of genes in plant and animal populations, and enhanced gathering of
evidence at crime scenes.

The mode of growth of bacterial populations has also proved to be

exploitable as a production tool. A prime example is the surface-adherent
mode of bacterial growth that is termed a biofilm. Although not known at
the time, the production of vinegar hundreds of years ago was, as now,
based on the percolation of water through biofilms growing on wood
shavings. Immobilized bacteria can produce all manner of compounds. As
well, the cells can provide a physical barrier to the flow of fluid. This
dynamic aspect has been utilized in a so far small-scale way to increase
the production of oil from fields oil thought to be depleted. Bacteria can plug
up the zones were water and oil flows most easily. Subsequent pumping of
water through the field forces the oil still resident in lower permeability
areas to the surface.

Control of Microorganisms

Control of microorganisms is essential in order to prevent the

transmission of diseases and infection, stop decomposition and spoilage,
and prevent unwanted microbial contamination. Microorganisms are
controlled by means of physical agents and chemical agents. Physical
agents include such methods of control as high or low temperature,
desiccation, osmotic pressure, radiation, and filtration. Control by chemical
agents refers to the use of disinfectants, antiseptics, antibiotics, and
chemotherapeutic antimicrobial chemicals.
The basis of chemotherapeutic control of bacteria is selective toxicity.
Selective toxicity means that the chemical being used should inhibit or kill
the intended pathogen without seriously harming the host. A broad
spectrum agent is one generally effective against a variety of Gram-positive
and Gram-negative bacteria; a narrow spectrum agent generally works
against just Gram-positives, Gram-negatives, or only a few bacteria. As
mentioned above, such agents may be cidal or static in their action. A cidal
agent kills the organism while a static agent inhibits the organism's growth
long enough for body defenses to remove it.
There are two categories of antimicrobial chemotherapeutic agents:
antibiotics and synthetic drugs. Antibiotics are metabolic products of one
microorganism that inhibit or kill other microorganisms. Chemotherapeutic
synthetic drugs are antimicrobial drugs synthesized by chemical
procedures in the laboratory. Many of today's antibiotics are now actually
semi-synthetic and some are even made synthetically.
Antibiotics are metabolic products of one microorganism that inhibit or kill
other microorganisms. Why then do bacteria produce antibiotics? There is
growing support for multiple actions for microbial antibiotic production:
 ● If produced in large enough amounts, antibiotics may be used as a
weapon to inhibit or kill other microbes in the vicinity to reduce
competition for food.
● Antibiotics produced in sublethal quantities may function as
interspecies quorum sensing molecules enabling a number of
different bacteria to form within a common biofilm where metabolic
end products of one organism may serve as a substrate for another.
All the organisms are protected within the same biofilm.
● Antibiotics produced in sublethal quantities may function as
interspecies quorum sensing molecules enabling some bacteria to
manipulate others to become motile and swim away thus reducing
the competition for food.
● Antibiotics action may result in the degradation of bacterial cell walls
or DNA and these products can act as cues that trigger other bacteria
to produce a protective biofilm.
● Antibiotics produced in sublethal quantities may trigger intraspecies
quorum sensing. Exposure to low concentrations of an antibiotic may
trigger bacteria to produce quorum sensing molecules that trigger the
population to produce a protective biofilm. The biofilm then protects
the population from greater concentrations of the antibiotic.

Learning Task:

1. What happens when one organ of the body fails to function? What could
be the effects to other parts of the body?

2. Give an example of a microorganism and discuss its economic and

medical importance.
 Topic VIII – Biotechnology

Learning Objectives:

1. Discuss and define biotechnology.

2. Compare and contrast biotechnology and genetic engineering.
3. Discuss recombinant technology and its use and principles.
4. Explain the principles of the polymerase chain reaction and its
importance in Biotechnology.
5. List uses of biotechnology in the fields of medicine, environment,
food, plant and animal science.
6. Discuss the mechanism of the development of these biotechnology
products.

Biotechnology and Genetic Engineering

In the early 1990s, an emerging disease was destroying Hawaii’s

production of papaya and threatening to decimate the $11 million industry.
Fortunately, a man named Dennis Gonsalves, who was raised on a sugar
plantation and then became a plant physiologist at Cornell University, would
develop papaya plants genetically engineered to resist the deadly virus. By
the end of the decade, the Hawaiian papaya industry and the livelihoods of
many farmers were saved thanks to the free distribution of Dr. Gonsalves
seeds.

The symptoms of papaya ringspot virus are shown on the tree (a) and fruit (b). “This work” is in
the Public Domain, CC0.

The development of a new strain of crop is an example of agricultural

biotechnology: a range of tools that include both traditional breeding
techniques and more modern lab-based methods. Traditional methods date
back thousands of years, whereas biotechnology uses the tools of genetic
engineering developed over the last few decades. Genetic engineering is
the name for the methods that scientists use to introduce new traits to an
organism. This process results in genetically modified organisms, or GMO.
For example, plants may be genetically engineered to produce
characteristics to enhance the growth or nutritional profile of food
crops. GMO that are crop species are commonly called genetically
engineered crops, or GE crops for short.
Biotechnology would not be possible without genetic engineering. In
modern terms, this process manipulates cells’ genetic information using
laboratory techniques in order to change the traits of living organisms.
Scientists may use genetic engineering in order to change the way an
organism looks, behaves, functions, or interacts with specific materials or
stimuli in its environment. Genetic engineering is possible in all living cells;
this includes micro-organisms such as bacteria and individual cells of
multicellular organisms, such as plants and animals. Even the human
genome can be edited using these techniques.
 Sometimes, scientists alter genetic information in a cell by directly
altering its genes. In other cases, pieces of DNA from one organism are
implanted into the cells of another organism. The new hybrid cells are
called transgenic.

Nearly all the fruits and vegetables found in your local market would
not occur naturally. In fact, they exist only because of human intervention
that began thousands of years ago. Humans created the vast majority of
crop species by using traditional breeding practices on naturally-occurring,
wild plants. These practices rely upon selective breeding (human
assisted-breeding of individuals with desirable traits). Traditional breeding
practices, although low-tech and simple to perform, have the practical
outcome of modifying an organism’s genetic information, thus producing
new traits.

An interesting example is maize (corn). Biologists have discovered

that maize was developed from a wild plant called teosinte. Through
traditional breeding practices, humans living thousands of years ago in
what is now Southern Mexico began selecting for desirable traits until they
were able to transform the plant into what is now known as maize. In doing
so, they permanently (and unknowingly) altered its genetic instructions,
allowing for new traits to emerge. Considering this history, we might ask the
question: is there really such a thing as “non-GMO” maize?

A wild grass called teosinte was genetically modified through selective breeding to produce what
is now known as maize (corn). This process of transformation started thousands of years ago by
indigenous people of what is now Mexico. “This work” by Nicolle Rager Fuller, National Science
Foundation is in the Public Domain, CC0.
 This history of genetic modification is common to nearly all crop
species. For example, cabbage, broccoli, Brussel sprouts, cauliflower, and
kale were all developed from a single species of wild mustard plant. Wild
nightshade was the source of tomatoes, eggplant, tobacco, and potatoes,
the latter developed by humans 7,000 – 10,000 years ago in South
America.

Traditional Breeding v. Modern Genetic Engineering

To produce new traits in livestock, pets, crops, or other type of

organism, there almost always has to be an underlying change in that
organism’s genetic instructions. What many people might not understand is
that traditional breeding practices do, in fact, result in permanent genetic
changes and is therefore a type of genetic modification. This
misunderstanding may arise because traditional breeding practices do not
require sophisticated laboratory equipment or any knowledge of genetics,
which some may see as a prerequisite for genetic modification.

How do traditional breeding practices compare to modern genetic

engineering? Both result in changes to an organism’s genetic information,
but the magnitude of those changes varies amongst the two techniques.
Traditional breeding shuffles all of the genes between the two organisms
being bred, which can number into the tens of thousands (maize, for
example, has 32,000 genes). When mixing such a large number of genes,
the results can be unpredictable. Modern genetic engineering is more
precise in the sense that biologists can modify just a single gene. Also,
genetic engineering can introduce a gene between two distantly-related
species, such as inserting a bacterial gene into a plant. Such transfer might
seem unusual, but it is not without its equivalent in nature. In a process
called horizontal gene transfer, DNA from one species can be inserted into
a different species. One recent study, for example, has found that humans
contain about 150 genes from other species, including bacteria.
Both traditional breeding and modern genetic engineering produce genetic
modifications. Genetic engineering allows for fewer and more precise genetic
modifications. FDA graphic by Michael J. Ermarth (Methods of Plant Breeding) [CC0
Public Domain], via Wikimedia Commons.

Potential Benefits of Genetic Engineering

Enhanced nutrition

White rice and Golden rice. Genetically engineered

“Golden Rice” contains up to 35 μg β-carotene per gram of rice, which could prevent millions of cases of
blindness worldwide.
Advances in biotechnology may provide consumers with foods that are
nutritionally-enriched, longer-lasting, or that contain lower levels of certain
naturally occurring toxins present in some food plants. For example,
developers are using biotechnology to try to reduce saturated fats in
cooking oils, reduce allergens in foods, and increase disease-fighting
nutrients in foods. Biotechnology may also be used to conserve natural
resources, enable animals to more effectively use nutrients present in feed,
decrease nutrient runoff into rivers and bays, and help meet the increasing
world food and land demands.

Cheaper and More Manageable Production

Biotechnology may provide farmers with tools that can make production
cheaper and more manageable. For example, some biotechnology crops
can be engineered to tolerate specific herbicides, which make weed control
simpler and more efficient. Other crops have been engineered to be
resistant to specific plant diseases and insect pests, which can make pest
control more reliable and effective, and/or can decrease the use of
synthetic pesticides. These crop production options can help countries
keep pace with demands for food while reducing production costs.

Improved pest control

Biotechnology has helped to make both pest control and weed

management safer and easier while safeguarding crops against disease.
For example, genetically engineered insect-resistant cotton has allowed for
a significant reduction in the use of persistent, synthetic pesticides that may
contaminate groundwater and the environment. In terms of improved weed
control, herbicide-tolerant soybeans, cotton, and corn enable the use of
reduced-risk herbicides that break down more quickly in soil and are
non-toxic to wildlife and humans.

Human Health Risk

At least some of the genes used in GE crops may not have been
used in the food supply before, so GM foods may pose a potential risk for
human health, such as producing new allergens. But this is also true of
crops generated by traditional breeding practices (because both produce
genetic modifications and thus new traits).
 Like other ‘controversial’ scientific issues, the scientific consensus on
GE crops is quite clear: they are safe. The UN’s Food and Agriculture
Organization has concluded that risks to human and animal health from the
use of GMOs are negligible. NASEM’s GE Crop Report found “no
substantiated evidence of a difference in risks to human health between
current commercially available genetically engineered (GE) crops and
conventionally bred crops, nor did it find conclusive cause-and-effect
evidence of environmental problems from the GE crops.” The American
Medical Association’s Council on Science and Public Health, in 2012,
stated that “Bioengineered foods have been consumed for close to 20
years, and during that time, no overt consequences on human health have
been reported and/or substantiated in the peer-reviewed literature.” Similar
statements have been made by the US National Resource Council and the
American Association for the Advancement of Science, which publishes the
preeminent scholarly journal, Science.

The potential of GE crops to be allergenic is one of the potential

adverse health effects and it should continue to be studied, especially
because some scientific evidences indicates that animals fed GE crops
have been harmed. NASEM’s GE Crop Report concluded that when
developing new crops, it is the product that should be studied for potential
health and environmental risks, not the process that achieved that product.
What this means is, because both traditional breeding practices and
modern genetic engineering produce new traits through genetic
modification, they both present potential risks. Thus, for the safety of the
environment and human health, both should be adequately studied.

What is recombinant DNA technology?

All DNA is made up of a base consisting of sugar, phosphate and

one nitrogen base. There are four nitrogen bases,
adenine (A), thymine (T), guanine (G), and cytosine (C). The nitrogen
bases are found in pairs, with A & T and G & C paired together. The
sequence of the nitrogen bases can be arranged in an infinite way, and
their structure is known as the famous "double helix". The sugar used in
DNA is deoxyribose. The four nitrogen bases are the same for all
organisms. The sequence and number of bases is what creates
diversity. DNA does not actually make the organism; it only
makes proteins. The DNA is transcribed into mRNA and mRNA is
translated into protein, and the protein then forms the organism. By
changing the DNA sequence, the way in which the protein is formed
changes. This leads to either a different protein, or an inactive protein.

Now that we know what DNA is, this is where the recombinant
comes in. Recombinant DNA is the general name for taking a piece of one
DNA, and combining it with another strand of DNA. Thus, the name
recombinant!
Recombinant DNA is also sometimes referred to as "chimera." By
combining two or more different strands of DNA, scientists are able to
create a new strand of DNA. The most common recombinant process
involves combining the DNA of two different organisms.

How is Recombinant DNA made?

There are three different methods by which Recombinant DNA is made.
They are Transformation, Phage Introduction, and Non-Bacterial
Transformation. Each are described separately below.

Transformation
The first step in transformation is to select a piece of DNA to be inserted
into a vector. The second step is to cut that piece of DNA with a restriction
enzyme and then ligate the DNA insert into the vector with DNA Ligase.
The insert contains a selectable marker which allows for identification of
recombinant molecules. An antibiotic marker is often used so a host cell
without a vector dies when exposed to a certain antibiotic, and the host with
the vector will live because it is resistant.

The vector is inserted into a host cell, in a process called transformation.

One example of a possible host cell is E. Coli. The host cells must be
specially prepared to take up the foreign DNA.

Selectable markers can be for antibiotic resistance, color changes, or any

other characteristic which can distinguish transformed hosts from
untransformed hosts. Different vectors have different properties to make
them suitable to different applications. Some properties can include
symmetrical cloning sites, size, and high copy number.

Non-Bacterial Transformation
This is a process very similar to Transformation, which was described
above. The only difference between the two is non-bacterial does not use
bacteria such as E. Coli for the host.

In microinjection, the DNA is injected directly into the nucleus of the cell
being transformed. In biolistics, the host cells are bombarded with high
velocity microprojectiles, such as particles of gold or tungsten that have
been coated with DNA.

Phage Introduction
Phage introduction is the process of transfection, which is equivalent to
transformation, except a phage is used instead of bacteria. In vitro
packagings of a vector is used. This uses lambda or MI3 phages to
produce phage plaques which contain recombinants. The recombinants
that are created can be identified by differences in the recombinants and
non-recombinants using various selection methods.

How does rDNA work?

Recombinant DNA works when the host cell expresses protein from the
recombinant genes. A significant amount of recombinant protein will not be
produced by the host unless expression factors are added. Protein
expression depends upon the gene being surrounded by a collection of
signals which provide instructions for the transcription and translation
of the gene by the cell. These signals include the promoter, the ribosome
binding site, and the terminator. Expression vectors, in which the foreign
DNA is inserted, contain these signals. Signals are species specific. In the
case of E. Coli, these signals must be E. Coli signals as E. Coli is unlikely
to understand the signals of human promoters and terminators.

Problems are encountered if the gene contains introns or contains signals

which act as terminators to a bacterial host. This results in premature
termination, and the recombinant protein may not be processed correctly,
be folded correctly, or may even be degraded.

Production of recombinant proteins in eukaryotic systems generally takes

place in yeast and filamentous fungi. The use of animal cells is difficult due
to the fact that many need a solid support surface, unlike bacteria, and
have complex growth needs. However, some proteins are too complex to
be produced in bacterium, so eukaryotic cells must be used.
Why is rDNA important?
Recombinant DNA has been gaining in importance over the last few years,
and recombinant DNA will only become more important in the 21st century
as genetic diseases become more prevelant and agricultural area is
reduced. Below are some of the areas where Recombinant DNA will have
an impact.
● Better Crops (drought & heat resistance)
● Recombinant Vaccines (ie. Hepatitis B)
● Prevention and cure of sickle cell anemia
● Prevention and cure of cystic fibrosis
● Production of clotting factors
● Production of insulin
● Production of recombinant pharmaceuticals
● Plants that produce their own insecticides
● Germ line and somatic gene therapy

What is PCR?

Polymerase chain reaction (PCR) is a common laboratory

technique used to make many copies (millions or billions!) of a particular
region of DNA. This DNA region can be anything the experimenter is
interested in. For example, it might be a gene whose function a researcher
wants to understand, or a genetic marker used by forensic scientists to
match crime scene DNA with suspects.

Typically, the goal of PCR is to make enough of the target DNA

region that it can be analyzed or used in some other way. For instance,
DNA amplified by PCR may be sent for sequencing, visualized by gel
electrophoresis, or cloned into a plasmid for further experiments.

PCR is used in many areas of biology and medicine, including

molecular biology research, medical diagnostics, and even some branches
of ecology. PCR is used in many research labs, and it also has practical
applications in forensics, genetic testing, and diagnostics. For instance,
PCR is used to amplify genes associated with genetic disorders from the
DNA of patients (or from fetal DNA, in the case of prenatal testing). PCR
can also be used to test for a bacterium or DNA virus in a patient's body: if
the pathogen is present, it may be possible to amplify regions of its DNA
from a blood or tissue sample.
Genetically Modified Organism (GMO)

Genetically modified organism (GMO), organism whose genome

has been engineered in the laboratory in order to favour the expression of
desired physiological traits or the generation of desired biological products.
In conventional livestock production, crop farming, and even pet breeding,
it has long been the practice to breed select individuals of a species in
order to produce offspring that have desirable traits. In genetic modification,
however, recombinant genetic technologies are employed to produce
organisms whose genomes have been precisely altered at the molecular
level, usually by the inclusion of genes from unrelated species of organisms
that code for traits that would not be obtained easily through conventional
selective breeding.
Genetically modified organisms (GMOs) are produced using scientific
methods that include recombinant DNA technology and
reproductive cloning. In reproductive cloning, a nucleus is extracted from a
cell of the individual to be cloned and is inserted into the
enucleated cytoplasm of a host egg (an enucleated egg is an egg cell that
has had its own nucleus removed). The process results in the generation of
an offspring that is genetically identical to the donor individual. The
first animal produced by means of this cloning technique with a nucleus
from an adult donor cell (as opposed to a donor embryo) was a sheep
named Dolly, born in 1996. Since then a number of other animals,
including pigs, horses, and dogs, have been generated by reproductive
cloning technology. Recombinant DNA technology, on the other hand,
involves the insertion of one or more individual genes from an organism of
one species into the DNA (deoxyribonucleic acid) of another.
Whole-genome replacement, involving the transplantation of
one bacterial genome into the “cell body,” or cytoplasm, of another
microorganism, has been reported, although this technology is still limited
to basic scientific applications.

GMOs produced through genetic technologies have become a part of

everyday life, entering into society through agriculture, medicine, research,
and environmental management. However, while GMOs have benefited
human society in many ways, some disadvantages exist; therefore, the
production of GMOs remains a highly controversial topic in many parts of
the world.

GMOs in agriculture
 Genetically modified (GM) foods were first approved for
human consumption in the United States in 1994, and by 2014–15 about
90 percent of the corn, cotton, and soybeans planted in the United States
were GM. By the end of 2014, GM crops covered nearly 1.8 million square
kilometres (695,000 square miles) of land in more than two dozen countries
worldwide. The majority of GM crops were grown in the Americas.

Engineered crops can dramatically increase per area crop yields and,
in some cases, reduce the use of chemical insecticides. For example, the
application of wide-spectrum insecticides declined in many areas growing
plants, such as potatoes, cotton, and corn, that were endowed with
a gene from the bacterium Bacillus thuringiensis, which produces a natural
insecticide called Bt toxin. Field studies conducted in India in which Bt
cotton was compared with non-Bt cotton demonstrated a 30–80 percent
increase in yield from the GM crop. This increase was attributed to marked
improvement in the GM plants’ ability to overcome bollworm infestation,
which was otherwise common. Studies of Bt cotton production in Arizona,
U.S., demonstrated only small gains in yield—about 5 percent—with an
estimated cost reduction of $25–$65 (USD) per acre owing to
decreased pesticide applications. In China, where farmers first gained
access to Bt cotton in 1997, the GM crop was initially successful. Farmers
who had planted Bt cotton reduced their pesticide use by 50–80 percent
and increased their earnings by as much as 36 percent. By 2004, however,
farmers who had been growing Bt cotton for several years found that the
benefits of the crop eroded as populations of secondary insect pests, such
as mirids, increased. Farmers once again were forced to spray
broad-spectrum pesticides throughout the growing season, such that the
average revenue for Bt growers was 8 percent lower than that of farmers
who grew conventional cotton. Meanwhile, Bt resistance had also evolved
in field populations of major cotton pests, including both the cotton
bollworm (Helicoverpa armigera) and the pink bollworm (Pectinophora
gossypiella).

Other GM plants were engineered for resistance to a specific

chemical herbicide, rather than resistance to a natural predator or
pest. Herbicide-resistant crops (HRC) have been available since the
mid-1980s; these crops enable effective chemical control of weeds, since
only the HRC plants can survive in fields treated with the corresponding
herbicide. Many HRCs are resistant to glyphosate (Roundup), enabling
liberal application of the chemical, which is highly effective against weeds.
Such crops have been especially valuable for no-till farming, which helps
prevent soil erosion. However, because HRCs encourage increased
application of chemicals to the soil, rather than decreased application, they
remain controversial with regard to their environmental impact. In addition,
in order to reduce the risk of selecting for herbicide-resistant weeds,
farmers must use multiple diverse weed-management strategies.

Another example of a GM crop is “golden” rice, which originally was

intended for Asia and was genetically modified to produce almost 20 times
the beta-carotene of previous varieties. Golden rice was created by
modifying the rice genome to include a gene from the daffodil Narcissus
pseudonarcissus that produces an enzyme known as phyotene synthase
and a gene from the bacterium Erwinia uredovora that produces an
enzyme called phyotene desaturase. The introduction of these genes
enabled beta-carotene, which is converted to vitamin A in the human liver,
to accumulate in the rice endosperm—the edible part of the rice
plant—thereby increasing the amount of beta-carotene available for vitamin
A synthesis in the body. In 2004 the same researchers who developed the
original golden rice plant improved upon the model, generating golden rice
2, which showed a 23-fold increase in carotenoid production.

Another form of modified rice was generated to help

combat iron deficiency, which impacts close to 30 percent of the world
population. This GM crop was engineered by introducing into the rice
genome a ferritin gene from the common bean, Phaseolus vulgaris, that
produces a protein capable of binding iron, as well as a gene from the
fungus Aspergillus fumigatus that produces an enzyme capable of
digesting compounds that increase iron bioavailability via digestion of
phytate (an inhibitor of iron absorption). The iron-fortified GM rice was
engineered to overexpress an existing rice gene that produces a
cysteine-rich metallothioneinlike (metal-binding) protein that enhances iron
absorption.

A variety of other crops modified to endure the weather extremes common

in other parts of the globe are also in production.

GMOs in medicine and research

 GMOs have emerged as one of the mainstays of biomedical research
since the 1980s. For example, GM animal models of human genetic
diseases enabled researchers to test novel therapies and to explore the
roles of candidate risk factors and modifiers of disease outcome. GM
microbes, plants, and animals also revolutionized the production of
complex pharmaceuticals by enabling the generation of safer and
cheaper vaccines and therapeutics. Pharmaceutical products range from
recombinant hepatitis B vaccine produced by GM baker’s yeast to
injectable insulin (for diabetics) produced in GM Escherichia coli bacteria
and to factor VIII (for hemophiliacs) and tissue plasminogen activator (tPA,
for heart attack or stroke patients), both of which are produced in GM
mammalian cells grown in laboratory culture. Furthermore, GM plants that
produce “edible vaccines” are under development. An edible vaccine is an
antigenic protein that is produced in the consumable parts of a plant (e.g.,
fruit) and absorbed into the bloodstream when the parts are eaten. Once
absorbed into the body, the protein stimulates the immune system to
produce antibodies against the pathogen from which the antigen was
derived. Such vaccines could offer a safe, inexpensive, and painless way to
provide vaccines, particularly in less-developed regions of the world, where
the limited availability of refrigeration and sterile needles has been
problematic for some traditional vaccines. Novel DNA vaccines may be
useful in the struggle to prevent diseases that have proved resistant to
traditional vaccination approaches, including HIV/AIDS, tuberculosis,
and cancer.

Genetic modification of insects has become an important area of

research, especially in the struggle to prevent parasitic diseases. For
example, GM mosquitoes have been developed that express a small
protein called SM1, which blocks entry of
the malaria parasite, Plasmodium, into the mosquito’s gut. This results in
the disruption of the parasite’s life cycle and renders the mosquito
malaria-resistant. Introduction of these GM mosquitoes into the wild could
help reduce transmission of the malaria parasite. In another example,
male Aedes aegypti mosquitoes engineered with a method known as the
sterile insect technique transmit a gene to their offspring that causes the
offspring to die before becoming sexually mature. In field trials in a Brazil
suburb, A. aegypti populations declined by 95 percent following the
sustained release of sterile GM males.
 Finally, genetic modification of humans via gene therapy is becoming
a treatment option for diseases ranging from rare metabolic disorders to
cancer. Coupling stem cell technology with recombinant DNA methods
allows stem cells derived from a patient to be modified in the laboratory to
introduce a desired gene. For example, a normal beta-globin gene may be
introduced into the DNA of bone marrow-derived hematopoietic stem cells
from a patient with sickle cell anemia; introduction of these GM cells into
the patient could cure the disease without the need for a matched donor.

Some Genetically Modified Organisms developed in the Philippines

o Longer-lasting papayas

Institute of Plant Breeding in UPLB developed delayed-ripening papaya

that is resistant to ring-spot virus (PRSV). The initial project assisted by the
Australian government developed a papaya variety with a 14-day shelf life,
or double the usual 6 days. The scientists achieved this by suppressing the
generation of key enzyme in the ethylene biosynthesis pathway –ACC
synthase – through genetic manipulation. ACC synthase triggers ethylene
production, which causes ripening of fruits.

o Protein enriched copra meal (PECM) as feed protein for tilapia, milkfish
and shrimp aquaculture

Primarily used as animal feed, copra meal is an important feed resource in

the Philippines. In 2014, the Philippines produced about 750,000 metric
tons of copra meal as coconut by-product. About 60% of this was locally
utilized mainly as animal feed. There are, however, several concerns on the
use of soybean meals as feeding ingredient. This includes its fluctuating
market price, its being expensive import commodity, its erratic supply, and
the fact that it even competes for human food. To address the issue on high
cost of soybean importation and to ensure the quality of animal feeds, the
Philippine Council for Agriculture, Aquatic and Natural Resources Research
and Development of the Department of Science and Technology
(DOSTPCARRD) supported research and development (R&D) programs
on feed resources under its Industry Strategic Science and Technology
(S&T) Program (ISP). One of the program’s accomplishments is the use of
formulated feeds for swine, poultry and aquatic animals with Protein
Enriched Copra Meal (PECM) that was developed by the National Institute
of Molecular Biology and Biotechnology of the University of the Philippines
Los Banos (UPLB-BIOTECH). Through solid-state fermentation technology,
the PECM is enriched with microorganisms that increase the protein
content of copra meal to about 36 to 44% crude protein content,
comparable to the 46% of soybean meal. A group of researchers from the
Institute of Aquaculture, College of Fisheries and Ocean Sciences of the
University of the Philippines Visayas studied the possibility of substituting
50% soybean meal, as a major feed protein source, with PECM.

o Tomato Leaf Curve Virus (ToLCV)- resistant Variety

The Institute of Plant Breeding (IPB) of the University of the Philippines Los
Banos (UPLB) has developed tomato breeding line resistant to tomato leaf
curl virus (ToLCV) in the hope of reviving tomato’s robust production in the
country.

The two-year project was completed by a team composed mainly of local

scientist at the IPB-UPLB with financial support from the Department of
Agriculture Biotech Program. The research team developed the candidate
ToLCV-resistant lines from the local tomato varieties by interbreeding local
varieties with ToLCV-resistant tomato lines acquired from the Asian
Vegetable Research and Development Center (AVRDC) – The World
Vegetable Center.

o Bt corn

Bt corn in the Philippines was engineered to be specifically resistant to the

Asian corn borer (ACB), Ostrinia furnacalis (Guenee), the most devastating
corn pests in the industry. It was introduced as a “practical and ecologically
sustainable solution” for poor corn farmers, a major bullet to combat
poverty and improve livelihood.

Role of GMOs in environmental management

Another application of GMOs is in the management of environmental

issues. For example, some bacteria can produce biodegradable plastics,
and the transfer of that ability to microbes that can be easily grown in the
laboratory may enable the wide-scale “greening” of the plastics industry. In
the early 1990s, Zeneca, a British company, developed a microbially
produced biodegradable plastic called Biopol (polyhydroxyalkanoate, or
PHA). The plastic was made with the use of a GM bacterium, Ralstonia
eutropha, to convert glucose and a variety of organic acids into a
flexible polymer. GMOs endowed with the bacterially encoded ability to
metabolize oil and heavy metals may provide efficient bioremediation
strategies.

Sociopolitical relevance of GMOs

While GMOs offer many potential benefits to society, the potential

risks associated with them have fueled controversy, especially in the food
industry. Many skeptics warn about the dangers that GM crops may pose to
human health. For example, genetic manipulation may potentially alter the
allergenic properties of crops. Whether some GM crops, such as golden
rice, deliver on the promise of improved health benefits is also unclear. The
release of GM mosquitoes and other GMOs into the environment also
raised concerns. More-established risks were associated with the potential
spread of engineered crop genes to native flora and the
possible evolution of insecticide-resistant “superbugs.”

From the late 1990s, the European Union (EU) addressed such
concerns by implementing strict GMO labeling laws. In the early 2000s, all
GM foods and GM animal feeds in the EU were required to be labeled if
they consisted of or contained GM products in a proportion greater than 0.9
percent. By contrast, in the United States, foods containing GM ingredients
did not require special labeling, though the issue was hotly debated at
national and state levels. Many opponents of GM products focused their
arguments on unknown risks to food safety. However, despite the concerns
of some consumer and health groups, especially in Europe, numerous
scientific panels, including the U.S. Food and Drug Administration,
concluded that consumption of GM foods was safe, even in cases involving
GM foods with genetic material from very distantly related organisms.

The strict regulations on GM products in the EU have been a source

of tension in agricultural trade. In the late 1990s, the EU declared
a moratorium on the import and use of GM crops. However, the
ban—which led to trade disputes with other countries, particularly
the United States, where GM foods had been accepted openly—was
considered unjustified by the World Trade Organization. In consequence,
the EU implemented regulatory changes that allowed for the import of
certain GM crops. Within Europe, however, only one GM crop, a type of
insect-resistant corn (maize), was cultivated. Some countries, including
certain African states, had likewise rejected GM products. Still other
countries, such as Canada, China, Argentina, and Australia, had open
policies on GM foods.

The use of GMOs in medicine and research has produced a debate

that is more philosophical in nature. For example, while genetic
researchers believe they are working to cure disease
and ameliorate suffering, many people worry that current gene therapy
approaches may one day be applied to produce “designer” children or to
lengthen the natural human life span. Similar to many other technologies,
gene therapy and the production and application of GMOs can be used to
address and resolve complicated scientific, medical, and environmental
issues, but they must be used wisely.

Learning Task:

1. Identify one example of genetic engineering and explain the genetic

change involved in the process.
References

Textbook
Berg, Linda L. 2012. Introductory to Botany Cengage Learning

Mader, Sylvia, Biology-Inquiry to Life, McGrawHill 2nd Edition, New York, 2015

Module Ged 109 Science, Technology and Society

Starr, Cecie et al. 2012. Biology: Applications and Concepts

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