LESSON 1 INTRODUCTION TO ZOOLOGY

Course Description
Biological principles related to zoology, life cycle, morphological characteristics and relationships
representative of the more important animal phyla, collection, and classification

Course Outcome
Distinguish among various levels of animal life
Identify animal tissues and organ systems in relation to their function
Describe the basic mechanism and processes associated with the different organ systems
Explain the concepts regarding the central dogma of molecular genetics
Recognize the different taxa of animals

Zoology
Study of animal life
Zoologists strive to understand:
The origin of animal diversity.
How animals perform basic life processes.
How they are able to inhabit various ecosystems.

SUBDISCIPLINE & DESCRIPTION

Anatomy: Study of the structure of entire organisms and their parts
Cytology: Study of the structure and function of cells
Ecology: Study of the interaction of organisms with their environment
Embryology: Study of the development of an animal from the fertilized egg to birth or hatching
Genetics: Study of the mechanisms of transmission of traits from parents to offspring
Histology: Study of tissues
Molecular biology: Study of subcellular details of animal structure and function
Parasitology: Study of animals that live in or on other organisms at the expense of the host
Physiology: Study of the function of organisms and their parts
Systematics: Study of the classification of, and the evolutionary interrelationships among, animal groups

EXAMPLES OF SPECIALIZATIONS IN ZOOLOGY BY TAXONOMIC CATEGORIES

Entomology: Study of insects
Herpetology: Study of amphibians and reptiles
Ichthyology: Study of fishes
Mammalogy: Study of mammals
Omithology: Study of birds
Protozoology: Study of protozoa
FUNDAMENTAL PROPERTIES OF LIFE
Does Life Have Defining Properties?
What is life?
● No simple definition.
● The history of life shows extensive and ongoing change called evolution.
● Answer must be based on the common history of life on earth.

GENERAL PROPERTIES OF LIVING SYSTEMS

• Chemical Uniqueness
• Complexity and Hierarchical Organization
• Reproduction
• Genetic Program
• Metabolism
• Development
• Environmental Interaction

CHEMICAL UNIQUENESS
• Living systems demonstrate a unique and complex molecular organization.
• Living organisms assemble large molecules – macromolecules – that are more complex than molecules
found in nonliving matter.
• Four categories of biological macromolecules – NA, CHON, CHO, Lipids
• These 4 groups differ in their:
• Components
• Types of bonds holding them together
• Functions
• Macromolecules evolved early in the history of life.
• Found in every form of life today.

• Proteins are made up of 20 different amino acid subunits.

• Enormous variability allows for the diversity of proteins and consequently of living forms.
•Nucleic acids, carbohydrates & lipids are also organized in a way This gives living systems a large
potential for diversity.

COMPLEXITY AND HIERARCHICAL ORGANIZATION

•Molecules are organized into patterns in the living world that do not exist in the nonliving world.
•New characteristics can appear at any level of organization – emergent properties.
•Emergent properties depend upon the characteristics found at lower hierarchical levels – to some extent.
• The development of spoken language requires hearing.
• But, many different languages have arisen.
Different Hierarchical Levels of Biological Complexity That Display Reproduction, Variation, and
Heredity

Level Timescale of Fields of Study Methods of Study Some Emergent

Reproduction Properties

Cell Hours Cell biology Microscopy (light, Chromosomal

(mammalian cell electron), replication
= ~16 hours) biochemistry (meiosis, mitosis),
synthesis of
macromolecules
(DNA, RNA,
proteins, lipids,
polysaccharides)

Organism Hours to days Organismal Dissection, Structure,

(unicellular); anatomy, genetic crosses, functions and
days to years physiology, clinical studies, coordination of
(multicellular) genetics physiological tissues, organs
experimentation and organ systems
(blood pressure,
body temperature,
sensory
perception,
feeding)

Population Up to thousands Population Statistical analysis Social structures,

of years biology, of variation, systems of
population abundance, mating, age
genetics, ecology geographical distribution of
distribution organisms, levels
of variation,
action of natural
selection

Species Thousands to Systematics and Study of Method of

millions of years Evolutionary reproductive reproduction,
biology, barriers, reproductive
community phylogeny, barriers
ecology paleontology.
ecological
interactions
REPRODUCTION
• Living systems can reproduce themselves
• Even species may split to produce new species - speciation.
• Heredity and variation are present at all of these levels.
• Heredity – faithful transmission of traits from one generation to the next.
• Variation – production of differences among the traits of individuals.
• Result: offspring are similar to – but not exactly like parents.

POSSESSION OF GENETIC PROGRAM

•Genetic program – provides fidelity of inheritance.
•Genetic information is coded in DNA
•DNA is a long chain of nucleotides – a sugar, phosphate + nitrogenous base (A, C, G, & T).
• The sequence of nucleotides codes for the order of amino acids in the protein specified.
• The genetic code - correspondence between the sequence of bases in D N A and the sequence of
amino acids in a protein.
• The genetic code is universal among living organisms from bacteria through humans.
METABOLISM
Living organisms maintain themselves by acquiring nutrients from their environments.
• Metabolism includes all of the chemical reactions occurring within an
organism.
• Digestion
• Respiration
• Synthesis of molecules and structures
• It includes destructive (catabolic) and constructive (anabolic) reactions.
• Physiology – the study of complex metabolic functions

DEVELOPMENT
• All organisms pass through characteristic stages in their life cycle.
• Development includes characteristic changes an organism passes through from its beginning (usually as
a fertilized egg) through adulthood.
• Metamorphosis – transformation from one life stage to another.
• Tadpole to frog
• Caterpillar to butterfly
ENVIRONMENTAL INTERACTION
•Living organisms interact with their environments.
•Ecology is the study of this interaction between organisms and between organisms and their
environment.

MOVEMENT
Living systems and their parts show precise and controlled movements arising from within the system.
• Living systems extract energy from their environments permitting the initiation of controlled
movements.
• Movements at the cellular level are required for: Reproduction, Growth, Responses to stimuli,
Development in multicellular organisms
• On a larger scale: Entire populations or species may disperse from one geographic location to another
over time.
• Movement of nonliving matter:
• Not precisely controlled by the moving objects
• Often involves external forces.

PHYSICAL LAWS
•First Law of Thermodynamics – Law of Conservation: Energy can not be created or destroyed, but can
be transformed.
•Second Law of Thermodynamics – Physical systems proceed toward a state of entropy or disorder.
Energy is required to maintain the complex organization in living organisms.

ZOOLOGY AS PART OF BIOLOGY

•Animals originated in the Precambrian seas over 600 million years ago.
•Characteristics of Animals:
• Eukaryotes: cells contain membrane-enclosed nuclei.
• Heterotrophs: Not capable of manufacturing their own food and must rely on
external food sources.
• Cells lack cell walls

THE NATURE OF SCIENCE

Science is a way of asking questions about the natural world.
• It is guided by natural law.
• It has to be explanatory by reference to natural law.
• It is testable against the observable world.
• Its conclusions are tentative and therefore not necessarily the final word.
• It is falsifiable.
SCIENTIFIC METHOD - HYPOTHETICODEDUCTIVE METHOD

February 2, 2022
• First is the observation phase, where new observations are made. This is also the time where previous
data are examined.
• Next, a hypothesis is formulated to attempt to explain the available data and observations.
• A hypothesis must be testable!!!
• Hypothesis:
• Potential answers to questions being asked.
• Derived from prior observations of nature or from theories based on such observations.
• Often constitute general statements about nature that may explain a large number of diverse
observations.
• If a hypothesis is very powerful in explaining a wide variety of related phenomena, it attains the
level of a theory.

• Scientists can then draw a conclusion based on the data. The conclusion may involve accepting or
rejecting the initial hypothesis. Further experiments may require an adjustment to the conclusions.
• Hypotheses are said to be supported, but not proven.
• New hypotheses are generated from the conclusions, and the process starts again.
• A theory results when a group of related hypotheses are supported by many experiments and
observations.
• Theories are the ideas that scientists are MOST SURE OF!
• Theory of gravity
• Theory of natural selection

EVOLUTION AND HEREDITY

• Powerful theories that guide extensive research are called paradigms.
• The refutement and replacement of a paradigm is known as a scientific revolution.
• Two major paradigms that guide zoological research:
1.Darwin’s Theory of Evolution
2.The Chromosomal Theory of Inheritance

THEORY OF EVOLUTION
• Charles Darwin – On the Origin of Species by Means of Natural Selection,1859.
• Five related theories:
• Perpetual change: The world and the organisms living in it are always changing. Supported by
the fossil record. The properties of organisms undergo transformation across generations
throughout time.Theory upon which the remaining 4 are based.
• Common descent: All forms of life descended from a common ancestor through a branching of
lineages. Life’s history has the structure of a branching evolutionary tree known as a phylogeny.
Serves as the basis for our taxonomic classification of animals. Descent with modification.
Supported by molecular work.
 • Multiplication of species: New species are produced by the splitting and transforming of older
species.
• Gradualism: Large differences result from the accumulation of small changes over long periods
of time. Occasionally, changes can happen more quickly.
• Natural selection: Differential success in the reproduction of different phenotypes resulting from
the interaction of organisms with their environment.
Natural selection requires:
Variation within the population.
This variation must be heritable.
Organisms with a particular variation will have more offspring.
Over time, these successful variations will spread through the population. Natural selection explains why
organisms are constructed to meet the demands of their environments. Adaptation results when the most
favorable variants accumulate over evolutionary time.

All vertebrate forelimbs share an underlying structure utilizing the same parts,but have evolved a diverse
array of adaptations,as seen in the wing of a bat,the flipper of a whale, & a human arm.

MENDELIAN HEREDITY
Gregor Mendel performed experiments on garden peas leading to an understanding of how chromosomal
inheritance works. Mendel chose peas to study inheritance because they possess several contrasting traits
without intermediates.
• Green vs.yellow peas
• Tall vs. short plants
• Wrinkled vs.smooth peas
• Purple vs. white flowers
The peas can self-fertilize or outcross. Mendel could control who the parents were. Mendel always started
with true-breeding parents. E.g. self-fertilized white-flowered parents always produced white-flowered
offspring. He could cross true-breeding white with true-breeding purple – this is the parental generation.
Resulting in all purple offspring – this is the F1 generation.

Allowing the hybrid F1 generation to self pollinate gives the F2 generation with 3 purple: 1 white
offspring. He kept careful quantitative records that allowed him to find patterns.
CONTRIBUTIONS OF CELL BIOLOGY
Microscopes allowed scientists to study the production of gametes (eggs & sperm).
They could watch the movement of chromosomes.
Result: the chromosomal theory of inheritance.
Heritable information is contained on chromosomes.

History of zoology since 1859

This article considers the history of zoology since the theory of evolution by natural selection proposed by
Charles Darwin in 1859. The result was a reconstruction of the classification of animals upon a
genealogical basis, fresh investigation of the development of animals, and early attempts to determine
their genetic relationships. The end of the 19th century saw the fall of spontaneous generation and the rise
of the germ theory of disease, though the mechanism of inheritance remained a mystery. In the early 20th
century, the rediscovery of Mendel’s work led to the rapid development of genetics by
Thomas Hunt Morgan and his students, and by the 1930s the combination of population genetics and
natural selection in the "neo-Darwinian synthesis".
In 1859, Charles Darwin placed the whole theory of organic evolution on a new footing, by his discovery
of a process by which organic evolution can occur, and provided observational evidence that it had done
so. This changed the attitudes of most exponents of the scientific method. Darwin’s discoveries
revolutionized the zoological and botanical sciences, by introducing the theory of evolution by natural
selection as an explanation for the diversity of all animal and plant life. The subject matter of this new
science, or branch of biological science, had been neglected: it did not form part of the studies of the
collector and systematist, nor was it a branch of anatomy, nor of the physiology pursued by medical men,
nor again was it included in the field of microscopy and the cell theory.

It cannot be said that previously to Darwin there had been any very profound study of teleology, but it had
been the delight of a certain type of mind, that of the lovers of nature or naturalists par excellence as they
were sometimes termed, to watch the habits of living animals and plants and to point out the remarkable
ways in which the structure of each variety of organic life was adapted to the special circumstances of life
of the variety or species. The astonishing colours and grotesque forms of some animals and plants which
the museum zoologists gravely described without comment were shown by these observers of living
nature to have their significance in the economy of the organism possessing them; and a general doctrine
was recognized, to the effect that no part or structure of an organism is without definite use and
adaptation, being designed by the Creator for the benefit of the creature to which it belongs, or else for the
benefit, amusement or instruction of his highest creatureman.

Teleology in this form of the doctrine of design was never very deeply rooted amongst scientific
anatomists and systematists. It was considered permissible to speculate somewhat vaguely on the subject
of the utility of this or that startling variety of structure; but few attempts, though some of great
importance, were made systematically to explain by observation and experiment the adaptation of organic
structures to particular purposes in the case of the lower animals and plants. Teleology had, indeed, an
important part in the development of physiology - the knowledge of the mechanism, the physical and
chemical properties, of the parts of the body of man and the higher animals allied to him.

Darwin’s theory had as one of its results the reformation and rehabilitation of teleology. According to that
theory, every organ, every part, colour and peculiarity of an organism, must either be of benefit to that
organism itself or have been so to its ancestors: no peculiarity of structure or general conformation, no
habit or instinct in any organism, can be supposed to exist for the benefit or amusement of another
organism, not even for the delectation of man himself.

A very subtle and important qualification of this generalization has to be recognized (and was recognized
by Darwin) in the fact that owing to the interdependence of the parts of the bodies of living things and
their profound chemical interactions and peculiar structural balance (what is called organic polarity) the
variation of one single part (a spot of colour, a tooth, a claw, a leaflet) may, and demonstrably does in
many cases entail variation of other parts what are called correlated variations. Hence many structures
which are obvious to the eye, and serve as distinguishing marks of separate species, are really not
themselves of value or use, but are the necessary concomitants of less obvious and even altogether
obscure qualities, which are the real characters upon which selection is acting. Such correlated variations
may attain to great size and complexity without being of use.
Necessarily, according to the theory of natural selection, structures either are present because they are
selected as useful or because they are still inherited from ancestors to whom they were useful, though no
longer useful to the existing representatives of those ancestors. Structures previously inexplicable were
now explained as survivals from a past age, no longer useful though once of value. Every variety of form
and colour was urgently and absolutely called upon to produce its title to existence either as an active
useful agent or as a survival. Darwin himself spent a large part of the later years of his life in thus
extending the new teleology.

The old doctrine of types, which was used by the philosophically minded zoologists (and botanists) of the
first half of the 19th century as a ready means of explaining the failures and difficulties of the doctrine of
design, fell into its proper place under the new dispensation. The adherence to type, the favourite
conception. of the transcendental morphologist, was seen to be nothing more than the expression of one of
the laws of thremmatology, the persistence of hereditary transmission of ancestral characters, even when
they have ceased to be significant or valuable in the struggle for existence, whilst the so called evidences
of design which was supposed to modify the limitations of types assigned to Himself by the Creator were
seen to be adaptations due to the selection and intensification by selective breeding of fortuitous
congenital variations, which happened to prove more useful than the many thousand other variations
which did not survive in the struggle for existence.

Thus not only did Darwins theory give a new basis to the study of organic structure, but, whilst rendering
the general theory of organic evolution equally acceptable and necessary, it explained the existence of low
and simple forms of life as survivals of the earliest ancestry of the more highly complex forms, and
revealed the classifications of the systematist as unconscious attempts to construct the genealogical tree or
pedigree of plants and animals. Finally, it brought the simplest living matter or formless protoplasm
before the mental vision as the starting point whence, by the operation of necessary mechanical causes,
the highest forms have been evolved, and it rendered unavoidable the conclusion that this earliest living
material was itself evolved by gradual processes, the result also of the known and recognized laws of
physics and chemistry, from material which we should call not living.

It abolished the conception of life as an entity above and beyond the common properties of matter, and led
to the conviction that the marvellous and exceptional qualities of that which we call living matter are
nothing more nor less than an exceptionally complicated development of those chemical and physical
properties which we recognize in a gradually ascending scale of evolution in the carbon compounds,
containing nitrogen as well as oxygen, sulphur and hydrogen as constituent atoms of their enormous
molecules. Thus mysticism was finally banished from the domain of biology, and zoology became one of
the physical sciences: the science which seeks to arrange and discuss the phenomena of animal life and
form, as the outcome of the operation of the laws of physics and chemistry.
A subdivision of zoology which was at one time in favour is simply into morphology and physiology, the
study of form and structure on the one hand, and the study of the activities and functions of the forms and
structures of the other. But a logical division like this is not necessarily conducive to the ascertainment
and remembrance of the historical progress and present significance of the science. No such distinction of
mental activities as that involved in the division of the study of animal life into morphology and
physiology has ever really existed: the investigator of animal forms has never entirely ignored the
functions of the forms studied by him, and the experimental inquirer into the functions and properties of
animal tissues and organs has always taken very careful account of the forms of those tissues and organs.
A more instructive subdivision must be one which corresponds to the separate currents of thought and
mental preoccupation which have been historically manifested in western Europe in the gradual evolution
of what is today the great river of zoological doctrine to which they have all been rendered contributory.

Theories on the Origin of Life

• Theory of Special Creation
• Theory of Spontaneous Generation
• Theory of Biogenesis
• Theory of Biochemical Evolution
• Theory of Panspermia

The theory of special creation is accepted by most of the world's religions. It stated that life was created
by the wishes of a divine being or some supernatural power, the Creator or God. There are three important
postulates in the theory of special creation.
1. All the different kinds of life (microorganisms, fungi, algae, animals and plants) were created at
the same time or at short intervals without any relationship with one another.
2. They were created in the same form in which they exist at present, having undergone no change
since their creation.
3. Their bodies and organs have been specially designed to fully meet the needs of the environment
in which they have been created.
The theory of special creation is purely a religious concept, acceptable only on the basis of faith. It is not
a scientific fact. Scientific facts are based on natural laws. Hence, it does not. enjoy general acceptance.
Scientific truth is tentative for a scientist whereas theological truth is absolute for atheist. The process of
special creation occurred only once. Therefore, it cannot be observed. Science relies on observation and
hence, cannot prove or disprove the special creation theory.

The theory of spontaneous generation held that living creatures could arise from nonliving matter and
that such processes were commonplace and regular. ... It was hypothesized that certain forms such as fleas
could arise from inanimate matter such as dust, or that maggots could arise from dead flesh. It was once
believed that life could come from nonliving things, such as mice from corn, flies from bovine manure,
maggots from rotting meat, and fish from the mud of previously dry lakes. Spontaneous generation is the
incorrect hypothesis that nonliving things are capable of producing life.
The formation of monomers
Stanley Miller and Urey recreate these conditions in vitro
The water is heated, and the mixture circulates for many days.

Results
After a week 15 amino acids in the mixture
Other biologically important molecules had been formed including ethanoic acid, lactic acid and urea
Later similar experiments were done using CO2 that produced nucleotides
Additional organic material may have been delivered by comets.

Biogenesis is the theory that living things can only come from other living things. It was developed in
1858 by Rudolf Virchow as a counter-hypothesis to spontaneous generation. ... In 1861, Louis Pasteur
conducted experiments to support the biogenesis theory. Conceptually, biogenesis is primarily attributed
to Louis Pasteur and encompasses the belief that complex living things come only from other living
things, by means of reproduction.

Spontaneous générations, a persistant idea

Maggots from meat
Bumble bees from dead horses
Mice from sweaty shirts and wheat
1668 Francesco Redi kept meat in open air/sealed/under gauze.

Microscopy
• Microscopy made the problem worse
• Fresh boiled meat broth contains no microbes
• Allowed to stand it becomes cloudy and putrid – full of microbes
• Needham (1745) sealed flaskes of boiled broth
• Microbes appeared.

Spallanzani (1770)
Suspected infection from the air before sealing
Boiled broth and removed the air
No microbes appeared
Criticism spontaneous generation needed air.
Microbes are responsible for infection
Robert Koch, Louis Pasteur and anthrax

Pasteur (1859): All life comes from life

Sterilised by boiling
Swan-kneck flask permitted access to air.
Biochemical evidence of evolution is based on the fact that certain enzymes and chemical processes are
found in the cells of all or nearly all life on Earth. The first living systems probably resided in a molecular
garden of Eden, where all the building blocks that contemporary organisms must work hard at
synthesizing were available free. Under such conditions the numbers of organisms must have increased
very rapidly. But such increases cannot go on indefinitely. In time the supply of some molecular building
block must have become short. Those primitive organisms that had the ability to synthesize the scarce
building block, say A, from a more abundant one, say B, clearly had a competitive advantage over those
organisms that could not perform such a synthesis. In time, however, the secondary source of supply, B,
would have also become depleted and those organisms that could produce it from a third building block,
C, would have preferentially replicated. A U.S. biochemist, N.H. Horowitz, proposed that in this way the
enzymatic reaction chains of contemporary organisms--each step catalyzed by a particular enzyme--
originally evolved.

From monomers to polymers

Amino acids polypeptides, could have occurred when dry or highly concentrated monomers are heated
Condensation reactions take place forming: peptide bonds between amino acids or phosphodiester bonds
form between nucleotides.

Early catalysts
As molecules adsorb to the clay mineral particles they become concentrated (stick to the surface particles)
Clay particles (coacervates) may have been essential catalysts in the formation of polymers.

The first polynucleotides

Polynucleotides show a tendency to copy themselves using complementary base pairing
This was probably catalysed by the presence of clay particles and metal ions
These single-stranded polynucleotides would have been the equivalent of RNA.

1. RNA was probably the first hereditary molecule having the ability to copy itself
2. RNA shows enzymic (catalytic) properties - called ribozymes
3. Polynucleotides are very good molecules at storing and transmitting information but they lack the
versatility for all the chemical functions of a cell.
DNA AND RNA DIFFERENCE

Even the evolution of enzymatic reaction chains may have occurred in free nucleic acids before the origin
of the cell. The cell may have arisen in response to the need for maintaining a high concentration of
scarce building blocks or enzymes, or as protection against the gradually increasing abundance of oxygen
on the primitive Earth. Oxygen is a well-known poison to many biological processes, and in
contemporary higher organisms the mitochondria that handle molecular oxygen are kept in the cytoplasm,
far from contact with the nuclear material. Even today processes are known whereby polyamino-acids
form small spherical objects, microns to tens of microns across, with some of the properties of cells.
These objects, called proteinoid microspheres, are certainly not cells, but they may indicate processes by
which the ancestors of cells arose.

Panspermia (from Ancient Greek πᾶν (pan), meaning 'all', and σπέρμα (sperma), meaning 'seed') is the
hypothesis that life exists throughout the Universe, distributed by space dust, meteoroids, asteroids,
comets, planetoids, and also by spacecraft carrying unintended contamination by microorganisms. The
Greek philosopher Anaxagoras (500-428 BCE) asserted that the seeds of life are present everywhere in
the universe (Nicholson, Trends Microbiol 17:243-250, 2009). He coined the term panspermia to describe
the concept as life traveling between planets as seed. Panspermia is a Greek word that translates literally
as "seeds everywhere". The panspermia hypothesis states that the "seeds" of life exist all over the
Universe and can be propagated through space from one location to another. Some believe that life on
Earth may have originated through these "seeds".
LESSON 2 ANIMAL CELLS

CELL THEORY
Cells represent the basic structural and functional unit of life.
Important unifying concept in biology.
All organisms are composed of one or more cells.
All tissues & organs are composed of cells.
There is no life without cells!
Cell theory states that all living organisms are composed of cells.
Cells come from preexisting cells.
Cells are fabric of life

PROKARYOTIC VS. EUKARYOTIC CELLS

All cells:
● Have DNA
● Use the same genetic code
● Synthesize proteins
● Use ATP in similar ways
● This implies common ancestry.
 Characteristics Prokaryotic cell Eukaryotic cell

Cell size Mostly small (1-10 µm) Mostly large (10-100 µm)

Genetic system DNA with some DNA- binding DNA complexed with DNA-
protein; simple, circular DNA binding proteins in complex
molecule in nucleoid; nucleoid linear chromosomes within
is not membrane bound nucleus with membranous
envelope; circular mitochondrial
and chloroplast DNA

Cell Division Direct by binary fission or Some form of mitosis; centrioles

budding; no mitosis in many; mitotic spindle present

Sexual system Absent in most; highly modified Present in most; male and
if present female partners; gametes that
fuse to form zygote

Nutrition Absorption by most; Absorption, ingestion,

photosynthesis by some photosynthesis by some

Energy Metabolism No mitochondria; oxidative Mitochondria present; oxidative

enzymes bound to cell enzymes packaged therein; more
membrane, not packaged unifi ed pattern of oxidative
separately; great variation in metabolism
metabolic pattern

Intra-cellularmovement (None) Cytoplasmicstreaming, phagocytosis, pinocytosis

Flagella/cilia (If present, not with “9 2” microtubular pattern) With “9 2” microtubular pattern
Cell Wall (Cell wall Contains disaccharide chains cross-linked with peptides) If present, not with
disaccharide polymers linked with peptides

THE EUKARYOTIC CELL

Eukaryotic cellular structure is more complex due to organelles
Organelles segregate functions, allows cell size to increase
CELL COMPONENTS
Protoplasm – viscid translucent colloid material in the cell
Substances that make up the cell protoplasm
•Water
•Electrolytes – transmission of impulses and provide chemicals for cellular reactions
•Proteins – 10- 20% of cell mass
•Lipids – form membranous barriers that separate different intracellular compartment
•Carbohydrates – nutrition for cells

COMPONENTS OF EUKARYOTIC CELLS

The plasma membrane surrounds the cell.
The nucleus is the largest organelle. Double layered nuclear envelope.
Cytoplasm refers to the cellular material between the cell membrane and nuclear envelope.
Organelles such as the mitochondria, Golgi complex, centrioles, and endoplasmic reticulum are found in
the cytoplasm.

PLASMA MEMBRANE
Two layers of phospholipid molecules oriented with hydrophilic heads toward the outside and
hydrophobic tails inside.
Fluid-like – flexible

The nonpolar nature of the hydrophobic ends in the interior of the membrane prohibit polar substances
from crossing the membrane. Glycoproteins embedded in the membrane function in the transport of
molecules across the membrane.

SOME FUNCTIONS OF CELLMEMBRANE PROTEINS

Channel
Transporter (Carrier)
Receptor
Enzyme
Cytoskeleton Anchor
Cell Identity Marker

NUCLEUS
The nuclear envelope contains molecules between pores to allow to move nucleus &cytoplasm.
Chromosomes are contained in the nucleus.
Chromatin refers to loosely condensed DNA & proteins.
Nucleoli are specialized parts of certain chromosomes that carry multiple copies of the DNA used to
synthesize ribosomal RNA.
This rRNA combines with protein to from the two subunits of ribosomes.
Ribosomes leave the nucleus through pores in the nuclear envelope.
ENDOPLASMIC RETICULUM
The nuclear joins a envelope with cytoplasmic membranous (the system)
Endoplasmic reticulum (ER).
• Rough endoplasmic reticulum (RER) is covered with ribosomes. Smooth (SER) is not.
• Ribosomes on the RER synthesize proteins that enter the ER that will either be incorporated into the
plasma membrane, exported from the cell, or they may be bound for lysosomes.
• Lipids and phospholipids are synthesized in the SER.

GOLGI COMPLEX
The Golgi complex is a stack of membranous vesicles where storage, modification, and packaging of
protein products occurs. Small vesicles of ER membrane containing polypeptide or protein detach and
then fuse with sacs on the cis or “forming face” of a Golgi complex. After modification, the polypeptides
or proteins become incorporated into vesicles that detach from the trans or “maturing face” of the
complex.

ASSEMBLING & SECRETING PROTEINS

LYSOSOMES
Lysosomes contain enzymes (proteins) that can breakdown foreign material like bacteria or worn out
cellular components. Contents of lysosome would kill cell if membrane ruptured. May pour enzymes into
food vacuoles.

MITOCHONDRIA
Mitochondria are the powerhouses of cells. ATP is produced here. Composed of a double membrane - the
inner membrane is folded into cristae. Mitochondria are self-replicating, containing their own circular
DNA molecule.

NON MEMBRANOUS ORGANELLES

Cytoskeleton – a system of fibers that maintains cell structure and permit it to change shape and move
Actin filaments are thin threads that function in cell division and cell motility.
Microtubules function in cell division and serve as a "temporary scaffolding" for other organelles.
Intermediate filaments are between the size of the microtubules and the actin filaments

CYTOSKELETON
Microfilaments are made of the proteins actin and myosin and function in a cell’s ability to contract as
seen in muscle cells. Actin microfilaments move molecules and organelles through the cytoplasm.

Microtubules are larger tubular structures composed of the protein tubulin.

Move chromosomes during cell division.
Part of the structure of cilia & flagella.
Microtubules radiate out from the centrosome – the microtubule organizing center.
Located near nucleus.
Not membrane bound.
Centrioles are found in the centrosome.
Centrioles composed of 9 triplets of microtubules.
Replicate before cell division.

CYTOSKELETON
Intermediate fibers fall in between microfilaments and microtubules in size.

SURFACE OF CELLS CILIA & FLAGELLA

● Cilia & flagella are motile extensions of the cell surface. In many single celled organisms they are
a source of locomotion. In multicellular animals they usually sweep material past the fixed cell.
● Nine pairs of microtubules enclose a central pair.
● At the base is a basal body - identical to a centriole.

PSEUDOPODIA
● Some single-celled organisms, migrating cells in embryos, and white blood cells show ameboid
movement.
● Cytoplasmic streaming through the action of actin microfilaments extends a pseudopodium
outward.
● Some have specialized pseudopodia with microtubules that are assembled & disassembled to
allow movement.

JUNCTIONS
Tight junctions form when cell membranes of adjacent cells fuse. Function as seals.
Adhesion junctions occur under tight junctions. Transmembrane proteins link across a small space and
connect to microfilaments.
● Desmosomes act as spot welds and increase the strength of the tissue.
● Hemidesmosomes are found at the base of cells and anchor them to connective tissue.
● Gap junctions are canals between cells that provide intercellular communication.

MICROVILLI
Microvilli are small fingerlike projections that have bundles of actin microfilaments. They serve to
increase the surface area of the tissue as in the intestine.

MEMBRANE FUNCTION
Membranes surround the outside of the cell and the organelles inside it.
The plasma membrane acts as a selective gatekeeper.
A substance may cross the membrane:
● By diffusion
● By a mediated transport system
● By endocytosis
DIFFUSION & OSMOSIS
Diffusion is the movement of molecules from an area of high concentration to an area oflow
concentration. This tends to equalize the concentration.
Down the concentration gradient.
Solutes are molecules (e.g. salt) that are found in a solution.
Cell membranes are selectively permeable – water can pass through, but not most solutes.
Gases (oxygen & carbon dioxide), urea, lipid soluble solutes can cross the membrane.

Osmosis - if there is a membrane between two solutions with unequal concentration of solutes that can not
cross the membrane, water will flow toward the side with less water/ more solute until the two sides have
equal concentrations. Does osmosis or diffusion require energy? No, molecules move along a
concentration gradient.

Animals utilize osmosis to control internal fluid and solute levels.

The blood of marine fishes has 1/3 the salt content of the water. They are hypoosmotic to seawater.
Freshwater fishes have blood that is saltier than water. They are hyperosmotic to the water.
If the solute concentrations were the same, the two solutions would be isoosmotic.

DIFFUSION THROUGH CHANNELS

• Charged substances, like water and dissolved ions, can’t simply diffuse across the cell membrane.
• They pass through channels created by transmembrane proteins.
• Some channels always open.
• Some are gated channels.

Gated channels require a signal to open or close them.

• Chemically-gated channels open or close when a signaling molecule binds to a binding site on the
transmembrane protein.
• Voltage-gated channels open or close when the ionic charge across the membrane changes.

CARRIER MEDIATED TRANSPORT

Sugars & amino acids must be able to enter cells and waste products must be able to leave.
These molecules cross the membrane with the help of transporter proteins.
Transporter proteins are specific.
• Facilitated diffusion
• Active transport

FACILITATED DIFFUSION
In facilitated diffusion, the transporter protein binds to the substrate molecule on one side of the plasma
membrane then changes shape to release it on the other side. Takes place in the direction of the
concentration gradient. Facilitated Diffusion molecules move down a concentration gradient with the aid
of special proteins.
ACTIVE TRANSPORT
Active transport requires energy (ATP) (form of energy synthesized in mitochondria) to transport
molecules in the direction opposite the concentration gradient. Moves against the concentration gradient.

ENDOCYTOSIS
Endocytosis is the ingestion of material by cells. It is a process by which a cell surrounds and takes in
material from its environment. The material is engulfed and enclosed by a portion of the cell’s plasma
membrane; resulting vacuole with its contents moves to the inside of the cell.
• Phagocytosis – cell eating – method of feeding by single-celled organisms. Solid particles are ingested
into the cell.
• Pinocytosis – small molecules or ions are enclosed in vesicles called caveolae; liquid is taken into the
cell.
• Receptor-mediated endocytosis – method of bringing large molecules into a cell with the help of the
protein clathrin.

EXOCYTOSIS
•Exocytosis - membranes of a vesicle inside the cell can fuse with the plasma membrane to discharge the
contents of the vesicle outside the cell; Moves materials out of the cell via secretory vesicles; is the
expulsion or secretion of materials from a cell.
•Transcytosis – a substance may be picked up on one side of the cell, transported completely across the
cell and discharged on the other side.

MITOSIS AND CELL DIVISION

Mitosis is the process of nuclear cell division in nonreproductive, or somatic, cells.
A fertilized egg, or zygote, divides by mitosis to produce a multicellular organism.
Damaged cells are replaced by mitosis.

CHROMOSOMES
In cells that are not dividing, the DNA is loosely organized so that individual chromosomes can’t be
distinguished – it is now referred to as chromatin. Before division, chromatin becomes more compact and
chromosomes can be recognized.
 ● All nonreproductive cells in a species have the same number of chromosomes. (46 in humans)
● Half of these chromosomes come from each parent.
● Result is two sets of chromosomes. (Diploid)
● Chromosome 1 from Mom and chromosome 1 from Dad are called homologous chromosomes.

CELL DIVISION
There are two phases of cell division:
Mitosis – nuclear cell division
• Interphase
• Prophase
• Metaphase
• Anaphase
• Telophase
Cytokinesis – division of the cytoplasm. Multiple nuclear divisions not accompanied by cytokinesis result
in a multinucleate cell.

Prophase: Chromosomes condense enough to be seen with a light microscope. Spindle forms between the
2 centrioles. Spindle fibers attach to kinetochores.
Metaphase: Alignment of chromosomes center of the along cell (metaphase plate). Fibers attached to
kinetochores on both sides of each chromosome.
Anaphase: Separation of the sister chromatids. Centromere splits apart – sister chromatids move toward
opposite poles. Disassembly of the tubulin subunits shortens the microtubules.
Telophase: re- formation of the nuclei once the chromosomes are at opposite poles. Chromosomes
unwind.
Cytokinesis: division of the cytoplasm. Two complete, diploid cells that are identical to the original cell.
During cytokinesis in animal cells, the cell pinches in two. A cleavage furrow produced by
microfilaments deepens until the cell splits.
THE CELL CYCLE
Cells come from preexisting cells through the process of cell division.
Cell division – mitosis and cytokinesis – occupy a very small portion of the cell cycle.

Interphase includes:
•G1 – growth phase where RNA and functional proteins are synthesized.
•S – DNA replication.
•G2 – growth phase where structural proteins are made.
Mitosis
Cytokinesis

CHROMOSOME STRUCTURE
During S phase, each of the 2 homologues replicates, resulting in identical copies called sister chromatids.
Chromatids remain connected at a linkage site called the centromere.

CELLULAR METABOLISM
CELLULAR RESPIRATION
•Cellular respiration – the oxidation of food molecules to obtain energy.
•Electrons are stripped away.
•Different from breathing (respiration).

Aerobic versus Anaerobic Metabolism

Heterotrophs
• Aerobes: Use molecular oxygen as the final electron acceptor
• Anaerobes: Use other molecules as final electron acceptor
Energy yield much lower ATP yield
When oxygen acts as the final electron acceptor (aerobes): Almost 20 times more energy is released than
if another acceptor is used (anaerobes).
Advantage of aerobic metabolism: Smaller quantity of food required to maintain given rate of
metabolism.

AEROBIC RESPIRATION
In aerobic respiration,ATP forms as electrons are harvested, transferred along the electron transport chain
and eventually donated to O2 gas.
• Oxygen is required!
• Glucose is completely oxidized.
CELLULAR RESPIRATION - 3 STAGES
● Food is digested to break it into smaller pieces – no energy production here.
● Glycolysis – coupled reactions used to make ATP.
Occurs in cytoplasm
Doesn’t require O2
● Oxidation – harvests electrons and uses their energy to power ATP production.
Only in mitochondria
More powerful

ANAEROBIC RESPIRATION
Anaerobic respiration occurs in the absence of oxygen.
Different electron acceptors are used instead of oxygen (sulfur, or nitrate).
Sugars are not completely oxidized, so it doesn’t generate as much ATP.

GLYCOLYSIS
● Glycolysis – the first stage in cellular respiration.
● A series of enzyme catalyzed reactions.
● Glucose converted to pyruvic acid.
● Small number of ATPs made (2 per glucose molecule), but it is possible in the absence of oxygen.
● All living organisms use glycolysis.
● Uphill portion primes the fuel with phosphates.
● Uses 2 ATPs
● Fuel is cleaved into 3-C sugars which undergo oxidation.
● NAD+ accepts e-s & 1 H+ to produce NADH
● NADH serves as a carrier to move high energy e-s to the final electron transport chain.
● Downhill portion produces 2 ATPs per 3-C sugar (4 total).
● Net production of 2 ATPs per glucose molecule.
Summary of the enzymatically catalyzed reactions in glycolysis:

HARVESTING ELECTRONS FROM CHEMICAL BONDS

When oxygen is available, a second oxidative stage of cellular respiration takes place.
First step – oxidize the 3-carbon pyruvate in the mitochondria forming Acetyl-CoA.
Next, Acetyl-CoA is oxidized in the Krebs cycle.
PRODUCING ACETYL-COA
The 3-carbon pyruvate loses a carbon producing an acetyl group.
Electrons are transferred to NAD+ forming NADH.
The acetyl group combines with CoA forming Acetyl-CoA.
Ready for use in Krebs cycle.

The Krebs cycle is the next stage in oxidative respiration and takes place in the mitochondria.
Acetyl-CoA joins cycle, binding to a 4-carbon molecule to form a 6-carbon molecule.
2 carbons removed as CO,, their electrons donated to NAD-, 4-carbon molecules left.
2 NADH produced.
More electrons are extracted and the original 4-carbon material is regenerated.
1 ATP, 1 NADH, and 1 FADH, produced.
Each glucose provides 2 pyruvates, therefore 2 turns of the Krebs cycle.
Glucose is completely consumed during cellular respiration

USING ELECTRONS TO MAKE ATP

NADH & FADH2 contain energized electrons.
NADH molecules carry their electrons to the inner mitochondrial membrane where they transfer electrons
to a series of membrane bound proteins – the electron transport chain.

BUILDING AN ELECTROCHEMICAL GRADIENT

In eukaryotes, aerobic metabolism takes place in the mitochondria in virtually all cells.
The Krebs cycle occurs in the matrix, or internal compartment of the mitochondrion.
Protons (H+) are pumped out of the matrix into the intermembrane space.

PRODUCING ATP- CHEMIOSMOSIS

A strong gradient with many protons outside the matrix and few inside is set up.
Protons are driven back into the matrix.
They must pass through special channels that will drive synthesis of ATP.
Oxidative phosphorylation

REVIEW OF CELLULAR RESPIRATION

1 ATP generated for each proton pump activated by the electron transport chain.
• NADH activates 3 pumps.
• FADH2 activates 2 pumps.
The 2 NADH produced during glycolysis must be transported across the mitochondrial membrane using 2
ATP.
• Net ATP production = 4
FERMENTATION
In the absence of oxygen, the end-product of glycolysis, pyruvate, is used infermentation.
During glycolysis, all the NAD+ becomes saturated with electrons (NADH). When this happens,
glycolysis will stop.
2 NADH and 2 ATP produced.
Pyruvate is used as the electron acceptor resetting the NAD+ for use in glycolysis.

2 TYPES
● Animals add extracted electrons to pyruvate forming lactate.
Reversible when oxygen becomes available.
Muscle fatigue
● Yeasts, single-celled fungi, produce ethanol.
Present in wine & beer.
Alcoholic fermentation

METABOLISM OF LIPIDS
Triglycerides are broken down into glycerol and 3 fatty acid chains.
• Glycerol enters glycolysis.
• Fatty acids are oxidized and 2-C molecules break off as acetyl-CoA.
• Oxidation of one 18-C stearic acid will net 146 ATP.
• Oxidation of three glucose (18 Cs) nets 108 ATP.
• Glycerol nets 22 ATP, so 1 triglyceride nets 462 ATP.

METABOLISM OF PROTEINS
Proteins digested in the gut into amino acids which are then absorbed into blood and extracellular fluid.
•Excess proteins can serve as fuel like carbohydrates and fats.
•Nitrogen is removed producing carbon skeletons and ammonia.
•Carbon skeletons oxidized.

•Ammonia is highly toxic, but soluble.

•Can be excreted by aquatic organisms as ammonia.
•Terrestrial organisms must detoxify it first.

REGULATING CELLULAR RESPIRATION

•Rate of cellular respiration slows down when your cells have enough ATP.
•Enzymes that are important early in the process have an allosteric (regulating) site thatwill bind to ATP.
•When lots of ATP is present, it will bind to this site, changing the shape of the enzyme, halting cellular
respiration.
•Enzyme activity is controlled by presence or absence of metabolites that cause conformational changes
in enzymes.
•Improves or decreases effectiveness as catalyst.

BIOLOGICAL MOLECULES

Why is Carbon is Central to Life?

Carbon makes the core of all organic compounds
Carbon is the central element to life because all biological molecules are built on a carbon framework.
Carbon’s outer shell has only four of the eight electrons necessary for maximum stability in most
elements.
Carbon atoms are thus able to form stable, covalent bonds with a wide variety of atoms, including other
carbon atoms.

Overview: The Molecules of Life

All living things are made up of 4 classes of large biological molecules: carbohydrates, lipids, proteins,
and nucleic acids
Macromolecules are large molecules composed of thousands of covalently connected atoms
Molecular structure and function are inseparable

The Synthesis and Breakdown of Polymers

A dehydration reaction occurs when 2 monomers bond together through the loss of a water molecule
Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the
dehydration reaction.
Macromolecules are polymers, built from monomers
A polymer is a long molecule consisting of many similar building blocks
These small building-block molecules are called monomers
Three of the four classes of life’s organic molecules are polymers: Carbohydrates, Proteins, Nucleic Acids

Given the rich complexity of life on Earth, it might be surprising that the most important large molecules
found in all living things - from bacteria to elephants - can be sorted into just 4 main classes:
carbohydrates, lipids, proteins, and nucleic acids.
On the molecular scale, members of 3 of these classes - carbohydrates, proteins, and nucleic acids - are
huge & are therefore called macromolecules.
The architecture of a large biological molecule plays an essential role in its function.
Like water and simple organic molecules, large biological molecules exhibit unique emergent properties
arising from the orderly arrangement of their atoms.
A protein may consist of thousands of atoms that form a molecular colossus with a mass well over
100,000 Daltons.

CARBOHYDRATES
Carbohydrates are formed from the building blocks or monomers of simple sugars, such as glucose. These
monomers can be linked to form larger carbohydrate polymers, which are known as polysaccharides or
complex carbohydrates.

Monosaccharides
- Glucose – blood sugar or dextrose
- Fructose – fruit sugar
- Galactose – milk sugar

Disaccharides
- Lactose – milk sugar: glucose + galactose
- Maltose – malt sugar: glucose + glucose
- Sucrose – table sugar: glucose + fructose
Carbohydrates serve as fuel and building material. Include sugars and the polymers of sugars. The
simplest carbohydrates are monosaccharides or single sugars. Carbohydrate macromolecules are
polysaccharides, polymers composed of many sugar building blocks

Monosaccharides have molecular formulas that are usually multiples of CH2O

Glucose (C6H12O6) is the most common monosaccharide
Monosaccharides serve as a major fuel for cells and as raw material for building molecules
Monosaccharides are classified by
the location of the carbonyl group as aldose or ketose
the number of carbons in the carbon skeleton
Triose: 3 carbons
Pentose: 5 carbons examples: ribose & ribulose
Hexose: 6 carbons examples: glucose, galactose, & fructose
Though often drawn as linear skeletons, in aqueous solutions many sugars form rings.

A disaccharide is formed when dehydration reaction joins 2 monosaccharides. This covalent bond is
called glycosidic linkage.
Polysaccharides
the polymers of sugars, have storage and structural roles
the structure and function of a polysaccharide are determined by its sugar monomers and the positions of
glycosidic linkages

Storage Polysaccharides
Starch: storage polysaccharides of plants, consists entirely of glucose monomers. Plants store surplus
starch as granules within chloroplasts and other plastids the simplest form of starch is amylose

Glycogen
a stored form of polysaccharide in animals
humans and other vertebrates store glycogen mainly in liver and muscle cells
Structural Polysaccharides
Cellulose: major component of the tough wall of plant cells
Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ
The difference is based on 2 ring forms for glucose: alpha ( α ) and beta ( β )

Polymers with α glucose are helical

Polymers with β glucose are straight
In straight structures, H atoms on one strand can bond with OH groups on other strands
Parallel cellulose molecules held together this way are grouped into microfibrils, which form strong
building materials for plants

Enzymes that digest starch by hydrolyzing α linkages can’t hydrolyze β linkages in cellulose
Cellulose in human food passes through the digestive tract as insoluble fiber
Some microbes use enzymes to digest cellulose
Many herbivores, from cows to termites, have symbiotic relationships with these microbes

Chitin
another structural polysaccharide
found in exoskeleton of arthropods like insects, spiders, crustaceans, etc.
provides structural support for the cell walls of many fungi
chitin adds rigidity and structural support to the thin cells of the fungus, and makes fresh mushrooms crisp
Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision
heals.
LIPIDS
•composed of carbon, hydrogen, and oxygen with no definite ratio
•important component of cell membrane
•do not readily dissolve in water - the defining characteristic of all lipids
•provide insulation barriers to avoid thermal, electrical, and physical shock.
•form the waterproof waxy coatings of plant leaves known as cutin.
Note:
Proteins are considered polymers because they are made of small repeating units, but lipids are not. The
repeating unit of proteins are amino acids. The structures of lipids vary widely with many containing long
hydrocarbon tails or carbon ring structures, but no monomers.

Lipids are a diverse group of hydrophobic molecules

Lipids are the one class of large biological molecules that do not form polymers
The unifying feature of lipids is having little or no affinity for water
Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent
bonds
The most biologically important lipids are fats, phospholipids, and steroids

Energy storage: major function of fats

Humans and other mammals store fats in adipose cells
Adipose tissue cushions vital organs and insulates the body
Among the most important lipids are the triglycerides, composed of a glyceride and 3 fatty acids.
Most of the fats that human beings consume are triglycerides.

Fats
Fats are constructed from two types of smaller molecules: glycerol and fatty acids
Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon
A fatty acid consists of a carboxyl group attached to a long carbon skeleton
Fats separate from water because water molecules form hydrogen bonds with each other and exclude the
fats
In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or
triglyceride

Fatty acids vary in length (number of carbons) and in the number and locations of double bonds
Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds
Unsaturated fatty acids have one or more double bonds

Fats made from saturated fatty acids are called saturated fats, and are solid at room temperature. Most
animal fats are saturated. Fats made from unsaturated fatty acids are called unsaturated fats or oils, and
are liquid at room temperature. Plant fats and fish fats are usually unsaturated. A diet rich in saturated fats
may contribute to cardiovascular disease through plaque deposits. Hydrogenation is the process of
converting unsaturated fats to saturated fats by adding hydrogen. Hydrogenating vegetable oils also
creates unsaturated fats with trans double bonds. These trans fats may contribute more than saturated fats
to cardiovascular disease.

The major function of fats is energy storage. Humans and other mammals store their fat in adipose cells.
Adipose tissue also cushions vital organs and insulates the body. Certain unsaturated fatty acids are not
synthesized in the human body: Linoleic (omega-6 family) and linolenic acids (omega- 3 family). These
must be supplied in the diet. These essential fatty acids include the omega-3 fatty acids, required for
normal growth, and thought to provide protection against cardiovascular disease.

Phospholipids
2 fatty acids and a phosphate group are attached to glycerol
The 2 fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic
head
When phospholipids are added to water, they self-assemble into a bilayer, with the hydrophobic tails
pointing toward the interior
The structure of phospholipids results in a bilayer arrangement found in cell membranes
Phospholipids are major component of all plasma membranes or biological membranes

Steroids
another important variety of lipids
Characterized by a carbon skeleton consisting of 4 fused rings
Cholesterol, an important steroid, is a component in animal cell membranes
Although cholesterol is essential in animals, high levels in the blood may contribute to cardiovascular
disease
Examples of steroids are cholesterol and hormones like testosterone and estrogen

Waxes
Waxes have an important “sealing” function in the living world. Almost all plant surfaces exposed to air,
for example, have a protective covering made largely of wax called cutin.

Proteins (a polymer) are macromolecules composed of amino acid subunits or monomers. •These amino
acids are covalently attached to one another to form long linear chains called polypeptides, which then
fold into a specific 3-dimensional (3-D) shape. Proteins account for more than 50% of the dry mass of
most cells.

Protein Functions
Structural support, storage, transport, cellular communications, movement, and defense against foreign
substances.
Enzymatic proteins
Function: Selective acceleration of chemical reactions
Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecules.

Defensive proteins
Function: Protection against disease
Example: Antibodies inactivate and help destroy viruses and bacteria.

Storage proteins
Function: Storage of amino acids
Examples: Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants have
storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for
the developing embryo.

Transport proteins
Function: Transport of substances
Examples: Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs
to other parts of the body. Other proteins transport molecules across cell membranes.

Hormonal proteins
Function: Coordination of an organism's activities
Example: Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus
regulating blood sugar concentration

Contractile and motor proteins

Function: Movement
Examples: Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin
proteins are responsible for the contraction of muscles.

Receptor proteins
Function: Response of cell to chemical stimuli
Example: Receptors built into the membrane of a nerve cell detect signaling molecules released by other
nerve cells.

Structural proteins
Function: Support
Examples: Keratin is the protein of hair, horns, feathers, and other skin appendages. Insects and spiders
use silk fibers to make their cocoons and webs, respectively. Collagen and elastin proteins provide a
fibrous framework in animal connective tissues.
Enzymes
Enzymes are a type of protein that acts as a catalysts to speed up chemical reactions. Enzymes can
perform their functions repeatedly, functioning as workhorses that carry out the processes of life.

Polypeptides
Unbranched polymers built from the same set of 20 amino acids
Protein is a biologically functional molecule that consists of one or more polypeptides.
If a polypeptide can function by itself, then it is a protein.
If a polypeptide cannot function on its own and needs to be associated with other polypeptides in order to
function, it is a polypeptide but not a protein.

Amino Acids
Amino acids are organic molecules with carboxyl and amino groups
Amino acids differ in their properties due to differing side chains represented by the R groups

Amino Acid Polymers

Amino acids are linked by peptide bonds
A polypeptide is a polymer of amino acids
Polypeptides range in length from a few to more than a thousand monomers
Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an
amino end (N-terminus)

negatively charged r-group: aspartate, glutamate

Nonpolar, aliphatic R groups: glycine, alanine, valine, leucine, methionine, isoleucine
Polar, uncharged R groups: Serine, Threonine, Cysteine, Proline, Asparagine, Glutamine
Aromatic R groups: Phenylalanine, Tyrosine, Tryptophan
Positively charged R groups: Lysine, Arginine, Histidine

The sequence of amino acids determines a protein's three-dimensional structure

A protein's structure determines its function

Protein Structure and Function

A functional protein consists of one or more polypeptides often precisely twisted, folded, and coiled into a
unique shape. Enzymes have precise shapes.
Some proteins have areas that are not precisely folded (~30% of them).

Shapes of Proteins
globular protein: folds into a compact globular structure
Examples: hemoglobin, hormones, and enzymes

fibrous protein - it folds into a long fiber-like chain

Examples:
collagen - most abundant protein in vertebrates' bones, cartilage, and skin
keratin - component of hair, skin, and nails
fibroin - silk made by mulberry silk moth

Four Levels of Protein Structure

Primary structure: the unique sequence of amino acids in a protein is like the order of letters in a long
word. The primary structure of any protein is simply its sequence of amino acids. This sequence
determines everything else about the protein's final shape.
Secondary structure: found in most proteins, consists of coils and folds in the polypeptide chain.
Structural motifs, such as the corkscrew-like alpha helix, beta pleated sheets, and the less organized
"random coils" are parts of many polypeptide chains, forming their secondary structure.
Tertiary structure: is determined by interactions among various side chains (R groups). These motifs may
persist through a set of larger-scale turns that make up the tertiary structure of the molecule.
Quaternary structure: results when protein consists of multiple polypeptide chains. Several polypeptide
chains may be linked together in a given protein, in this case hemoglobin, with their configuration
forming its quaternary structure.

Primary Protein Structures

determined by inherited genetic
A typical primary protein structure consists of hundreds of Amino Acids arranged in linear pattern.

Secondary structure is the result of hydrogen bonding. The coils and folds of secondary structure result
from hydrogen bonds between repeating constituents of the polypeptide backbone. Typical secondary
structures are a coil called a helix and a folded structure called a B pleated sheet.

Tertiary structure is the overall 3-dimensional shape of the polypeptide and is determined by interactions
between R groups, rather than interactions between backbone constituents. These interactions between R
groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions.
Strong covalent bonds called disulfide bridges may reinforce the protein's structure.

Quaternary structure results when two or more polypeptide chains form one macromolecule
Collagen is a fibrous protein consisting of three polypeptides coiled like a rope
Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains
Transthyretin protein (four identical polypeptides)

Structure of Human Hemoglobin

What Determines Protein Structure
In addition to primary structure, physical, and chemical conditions can affect structure

Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to
unravel
This loss of a protein’s native structure is called denaturation
A denatured protein is biologically inactive
Protein Folding in the Cell
It is hard to predict a protein’s structure from its primary structure
Most proteins go through several stages on their way to a stable structure
Chaperonins are protein molecules that assist the proper folding of other proteins
Diseases such as Alzheimer’s, Parkinson’s, and mad cow disease are associated with misfolded proteins

Lipoproteins
biological molecules that are combinations of lipids and proteins
High-density (HDL) & Low-density lipoprotein (LDL)
transport cholesterol in human beings
important determinants of human heart disease

Glycoproteins
combinations of carbohydrate (glycogen)and proteins
the signal-receiving receptors found on cell surfaces often are glycoproteins

Type
Enzymes (Quicken chemical reactions) Sucrase: Positions sucrose (table sugar) in such a way that it can
be broken down into component parts of glucose and fructose
Hormones (Chemical messengers) Growth hormone: Stimulates growth of bones
Transport (Move other molecules) Hemoglobin: Transports oxygen through blood
Contractile (Movement) Myosin and actin: Allow muscles to contract
Protective (Healing; defense against invader) Fibrinogen: Stops bleeding, Antibodies: Kill bacterial
invaders
Structural (Mechanical support) Keratin: Hair, Collagen: Cartilage
Storage (Stores nutrients) Ovalbumin: Egg white, used as nutrient for embryos
Toxins (Defense, predation) Bacterial diphtheria toxin
Communication (Cell signaling) Glycoprotein: Receptors on cell surface

Nucleic acids store, transmit, and help express hereditary information

The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene
Genes are made of DNA, a nucleic acid made of monomers called nucleotides
DNA is a repository of genetic information.
The sequence of its bases encodes the information for the production of the huge array of proteins
produced by living things.
The Roles of Nucleic Acids
There are two types of nucleic acids
- Deoxyribonucleic acid (DNA)
- Ribonucleic acid (RNA)
DNA provides directions for its own replication
DNA directs synthesis of messenger RNA (MRNA) and, through mRNA, controls protein synthesis
Protein synthesis occurs in ribosomes

The Components of Nucleic Acids

Nucleic acids are polymers called polynucleotides
Each polynucleotide is made of monomers called nucleotides
Each nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups
The portion of a nucleotide without the phosphate group is called a nucleoside

DNA and Proteins as Tape Measures of Evolution

The linear sequences of nucleotides in DNA molecules are passed from parents to offspring
Two closely related species are more similar in DNA than are more distantly related species
Molecular biology can be used to assess evolutionary kinship

Nucleic Acids
Ribonucleic acid (RNA) and Deoxyribonucleic acid (DNA)
Important in protein synthesis (RNA) and in heredity (DNA)
Building block is nucleotide
Made of ribose sugar (RNA) or deoxyribose (DNA), nitrogenous base, and phosphate

Summary Table of Biological Molecules

Type of Molecule Subgroups Examples and Roles

Carbohydrates Monosaccharides Glucose: Energy source

Disaccharides Sucrose: Energy source
Polysaccharides Glycogen: Storage form of
glucose
Starch: Carbohydrate storage in
plants; used by animals in
nutrition
Cellulose: Plant cell walls,
structure; fiber in animal
digestion
Chitin: External skeleton of
arthropods

Lipids Triglycerides Fats, Oils (butter, corn oil):

3 Fatty acids and glycerol Food, energy, storage, insulation
Fatty acids Stearic Acid: Food, energy
 Components of Triglycerides sources
Steroids Cholesterol: Fat digestion,
Four-ring structure hormone precursor, cell
Phospholipids membrane component
Polar head, nonpolar tails Cell membrane structure

Proteins Enzymes: Chemically active Sucrase: Breaks down sugar

Structural Keratin: Hair
Lipoproteins: Protein-lipid HDLS, LDLS: Transport of
molecule lipids
Glycoproteins: Protein-sugar Cell surface receptors
molecule

Nucleic acids Deoxyribonucleic acid (DNA) DNA contains information for

Ribonucleic acid (RNA) the production of proteins.
One variety of RNA carries
DNA's information to the sites
of protein production, the
ribosomes; another variety of
RNA helps make up ribosomes.

Cellular Anatomy & Physiology

The Properties of Life
1. Cellular composition
2. Organization
3. Metabolic Pathways
4. Homeostasis
5. Growth
6. Reproduction
7. Regulation and Control

Levels of Organization of Life

Biosphere
Ecosystem
Community
Population
Multicellular Organism (individual)
Organ System
Organ
Tissue
Cell
a. smallest living unit
b. may be free living
c. may live as part of multicellular organisms
Organelle
Molecule
Atom
Subatomic Particles

BASIC PROPERTIES OF CELLS

Cells have highly complex and organized design.
Cells posses a genetic program and the means to use it.
Cells are capable of producing more of themselves.
Cells acquire and utilize energy.
Cells carry out a variety of chemical reactions.
Cells engage in numerous mechanical activities.
Cells are able to respond to stimuli.
Cells are capable of self-regulation.

Modern Tenets of the Cell Theory

1. All known living things are made up of cells.
2. The cell is the structural and functional unit of all living organisms.
3. All cells come from pre-existing cells by division.
4. Cells contain hereditary information which is passed from cell to cell during cell division.
5. All cells are basically the same in chemical composition.
6. All energy flow (metabolism & biochemistry) of life occurs within cells.

Cell Classification
based on complexity of structural organization
Relative Sizes: Atom, Macromolecules, Flu Virus, Cells, and Adult Human Female
COMPARISON
Parameter Prokaryotic Eukaryotic

Average size 0.1-10 um 10-100 um

Complexity Simple Complex

Organelle No membrane Membrane-bound

Nucleus No nuclear membrane Membrane-bound

(Nucleoid region)

Ribosome 70S (30S + 50S subunits) 80S (40S + 60S subunits)

Organisms Bacteria, Archae, Cyanobacteria Protista, Fungi,

(Blue-green algae) Plantae, Animalia

Differences Between Plant & Animal Cells

Plant Cells
Usually larger in size, regular in shape
Presence of cellulose in cell wall outside the cell membrane
Presence of chloroplasts containing chlorophyll
Presence of large vacuoles containing cell sap
Nucleus is located more on the periphery due to the large water-filled vacuole in the center of the cell
Have starch granules: food reserves
Animal Cells
Usually smaller in size, irregular in shape
Absence of cell wall
Absence of chloroplasts
Vacuoles are absent, or when present, they are small containing excretory or secretory products
Nucleus usually found at the central region of the cell
Have glycogen: food reserves

CELL ORGANELLES
Damage to the membrane by alcohols, quaternary ammonium (detergents), and polymyxin antibiotics can
cause leakage of cell contents.
1. Plasma membrane or Cell membrane holds the phospholipid bilayer composed of peripheral proteins,
integral proteins, transmembrane proteins, glycocalyx, sterols, and cholesterol, arranged in a fluid-mosaic
pattern; gives the cell its integrity and regulates what comes in and goes out of the cell, so that it doesn’t
lose too many nutrients, or take in too many ions; holds the different components of the cell together and
to protect it from the environment outside the cell. It also does a pretty good job of keeping harmful
things out.

Fluid-Mosaic Model of Cell Membrane

pattern of different types of molecules put together = mosaic

Membrane molecules are constantly moving in two dimensions, in a fluid fashion, similar to icebergs
floating in the ocean.

There are 3 main factors that influence cell membrane fluidity:

cholesterol
unsaturated fatty acids
temperature

Plasma Membrane Specializations

Microvilli: Finger-like projections; increase the surface area for absorption
Membrane Junctions: Tight junctions; Desmosomes; Gap junctions
Cytoplasm: substance inside the plasma membrane and outside the nucleus
Cytosol: fluid portion of cytoplasm
Cytoplasmic streaming: movement of cytoplasm throughout the cells

The Cell Wall and Glycocalyx

Cell wall: cellular structure found in plants, algae, and fungi
Carbohydrates: cellulose, chitin, glucan, mannan
Glycocalyx: carbohydrates extending from animal plasma membrane; Bonded to proteins and lipids in
membrane

2. Nucleus
has a double membrane that separates it from the cytoplasm, has pores -- > nucleopores
contains DNA in the form of chromatin threads that clump up during cell division to form chromosomes
controls structure and function through genes

3. Cytoplasm
the cellular material outside the nucleus and inside the plasma membrane
Site of most cellular activities
Contains:
Cytosol - semitransparent fluid that suspends other structures in cytoplasm.
Organelles – small organs suspended in the cytosol that perform specific

The Nucleolus
the largest structure in the nucleus of eukaryotic cells
best known as the site of ribosome biogenesis
participates in the formation of signal recognition particles and play a role in the cell's response to stress.
made of proteins, DNA and RNA and form around specific chromosomal regions called nucleolar
organizing regions (NOR).
Malfunction of nucleoli can be the cause of several human conditions called "nucleolopathies" and the
nucleolus has been investigated as a target for cancer chemotherapy.
The Intracellular Compartments
Characteristics of Intracellular Compartments
● Membrane-bound compartments
● House various cellular activities and
● metabolic activities
● Biosynthesis of secretory products
● Breakdown of long-chain fatty acids
● Regulation of trafficking within the cell

Endomembrane System
Occurs in Eukaryotic cell
Closely associated to the nuclear membrane
is defined more accurately as the set of membranes that form a single functional unit, either being
connected directly, or exchanging material through vesicle transport
Materials flow in involved structures through transport vesicles; shuttles compounds between organelles
Transport vesicle: carry membrane lipids and membrane proteins to their proper destinations and carry
soluble materials for synthesis of secretions

Organelles of the Endomembrane System

Nuclear membrane
Endoplasmic reticulum
Golgi apparatus
Lysosomes
Vesicles
Endosomes
Plasma/cell membrane
Endomembrane System does NOT include the chloroplasts, mitochondria, and peroxisome. Why?

Relative Volume Occupied by the Membrane-Enclosed Organelles in A Liver Cell (Hepatocyte)

INTRACELLULAR PERCENT OF TOTAL CELL APPROXIMATE
COMPARTMENT VOLUME NUMBER PER CELL

Cytosol 54 1

Mitochondrion 22 1700

Endoplasmic reticulum 12 1

Nucleus 6 1

Golgi Apparatus 3 1

Peroxisome 1 400

Lysosome 1 300
 Endosome 1 200

Organelle
Endoplasmic reticulum: Protein synthesis and processing, ion storage and steroid production, drug
deactivation, carbohydrate breakdown; “transport network of the cell”
Golgi complex: Assembly of lipids and proteins, involved in further CHON glycosylation, exocytosis and
endocytosis transports, forms endosomes
Lysosomes: Cellular digestion
Vacuole (plant): Multifunctional
Peroxisomes: Hydrogen peroxide metabolism

Rough Endoplasmic Reticulum

flattened structure/sheet
with ribosomes attached to the cytosolic side (outer surface) of the membrane away from the ER lumen
translation sites; new proteins immediately enter the ER lumen
processing of proteins

Endoplasmic Reticulum
Two types are distinguished morphologically but are not separate organelles
Transport of materials between the 2 ERs does not require vesicles (Both ERs are connected through their
lumen)
Cisternae: membrane-bound sacs
ER lumen: space within cisternae
ER enzymes: involved in protein synthesis and cellular export of proteins; and biosynthesis of lipids
(triacylglycerols, cholesterol and related compounds)
Biosynthesis of lipids is the major source of membrane lipids.
Continued network of flattened sacs, tubules and vesicles, occupying the cytoplasmic area
The ER is a network of membrane sheets and tubules

Cells characterized by the biosynthesis of secretory proteins have very prominent RER networks (liver
cells)
Cells producing steroid hormones contain excessive SER (Leydig cells of the testes) Smooth Endoplasmic
Reticulum
Smooth Endoplasmic Reticulum
tubular structure
lacks ribosomes
involves in drug detoxification
carbohydrate metabolism
calcium storage
steroid biosynthesis (male & female sex hormones and hormones in adrenal cortex)

Golgi Structure. A Golgi stack consists of a small number of flattened cisternae. (a) At the cis face,
transition vesicles arriving from the ER fuse with membranes of the cis-Golgi network (CGN). At the
trans face, transport vesicles arise by budding from the trans-Golgi network (TGN). The transport vesicles
carry lipids and proteins to other components of the endomembrane system or form secretory vesicles. (b)
This electron micrograph shows a Golgi stack lying next to the nuclear envelope of an algal cell (TEM).

Discovered by the Italian Biologist, Camillo Golgi (1898)

The number of Golgi stacks may vary depending on the nature of the cell.

Golgi Apparatus
membrane formation and secretion, packages proteins
a major collection and dispatch station of protein products received from the endoplasmic reticulum (ER).
proteins synthesized in the ER are packaged into vesicles, which then fuse with the Golgi apparatus.
These cargo proteins are modified and destined for secretion via exocytosis or for use in the cell.

Golgi Complex
In most eukaryotes, the Golgi apparatus is made up of a series of compartments and is a collection of
fused, flattened membrane-enclosed disks known as cisternae (singular: cisterna, also called
"dictyosomes"). Vesicular clusters bud off the endoplasmic reticulum.

A mammalian cell typically contains 40 to 100 stacks of cisternae.

This collection of cisternae is broken down into cis, medial, and trans compartments, making up two main
networks: the cis Golgi network (CGN) and the trans Golgi network (TGN).

The CGN is the first cisternal structure, and the TGN is the final, from which proteins are packaged into
vesicles destined to lysosomes, secretory vesicles and/or the cell surface.

Functions of Golgi Complex

● protein glycosylation
● protein and lipid trafficking
● lysosomal formation
● cellular transport processes
● can be thought of as similar to a post office: it packages and labels items which are sent to
different parts of the cell or to the extracellular space
 ● tends to be larger and more numerous in cells that synthesize and secrete large amounts of
substances, i.e., the antibody-secreting plasma B cells of the immune system have prominent

CGN
- Close to the ER
- vesicle fuses with CGN

TGN
Substances leave the Golgi complex in transport vesicles.
protein processing occurs in medial cisternae of the Golgi complex.

Golgi Apparatus: Pathways of Vesicular Formation

Mitochondrion
- double membrane and has folds called cristae
- contains enzymes for the synthesis of ATP
- contains DNA, thus can self-replicate
- its origin is explained by Endosymbiosis theory
Smooth outer Membrane
Folded inner membrane
Cristae: inner membrane folds
Matrix: space inside the cristae

mitochondria and plastids evolved from prokaryotic cells that took residence in larger cells and eventually
lost their independence; the cells containing the endosymbionts became dependent upon them for food
processing, and in turn provide them with a protected and rich environment (a mutualistic relationship)

Endosymbiont Theory
Supporting evidences
● the size scale is right - mitochondria and plastids are on the high end of the size of typical bacteria
● endosymbionts also have their own DNA and their own “cell” division; in many ways they act
like bacterial cells
● the DNA sequence and arrangement (circular chromosomes)of endosymbionts is closer to that of
bacteria than to that found in the eukaryotic nucleus
● endosymbionts have their own ribosomes, which are much like bacterial ribosomes
● there are other known, more modern endosymbiotic relationships: algae in corals, bacteria within
protozoans in termite guts
● DNA sequencing of endosymbionts is being used to trace the evolutionary history of the
endosymbionts
● appears that endosymbiosis began about 1.5 to 2 billion years ago (around when the first
eukaryotic cells appeared)
● mitochondria appear to have a monophyletic origin (one initial endosymbiotic event, giving rise
to all mitochondria in eukaryotic cells today)
● plastids appear to have a polyphyletic origin (more than one initial endosymbiotic event giving
rise to different plastid lines present today in algae and plants)
The subcompartments of mitochondria and chloroplasts

Ribosome
● found ‘free’ in the cytoplasm or bound to the endoplasmic reticulum (ER) to form the rough ER
● Ribosomes are different from other organelles because they have no membrane around them that
separates them from other organelles.
● When they are producing certain proteins they can become membrane-bound to the Endoplasmic
reticulum, thus
● Ribosomes are often associated with the intracellular membranes that make up the rough
endoplasmic reticulum.
● But they can also be free floating while performing their function.
● functions as a micro-machine for making proteins

formed from 2 subunits locking together that functions to:

(1) Translate encoded information from the cell nucleus provided by messenger ribonucleic acid (mRNA)
(2) Link together amino acids selected and collected from the cytoplasm by transfer ribonucleic acid
(tRNA). The order which the amino acids are linked together is determined by the mRNA.
(3) Export the polypeptide produced to the cytoplasm where it will form a functional protein.
The differences in size, sequence, structure, and the ratio of protein to RNA of ribosomes in bacteria and
humans allow some antibiotics to kill bacteria by inhibiting their ribosomes, while leaving human
ribosomes unaffected.

Svedberg (S)
• nonmetric unit for the sedimentation rate of a particle of a given size and shape that
measures how fast the particle 'settles‘ at the bottom.
• It is often used to reflect the rate at which a molecule travels to the bottom of a test tube under the
centrifugal force of a centrifuge.
(a) Ribosomes attach to ER membranes if they are synthesizing polypeptides destined for the
endomembrane system or for export from the cell. As synthesis continues, the newly forming polypeptide
is transferred across the ER membrane by COTRANSLATIONAL IMPORT. The completed polypeptide
either remains in the ER or is transported via various vesicles to another compartment of the
endomembrane system. (Integral membrane proteins are inserted into the ER membrane as they are made,
rather than being released into the ER lumen.)
(b) Ribosomes remain free in the cytosol if they are synthesizing polypeptides destined for the cytosol or
for import into the nucleus, mitochondria, chloroplasts, or peroxisomes. When the polypeptide is
complete, it is released from the ribosome and either remains in the cytosol or is transported into the
appropriate organelle by POSTTRANSLATIONAL IMPORT. Polypeptide uptake by the nucleus occurs
via the nuclear pores, using a mechanism different from that involved in posttranslational uptake by other
organelles.

LYSOSOME
● a membrane-bound organelle found in nearly all animal cells
● spherical vesicle which contains hydrolytic enzymes that can break down virtually all kinds of
biomolecules
● involved in various cell processes, like secretion, plasma membrane repair, cell signaling, and
energy metabolism
● acts as the floating waste disposal system of the cell by digesting unwanted materials in the
cytoplasm, both from outside the cell and obsolete components inside the cell
● material from the outside the cell is taken-up through endocytosis, while material from the inside
of the cell is digested through autophagy
● Discovered in 1950 by Christian de Duve and his colleagues
● Vary considerably in size (generally 0.5 μm in diameter)
● Enclosed by a single membrane
● Contain digestive enzymes (acid hydrolases) which are stored in the lysosomal lumen
● They are found in animal cells, but absent in plant cells.
Enzymes
All enzymes are hydrolases
- hydrolytic enzymes with a pH optimum 5.0
- List of enzymes includes
5 phosphatases
14 proteases and peptidases
2 nucleases
6 lipases
13 glycosidases
7 sulfatases

Functions of Lysosomes
Digest excess or worn-out and damaged organelles and other intracellular structures no longer needed by
the cell
Capable of degrading all the major classes of biological macromolecules
Degrade extracellular materials brought into the cell by endocytosis

Importance of Lysosomes
● Nutrition
● Defense
● recycling of cellular components
● differentiation

Lysosomes Developed From Endosomes

Early endosomes: vesicles budding off the trans-Golgi network that are sites for the sorting and recycling
of extracellular material brought into the cell by endocytosis.
Late endosomes: vesicle containing newly synthesized acid hydrolases plus material fated for digestion;
activated either by lowering the pH of the late endosome or transferring its material to an existing
lysosome. These are not engaged in digestive activity.

Why are lysosomes not damaged by their own enzymes?

The lumenal side of lysosomal membrane is highly glycosylated
- forms a nearly continuous carbohydrate coating
- provides protection from lysosomal proteases

Types of Lysosomes (Based on different origin)

1. Heterophagic lysosomes – those containing substances from extracellular origin
2. Autophagic lysosomes - those containing substances from intracellular origin
Lysosomes in Nutrition and Defense
Nutrition
soluble products of digestion (sugar, amino acids and nucleotides) are transported across the lysosomal
membrane into the cytosol and are used as source of nutrients of the cell; and as energy-source
Only indigestible material remains in the lysosome which becomes a residual body.

Defense
Lysosomal enzymes function in the degradation of foreign materials brought about into eukaryotic cells
by phagocytosis and cell-mediated phagocytosis.

Autophagy (self-eating) is the digestion of old or unwanted organelles or other cell structures.
Macrophagy – begins when an organelle or other structure becomes wrapped in a double membrane
derived from the ER.
Microphagy – involves formation of a much smaller autophagic vacuole, surrounded by a single
phospholipid bilayer that encloses small bits of cytoplasm rather than whole organelle.

Controversy in Botany
The term lysosome is applied to those vesicular organelles ONLY in ANIMALS while vacuoles are to
plants, fungi, and algae.
Plant vacuoles contain their own hydrolytic enzymes and perform the classic lysosomal activity, which is
autophagy. These vacuoles are therefore seen as fulfilling the role of the animal lysosome which made
some botanists strongly argued that these vacuoles are lysosomes.

However, this is not universally accepted as the vacuoles are strictly not similar to lysosomes, such as in
their specific enzymes and lack of phagocytic functions.
Vacuoles DO NOT HAVE catabolic activity and DO NOT undergo exocytosis as lysosomes do.

Peroxisomes
● membrane-enclosed organelles that contain 50 different enzymes involved in a variety of
biochemical pathways
● are morphologically similar to lysosomes
● Major function of peroxisome: breakdown of very long-chain fatty acids through beta-oxidation.
In animal cells, the long fatty acids are converted to medium-chain fatty acids, which are
subsequently shuttled to mitochondria where they are eventually broken down to CO2 and H2O.
● originally defined as organelles that carry out oxidation reactions leading to the production of
hydrogen peroxide (H2O2)
● H2O2 is harmful to the cell, so peroxisomes decompose H2O2 through its enzyme catalase.
H2O2 is either converted to water or used to oxidize another organic compound.
In animal cells, fatty acids are oxidized in both peroxisomes and mitochondria. But in yeasts and plants,
fatty acid oxidation is restricted to peroxisomes.
 ● are single bounded organelle
● are not derived from the ER, thus not part of the endomembrane system
● Smaller than mitochondria, and have varying sizes
● oxidation of fatty acids; destroys H2O2
● Found in all eukaryotic cells but are prominent in
a. mammalian kidney & liver cells
b. algae & photosynthetic plant cells
c. germinating plants
● Defining characteristics: the presence of CATALASE, an enzyme essential for the degradation of
H2O2
● H2O2 is a potentially toxic compound formed by a variety of oxidative reactions catalyzed by
oxidases.
● Contain at least one oxidase that forms the toxic molecule H2O2, as well as catalase, an enzyme
that breaks the H2O2 down into nontoxic oxygen and H2O
● The generation and degradation of H2O2 occur within the same organelle. What an irony!

Functions of Peroxisomes
Most peroxisomal functions are linked to hydrogen peroxide metabolism.
5 general functions
- hydrogen peroxide metabolism
- detoxification of harmful compounds
- oxidation of fatty acids
- metabolism of nitrogen-containing compounds
- catabolism of unusual products

Types of Peroxisomes (exclusive to plants)

Leaf peroxisomes. This is in close contact with chloroplasts and mitochondria. The close proximity of the
three organelles reflects their mutual involvement in glycolate pathway
Glyoxysomes. Occur in seedlings of plant species that store carbon and energy reserves in the seed as fat

Cytoskeleton
Network of protein structures extending throughout the cytoplasm serves as bones and muscles of the cell
Components of Cytoskeleton
- intermediate filaments
- microtubules
- microfilaments
Microtubules
- projections from the cell membrane
- arrangement: 9 pairs + 2 arrays
- cilia are small and numerous
- flagella: usually singular and long

Flagellum, Fimbriae, and Pilus

Centrioles
• collections of microtubules (9 triplets)
• found in pairs (1 pair = centrosome)
• separate chromosomes during cell division
• Rod-shaped bodies that direct the formation of mitotic spindle during cell division

Centrosome
Centrosome is made up of two centrioles
Centrosomes are microtubule-organizing centers (MTOCS) that contain y-tubulin

Cytoplasmic Inclusions
Substances in the cell like hemoglobin, glycogen and fats

Other examples:
Metachromatic granules (volutin) - phosphate reserves in certain bacteria
Polysaccharide granules - energy reserves
Lipid inclusions - energy reserves
Sulfur granules - energy reserves
Carboxysomes – bacterial microcompartments for CO2 fixation
Gas vacuoles - protein-covered cylinders
Magnetosomes - iron oxide (destroys H2O2)
Transport Across the Plasma Membrane
TOPICS OUTLINE
I. Plasma Membrane:
Composition: The Fluid Mosaic Model
Function
II. Methods of Transport Across
the Cell Membrane
A. Passive Transport
1. Simple Diffusion
2. Facilitated Diffusion
a. Channel Proteins/Ion Channels
b. Carrier/Transport Proteins
3. Osmosis & Tonicity
B. Active Transport
1. Ion Pump
2. Bulk Transport
a. Endocytosis: It is the means by which larger molecules and particles move through membranes
enclosed by vesicles that are formed by sections of infolding/invaginating cell membrane.
receptor-mediated endocytosis
phagocytosis & pinocytosis
b. Exocytosis

Fluid-Mosaic Model of Plasma

movements of phospholipid molecules
• A feature of Singer-Nicolson model
• Lateral mobility: movement parallel to membrane surface
• Some membranes like those of RBCs can have restricted mobility
one side of phospholipid
layer can be attached to
cytoskeleton

membrane Proteins
membrane lipids
• Some major classes of lipids in membranes: phospholipids, glycolipids, and sterols
• Fatty acids are essential to membrane structure and function
• Membrane asymmetry is due to unequal distribution of lipids between the 2 monolayers
• Most lipids are free to move laterally that creates an impression of membrane fluidity

EO Proteins
Integral proteins (Amphipathic)
Peripheral proteins (Not amphipathic)
Proteins can function as carrier, channel, ion pump (integral proteins) and enzyme and some controllers of
intracellular function (peripheral proteins).
INTEGRAL PROTEINS
Amphipathic
Hydrophobic region in the midsection of the bilayer
Hydrophilic region exposed to aqueous solutions on outside and inside of cell

different types of membrane proteins

GPI glycosylphosphatidylinositol - cell membrane
● GPI-anchored peripheral proteins: released by Phospholipase C for phosphatidylinositol linkages
● AMPs: antimicrobial peptides-act like detergents disrupting membrane structure causing holes to
destroy permeability & kill cells; also anti-viral in membrane enclosed viruses like HIV.

phospholipid
Hydrophilic head - water loving
Hydrophobic tail - water hating

Phospholipids are Building Blocks of Cellular Membranes. The hydrophilic head group and hydrophobic
tails are the keys to phospholipid function.

nonpolar hydrophobic tails (fatty acids) exposed to oil

polar hydrophilic heads exposed to water

Membrane Permeability
Plasma membranes are semi-permeable: this means that some substances can pass through and others
cannot.
What is it that determines what substances pass through?
The substance has to be very soluble in the oily phospholipid bilayer. Steroid hormones, oxygen and CO2
are examples of such molecules.
SOLUBLE: steroid hormone, oxygen, carbon dioxide
INSOLUBLE: Glucose, Protein, Lipid

Membrane Flow: is the continual movement and recycling of the plasma membrane; The ER, Golgi
apparatus, and vesicles constantly recycle the lipids, protein channels, and enzymes.
Relative permeability of a phospholipid bilayer to various
Type of substance Examples Behavior

Gases CO2, N2, O2 Permeable

Small uncharged polar Urea, water, and ethanol Permeable, totally or partially
molecules

Large uncharged polar glucose, fructose Not permeable

molecules

lons K+, Na+, Cl-, HCO3-, Not permeable

Charged polar molecules ATP, amino acids, and Not permeable

glucose-6-phosphate

Methods of Transport Across Membranes

1. Passive Transport
a. Diffusion/Simple Diffusion: net movement of material from high to low concentration area. Ex:
O2 & CO2 transport across the plasma membrane
b. Osmosis: diffusion of water across a differentially permeable plasma membrane
c. Facilitated Diffusion: diffusion of materials with the aid of carrier proteins ex: transport of
glucose and amino acids
2. Active Transport
a. ion pump
b. bulk transport
phagocytosis: (a) endocytosis (b) exocytosis

Passive transport occurs without expenditure of energy. Molecules move using their own kinetic energy.
Passive transport allows cells to get water, oxygen and other small molecules that they need. It also allows
the cell to get rid of waste such as carbon dioxide.

1. Diffusion: the movement of particles down its concentration gradient - i.e., as molecules or ions, from a
region of higher concentration to a region of lower concentration
2. Facilitated Diffusion: differs from simple diffusion because it involves "facilitation" of the process by
proteins that form part of the structure of the membrane. Not to be confused with simple diffusion, is a
form of passive transport mediated by transport proteins or channel proteins embedded within the cellular
membrane to facilitate solute movement across the plasma membrane. Allows the passage of lipophobic
molecules through the cell membrane’s lipid bilayer. Molecules, particles, and ions travel freely across the
cellular membrane from high concentration to low concentration in an attempt to achieve equilibrium.
a. Channel proteins have hollow cores that enable ions and small polar molecules to cross the
membrane by passing through channel proteins (provides a "channel" for passage of particle)
b. Carrier proteins bind to a particle, e.g. a large polar sugar molecule, then move it across the
membrane, releasing it on the other side of the phospholipid bilayer. ("Carries" particle)
Diffusion: Molecules in solution tend to slowly spread apart over time. Movement of molecules or ions
from an area of higher concentration to an area of lower concentration.

factors that affect diffusion

• Molecules move constantly in a random manner at a rate that depends on their mass, their environment,
and the amount of heat energy they possess, which in turn is a function of temperature.
• This movement accounts for the diffusion of molecules through whatever medium in which they are
localized.
• A substance will tend to move into any space available to it until it is evenly distributed throughout it.
• After a substance has diffused completely through a space removing its concentration gradient,
molecules will still move around in the space, but there will be no net movement of the number of
molecules from one area to another.
• This lack of a concentration gradient in which there is no net movement of a substance is known as
dynamic equilibrium.

1. Extent of the concentration gradient: The greater the difference in concentration, the more rapid
the diffusion. The closer the distribution of the material gets to equilibrium, the slower the rate of
diffusion becomes.
2. Mass of the molecules diffusing: Heavier molecules move more slowly; therefore, they diffuse
more slowly. The reverse is true for lighter molecules.
3. Temperature: Higher temperatures increase the energy and therefore the movement of the
molecules, increasing the rate of diffusion. Lower temperatures decrease the energy of the
molecules, thus decreasing the rate of diffusion.
4. Solvent density: As the density of a solvent increases, the rate of diffusion decreases. The
molecules slow down because they have a more difficult time getting through the denser medium.
If the medium is less dense, diffusion increases. Because cells primarily use diffusion to move
materials within the cytoplasm, any increase in the cytoplasm's density will inhibit the movement
of the materials. Example: a person experiencing dehydration: As the body's cells lose water, the
rate of diffusion decreases in the cytoplasm, and the cells' functions deteriorate. Neurons tend to
be very sensitive to this effect. Dehydration frequently leads to unconsciousness and possibly
coma because of the decrease in diffusion rate within the cells.

Factors governing diffusion across lipid membranes

1. Solute size
2. Solute polarity
3. Ion permeability
 5. Solubility: nonpolar or lipid-soluble materials pass through plasma membranes more easily than
polar materials, allowing a faster rate of diffusion.
6. Surface area and thickness of the plasma membrane: Increased surface area increases the rate of
diffusion, whereas a thicker membrane reduces it.
7. Distance traveled: The greater the distance that a substance must travel, the slower the rate of
diffusion. This places an upper limitation on cell size. A large, spherical cell will die because
nutrients or waste cannot reach or leave the center of the cell. Therefore, cells must either be
small in size, as in the case of many prokaryotes, or be flattened, as with many single-celled
eukaryotes.

Osmosis: Water molecules move down the concentration gradient or from an area of greater to lower
concentration across a semipermeable membrane.

tonicity is a relative term

Hypotonic: contains a low concentration of solute relative to another solution
Hypertonic: contains a high concentration of solute relative to another solution
Isotonic: both solutions have same concentrations of solute.

Over time molecules will move across the membrane until the concentration of solutes is equal on both
sides. This type of solution is called ISOTONIC.

• Cytoplasm is a solution of solids solutes dissolved in water.

• Water moves into and out of cells because of the different concentrations of the solutes.
• Illustrations above are examples of RBCs in different types of solutions and shows what happen to the
red blood cells.

PLANT CELLS
Hypotonic Solution
TURGID CELL: water enters by osmosis, vacuole swells and pushes against cell wall.
Turgor pressure builds in the cell and causes osmosis to stop because of the rigid cell wall.

Hypertonic Solution
FLACCID CELL: water lost from cell, vacuole shrinks, cell loses shape
Plants will wilt when cells lose water through osmosis.
plant and animal cells placed in various solutions

cytolysis and plasmolysis

cytolysis: Cells placed in distilled water; Cells swell and burst
Plasmolysis: Cells placed in concentrated salt solution; Cells shrink and shrivel; RBCs become crenated
Note: Crenation describes the formation of abnormal notched or scalloped surfaces on cells as a result of
water loss through osmosis.

If osmosis continued, the animal cell would burst. This would be bad news for animals. Consequently
there are processes in the animal’s body which control osmosis. Mainly, this is done by keeping the
concentration of body fluids outside the cell the same as it is inside.

Perch: The fish gets rid of the excess water by means of its kidneys.

gills absorb water by osmosis

blood carries water to kidneys
kidneys expel excess water
in the form of dilute urine
seawater fish
Herring Fish
Sea water is a more concentrated solution than the fish’s blood. What will be the osmotic effect ? A sea
water fish will lose water by osmosis through its gills. The fish drinks sea water and the gills expel the
excess salt from the blood, so keeping its concentration constant.

In a plant cell, the cell membrane acts as a selectively permeable membrane.

The cell wall is freely permeable to water.
The vacuole contains a solution of salts and sugars.
If there is water outside the cell, it will diffuse by osmosis into the vacuole.
The vacuole will expand, pushing the cytoplasm outwards against the cell wall.
The cellulose cell wall cannot stretch, so the vacuole cannot continue to expand.
But the pressure of the vacuole against the cell wall makes the cell very firm.
A plant cell in this condition is said to be turgid.
If all the cells in the plant are turgid, the plant will be firm and upright and the leaves would be expanded.

Limp and Turgid Plant Cells

Limp: These cells are short of water; the tissue is limp and the plant is wilting.
Turgid: The cells have taken up water by osmosis; the cells are turgid and the tissue is firm. Limp and
Turgid Plant Cells

(1) wilting
(2) recovering
(3) recovered
Busy Lizzie

facilitated diffusion works by having channel proteins of different

sizes (like a sieve) or ion channels which allow larger, or charged
molecules to diffuse in/out of cell; The passage of materials is aided
both by a concentration gradient and by a transport protein.
simple diffusion: Materials move down their concentration gradient
through the phospholipid bilayer

ANALOGY
NO ENERGY NEEDED:
Diffusion
Osmosis
Facilitated Diffusion

ENERGY NEEDED: Active Transport

Active Transport
ATP pump, Symport, Antiport,
Molecules again move through a transport protein, but now energy must be expended to move them
against their concentration gradient. Most living cells maintain internal environments that are different
from their extracellular environment, as well as concentration differences between the cytosol and internal
compartments. In human tissues, for example, all cells have a higher concentration of Na+ outside the cell
than inside, and a higher concentration of K+ inside the cell than outside. These concentration gradients
of Na+ and K+ represent a form of energy storage, similar to a battery. An example of a concentration
difference between the cytosol and an internal compartment is found in lysosome, where the
concentration of hydrogen ions (H+) can be 100 to 1000 times greater than the concentration outside, in
cytosol.

Like pushing an object uphill, moving a molecule against a concentration gradient requires energy. Cells
have evolved active transport proteins that can use energy to establish and maintain concentration
gradients. Active transport enzymes couple net solute movement across a membrane to ATP hydrolysis.
An active transport pump may be a uniporter or antiporter.

ATP-powered Pumps ATP-powered pumps (ATPases) couple the splitting, or hydrolysis, of ATP with the
movement of ions across a membrane against a concentration gradient. ATP is hydrolyzed directly to
ADP and inorganic phosphate, and the energy released is used to move one or more ions across the cell
membrane. As much as 25% of a cell's ATP reserves may be spent in such ion transport. Examples
include: The Na+-K+ ATPase pumps Na+ out of the cell while it pumps K+ in. Because the pump moves
three Na+ to the outside for every two K+ that are moved to the inside, it creates an overall charge
separation known as polarization. This electrical potential is required for nervous system activity, and
supplies energy needed for other types of transport such as symport and antiport.

Ca++ ATPases are responsible for keeping intracellular

Ca++ at low levels, a necessary precondition for muscle contraction.

If a proton gradient is established by the breakdown of other molecules, the transport process works in
reverse to synthesize ATP from ADP and phosphate, using the energy of the proton gradient.

Step 1. Three Na+ ions bind to cytoplasmic high-affinity binding sites.

Step 2. ATP is hydrolyzed, transferring a phosphate group to the pump.
Step 3. The pump conformation changes, moving Na+ ions to the extracellular side of the membrane.
Step 4. Na+ ions dissociate, and two K+ ions bind to high-affinity extracellular sites.
Step 5. The bond linking phosphate to the pump protein is hydrol yzed, releasing inorganic phosphate.
Step 6. The pump conformation changes, moving K+ ions to low-affinity cytoplasmic sites.
Step 7. K+ ions dissociate, and the pump is ready for another cycle.
Example
Action Potential: Generation and Transmission of neural impulse
Exergonic hydrolysis of ATP to drive endergonic influx of K +ions and outward efflux of Na+ ions
resulting to asymmetric distribution of ions.

Antiport
In antiport, a cell uses movement of an ion across a membrane and down its concentration gradient to
power the transport of a second substance "uphill" against its gradient. In this process, the two substances
move across the membrane in opposite directions.

summarizing operation of an antiporter

Step 1. Two substrates bind to the opposite sides of the transporter. One substrate (Na+ ion) is traveling
"downhill", and will energize transport of the other substrate (Ca2+ ion).
Step 2. The transporter changes orientation with respect to the inner and outer surfaces of the membrane.
Step 3. After being transported across the membrane, both substrates are released, and the protein is ready
for another cycle.

Example process is the transport of Ca2+ ions out of cardiac muscle cells. Muscle cells are triggered to
contract by a rise in intracellular Ca2+ concentration, so it is imperative that Ca2+ be removed from the
cytoplasm so that the muscle can relax before contracting again. This antiport system is so effective that it
can maintain the cellular concentration of Ca2+ at levels 10,000 times lower than the external
concentration.

Symport: Example process is the transport of amino acids across the intestinal lining in the human gut.
To transport some substances against a concentration gradient, cells use energy already stored in ion
gradients, such as proton (H+) or sodium (Na+) gradients, to power membrane proteins called
transporters. When the transported molecule and the co-transported ion move in the same direction, the
process is known as symport.

Step 1. Two substrates bind to the extracellular side of the transporter. One substrate (Na+ion) is traveling
"downhill", and will energize transport of the other substrate (ami no acid).
Step 2. The transporter changes orientation with respect to the inner and outer surfaces of the membrane.
Step 3. After being transported across the membrane, both substrates are released, and the protein is ready
for another cycle.

SUPPLEMENTAL CONCEPTS
The plasma membrane is a highly dynamic organelle and fences off pathogens with considerable
efficiency. Besides segregation, it coordinates cell migration, information processing, and endo- and
exocytosis during signaling and homeostasis. It also transmits information between neighboring cells or
cells at a distance. Viruses take advantage of the plasma membrane in various ways. They bind to
attachment factors, move laterally, and interact with secondary signaling receptors, or engage into
endocytosis or fusion with the plasma membrane. All of these events determine if a particular cell gets
infected or resists against the pathogen. For many viruses, the interactions with attachment factors and
receptors are well characterized, and endocytic pathways have been mapped and in part integrated with
cell signaling. Only recently, however, attention has been focused on lateral motions of viruses at the
plasma membrane prior to uptake.

MIDTERM
CELLULAR RESPIRATION

Inside every cell of all living things, energy is required to carry out life processes. Energy is needed to
break down and build up molecules and to transport many molecules across the plasma membranes. All of
life’s work demands energy. A lot of energy is also simply lost to the environment as heat. The story of
life is a story of energy flow — its capture, its change of form, its use for work, and its loss as heat.
Energy , unlike matter, cannot be recycled, so organisms require a constant input of energy. Life runs on
chemical energy. Where do living organisms get this chemical energy? Where do organisms get energy
from? The chemical energy that organisms need comes from food. Food consists of organic molecules
that store energy in their chemical bonds. Glucose is a simple carbohydrate that stores chemical energy in
a concentrated, stable form. In our body, glucose is the form of energy that is carried in blood and taken
up by each of our trillions of cells. Cells carry out cellular respiration to extract energy from the bonds of
glucose and other food molecules. Cells can store the extracted energy in the form of ATP (adenosine
triphosphate). This inviting campfire can be used for both heat and light. Heat and light are 2 forms of
energy that are released when a fuel like wood is burned. The cells of living things also obtain energy by
"burning." They "burn" glucose in the process called cellular respiration.

● a set of metabolic reactions and processes that take place in the cells of organisms to convert
chemical energy from oxygen molecules or nutrients into adenosine triphosphate (ATP), and then
release waste products
● the process by which living cells break down glucose molecules and release energy
● The process is similar to burning, although it doesn’t produce light or intense heat as a campfire
does. This is because cellular respiration releases the energy in glucose slowly, in many small
steps. It uses the energy that is released to form molecules of ATP, the energy-carrying molecules
that cells use to power biochemical processes
● involves many chemical reactions, but they can all be summed up with this chemical equation:
Glycolysis in the Cytoplasm

Citric Acid Cycle in the Mitochondria

MAJOR STAGES OF CELLULAR RESPIRATION
To see how a glucose molecule is converted into carbon dioxide (CO2) and how its energy is harvested as
ATP and NADH/FADH2 in one of our body's cells, let’s walk step by step through the 4 stages of cellular
respiration.
1. Glycolysis (glai·kaa·luh·suhs) glucose - a six-carbon sugar - undergoes a series of chemical
transformations. It gets converted into 2 pyruvate molecules, a three-carbon organic molecule. In
these reactions, ATP is made, and NAD+ is converted to NADH. Glycolysis can occur without
O2: fermentation
2. Pyruvate oxidation (pai-roo-veit) Each pyruvate from glycolysis goes into the mitochondrial
matrix – the innermost compartment of mitochondria. There, it’s converted into a two-carbon
molecule bound to Coenzyme A, known as Acetyl CoA. CO2 is released and NADH is generated.
3. Citric acid cycle The Acetyl-CoA from pyruvate oxidation combines with oxaloacetate (a four-
carbon molecule) and goes through a cycle of reactions, ultimately regenerating the four-carbon
starting molecule. Hence a cycle. ATP, NADH and FADH2 are produced, and CO2 is released.
4. Oxidative phosphorylation (TCE and Chemiosmosis) NADH and FAD2 deposit their electrons
in the electron transport chain (ETC), turning back into their "empty" forms NAD+ and FAD. As
electrons move down the chain, energy is released and used to pump protons out of the matrix,
forming a gradient. Protons flow or stream back into the matrix through an enzyme called ATP
synthase, making ATP. At the end of the ETC, oxygen (O2) accepts electrons and takes up
protons or H+ to form water (H2O).

Pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation - require O2 to occur. Only
oxidative phosphorylation uses O2 directly, but the other 2 stages can't run without oxidative
phosphorylation.

Summary of Glycolysis
 ● In Chemistry, intermediate means a molecule or substance or compound formed from the
reactants and reacts further to produce the final essential product(s).
● Most chemical reactions are stepwise (step by step) which take more than one basic or primary
step to complete the entire process.
● In the process of converting biomolecules into several intermediates in the TCA Cycle, NADH
& FADH2 are formed.
● These 2 energy-rich molecules (NADH & FADH2) proceed to another series of chemical
reactions in the Electron Transport Chain (ETC).

Tricarboxylic Acid Cycle (TCA) refers to the 3 carboxyl groups (-COOH) found in the first 2
intermediates of the cycle: Citrate, Isocitrate

The overall reaction of the Tricarboxylic Acid Cycle

Where’s all the have ATP gone?

You may be thinking that the ATP output of the TCA Cycle seems pretty unimpressive. All that series of
chemical reactions for just one ATP or GTP? It’s true that the cycle doesn’t produce much ATP directly.
However, it can make a lot of ATP indirectly, by way of the NADH and FADH2 it generates. These
electron carriers, NADH and FADH2, will connect with the last stage of cellular respiration, depositing
their electrons into the ETC to drive synthesis of ATP molecules through oxidative phosphorylation. The
TCA Cycle is a central driver of cellular respiration. It takes Acetyl-CoA produced by the oxidation of
pyruvate and originally derived from glucose - as its starting material and, in a series of redox reactions,
the cycle harvests much of its energy in the form of NADH, FADH2, and ATP molecules. The reduced
electron carriers NADH and FADH2 generated in the TCA cycle will pass their electrons into the ETC.
Through oxidative phosphorylation, most of the ATP molecules produced in cellular respiration are
generated.
Oxidative Phosphorylation
● takes place in the inner membrane of mitochondrion
● the pathway that forms ATP as a result of the transfer of electrons from NADH or FADH2 to O2
by a series of electron carriers.
● is powered by the movement of electrons through the electron transport chain made of a series of
proteins embedded in the inner membrane of the mitochondrion.
● is made up of 2 closely connected processes: the electron transport chain and chemiosmosis or
phosphorylation reaction.
● In electron transport chain (ETC), electrons are passed from one electron acceptor to the next e-
acceptor.
● energy released in these electron transfers is used to form an electrochemical gradient resulting in
the synthesize ATP.
● electrochemical gradient indicates the difference in solute concentration across a membrane, and
the difference in charge across the inner membrane of mitochondrion

Why do we need oxygen? Like many other organisms, we need oxygen to live. If you’ve ever tried to
hold your breath for too long, lack of oxygen can make you feel dizzy or even black out, and prolonged
lack of oxygen can cause death. But have you ever wondered what exactly our body does with all that
oxygen? The reason we need oxygen is so our cells can use this molecule during oxidative
phosphorylation, the final stage of cellular respiration. In ETC of Oxidative Phosphorylation, electrons
are passed from one electron acceptor to another, and energy released in these electron transfers is used to
form an electrochemical gradient. Oxygen sits at the end of the ETC, where it accepts electrons and picks
up protons to form water. If oxygen isn’t there to accept electrons (for instance, because a person is not
breathing in enough oxygen), the ETC will stop functioning, and ATP will no longer be produced by
chemiosmosis. Without enough ATP, cells can’t carry out the reactions they need to function, and, after a
long enough period of time, may even die.

All of the electrons that enter the ETC come from NADH and FADH2, the 2 molecules produced during
earlier stages of cellular respiration: glycolysis, pyruvate oxidation, and the citric acid cycle. NADH is
very good at donating electrons in redox reactions (that is, its electrons are at a high energy level), so it
can transfer its electrons directly to complex I, turning back into NAD+ . As electrons move through
complex I in a series of redox reactions, energy is released, and the complex uses this energy to pump
protons from the matrix into the intermembrane space. FADH2 is not as good at donating electrons as
NADH (its electrons are at a lower energy level), so it cannot transfer its electrons to complex I. Instead,
it feeds them into the transport chain through complex II, which does not pump protons across the
membrane.
Oxidative Phosphorylation
Carried out by 4 closely related membrane-bound complexes (Complex I, II, III, IV), 2 electron carriers
NADH & FADH2, and coenzyme Q and cytochrome C.
● In a series of oxidation-reduction reactions, electrons from FADH2 and NADH are transferred
from one complex to the next until they reach O2 molecule.
● O2 is reduced to H2O. ½ O2 + 2H+ H2O + energy
● As a result of electron transport, protons are pumped across the inner membrane to the
intermembrane space.

Mitochondrion: The Site of Cellular Respiration

Intermembrane space Small space to quickly accumulate protons
Matrix Has appropriate enzymes and a suitable pH for the Krebs cycle
Outer membrane Contains transport proteins for shuttling pyruvate into mitochondrion
Inner membrane Contains ETC and ATP synthase for oxidative phosphorylation
Cristae Highly folded so as to increase SA:Vol ratio

Complexes I, III, and IV of the ETC are proton pumps. As electrons move energetically downhill, the
complexes capture the released energy and use it to pump H+ ions from the matrix to the intermembrane
space. This pumping forms an electrochemical gradient across the inner mitochondrial membrane. The
gradient is sometimes called the proton-motive force that is a form of stored energy, kind of like a battery.
Like many other ions, protons can't pass directly through the phospholipid bilayer of the membrane
because its core is too hydrophobic. Instead, H+ ions can move down their concentration gradient only
with the help of channel proteins that form hydrophilic tunnels across the membrane. In the inner
mitochondrial membrane, H+ ions have just one channel available: a membrane enzyme known as ATP
synthase. Conceptually, ATP synthase is a lot like a turbine in a hydroelectric power plant. Instead of
being turned by water, it’s turned by the flow of H+ ions moving down their electrochemical gradient. As
ATP synthase turns, it catalyzes the addition of a phosphate to ADP (phosphorylation) and form the ATP.
Oxidative Phosphorylation: ETC + Chemiosmosis
A. As electrons (e~) move through the electron transport chain, hydrogen lons (H+) are pumped
from the matrix into the intermembrane space.
B. A hydrogen ion gradient is formed, with a higher concentration of lons in the intermembrane
space than in the matrix.
C. When hydrogen ions flow back into the matrix down their concentration gradient, ATP is
synthesized from ADP + P, by an ATP synthase complex.

Coupling of Oxidation & Phosphorylation Reactions

To explain how electron and H+ transport produce the chemical energy of ATP, Peter Mitchell proposed
the Chemiosmotic Theory:
● The energy-releasing oxidations give rise to proton pumping and a pH gradient is created across
the inner mitochondrial membrane.
● There is a higher concentration of H+ (protons) in the intermembrane space than the matrix of
mitochondrion.
● This proton gradient or electrochemical gradient provides the driving force to propel the protons
back into the mitochondrion through the enzyme complex called proton translocating ATPase.

Proton gradient: difference in the concentration of protons across the membrane During oxidative
phosphorylation, high energy electron is passed along ETC in the inner mitochondrial membrane in
eukaryotes. This linked set of proteins carry out redox reactions which release energy. The energy
released by electrons flowing through this transport chain, pumps H ions out of the matrix space across
the inner mitochondrial membrane. The gradient created drives H ions to stream back across the
membrane, through an enzyme called ATP synthase. This process is called chemiosmosis.
Coupling of Oxygen and Phosphate
● Protons flow back into the matrix through channels in the F0 unit of ATP synthase.
● The flow of protons is accompanied by formation of ATP in the F1 unit of ATP synthase.

The functions of oxygen are:

● To oxidize NADH to NAD+ and FADH2 to FAD so that these molecules can return to participate
in the Citric acid cycle.
● Provide energy for the conversion of ADP to ATP.

Oxidative Phosphorylation: ETC + Chemiosmosis

As electrons are passed from one e- acceptor to the next (move down) in the ETC, some of the carriers
transport H+ ions from one side of the membrane to the other which causes a H+ gradient to form across
the membrane. This gradient is then used to drive ATP synthesis as the H+ ions move along their
concentration gradient through the ATP synthase protein found in the inner membrane of mitochondrion.
The proton gradient created in ETC is then used for chemiosmosis. As H+ ions flow down their gradient,
they pass through an enzyme called ATP synthase, which uses the flow of protons to make ATP.

Oxidative Phosphorylation
The overall reactions of oxidative phosphorylation:

Oxidation of each NADH yields 3ATP.

Oxidation of each FADH2 yields 2 ATP.
The table below describes the reactions involved when one glucose molecule is fully oxidized into carbon
dioxide. It is assumed that all the reduced coenzymes are oxidized by the electron transport chain and
used for oxidative phosphorylation.
STEP COENZYME YIELD ATP YIELD SOURCE OF ATP

Glycolysis preparatory phase -2 Phosphorylation of glucose and fructose 6-phosphate uses two
ATP from the cytoplasm.

Glycolysis pay-off phase 4 Substrate-level phosphorylation

2 NADH 3 OR 5 Oxidative phosphorylation : Each NADH produces net 1.5 ATP

(instead of usual 2.5) due to NADH transport over the
mitochondrial membrane

Oxidative decarboxylation of 2 NADH 5 Oxidative phosphoryiation

pyruvate

Krebs cycle 2 Substrate-level phosphorylation

6 NADH 15 Oxidative phosphorylation

2 FADH2 3 Oxidative phosphorylation

Total yield 30 OR 32 From the complete oxidation of one glucose molecule to

ATP carbon dioxide and oxidation of all the reduced coenzymes.

Although there is a theoretical yield of 38 ATP molecules per glucose during cellular respiration, such
conditions are generally not realized because of losses such as the cost of moving pyruvate (from
glycolysis), phosphate, and ADP (substrates for ATP synthesis) into the mitochondría. All are actively
transported using carriers that utilize the stored energy in the proton electrochemical gradient.

Synthesis of Glucose
Glycogenesis: the synthesis of glycogen from glucose
Gluconeogenesis: the synthesis of glucose from noncarbohydrate sources
These sources are most commonly pyruvate, citric acid cycle intermediates, and glucogenic amino acids.

GLUCOSE AS ENERGY SOURCE

● When glucose is in adequate supply, such as shortly after consumption of a meal, the hormone
insulin from the pancreas increases glycogen formation (glycogenesis) in the liver.
● When glucose levels drop between meals, the hormone glucagon is released from the pancreas
and stimulates the conversion of glycogen into glucose (by the process of glycogenolysis).
● If all glycogen supplies are depleted, then other substances in the body are converted into glucose
or intermediate products that can enter the above-outlined cellular respiration pathway.
● The conversion of fatty acids (from lipids) or amino acids (from proteins) into glucose or
intermediate products is called gluconeogenesis.
Cori Cycle (Lactic Acid Cycle) the metabolic pathway in which lactate produced by glycolysis in the
muscles moves to the liver, where gluconeogenesi s converts it back to glucose, then returns to the
muscles and is metabolized back to lactate.

PROTEIN AS ENERGY SOURCE

Proteins are used as an energy source only if protein intake is high, or if glucose and fat sources are
depleted, in which case amino acids from protein breakdown are converted into molecules that can enter
the TCA Cycle. These molecules are produced by either of two categories of reactions that alter the
structure of amino acids. Transamination transfers an amino group (NH2) from one amino acid to another,
whereas deamination removes an amino group from an amino acid. As they accumulate, the amino groups
removed by the process of deamination are altered to form a harmful waste product (ammonia), that must
be converted by the liver into urea which is excreted by the kidneys.

LIPID AS ENERGY SOURCE

Fats (lipids) are stored in adipose tissue. These stored fat molecules are synthesized in the body from the
breakdown products of fat digestion (glycerol and fatty acids), in a process known as lipogenesis. When
needed as an energy source, the fat reserves are mobilized, moved out of adipose tissue, and broken down
into glycerol and fatty acids in the liver by the process of lipolysis. Glycerol is changed into one of the
intermediate products of glycolysis, so enters the cell respiration pathway. Fatty acids are changed in a
series of reactions called beta-oxidation into acetyl CoA molecules, which enter cell metabolism at the
Kreb's Cycle or TCA Cycle. When fats are being used as the primary energy source such as in starvation,
fasting or untreated diabetes, an excess amount of acetyl CoA is produced, and is converted into acetone
and ketone bodies. This produces the sweet smell of acetone on the breath, noticeable in a diabetic state.
Summary of Key Questions
1. What are the principal compounds of the Common Metabolic Pathway
● ATP- a phosphate carrier
● CoA - the C2 fragment carrier that combines with oxaloacetate in the Citric Acid Cycle
● NADH+ and FADH2 - carry the H+ (protons) and electrons
● ADP - the unit common to all carriers. The nonactive end of the carriers acts as a handle
that fits into the active sites of the enzymes.

2. How do electron and H+ (proton) transport take place?

● The electrons of NADH enter the Electron Transport Chain (ETC).
● For each NADH, 6 H+ ions are expelled. For each FADH2, 4 H+ ions are expelled from
the matrix of the mitochondrion to the intermembrane space.
● The electrons passed to complex IV return to the matrix and combine with oxygen and
H+ to form water.

3. What is the role of the Chemiosmotic Pump in ATP production?

● Both the TCA and oxidative phosphorylation take place in the mitochondria
● When the H+ ions expelled by electron transport stream back into the mitochondrion,
they drive a complex enzyme called proton-translocating ATPase which makes 1 ATP
molecule for each 2 H+ ions that enter the mitochondrion.
● The proton-translocation ATPase is a complex “rotor engine”
● The proton channel part (F0) is embedded in the membrane and the Catalytic unit (F1)
converts mechanical energy to chemical energy of the ATP molecule.

4. How long does the chemical energy in ATP last?

Chemical energy is stored in ATP only for a short time – ATP is quickly hydrolyzed, usually within a
minute.

5. What is the energy yield resulting from electron and H+ transport?

● For each NADH from TCA Cycle = 3 ATP molecules are formed
● For each FADH2 = 2 ATP molecules are formed
● For each Acetyl-CoA that enters the TCA Cycle = 12 ATP molecules are produced in
Oxidative Phosphorylation.

Note:
TCA cycle runs twice for 1 glucose molecule. Glycolysis produces 2 molecules of pyruvate, each
molecule is converted into Acetyl-CoA. One molecule of Acetyl-CoA makes 1 cyclic function for TCA.
CATABOLIC PATHWAYS
1. What is the general outline of Catabolic Pathways?
● The foods we eat consist of carbohydrates, lipids, an proteins.
● There are specific breakdown pathways for each kind of nutrient.
2. What are the general details about glycolysis?
● The specific pathway of carbohydrates catabolism is glycolysis
● A reaction that occurs in the cytoplasm of the cell, converting glucose into pyruvate.
● Pyruvate is converted to Acetyl-CoA which is further catabolized in the common
pathway.
3. How does glycerol catabolism take place?
● Fats are broken down to glycerol and fatty acids
● Glycerol is catabolized in the glycolysis pathway and yields 20 ATP molecules.
4. How is the nitrogen of amino acids processed in catabolism?
● Proteins are broken down to amino acids. The nitrogen of the amino acids is first
transferred to glutamate.
● Glutamate is oxidatively deaminated to yield ammonia.
● Mammals get rid of the toxic ammonia (NH3) by converting it to Urea in the Urea Cycle;
urea is secreted in urine.

the ff. statements are true, regarding energy , except.

energy , like matter , can not be recycled, in organisms require a constant input of energy.

energy that comes from food are called, what?

chemical

it is called simple carbohydrates.

glucose

true about cellular respiration , except.

a set of metabolic reactions that take place in the cell to convert mechanical energy from oxygen or
nutrient to ATP.

which of the following is a 5 carbon sugar?

pentose

it is the central driver of cellular reapiration.

tricarboxylic acid cycle

which of the ff. reactions ,does not require oxygen to occur?

fermentation

true about oxidative phosphorylation , except.

takes place in the inner membrane of the ribosomes
the final stage of cellular respiration
oxidative phosphorylation

which of the ff. does not describe oxidative phosphorylation.

electron foe FADH2and NADH are transferred from one complex to the next untill they reach carbon
molecule.

the site of cellular respiration.

mitochondria

which of the ff. complexes in the electron transport chain , is not a proton pump?
complex 2

process whereby is synthesize for glucose.gluconeogenesis

gluconeogenesis

otherwise known as cori cycle.

lactic acid cycle

process whereby an amino acid is transferred from one amino acid to anothr.
transamination

site for fat storage.adipose tissue

adipose tissue

in the oxidation of NADH,it will yields how many ATP!S

3

process whereby glycolysis can occur with out O2.

fermentation

a reaction wghereby NAD is converted into NADH creating an ATP.

glycolysis

the precursor of polysaccharides

glucose
Animal Tissues

Epithelial tissue lines surfaces the body

Muscle tissue is made up of fibers that contract
Nervous tissue consists of cells with projections that transmit electrical signals

Connective tissues:
Loose connective tissue acts as padding under skin and elsewhere.
Bone and cartilage are connective tissues made up of cells in a hard or stiff extracellular matrix.
Blood is a connective tissue made up of cells in a liquid matrix.

Structure fits function at all levels of organization in the animal body

Anatomy: the study of structure
Physiology: is the study of function

Animals consist of a hierarchy of levels of organization

Tissues: array/group of similar cells that perform a common function
Organs: consist of a group of 2 or more tissues in living organism that been adapted to perform a specific
task or function
Organ systems: consist of multiple organs that together perform a vital body function

Levels of Organization
A. Cellular Level: Muscle Cell
B. Tissue Level: Muscle Tissue
C. Organ Level: Heart
D. Organ System Level: Circulatory System
E. Organism Level: All Organ Systems Functioning Together

Animals have 4 main categories of tissues

4 Types of Animal Tissues: Epithelial, Connective, Muscle, and Nervous
Tissues are an integrated group of similar cells that perform a common function
Tissues are combined to form organs
Tissues are groups of cells with a common structure and function

Epithelial Tissues or Epithelia come in 3 shapes

● Squamous - shaped like a fried egg
● Cuboidal - as tall as they are wide
● Columnar - taller than they are wide
Epithelial tissues are named according to
● the number of cell layers they have
● the shape of the cells on their apical surface
Transitional epithelium is a stratified tissue in which the cells are all have a fairly round shape when the
organ it lines is not distended (stretched out). When the tissue is stretched, the cells, especially those on
the surface, become flat. This allows organs lined with transitional epithelium to change shape without
damaging epithelial lining.

Simple cuboidal epithelial cells line tubules in the mammalian kidney, where they are involved in filtering
the blood.

Squamous epithelia cells (a) have a slightly irregular shape, and a small, centrally located nucleus. These
cells can be stratified into layers, as in (b) this human cervix specimen. (credit b: modification of work by
Ed Uthman; scale-bar data from Matt Russell)

Epithelia are Polar

• anchored on one surface, but free on another, the free side is typically exposed to the environment or
body fluids
• can be single layer or many layers thick Functions: protection, secretion, and absorption
• Epithelial cells are continuously sloughing off and are replaced by new ones through cell division
• Epithelial cells lining the small intestine

Epithelial tissue
● formed by cells that cover the body and organ surfaces
surface of skin, airways, inner lining of the digestive tract, reproductive tract
● provides a barrier between the external environment and the organ it covers
● protect organs from microorganisms, injury, and fluid loss
● because epithelium is found on the edges of organs, it has
● two distinct surfaces: (1) apical surface (2) basal surface
● the underside of epithelial tissue is anchored by a basement membrane to a connective tissue

Types of Epithelial Tissue

Other cellular features, such as cilia may also be described in the classification system. Some common
kinds of
epithelium are:
• Simple squamous epithelium
• Stratified squamous epithelium
• Simple cuboidal epithelium
• Transitional epithelium
• Pseudostratified columnar epithelium or Ciliated columnar epithelium
• Columnar epithelium
• Glandular epithelium

A. Simple squamous epithelium: lungs; Underlying tissue, Apical surface of epithelium, Basal lamina,
Cell nuclei
B. Simple cuboidal epithelium: kidney
C. Simple columnar epithelium: stomach
D. Stratified squamous epithelium: esophagus

Normal intestinal tissue (cross section of digestive tract)

Mucosa:
Epithelium
Connective tissue
Thin muscle layer

Submucosa
Thick muscle layers
Subserosa
Serosa

Different Types of Epithelial Tissues

Squamous: flat, irregular round shape; located in simple: lung alveoli, capillaries stratified: skin, mouth,
vagina
Cuboidal: cube shaped, central nucleus; located in glands, renal tubules
Columnar: tall, narrow, nucleus toward base tall, narrow, nucleus along cell; location in simple: digestive
tract, pseudostratified: respiratory tract
Transitional: round, simple but appear stratified; located in urinary bladder
Connective Tissues bind and support other tissues are grouped into 6 major types
1. Loose connective tissue
• is the most widespread connective tissue in animals
• consists of ropelike collagen & elastic fibers that are strong and resilient, helps to join skin to underlying
tissues
• called loose because fibers are loosely woven together

2. Fibrous connective tissue

• has densely packed collagen fibers
• forms tendons that attach muscle to bone; and ligament, a fibrous connective tissue which attaches bone
to bone, and usually serves to hold structures together and keep them stable.

3. Adipose tissue
• stores fat in large, closely packed cells held in a matrix of fibers, for storage of energy (fat), insulation,
padding for organs

4. Cartilage
• is a strong and flexible skeletal material, commonly surrounds the ends of bones
• cushions joints, forms support for ears and nose

5. Bone
• has a matrix of collagen fibers embedded in a hard mineral substance containing calcium, magnesium,
and phosphate

6. Blood
• transports substances throughout the body, WBCs fight infections

A. Loose connective tissue (under the skin): Cell nucleus, Collagen fiber, Elastic fibers
B. Fibrous connective tissue (forming a tendon): Cell nucleus, Collagen fibers
C. Adipose tissue: Fat droplets
D. Cartilage (at the end of a bone): Cartilage forming cells, Matrix
E. Bone: Central canal, Matrix, Bone forming cells
F. Blood: White blood cells, Red blood cell, Plasma

Connective Tissues
Adipose is a connective tissue is made up of cells called adipocytes. Adipocytes have small nuclei
localized at the cell edge. Loose connective tissue is composed of loosely woven collagen and elastic
fibers. The fibers and other components of the connective tissue matrix are secreted by fibroblasts.

Connective Tissue: Bone

(a) Compact bone is a dense matrix on the outer surface of bone. Spongy bone, inside the compact bone,
is porous with web-like trabeculae.
 (b) Compact bone is organized into rings called osteons. Blood vessels, nerves, and lymphatic vessels are
found in the central Haversian canal. Rings of lamellae surround the Haversian canal. Between the
lamellae are cavities called lacunae. Canaliculi are microchannels connecting the lacunae together.
(c) Osteoblasts surround the exterior of the bone. Osteoclasts bore tunnels into the bone and osteocytes
are found in the lacunae.

Blood is a connective tissue that has a fluid matrix, called plasma, and no fibers. Erythrocytes (red blood
cells), the predominant cell type, are involved in the transport of oxygen and carbon dioxide. Also present
are various leukocytes (white blood cells) involved in immune response.

Types of Connective Tissues

Tissue Cells Fibers Location

loose/areolar Fibroblasts, macrophages, some few: collagen, elastic, reticular around blood vessels; anchors
lymphocytes, some neutrophils epithelia

fibrous Fibroblasts, macrophages mostly collagen irregular: skin

regular: tendons, ligaments

cartilage Chondrocytes, chondroblasts hyaline: few collagen shark skeleton, fetal bones, human
fibrocartilage: large amount of ears, intervertebral discs
collagen

bone Osteoblasts, osteocytes, osteoclasts some: collagen, elastic Vertebrate skeletons

adipose adipocytes few adipose (fat)

blood RBCs, WBCs none blood

Muscle Tissue: functions in movement, most abundant animal tissue
Skeletal Muscle causes voluntary movements
Cardiac Muscle pumps blood, Only found in heart, Striated, Involuntary, undergoes rhythmic contractions
to produce heartbeat, Branched, interlocking cells propagate signal to contract almost simultaneously
Smooth Muscle moves walls of internal organs such as the intestines, Spindle-shaped cells, Musculature
of organs, blood vessels, and digestive tract, Involuntary, Contracts more slowly and for longer than
skeletal muscle

Nervous tissue senses stimuli and rapidly transmits information, forms a communication network
Neurons: carry signals by conducting electrical impulses
Other cells in nervous tissue
•insulate axons,
•nourish neurons, and
•regulate the fluid around neurons
The neuron has projections called dendrites that receive signals and projections called axons that send
signals. Also shown are two types of glial cells: astrocytes regulate the chemical environment of the nerve
cell, and oligodendrocytes insulate the axon so the electrical nerve impulse is transferred more efficiently.

Organs and Organ Systems

Organs are made up of tissues
• Each tissue performs specific functions
• The heart has extensive muscle that generates contractions, epithelial tissues that line the heart
chambers, prevent leaks, and form a smooth surface for blood flow, connective tissues that make the heart
elastic and strong, and neurons that regulate contractions.
• The small intestine is lined by a columnar epithelium, includes connective tissues that contain blood
vessels, has two layers of smooth muscle that help propel food
• The inner surface of the small intestine has many finger-like projections that increase the surface area
for absorption.

Organ systems work together to perform life’s functions

● Each organ system typically consists of many organs, has one or more functions, and works with
other organ systems to create a functional organism.
● the circulatory system delivers oxygen and nutrients to the body cells, transports CO2 to the
lungs, carries metabolic, wastes to the kidneys
● the respiratory system exchanges gases with the environment, supplying the blood with oxygen,
disposing of carbon dioxide.

the muscular system

• moves the body
• maintains posture
• produces heat.

integumentary system protects against

• physical injury
• infection
• excessive heat or cold
• drying out

the skeletal system

• supports the body
• protects organs such as the brain and lungs
• provides the framework for muscle movement

digestive system
• ingests and digests food
• absorbs nutrients
• eliminates undigested material
 Urinary system
• removes waste products from the blood, excretes urine
• regulates the chemical makeup, pH, and water balance of blood

endocrine system
• secretes hormones that regulate body activities

lymphatic system
• returns excess body fluid to the circulatory system

lymphatic & immune systems

• protect the body from infection and cancer

Nervous system coordinates body activities by

• detecting stimuli, integrating information, and directing responses

The female reproductive system

• supports a developing embryo
• produces milk

The reproductive system produces

• gametes and
• sex hormones

Function Epithelial tissue covers the body and Connective tissue binds and supports Muscle tissue functions in Nervous tissue forms a
lines its organs and cavities. other tissues. movement. communication network.

Structure Sheets of closely packed cells Sparse cells in extracellular matrix Long cells (fibers) with contractile Neurons with branching extensions;
proteins supporting cells

Example Columnar epithelium Loose connective tissue Skeletal muscle Neuron

these are large deposits of fats that bind and support other tissues.
adipose

epithelium is for protction, because of the ff reasons, except.

the acidity of the perspiration
it has plenty of water substance

part of the neuron that receives the signal.

dendrites
female endocrine structures , except ..
testis

thanx to this tissue , we are able to move.

chondrocytes
osteocytes
osteoclasts

polar structure that covers our body and other body surfaces.
epithelium

youve heard my lecture, you understood my explaination, because of this tissue.

nervous

type of neuron according to structure , except.

tripolar

two or more organs combined together is called.

system

the only connective tissue having no fibers.bone tissue

blood tissue

which of the ff. is not a function of the muscular system.

produce blood

these are not found in the digestive system .

ovaries

true about smooth muscle tissue , except.

voluntary

type of epithelium that line the organs for urine formation.

cuboidal
squamous
columnar

neuron according to functions , except.

unipolar

type of tissue considered as soldier cells.

white blood cells
outgrowths of the integumentary system , except
melanin

a stratified tissue in which the cells are flat when it is distented.

pseudo strtified
simple cuboidal
transitional

young bone cells

chondrocytes
osteocytes
osteoclasts

system that delivers oxygen and nutrients to the body.

circulatory system

MITOSIS
Overview: The Key Roles of Cell Division
The ability of organisms to produce more of their own kind best distinguishes living things from
nonliving matter.
The continuity of life is based on the reproduction of cells, or cell division.
In unicellular organisms, division of one cell reproduces the entire organism.
Cell division enables multicellular eukaryotes to develop from a single cell and, once fully grown, to
renew, repair, or replace cells as needed.
Cell division is an integral part of the cell cycle - the life of a cell from its formation to its own division.

Cell division results in the distribution of identical genetic material (DNA) to 2 daughter cells.
DNA is passed from one generation of cells to the next with remarkable fidelity.
All DNA in a cell constitutes the cell’s genome. A genome consists of a single DNA molecule (in
prokaryotic cells) or a number of DNA molecules (in eukaryotic cells).
The DNA molecules in a cell are packaged into chromosomes.

Distribution of Chromosomes During Eukaryotic Cell Division

● In preparation for cell division, DNA is replicated and chromosomes condense.
● Each duplicated chromosome has two sister chromatids - joined identical copies of the original
chromosome.
● Centromere closely attaches the 2 chromatids

Eukaryotic chromosomes consist of chromatin, a complex of DNA and protein.

Every eukaryotic species has a characteristic number of chromosomes in each cell nucleus
Somatic cells (nonreproductive cells) have 2 sets of chromosomes
Gametes (reproductive cells: sperm and eggs) have one set of chromosome

Eukaryotic cell division consists of

Mitosis: the division of the genetic material in the nucleus
Cytokinesis: the division of the cytoplasm
Gametes are produced by a variation of cell division called meiosis
Meiosis yields nonidentical daughter cells that have only one set of chromosomes, half as many as the
parent cell.

Mitosis is conventionally divided into 5 phases

(for some authors)
1. Prophase
2. Prometaphase
3. Metaphase
4. Anaphase
5. Telophase
6. Cytokinesis overlaps the latter stages of mitosis

Interphase
cell growth occurs duplication of chromosomes in preparation for cell division
about 90% of the cell cycle can be divided into subphases
● G1 phase (“first gap”)
● S phase (“synthesis”)
● G2 phase (“second gap”)
The cell grows during all 3 phases, but chromosomes are duplicated only during the S phase.

The Three Major Stages of the Cell Cycle

In Every Rule Is An Exception...
cells that do not divide:
● neurons
● cardiomyocytes
● skeletal muscle cells
● erythrocytes
● few pancreas cells
● liver cells - no cytokinesis

1. Interphase
2. Mitosis
a) Prophase
b) Metaphase
c) Anaphase
d) Telophase
3. Cytokinesis

Chromatins, Chromatids, Chromosomes... Which is Which?

At the end of S phase, a cell has twice as many chromatids as there were chromosomes in G1 phase
i.e. - human cell
- 46 chromosomes in G1 phase
- 46 pairs of sister chromatids in G2 phase
Chromosome is thus a relative term
In G1, anaphase, & telophase: Chromosome is equivalent to one chromatid
In G2, prophase, & metaphase: Chromosome refers to a pair of sister chromatids

Centromere and Kinetochore

The centromere is the part of a chromosome that links sister chromatids or a dyad.
During mitosis, spindle fibers attach to the centromere via the kinetochore.
The kinetochore forms in eukaryotes, assembles on the centromere and links the chromosome to
microtubule polymers from the mitotic spindle during mitosis and meiosis.

Centrioles evolved as a refinement of the cell, making mitosis a much more efficient and less error-prone
process

Spindle Apparatus
• Composed of microtubules that originate from centrioles
• Microtubules are formed polymerization of tubulin proteins

3 Types of Spindle Microtubules

• Aster microtubules: for positioning of the spindle apparatus
• Polar microtubules: help to “push” the poles away from each other
• Kinetochore microtubules: attached to the centromere

Kinetochore Spindle Fibers

The function of astral microtubules can be generally considered as determination of cell geometry.
They are absolutely required for correct positioning and orientation of the mitotic spindle apparatus, and
are thus involved in determining the cell division site.

The diagram depicts the organization of a typical mitotic spindle found in animal cells. Chromosomes are
attached to kinetochore microtubules via a multiprotein complex called the kinetochore. Polar
microtubules interdigitate at the spindle midzone and push the spindle poles apart via motor proteins.
Astral microtubules anchor the spindle poles to the cell membrane. Microtubule polymerization is
nucleated at the microtubule organizing center.

During prophase, the microtubules within the centrosome begin lengthening toward the chromosomes in
the nucleus. The microtubules are referred to as spindles at this point. Spindles orchestrate the careful
organization and segregation of chromosomes between daughter cells during mitosis. Some of the
microtubules extending from the centrosome also participate in cytokinesis after the last stage of mitosis.

Formation of the Spindle in Plant Cells

Most plants do not contain centrioles, but instead have microtubule clusters that function to direct the
distribution of chromosomes. They also participate in splitting the cell during cytokinesis. During
prophase, the plant cell begins to produce spindles from the organizing centers that grow into the nuclear
region and attach to the chromosomes. From there, they orchestrate the organization and segregation of
chromosomes between daughter cells during mitosis.

Interphase
• Intact nuclearn envelope
• Visible nucleolus
• Although you can’t tell it, the cell’s DNA and other cell components are undergoing a process called
replication (duplication process); chromosomes become double-stranded
• Chromosomes are decondensed
• chromosomes replicate
• The centrosome divides
Nuclear membrane
Decondens ed chromosomes
Two centrosomes (each with centriole pairs)

Prophase
• Nuclear envelope dissociates
• Centrosomes move to opposite poles
• mitotic spindle apparatus forms
Microtubules forming mitotic spindle
Sister chromatids
Centromere

Mitosis = Karyokinesis
Prophase
• Disappearing nuclear envelope and nucleolus
• Chromosomes (46 in each human cell = 23 pairs of chromosomes) coil and condense.
• Spindle fibers (microtubules) form and chromosomes become attached through the centromeres.
• Newly formed centrioles move to opposite ends of the cell.

The Mitotic Spindle

The mitotic spindle is a structure made of microtubules and associated proteins
It controls chromosome movement during mitosis
In animal cells, assembly of spindle microtubules begins in the centrosome, a type of microtubule
organizing center
The spindle includes the centrosomes, the spindle microtubules, and the asters
The centrosome replicates during interphase, forming two centrosomes that migrate to opposite ends of
the cell during prophase and prometaphase
An aster (radial array of short microtubules) extends from each centrosome

Prometaphase
• Spindle fibers bind kinetochores
• The 2 kinetochores on a pair of sister chromatids are attached to kinetochore MTs from opposite poles
• some spindle microtubules attach to the kinetochores of chromosomes and begin to move the
chromosomes
• Kinetochores are protein complexes that assemble on sections of DNA at centromeres

Metaphase
• Pairs of sister chromatids (chromosomes) align themselves at the metaphase plate.
• the centromeres of all the chromosomes are at the metaphase plate
• an imaginary structure at the midway point between the spindle’s two poles

Mitosis = Karyokinesis
Metaphase
Characterized by:
1. Chromosomes align across the “equator” or metaphase plate.
2. Centrioles stop at opposite ends of the cell.
3. Spindle apparatus is fully formed.

Anaphase
• Sister chromatids separate
• Centromeres separate
• Each chromatid is linked to only 1 pole
• Kinetochore MTs shorten
Chromosomes move to opposite poles
• Polar MTs lengthen
Poles themselves move further away from each other
• Spindle fibers (microtubules) shorten and separate the chromosomes at the metaphase plate.

The microtubules shorten by depolymerizing at their kinetochore ends. Chromosomes are also “reeled in”
by motor proteins at spindle poles, and microtubules depolymerize after they pass by the motor proteins

Telophase & Cytokinesis

• Chromosomes reach poles & decondense
• Nuclear membrane reforms
• Quickly followed by cytokinesis
In animal cells
- formation of a cleavage furrow
In plant cells
 - Formation of a cell plate

Telophase
1. Cleavage furrow forms.
2. Nuclear envelopes begin to form around 2 nuclei.
3. Chromosomes decondense.
4. Spindle fibers disappear.

Cytokinesis: Division of cytoplasm and its contents into 2 cells

Some Key Points

Mitosis ultimately produces two daughter cells genetically identical to the mother cell
● Barring rare mutations
Processes requiring mitotic cell division
● Development of multicellularity
● Organismal growth
● Wound repair
● Tissue regeneration

Prometaphase: Chromosomes associated to mitotic spindle

Metaphase: Chromosomes congressed in the metaphase plate
Anaphase: Sister chromatid separation

Cell Cycle
One outcome can be guaranteed from several ongoing studies: mitosis will continue to fascinate biologists
for the next century as it has done for the past 100 years!

MEIOSIS
two Part Cell Division
A cell division that produces GAMETES/SEX CELLS with a number of CHROMOSOMES as many as
half the number of chromosomes as the diploid cell.
DIPLOID (2n) – 2 sets of chromosomes
HAPLOID (n) – 1 set of chromosomes
Meiosis is a form of SEXUAL reproduction
TWO divisions - MEIOSIS I and MEIOSIS II

• Sex cells divide to produce gametes (sperm cells or oocytes)

• Gametes have only half of the number of chromosomes as the mother cell or only one set of
chromosomes
• Occurs only in gonads (testes or ovaries)
• Male: SPERMATOGENESIS
spermatogonium = 4 sperm cells
• Female: OOGENESIS
oogonium = 1 egg cell or ovum & 3 polar bodies

Meiosis I: Reduction Division

Cell division that reduces the chromosome number by 1/2
Four phases:
a. Prophase I
b. Metaphase I: Chiasmata hold homologues together. The kinetochores of sister chromatids fuse
and function as one. Microtubules can attach to only one side of each centromere.
c. Anaphase I: Microtubules pull the homologous chromosomes apart, but sister chromatids are held
together.
d. Telophase I

Mitosis
a. Metaphase: Homologues do not pair; kinetochores of sister chromatids remain separate;
microtubules attach to both kinetochores on opposite sides of the centromere.
b. Anaphase: Microtubules pull sister chromatids аpart.

MEIOSIS I : Interphase
similar to mitosis interphase
chromosomes (DNA) replicate in the synthesis (s) phase
each duplicated chromosome consists of two identical sister chromatids attached at their centromeres
centrioles replicate also

A pair of homologous chromosomes, each in the unduplicated state (most often, one from a male parent
and ts partner from a female parent)
A gene locus (plural, loci), the location for a specific gene on a specific type of chromosome
A pair of alleles (each being a certain molecular form of a gene) at corresponding loci on a pair of
homologous chromosomes
Three pairs of genes (at three loci on this pair of homologous chromosomes): same thing as three pairs of
alleles

Homologues/Homologs/ Homologous Chromosomes

Pair of chromosomes (maternal and paternal) that are similar in shape, size and gene loci
Homologous pairs (tetrads) carry GENES controlling the SAME inherited traits.
Each locus (gene location) is in the same position on homologues/homologs.
Humans have 23 pairs of homologous chromosomes:
a. First 22 pairs of autosomes
b. Last pair of sex chromosomes 10

Prophase I: Synapsis – Homologs Pair Up!

Non-Sister Chromatids - HOMOLOGS
Homologous chromosomes contain DNA that codes for the same genes. In this example, both
chromosomes have all the same genes in the same locations (repre- sented with colored strips), but
different 'versions' of those genes (represented by the different shades of each color). Sister chromatids
are exact replicas. but homologous chromosomes are not.

Longest and most complex phase

Chromosomes condense.
Synapsis occurs
- Homologous chromosomes pair up/lie side by side
- Homologous chromosomes come together to form a tetrad
Tetrad – consists of two chromosomes or four chromatids (sister and non-sister chromatids).

Prophase I: Crossing Over

Crossing over occurs between non-sister chromatids at sites called chiasmata
Crossing over: segments of non-sister chromatids break and reattach to the other chromatid sections of
chromosomes from homologues are swapped or exchanged during prophase I of meiosis.
In humans, 2-3 cross over parts are formed per chromosome pair.
The result: chromosomes after meiosis are genetically unique from one another having DNA
combinations derived from both parents.

Causes Genetic Recombination

Chiasmata: points where chromosomes come in contact and exchange genes
chiasma - singular
chiasmata – plural

Genetic Recombination
Crossing-over multiplies the already huge number of different gamete combinations produced through
independent assortment.

Anaphase I
Homologs or Homologous chromosomes separate and move towards the opposite poles.
Sister chromatids remain attached at their centromeres.

Telophase I
Each pole now has haploid (n) set of chromosomes
Cytokinesis occurs and two haploid daughter cells are formed.

Meiosis II
No Interphase II
No DNA Replication
Remember: Meiosis II is similar to Mitosis

Prophase II
Nucleus & nucleolus disappear
Chromosomes condense
Spindle fiber or mitotic spindle forms

Metaphase II
Chromosomes (not homologs) line up at equator of cell

Anaphase II
Sister Chromatids separate

Telophase II
Nuclei and Nucleoli reform, spindle fibers disappear
Cytokinesis or division of the cytoplasm occurs
4 new haploid cells are produced (1 ovum, 3 polar bodies in oogenesis)
Each haploid cell is genetically different from the other
Spermatogenesis
- takes 2 months from start to finish
- Every day, hundred of millions sperms are made!
- Spermatogonia (2n) are the cells in the testes that undergo meiosis specifically spermatogenesis

Primary spermatocytes (2n)

- formed during Meiosis I
- have 23 pairs of homologues including X and Y hromosomes

Spermatids (n)
- formed during Meiosis II
- have 23 chromosomes, one of which is an X or a Y
Spermatozoa (n) or sperm cell
- “streamlined” cell

Oogenesis
- Two divisions produce 3 polar bodies that degenerate or disintegrate and 1 viable egg ready to get
fertilized
- The 1 ovum gets all the resources (cytoplasm, mitochondria)
- Polar bodies die because of unequal division of cytoplasm
- Oogonia (2n) - 2 millions are formed in the ovaries of a girl fetus before birth!
- Primary oocytes (2n) – immature eggs formed when oogonium divides; contain 23 pairs of homologs
and 2 X chromosomes
- Developmental arrest in Meiosis I for 15-30 years, until a girl reaches puberty
- At the onset of puberty, follicle-stimulating hormone (FSH)
- triggers a few primary oocytes to progress through meiosis every 28 days.
Oocyte Maturation
During early fetal life, oogonia proliferate by mitosis.
Before birth, oogonia enlarge to form primary oocytes.
Primordial follicle: primary oocyte surrounded by a single layer of flattened epithelial cells
Primary follicle: enlarged primary oocyte surrounded by zona pellucida and a single layer of columnar
follicular epithelial cells
Secondary follicle: primary follicle with more than one layer of follicular cells

An overview of Spermatogenesis (human male)

An overview of Oogenesis (human female)

 The Fate of OOCYTES
• Primary oocytes are formed prenatally (before birth) and remain suspended in prophase 1 for years until
the onset of puberty.
• Long duration of first meiotic arrest may cause high frequency of meiotic errors such as non-disjunction.
• Completion of Meiosis I: a day before ovulation as its follicle matures resulting in a secondary oocyte
and the FIRST 2 polar bodies.
• After ovulation, each oocyte continues to Metaphase of Meiosis II.
• Meiosis II is completed only if fertilization occurs, resulting in a fertilized mature ovum and the second
polar body.

So in short, the oocyte is stuck in metaphase II until fertilization occurs?

• Yes, the secondary oocyte stays in metaphase II throughout ovulation until fertilization occurs.
• Upon fertilization, the secondary oocyte and polar body are formed.
• If no fertilization occurs, the secondary oocyte (still in meiosis II) is expelled via menstruation.

1. Prenatal (before birth) Primary oocytes are produced at fetal stage of female human. Growth is
arrested in Prophase I.
2. Postnatal (afterbirth) Primary oocytes remain dormant until puberty. Shortly before ovulation,
primary oocyte increases in size and complete first meiotic division to form secondary oocyte
with first polar body.
3. During Ovulation Secondary oocyte begins secondary division; is arrested in Metaphase II.
4. If Fertilization occurs 2nd meiotic division resumes & produces the 2nd polar body.

COMPARISON
mitosis meiosis
All chromosomes align at metaphase plate Homologous pairs of chromosomes align

One set of divisions: Two sets of divisions:

P–M–A–T PI - MI – AI – TI
PII – MII – AII – TII

2 daughter cells 4 daughter cells (male)

1 cell and 3 polar bodies (female)

daughter cells diploid daughter cells haploid (n; half the number of
(2n; same as original cell) chromosomes as the original diploid cell)

Growth and repair Formation of sex cells

Variation (reshuffling of genes)

Also known as genetic recombination
Important to population as the basic requirement for NATURAL SELECTION
All organisms are NOT alike.
The most fit and NOT the strongest survives to reproduce and pass on the heritable traits.

Fertilization: “putting it all together”

Karyotype
• An organized picture of human chromosomes arranged in pairs based on size, from largest to smallest.
• Pairs 1-22 are called AUTOSOMES
• Last pair is composed of SEX CHROMOSOMES

The drug colchicine inhibits the formation of spindle fibers. If you treat dividing cells with colchicine,
what would you expect the result to be?
Chromosomes would divide in interphase (S phase) and enter mitosis. However, the spindle apparatus
would not form, so the chromosomes would end up in the metaphase form and no further mitotic events
would take place. In fact, this kind of approach is used to produce the chromosomes shown in human
karyotypes (displays of the full chromosome set). In these karyotypes the chromosomes are highly visible
because they are at their most condensed, and they are in the X form because the chromosomes have
duplicated and the two chromatids of each chromosome are still attached by the centromere.

1. Centromere: A specialized thin region, often referred to as the ‘primary constriction’, on a

chromosome. It is composed of highly condensed heterochromatin that serves as the platform for
the assembly of kinetochores.
2. Kinetochore: A structure that assembles on mitotic chromosome to attach to microtubules of the
spindle.
3. Spindle assembly checkpoint: A surveillance mechanism that monitors the attachment state of
individual chromosomes. The checkpoint blocks anaphase onset until the kinetochores are
attached to microtubules of the spindle.
4. Congression: The process by which chromosomes align at the spindle equator.
5. Bi-oriented: describes the attachment of a chromosome to microtubules emanating from opposite
spindle poles.
6. Centromeric heterochromatin: Distinct regions of chromatin at the centromere of a chromosome
that are highly condensed and contribute to specifying the location of kinetochore assembly.
7. Astral microtubule: A microtubule that emanates from the spindle pole to the cell cortex
8. Mono-oriented: describes the attachment of a chromosome to microtubules coming from a single
spindle pole.

Taxonomy & Classification

The Three-Domain System
Domain Archaea (ar-KEE-ə)
• prokaryotic single celled organisms
• they lack peptidoglycan in the cell wall
• live in conditions that are too extreme for other forms of life. Thermophiles thrive at temperatures as hot
as 90°C and are found in deep- sea volcanic vents and hot springs.

Domain Bacteria
• includes the prokaryotes
• most bacterial species are heterotrophic; that is, they acquire their food from organic matter
• the largest number of bacteria are saprobic, meaning that they feed on dead or decaying organic matter
• Includes the pathogenic or disease-causing bacteria

Levels of Taxonomic Classification

Kingdom
Phylum
Class
Order
Genus
Species

Chordates with pharyngeal gill slits and a dorsal hollow nerve cord, at some time in their development,
are few distinguishing features of these organisms

Classification Categories
● The higher the category, the more inclusive.
● Organisms in the same domain have general characteristics in common.

DOMAIN ARCHAEA
• prokaryotic, unicellular organisms, with cell wall
• can survive the greatest extremes in temperature or salt concentration or absence of oxygen gas

DOMAIN BACTERIA
• prokaryotic, unicellular organisms, with cell wall
• cell walls contain peptidoglycan

KINGDOM PROTISTS
• diverse collection of organisms. While exceptions exist, they are primarily microscopic and unicellular,
or made up of a single cell.

KINGDOM FUNGI
• best characterized as eukaryotic, heterotrophic, and having the chitinous cell walls
• Molds or deuteromycota, are grouped into this kingdom that consists of mostly multicellular organisms
that are constructed of hyphae.

KINGDOM PLANTAE
• multicellular, terrestrial autotrophs with cell walls of cellulose, and alternating life cycles

KINGDOM ANIMALIA
• Multicellular, heterotrophs, diploid stages as their dominant generation in the life cycle

LIVING ORGANISM: All living organisms are divided into 3 domains

Archae
Eukaryotes
Bacteria

Each domain is divided into number of kingdoms

Under Eukaryotes:
Kingdom animalia
Kingdom plantae
Kingdom protista
Kingdom fungi

Under Kingdom Animalia:

Each Kingdom is divided into number of Phylums e.g Porifera, Cnidaria, Chordata
Chordata: Animals with notochord, tail, nerve cord would fall into this phylum
Each Phylum is divided into number of Classes e.g Mammalia, Amphibia, Reptilia
Mammalia: Animals with mammary gland, hair fur would fall into this class
Each Class Is divided into number of Subclasses e.g Monotremes , Placental mammals
Placental: Mammals that depend on placenta e.g. Carnivores (dog), Primates
Each Subclass Is divided into number of Orders e.g. Primates
Primates: Mammals that have enlarged brain, an opposable thumb. e.g humans, gorilla
Each Order is divided into number of Families e.g. Hominidae, Apes...
Hominidae: Mammals that can stand erect would fall into this family
Each Family Is divided into number of Genus e.g Homo
Homo: Mammals that walk upright on two legs
Each Genus is divided into number of Species
Sapience: Wise

Body Symmetry
Bilateral Symmetry: shown by animals having anterior, posterior, dorsal, and ventral surfaces on its body.
Only one slice can divide left and right sides into mirror-image halves.
Radial symmetry. Parts radiate from the center, so any slice through the central axis divides into mirror
images.
Body Cavity

(a) No body cavity: for example, flatworm

(b) Pseudocoelom: a body cavity only partially lined by the mesoderm, the middle tissue layer; for
example, roundworm
(c) True coelom: a fluid-filled body cavity completely lined by mesoderm, for example, annelid

THE INVERTEBRATES: Animals Without Backbones

Phylum Porifera
• Multicellular
• Body with pores (ostia)
• No organs or true tissues.
• No nervous system
• Adults sessile & attached to substratum.
• Skeleton of calcareous spicules, siliceous spicules, spongin or a combination.
• All aquatic, mostly marine.

CNIDARIANS
Cnidarians (phylum Cnidaria) are characterized by:
The presence of body tissues
Radial symmetry
Tentacles with stinging cells
Has secretory organelle called "cnida" contained in a cnidocyte
Cnidarians are carnivores that use tentacles, armed with cnidocytes ("stinging cells"), to capture prey.
The basic body plan of a cnidarian is a sac with a gastrovascular cavity, a central digestive compartment
with only one opening.
The body plan has two variations:
● The sessile polyp
● The floating medusa
Echinoderms
Echinoderms (phylum Echinodermata):
Lack body segments
Typically show radial symmetry as adults but bilateral symmetry as larvae
Have an endoskeleton
Have a water vascular system that facilitates movement and gas exchange
Echinoderms are a very diverse group.
Organisms characterized by either radial or bilateral symmetry, water vascular system and a generally
bottom-dwelling habit.
Deuterostome development
Dorsal hollow nerve cord
Molluscs
Molluscs (phylum Mollusca) are represented by soft-bodied animals, usually protected by a hard shell.
Many molluscs feed by using a file-like organ called a Radula to scrape up food.
The body of a mollusc has three main parts:
● A muscular foot used for movement
● A visceral mass housing most of the internal organs
● A mantle, which secretes the shell if present
Bivalves (hinged shell)

Flatworms
Flatworms (phylum Platyhelminthes) are the simplest bilateral animals.
Flatworms include forms that are:
● Parasites or
● Free-living in marine, freshwater, or damp habitats
Annelids
Annelids (phylum Annelida) have:
● Body segmentation, a subdivision of the body along its length into a series of repeated parts
● A coelom
● A complete digestive tract with
Two openings, a mouth and anus
One-way movement of food
The three main groups of annelids are:
● Earthworms, which eat their way through soil
● Polychaetes, marine worms with segmental appendages for movement and gas exchange
● Leeches, typically free-living carnivores but with some bloodsucking forms

Roundworms
Roundworms (phylum Nematoda) are:
● Cylindrical in shape, tapered at both ends
● The most diverse and widespread of all animals
Roundworms (also called nematodes) are:
● Important decomposers
● Dangerous parasites in plants, humans, and other animals
Arthropods
Arthropods (phylum Arthropoda) are named for their jointed appendages.
• There are about one million arthropod species identified, mostly insects.
• Arthropods are a very diverse and successful group, occurring in nearly all habitats in the biosphere.

The chitinous exoskeleton and jointed appendages are the distinct features of this class of organisms.
Coelomate: with body cavity completely surrounded by tissue derived from the mesoderm that provides
cushioning for internal organs.

Subphylum Crustacea
Crustaceans:
● Are nearly all aquatic
● Have multiple pairs of specialized appendages
● Include crabs, lobsters, crayfish, shrimps, and barnacles
Class Insecta
Which of the following is an egg-laying mammal?
platypus

Which of the following represents the best stage to view the shape, size and number of chromosomes?
Metaphase

How many chromatids are there in metaphase?

two each in mitosis and meiosis

This class feed on cnidarian polyps.

Class pycnogonida

Maine coon, ragdoll, and somali are breeds of:

Cats
Colchicine affects which element of mitosis in order to induce polyploidy?
Spindle formation

What is the waxy lipoprotein layer of the exoskeleton called?

Epicuticle

When, during the meiotic division, do the centromeres divide?

Anaphase II

Meiosis I : reductional division :: Meiosis II : ______________

Equational division

Interphase : centrosome divides :: ____________ : centrosome move to opposite direction

Anaphase

To create 128 cells, how many mitotic divisions does a single cell need?
7

Long bones with air cavities and lungs with air sacs are the features of class?
Aves

Where is zygotic meiosis occur?

Gonads

In the scientific classification taxonomy, which level will feature the largest selection of organisms?
Kingdom

The synapsis takes place between?

Two homologous chromosome

Arthropods nervous system consists of?

Brain, Ventral Nerve Cord, Segmental Ganglia

This is a type of metamorphosis when larva and adult have very different body forms.
Metamorphism

In Kingdom Animalia, the animals developed from two dissimilar haploid gametes. The large gamete is
called ________ and small gamete is called ____.
Egg, sperm

Which of the following is not the characteristics of metaphase?

The centromeres separate
The acoelomate animals are included in to which phylum?
Platyhelminths

Gametes: reproductive cells :: ____________: non-productive cells

Somatic cells

Why is meiosis is significant?

There is doubling of DNA contents in the cell

The crossing over occur at what stage of prophase I?

Zygotene

Snakes are belonging to which animal class?

Reptilia

When does pairing/synapsis, bivalent formation occur in meiosis?

Pachytene

Animals having a true coelom are included into what phylum?

Chordata

During mitosis, ER and nucleolus begin to disappear at

Early prophase

Animals of which phylum have jointed legs?

Arthropoda

Continuous variations are due to

Crossing over

Body segments of class arachnida.

Cephalothorax and abdomen

The cuttlefish belongs to what phylum?

Mollusca

Which organisms are classified into the class Aves?

Birds motherfucker

The scientific name of an organism consist of which two parts?

Genus and species
Meiosis I is reductional division and meiosis II is equational division because of?
Separation of chromatids

What is the event wherein the paternal and maternal chromosomes change their material with each other
in cell division?
Crossing over

According to binomial nomenclature, what is the scientific name of human?

Homo sapiens

Which of the following statements best explains the evolutionary advantages of meiosis?
Genetic recombination are possible from generation to generation

In binomial nomenclature the first part of the name indicates ______.

Genus

The meiotic division takes place in ______.

Reproductive cells

Cleavage furro forms.

Telophase

What performs by Meiosis II?

Separation of chromatids

Which of the following vertebrates is not a Reptile?

penguin

What is the reason for daughter cells to differ from parent cells and also each other in meiosis?
Segregation and independent assortment

Which of the following features are used by Protista organisms for locomotion?
Flagella

Which of the following is a characteristic of the class Aves?

They are endothermic

Where does the nuclear membrane appear during cell division in the apical meristem?
Telophase

The Mendelian factor (Aa) is segregated during?

Anaphase 1
Cell division is of two types – meiosis and mitosis. Meiosis is the process wherein the parent cell divides
two times to form four daughter cells comprising half the actual amount of genetic content. Hence the
daughter cells are haploid. It is through meiosis that gametes are produced.

1. The evolutionary advantage of meiosis can be best explained by which of these statements?
Genetic recombination is possible from one to next generation

2. One of these events does not take place during meiosis

One successive division without any DNA replication

3. The meiotic division takes place in

Reproductive cells

4. Name the event wherein the paternal and maternal chromosomes change their material with each other
in cell division
Crossing over

5. The reason for daughter cells to differ from parent cells and also each other in meiosis is;
Segregation, crossing over and independent assortment

6. Continuous variations are due to

Crossing over

7. Synapsis takes place between

Two homologous chromosomes

8. Mendelian factor (Aa) is segregated during

Anaphase I

9. The stage of prophase I wherein crossing over occurs is

Pachytene

10. Meiosis I is reductional division and meiosis II is equational division because of

Separation of chromatids

11. Which statements best explains the evolutionary advantage of meiosis?

Genetic recombination are possible from generation to generation

12. Meiotic division occurs in

reproductive cells

13. Meiosis l is reductional division. Meiosis Il is equational division due to

Separation of chromatids
14. Meiosis Il performs
Separation of chromatids

15. Segregation of Mendelian factor (Aa) occurs during

Anaphase I

16. Synapsis occurs between

Two homologous chromosomes

17. In Meiosis, the daughter cells differ from parent cell as well as amongst themselves due to
Segregation, independent assortment and crossing over

18. During which stage of prophase I of the crossing over takes place ?
Pachytene

19. Continuous variations are attributed to

Crossing over

20. When parental and maternal chromosomes change their materials with each other in cell division this
event called
Crossing over

In classification of animals, the scientists classified different organisms into groups or sub-groups in order
to study them easily. Animals are classified according to a system of seven ranks which are Kingdom,
Phylum, Class, Order, Family, genus and species as well.

The classification system in which animals are placed in two kingdoms was given by Robert Whittaker.
TRUE

The two kingdoms system include kingdoms:

Protictista and animalia

Kingdom protoctista includes

PROTOZOANS

In kingdom Animalia, animals are multicellular, diploid, prokaryotic and ingestive heterotrophs.
FALSE (eukaryotic)

In kingdom Animalia,the animals developed from two dissimilar haploid gametes. The large gamete is
called and small gamete is called
Egg, sperm
Parazoa (phylum porifera) lack tissue organ organization,so they are asymmetrical.
True

To which kingdom the animals that have tissue organ and organ system organization are included?
Eumetazoa

The animals with radial symmetry are included in the Radiata group of sub kingdom Eumetazoa.
True

Which phylum belongs to Radiata group of sub kingdom Eumetazoa?

Coelenterata (Cnidaria)

The animals which have bilateral symmetry are included in the Bilateria group of the sub kingdom
Eumetazoa.
True

The acoelomate(without body cavity)animals are included in to which phylum?

Platyhelminthes

The false coelom animals are called pseudocoel and are included in the phylum chordata.
False (Nematoda)

Animals having true coelom are included in the phylum:

chordata