Cytology

M O D U L A R S Y S T E M
CYTOLOGY
Bayram KENCÝ
Osman ARPACI
Musa ÖZET
Soner EFE
Zeki DENGÝZ
Duran KALA
Tan ERDOÐAN
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Biology is a rapidly developing branch of science. The major advances that are
made, continuously affect our life on earth. Some of these important advances are
included here. The results of a recent survey on the attitudes to existing literature
available to high school students showed that many were unhappy with the materi-
al used in teaching and learning. Those questioned identified a lack of the follow-
ing; accompanying supplementary material to main text books, current information
on new developments, clear figures and diagrams and insufficient attention to
design and planning of experiments. This book aims to improve the level of under-
standing of modern biology by inclusion of the following; main texts, figures and
illustrations, extensive questions, articles and experiments. Each topic is well illus-
trated with figures and graphs to ease understanding. Supplementary material in
the form of posters, transparencies and cassettes will shortly be available. It is the
intention and hope of the authors that the contents of this book will help to bridge
the current gap in the field of biology at this level.
The chapter summary and review questions are expanded enough to make
understanding better and easier.
Acknowledgements
I am grateful to all the people who have helped with this book. My special
thanks to BISSENBAEV Amangeldy, Gökhan BENDAÞ for their contributions and
suggestions.
I also wish to acknowledge the experts Cengiz ARAS, Bakhytzhan

NURAKHANOV, Talgat YECHSHZHANOV and Erkan CENGÝZ. These experts
gave me the benefit of their knowledge during writing in several subjects of biology.
Last but by no means least, I am particularly grateful my wife for her patient,
support and constant encouragement during the writing of this book.
Bayram KENCÝ
1. The Chemistry of Life . . . . . . . . . . . . . . . . .7 Vitamins . . . . . . . . . . . . . . . . . . . . . . . .38
The chemistry of life . . . . . . . . . . . . . . . . .8 Water soluble vitamins . . . . . . . . . . . . . .38
Bioelements . . . . . . . . . . . . . . . . . . . . . . .9 Lipid soluble vitamins . . . . . . . . . . . . . . .39
Organisation of matter . . . . . . . . . . . . . . .9 Nucleic acids . . . . . . . . . . . . . . . . . . . . .40
Atomic number, Summary . . . . . . . . . . . . . . . . . . . . . . .41

atomic weight and mass number . . . . . .11
Experiment . . . . . . . . . . . . . . . . . . . . . .42
Compounds and molecules . . . . . . . . . . .12
Information recall questions . . . . . . . . . .44
Chemical reactions . . . . . . . . . . . . . . . . .15
Hydrolysis - Dehydration synthesis . . . . .16

2. The Microuniverse . . . . . . . . . . . . . . . . . .49
Molecular basis of life . . . . . . . . . . . . . . .17
Exploring of the cell . . . . . . . . . . . . . . . .50
Water is essential to life . . . . . . . . . . . . .17 Types of cell . . . . . . . . . . . . . . . . . . . . . .51
Electrolytes . . . . . . . . . . . . . . . . . . . . . .20 Read me . . . . . . . . . . . . . . . . . . . . . . . .53
Read me . . . . . . . . . . . . . . . . . . . . . . . .20 The structure of eukaryotic cell . . . . . . . .54
Read me . . . . . . . . . . . . . . . . . . . . . . . .21 Structure of the plasma membrane . . . .55
Carbon and life . . . . . . . . . . . . . . . . . . . .22 The cytosol . . . . . . . . . . . . . . . . . . . . . .57
Carbohydrates (C,H,O) . . . . . . . . . . . . . .23 Organelles . . . . . . . . . . . . . . . . . . . . . . .58
Lipids (C, H, O, P, S) . . . . . . . . . . . . . . . .28 Read me . . . . . . . . . . . . . . . . . . . . . . . .63
Read me . . . . . . . . . . . . . . . . . . . . . . . .30 Cytosceleton . . . . . . . . . . . . . . . . . . . . .69
Read me . . . . . . . . . . . . . . . . . . . . . . . .31 Surface features of cells . . . . . . . . . . . .70
Proteins (C, H, O, N, S) . . . . . . . . . . . . . .33 Transport of materials through the
Functions of proteins . . . . . . . . . . . . . . .34 plasma membrane . . . . . . . . . . . . . . . . .75
Three dimensional structure of proteins . .35 Passive mechanisms . . . . . . . . . . . . . . .75
Read me . . . . . . . . . . . . . . . . . . . . . . . .37 Active mechanisms . . . . . . . . . . . . . . . .80

Endocytosis . . . . . . . . . . . . . . . . . . . . . .81 Read me . . . . . . . . . . . . . . . . . . . . . . .125
Exocytosis . . . . . . . . . . . . . . . . . . . . . . .81 Factors affecting the rate of

photosynthesis . . . . . . . . . . . . . . . . . . .126
Summary . . . . . . . . . . . . . . . . . . . . . . .83
CO2 Fixation and photorespiration . . . . .128
Experiment . . . . . . . . . . . . . . . . . . . . . .84
Bacterial photosynthesis . . . . . . . . . . . .133
Information recall questions . . . . . . . . . .86
Chemosynthesis . . . . . . . . . . . . . . . . .134
Read me . . . . . . . . . . . . . . . . . . . . . . .134
3. Metabolism . . . . . . . . . . . . . . . . . . . . . . .92
Summary . . . . . . . . . . . . . . . . . . . . . .135
Energy . . . . . . . . . . . . . . . . . . . . . . . .93
Experiment . . . . . . . . . . . . . . . . . . . . .136
Read me . . . . . . . . . . . . . . . . . . . . . . . .94
Information recall questions . . . . . . . . .138
Enzymes . . . . . . . . . . . . . . . . . . . . . . . .95
Read me . . . . . . . . . . . . . . . . . . . . . . . .99
5. Cellular Respiration Harvests Energy . . . .144
ATP (Adenosine Triphosphate) . . . . . . . .100
Aerobic respiration . . . . . . . . . . . . . . . .145
Read me . . . . . . . . . . . . . . . . . . . . . . .101
Aerobic respiration (An Overview) . . . . .147
Electron acceptors (Coenzymes) . . . . . .104
Aerobic respiration (A Closer Look) . . . .148
Read me . . . . . . . . . . . . . . . . . . . . . . .106
Glycolysis (Reactions) . . . . . . . . . . . . . .148
Summary . . . . . . . . . . . . . . . . . . . . . .107
Pyruvate oxidation . . . . . . . . . . . . . . . .150
Experiment . . . . . . . . . . . . . . . . . . . . .108
Krebs cycle . . . . . . . . . . . . . . . . . . . . .150
Electron transport chain (ETC)
and chemiosmosis . . . . . . . . . . . . . . . .152
4. Photosynthesis . . . . . . . . . . . . . . . . . . .114
Chemiosmotic
Necessary factors for photosynthesis . . .116 mechanism (A closer look) . . . . . . . . . .154
Read me . . . . . . . . . . . . . . . . . . . . . . .117 Read me . . . . . . . . . . . . . . . . . . . . . . .156
Photosynthetic reactions . . . . . . . . . . . .120 Catabolism of lipids . . . . . . . . . . . . . . .158

Catabolism of proteins . . . . . . . . . . . . .160 Experiment . . . . . . . . . . . . . . . . . . . . .203
Anaerobic respiration (Fermentation) . . .162 Information recall questions . . . . . . . . .204
The industrial importance of Appendix . . . . . . . . . . . . . . . . . . . . . . . . .209

fermentation . . . . . . . . . . . . . . . . . . . .164
Biological abbreviations . . . . . . . . . . . . .210
Read me . . . . . . . . . . . . . . . . . . . . . . .165
Understanding biological terms . . . . . . .211
Summary . . . . . . . . . . . . . . . . . . . . . .166
Scientific measurement . . . . . . . . . . . .212
Experiment . . . . . . . . . . . . . . . . . . . . .167
Glossary . . . . . . . . . . . . . . . . . . . . . . .213
Reference . . . . . . . . . . . . . . . . . . . . . .223
6. The Secret Of Life . . . . . . . . . . . . . . . . .174
Nucleic acids . . . . . . . . . . . . . . . . . . . .174
DNA (Deoxyribonucleic Acid) . . . . . . . . .176
RNA (Ribonucleic Acid) . . . . . . . . . . . . .180
Read me . . . . . . . . . . . . . . . . . . . . . . .181
Chromatin and chromosome . . . . . . . . .182
The cell cycle . . . . . . . . . . . . . . . . . . . .185
Mitosis . . . . . . . . . . . . . . . . . . . . . . . .186
Meiosis . . . . . . . . . . . . . . . . . . . . . . .189
Read me . . . . . . . . . . . . . . . . . . . . . . .193
Protein synthesis . . . . . . . . . . . . . . . . .194
Read me . . . . . . . . . . . . . . . . . . . . . . .198
Read me . . . . . . . . . . . . . . . . . . . . . . .201
Summary . . . . . . . . . . . . . . . . . . . . . .202
Cytology
chapter
THE CHEMISTRY
OF LIFE
1
The chemistry of life
THE CHEMISTRY OF LIFE
An adult human body Everything around us is made up of solids, liquids or gases. Despite their obvi-
contains nearly... ous differences in physical appearance, they are all made up of matter and share
1.4-1.6 Kg Calcium the same basic structure.
1 Kg Phosphorus Matter is anything that has weight and takes up space. All matter is composed
83-87 Gram Sodium of basic structures called elements. An element is a substance is a substance that
20-28 Gram Magnesium can not be broken down to other substances by chemical reactions.
3-5 Gram Iron Today 111 elements are known, although naturally occurring elements on
2-3 Gram Zinc earth only 92 of them, gold, copper, carbon, mercury and magnesium are exam-
CYTOLOGY
100-150 Milligram Copper ples. They have their own symbol, usually the first letter or two of its name. Some
115-130 Milligram Potassium of the symbols are derived from Latin or German names; for example, the symbol
20-50 Milligram Iodine for sodium is Na, from the Latin word natrium.
and trace amount of other Elements mostly exist in a mixtures or chemical combinations but some of
chemicals.
them exist in a pure form.
8
Bioelements Elements in the human body
Living organisms require about 25 chemical elements. Major elements
They are called bioelements, which are essential to life. Just
four of these, oxygen, carbon, hydrogen, nitrogen, make up Element Symbol Approximate %
96% of living matter. Phosphorus, sulfur, calcium, potassium Oxygen O 65.0
and other elements make up 4% of living matter. Carbon C 18.5
Some bioelements are required by an organism in only Hydrogen H 9.5
minute quantities, these are called trace elements. Iron, Nitrogen N 3.3
Cobalt, Copper and Iodine are examples. (Table-1.1) Calcium Ca 1.5
Phosphorus P 1.0
Organisation of matter Potassium K 0.4
Sulfur S 0.3
Atoms
Sodium Na 0.2
Elements are composed of atoms. An atom is the smallest Chlorine Cl 0.2
unit of matter. Atoms of an element are similar to each other, Magnesium Mg 0.1
but they differ from the atoms of any other elements. Atoms
are very small; they can be seen only strong electron micro- Trace elements
scopes. Chromium Cr
Cobalt Co
Structure of atom Copper Cu
All atoms are comprised of a nucleus containing protons Fluorine F
and neutrons with electrons spinning around them. Iodine I
Iron Fe Together less than
The overall charge on the nucleus at the centre of this
Manganese Mn 0.1 %
'microscopic solar system is positive due to the presence of
positively charged protons, and neutrons which carry no Zinc Zn
charge. (Table-1.2) Molybdenum Mo
Silicon Si
Negatively charged electrons orbit around them balancing
the positive charge of the protons. Tin Sn
Vanadium V
The number of electrons plays an important role in deter-
Selenium Se
mining the characteristics of an atom. If there are more elec-
trons than protons, the atom will be overall negative and con- Table1.1: Bioelements in human body
sequently unstable. (Figure-1.1)

Figure-1.1: Atom can be seen by the SEM
9
Atoms are the
simplest unit of an
element. They are
composed of a proton, neu-
tron and electron. Different
atoms are joined by chemical
bonds to form compounds.
Compounds are divided into
two main types, inorganic
and organic compounds.
Figure-1.1: The structure of atom
Electrons and energy

Electrons are constantly revolving around their nucleus within orbits. Since
there are many orbits in which electrons can move, they may be found at varying
distances from the central nucleus. Those electrons in orbits that are far from the
nucleus have more potential energy than those electrons in orbits close to it. This
can be understood by considering the position of a stone.
When the stone is on the ground it has no potential energy. However when it
is lifted it gains potential energy. This is lost when the object returns to its original
position. In the same way, an electron can gain energy from heat or light and can
move into a position in an orbit further away from the nucleus. This energy is
released when it returns to its original position. (Figure-1.2)
The ability of electrons to gain or lose energy according
to their position is extremely important for energy transfer
on earth.
For instance, radiant energy can excite electrons in
green plants and algae, moving them into a higher orbit.
This energy is then transferred as chemical bond energy in
photosynthetic organisms such as green plants and algae.
CYTOLOGY
Figure-1.2: Electrons have different energy level.
10
Atomic number, atomic weight and mass number Atoms have an
atomic symbol,
Atomic weight weight, and number.
The atomic weight of an element describes the number of protons and neu- The subatomic particles
trons within its nucleus. For example, the smallest atom hydrogen is composed of which are protons, neutrons,
only a single electron and a single proton. and electrons determine the
characteristics of atoms.
Atomic number
The atomic number is the number of protons in each element. Each element
has a unique number of protons. In uncharged atoms the number of protons is
equal to number of electrons.
Mass number
Mass number is the sum of protons plus neutrons in the nucleus of an atom.
The number and ratio of subatomic particles of a particular element is a factor
that determines whether it is stable or unstable. If the number of protons is equal
to the number of neutrons and electrons, it is termed as stable and unreactive. If
the number differs, the atom is unstable, reactive and capable of changing its
form, probably taking on the properties of an atom of another element as a result.
Isotopes
If the number of neutrons in a particular element differs even though the num-
ber of protons and electrons remains the same, this type of element is termed an
isotope. The chemical properties of an isotope of oxygen for example, are identi-
cal to normal oxygen but are physically different in that they are heavier due to the
extra neutrons within their nucleus. Thus an isotope has a greater atomic mass.
Two other examples of isotopes are nitrogen and carbon.
N14 normal element, N15 isotope Atoms that have
C12 normal element, C11, C14, C13 isotopes the same number of
protons but a different
Isotopes are frequently used in biological research. The uptake of an isotope number of neutrons and a
can be detected and its activity in subsequent reactions monitored. The radiation different weight are called
produced by some isotopes is frequently used in recombinant DNA techniques to isotopes.
follow changes in DNA structure.
Subatomic Particles
Particle Symbol Function Location Mass Charge

Electron e– Bonding Orbitals 0 –
Proton p Identity Nucleus 1 +
Neutron n Isotope Nucleus 1 0

Table 1.2: Subatomic particles
11
A compound is a
substance consist-
ing of two or more
elements combined in a fixed
ratio. A molecule is the
smallest unit of a compound,
just as an atom is the small-
est unit of an element.
Compounds and molecules

A compound is a substance consisting of two or more elements combined in
a fixed ratio.
A molecule is the smallest unit of a compound, just as an atom is the small-
est unit of an element. For example; water consists of hydrogen and oxygen ele-
ments in a 2:1 ratio. Another example is table salt, the combination of chloride and
sodium in a 1:1 ratio.
Formation of a compound changes the characteristics of elements. Pure sodi-
um is a metal and pure chloride is a poisonous gas, they form edible table salt.
Formation of Chemical Bonds

Atoms are combined to form molecules by chemical bonds. The number elec-
trons in an atom’s outermost shell, or valance electrons determines which type of
chemical bond can form. (Table-1.3)
CYTOLOGY
Atoms have a tendency to fill their outermost orbit with electrons. To achieve
this, they interact with another atom to donate, receive or share electrons. The
result of an association between two or more atoms is a molecule.
The component atoms of a compound in biological systems are held together
by three main types of bonds;
12
Ionic Bonding
Ionic bonding is a chemical bond formed between
ions as a result of the attraction of opposite electrical
charges.
Most atoms complete their orbitals by gaining or
losing electrons. For instance, a Cl atom has 7 elec-
trons in its outermost orbital and requires one extra
electron to complete it. If it receives one, it becomes
a negatively charged ion and is abbreviated as (Cl-). If
Na and Cl atoms react, one electron is donated from
the Na atom to the Cl atom. The Na atom is now a NaOH + HCl ⎯⎯→ NaCl + H2O
positive ion after losing one electron. Since opposite
charges attract each other, an electrostatic or ionic
bond forms between negatively charged and positive-
ly charged ions.
Covalent Bonding
A type of strong chemical bond formed by the
sharing of one or more pairs of electron.
Most atoms have an incomplete outermost orbital
and must gain or donate one or more electrons to
become stable. Since the energy needed for this is
considerable, instead two or more nonmetallic atoms
group together and share their outermost electrons. H + H ⎯⎯→ H2
Atoms have a
The attraction of atoms tendency to fill their
outermost orbit with
electrons. To achieve this,
Type Formed Strength Example they interact with another
atom to donate, receive or
share electrons. The result of
When one atom donates an Weak in an association between two
Ionic bonds Table salt
electron to another water or more atoms is a molecule.
When atoms share their CH4

Covalent bonds Strong

electron pairs
When negative charged

Hydrogen bonds atoms attract hydrogen Weak Water
atom
Van der walls When oppositely charged
regions of molecules attract Weak Protein Taboo1.3: The attraction of atoms
attractions one another
13
Hydrogen Bonding
Hydrogen bonding is a type of weak chem-
ical bond formed when the slightly positive
hydrogen atom of a polar covalent bond in one
molecule is attracted to the slightly negative
atom of a polar covalent bond in another mol-
ecule.
Hydrogen bonding has great importance
for biological systems since the majority of bio-
molecules have many such bonds.
Water, the most important biological sol-
vent is formed when two hydrogen atoms
come close to an oxygen atom. In water the
electrostatic attraction between the positive
hydrogen and the negative oxygen bonds the
atoms together.
Hydrogen bonding is particularly important
in DNA and RNA as the molecules must keep
a stable structure, but also be able to unzip
sections of their helix in order for genetic infor-
mation to be transcripted. Hydrogen bonds
also form between the amino acids of proteins,
giving them their vital and distinct forms.
In the plants, hydrogen bonding plays an
important role in the transport of water
through the xylem vessels. (Figure-1.3)
Figure-1.3: Hydrogen bonding and water transport through the
xylem(above). Hydrogen bonds in a DNA molecule (bellow)
MATTER
Name Definition
Element A pure chemical substance
Atom The smallest unit of element

CYTOLOGY
A pure substance formed from the atoms of different ele-

Compound
ments
Molecule The smallest unit of compound
14
Chemical reactions
A compound is formed when molecules are rearranged or bonds form between
atoms. The bonds that form may be ionic or covalent. The formation of bonds is
termed a chemical reaction and may be categorised according to the charge of
the reacting molecules, water uptake or release and synthesis or breakdown of
molecules.
oxidation - reduction (redox) reactions
anabolic - catabolic reactions
hydrolysis - dehydration synthesis
exothermic - endothermic reactions
The formation or
Oxidation - Reduction (redox) Reactions breakdown of a
A chemical reaction involves physical changes to all the reactants involved. For bond is accompa-
example, a compound may receive or donate electrons. Such reactions are known nied by energy supply or
as oxidation-reduction reactions or redox reactions. The compound donating elec- removal. The amount of
trons is said to be oxidised while the compound accepting electrons is said to be energy required for either
reduced. bond formation or break-
down is almost equal, the
C6H12O6 + 6O2 ⎯→ 6CO2 + 6H2O + Energy strongest bonds requiring
the most energy for both
(Oxidation of glucose) these processes. The unit of
measurement used to define
The mechanism of redox reactions is vitally important for the extraction of
the strength of a chemical
energy during the breakdown of complex food molecules in cellular respiration. bond is the calorie. It
This topic is dealt with in more detail in chapter 3. describes the amount of heat
Anabolic - Catabolic Reactions required to increase the tem-
perature of 1 g of water from
14.5 to 15.5 °C.
Catabolic Reactions
Organic compounds are broken down to their monomers by catabolic reac-
tions, most of which result in energy release. The oxidation of glucose for instance
involves the release of hydrogen atoms as well as energy from the molecule. These
then combine with oxygen to form water molecules.
C6H12O6 + 6O2 ⎯→ 6CO2 + 6H2O + Energy (38 ATP/686 Kcal/mol)
Anabolic Reactions

All reactions in a cell that build new giant molecules are known as anabolic
reactions. For instance, photosynthesis involves the synthesis of glucose. Energy
required for the formation of chemical bonds between molecules is obtained from
the radiant energy of the sun.
6CO2 + 6H2O + Light energy (686 Kcal/mol) ⎯⎯→ C6H12O6 + 6O2
15
Hydrolysis - Dehydration Synthesis
Chemical reactions can also be categorised according to the behaviour of
water in the reaction. For example in catabolic reactions, water is split by hydrolyt-
ic enzymes and its components are added to the bonds that are to be broken. This
is known as hydrolysis and the reaction is exothermic. The catabolism of maltose
is a good example of this type of reaction.
C12H22O11 + H2O ⎯→ 2 C6H12O6 (hydrolysis)
Anabolic reactions, the condensation of two amino acids or carbohydrates for

example, involves the formation of new bonds and the formation and release of
water. This is known as dehydration synthesis. During protein synthesis, water
molecules are released when two amino acids bond. This reaction is endergonic
and requires the same amount of energy as that needed to break the bond origi-
nally. This energy is obtained by the conversion of Adenosine triphosphate (ATP)
A compound is to Adenosine diphosphate (ADP).
formed when mole-
cules are rearranged
or bonds are formed between aa1 + aa2 ⎯→ dipeptide + H2O (dehydration)
atoms. The bonds that form
may be ionic or covalent. The The water that is formed is known as metabolic water and is of vital importance
formation of bonds is termed to animals that live in arid habitats or hibernate during the winter.
a chemical reaction and may
be categorised according to Endothermic - Exothermic Reactions
the charge of the reacting
molecules, water uptake or An endothermic or endergonic reaction is one that requires energy in order
release and synthesis or to form the necessary bonds in the synthesis of a new compound. For instance
breakdown of molecules. radiant energy is used to make new bonds between water and carbon dioxide,
forming glucose.
Light energy
6CO2+6H2O ⎯⎯⎯⎯⎯⎯⎯→ C6H12O6+6O2
An exothermic reaction is one that releases energy as the bonds of a com-

pound are broken. The energy that is released is used within the cell to form ATP
from ADP. The catabolism of glucose during cell respiration is a good example of
an exothermic reaction .
C6H12O6+6O2 → 6CO2+6H2O+38 ATP (686.4 kcal)

CYTOLOGY
16
Figure-1.4: Water molecule is polar
Molecular basis of life
Water is essential to life
Three-fourth of the earth's surface is covered by water. About two-third of your
body is water, and you can not exist long without water. Like you, all other organ-
isms need water. It is no accident that tropical rain forests are abounding with life,
Figure-1-5: The structure of water molecule
whereas dry deserts are almost lifeless except after a rain. The chemistry of life,
then, is water chemistry.
The amount of water present in a structure varies according to its function. For
example, all parts of an actively growing embryo have a high water content acting
as the medium for many reactions.
Structure of Water Molecules

A water molecule consists of one oxygen and a pair of hydrogen atoms. The

oxygen atom forms the core of the molecule with the hydrogen atoms attached to
it at an angle of 104.5°. Instead of being electrically neutral, a water molecule is
positively charged on one side. (Figure 1.4-5)
This is due to the exposed, unpaired protons of the H atoms, but this charge
is balanced by the negative charge from the electrons of oxygen. This feature gives
water its polar nature, allowing it to form hydrogen bonds with other structures.
17
Properties of Water
Water is the principle solvent of life

Water is a common solvent for most biochemical reactions. For instance, the
strong ionic bond between Na and Cl ions is reduced to one-eightieth in water.
This ability of many molecules to ionise in water is vital for the chemical reactions
that make life possible. (Figure 1.6)
High melting point regulates body temperature

Water molecules change from a liquid to a gaseous state as the temperature
increases. As each water molecule leaves the liquid state, it draws the energy
needed to do so from its environment, resulting in a drop in temperature. This
Figure-1.6: Water is a good solvent characteristic of water helps an organism to maintain a constant body tempera-
ture.
Figure-1.7: Water has high surface tension
Water exhibits cohesion and adhesion
The ability of water molecules to hydrogen bond with each other is called cohe-
sion. It is essential for the movement of water molecules through the narrow ves-
sels of an organism, such as the xylem of a plant or the blood vessels of a mam-
mal. Through the formation of a chain, they provide an unbroken medium
CYTOLOGY
through which soluble molecules can travel. Water molecules also stick to many
kinds of substances that are called adhesion, so these adhesive forces explain how
things get wet by water. Hydrogen bonding between water molecules enable it to
have a high degree of surface tension that explain how small animals can walk on
water. (Figure 1.7)
18
Water helps maintain a stable ionic balance
Water not only acts as a solvent for soluble organic and inorganic salts in the
body, but allows their movement through its structure by diffusion. This enables
the pH and ion concentration in tissues and hence osmotic pressure to be main-
tained. Since all cells eventually die if they are placed into pure water due to its
rapid intake, the ionic concentration of water and consequently that of the tissues
are balanced to the survival of an organism.
Water has low density at solid state making ice float

Water has a maximum density at +4°C, but varies above and below this tem-
perature. Water molecules change to a solid state at 0°C and simultaneously
expand due to hydrogen bonding between molecules. This reduces their density
resulting in ice formation above water still in the liquid state.
Figure-1.8: Living under iceberg
Aquatic organisms benefit from this important characteristic since it enables
them to survive at subzero temperatures during the winter (Figure 1.8).
Metabolic reactions need enough water concentration

Since water in a liquid state is essential for the transport of other molecules Water means life.
within it, particularly enzymes and their substrates, all metabolic activities cease if Water has unique
water molecules freeze or if their concentration is reduced to less than 15%. Due properties that allow
to the presence of insoluble molecules, water is rare in the skeletal system, in adi- cellular activities to occur and
pose tissue and in food storage regions. that make life on earth possi-
During long term starvation, the osmotic pressure of blood decreases and ble.
water accumulates at the tissues, resulting in a condition known as edema. This
can also result from cardiac insufficiency and the deposition of fat.
Water is essential to life
Properties Importance
Good solvent Water is vital for the chemical reactions that make life possible.
High heat capacity Water regulates constant body temperature.

High surface tension Difficult to break surface, small animals can walk on water.
Cohesive and adhesive Water molecules stick to each other, water flows, leaves get water from the soil.
Low density at solid state Aquatic organisms can survive at subzero temperature during winter.
19
Electrolytes
Acids, alkalis and salts dissociate into their constituent ions in water. Positively
charged ions are termed cations while negatively charged ions are termed anions.
These substances collectively known as electrolytes, enable the conduction of
electricity through water.
Acids have a pH that
is less than 7, and Acids
bases have a pH is
greater than 7. Buffers, which Acids increase the hydrogen ion concentration of a solution. Strong acids are
can combine with both corrosive and irritant. Weak acids have a sour taste and are found in many types
hydrogen ions and hydroxide of food and drink.
ions, help to keep the pH of Cola and some other soft drinks contain carbonic acid whereas citrus fruits
internal body fluids near pH 7 such as oranges contain citric acid and ascorbic acid. Some acids are also found
that is neutral. in the structure of proteins and all can be detected by the use of litmus paper. An
acidic substance results in a colour change from blue to red.
Base (Alkalis)
Alkalis reduce the hydrogen ion concentration of a solution. Strong base are
also corrosive. Litmus paper is also used to detect alkalis, and an alkaline sub-
stance results in a colour change from violet to blue. Organic alkalis contain most-
ly carbon and nitrogen within their structure. CH3NH2, NH4OH are examples of
organic alkalis.
READ ME pH
The pH of any solution is determined by the minus logarithm of the concentration of hydrogen. From this the con-
centration of hydroxide ions can also be established. A neutral solution has an ion concentration of 10–7 (mol/1)
and the number of hydrogen and hydroxide ions is balanced. The pH value of an acidic solution varies between
0 and 6.9 (100—10–7) and here the number of hydrogen ions is in excess. Similarly, the pH of an alkaline solution
varies between 7.1 and 14 (10–7—10–14) and the number of hydroxide ions is in excess. All organisms are sensi-
tive to pH changes within their body. Since their pH is neutral, acid and alkaline concentrations are virtually bal-
anced.
CYTOLOGY
20
Salts
A salt is the product of a neutralisation reaction of an acid and an alkali. The
combination of an anion from an acid with a cation from an alkali forms a salt. All
cells and the intercellular matrix of the body contain some salts. The most com-
mon cations are sodium, calcium, potassium and magnesium. In fact, the densi-
ty of Na and K ions in the intercellular matrix is almost identical to that of sea
water. The most common anions are chloride, bicarbonate, phosphate and sul- Figure-1.9: The structure of table salt
phate. Organisms maintain their ionic equilibrium by the action of excretory
organs or glands that secrete various ions and salts into the intercellular matrix
(Figure 1.9).
NaOH + HCl ⎯⎯→ NaCl + H2O
Buffers
The metabolic reactions of an organism all have specific requirements of pH
Human blood can
at which they can function at an optimum rate. It is in the best interests of an
only function opti-
organism therefore to maintain its homeostasis. For example, human blood can
mally in the pH
only function optimally in the pH range 7.35 to 7.45. Drinking coffee for instance
range 7.35 to 7.45. Drinking
will potentially reduce the pH to 5. In actual fact, buffers within the blood neutralise
coffee for instance will poten-
the excess hydrogen ions, restoring equilibrium in only a few seconds. Drinking
tially reduce the pH to 5. In
coffee is non-fatal since certain soluble chemicals in the blood ‘soak up' excess
actual fact, buffers within the
acids and also alkalis, effectively neutralising them. These chemicals are known as
blood neutralise the excess
buffers and are capable of resisting changes in pH due to the addition of small
hydrogen ions, restoring
amounts of acid (H+) or base (OH–). A buffer consists of a weak acid and its cor- equilibrium in only a few sec-
responding base without protons. Acetic acid behaves in this way. If extra hydrox- onds.
ide ions enter the solution, they react with the weak acid in a reversible reaction.
Any extra hydrogen ions react with the base, also in a reversible reaction resulting
in only a very small change in pH.
READ ME salt
The most important function of common salt is the regulation of osmotic pressure within the intercellular matrix.
Its deficiency results in a range of unpleasant conditions: disruption of the nitrogen balance in the body, degra-
dation of proteins, increase in the level of blood sugar, accumulation of urea in the blood, increase in density of
the blood, decrease in the rate of blood circulation, giddiness and cramps. In extreme cases, the combination of
all these is usually fatal. A small quantity of common salt in food is thought to be beneficial since it increases the

volume of gastric secretions. However since most foods contain common salt naturally, the addition of salt to food
during preparation and before eating is unnecessary.
The exception to this is in hot climates where quantities of salt are lost from the body by perspiration. In extreme
excess, salt leads to renal insufficiency, oversecretion of saliva, water retention, dilation of the pupils and inflam-
mation of the intestines and ultimately death.
21
Carbon and life
Although water is the universal medium for life on Earth, most of the chemi-
cals that make up living organisms are base on the carbon element. Both organ-
ic and inorganic forms of carbon occur widely in nature. Compounds that con-
Life as we know it is
dependent on car- tain carbon are called organic compounds and the branch of chemistry that spe-
bon-based mole- cialises in the study of carbon compound is called organic chemistry.
cules. Carbon is a versatile Carbon has unique properties that permit formation of carbon backbones of
atom. It has 4 electrons in its
the large molecules. The organic molecules such as proteins, carbohydrates,
outermost shell, and this
nucleic acids, vitamins and other molecules are all composed of carbon atoms
allows it to form covalent
bonds with as many as 4 bonded to one another and to atoms of other elements.
other atoms. The organic Inorganic molecules constitute nonliving matter, but even so they also play
molecules such as proteins, important roles in living things like salts do. Inorganic molecules such as diamond
lipids etc. make up cells.
and pencil lead are also made up of carbon skeleton.
Organic molecules are synthesised and used only in a living organism’s body.
They can contain C,H,O,N,P and S elements. The amount of these molecules
varies according to molecules types. Carbohydrates, lipids and nucleic acids con-
stitute the basic food sources involved in energy production and structure.
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Monomer and polymers

Some of the organic molecules in organisms are small and simple. They are
called monomers. Monomers are combined to each other to form polymers. For
example simple sugar glucose (monosaccharide) is a monomer within polysac-
charide starch.
22
Carbohydrates (C, H, O)
Structure and Function
Carbohydrates are made up of C, H and O atoms. Carbohydrates provide the
primary energy source for all organisms. Furthermore, they participate in the
structure of the plasma membrane and cell wall. They are categorised into three
groups; monosaccharides, disaccharides and polysaccharides.
Types of Carbohydrates
Monosaccharides
These are the simplest of all saccharides and cannot be hydrolysed. They are
categorised according to the number of carbon within their structure (Figure
1.10).
Triose sugars
These sugars have 3 carbon atoms such as glyceraldehyde and pyruvate.
Pentose sugars
These sugars have 5 carbon atoms such as ribose and deoxyribose. Ribose
Figure-1.10: Pentose sugar
and deoxyribose have the same number of carbon atoms but ribose has one more
oxygen. Ribose is found in the structure of RNA, NAD, FAD and ATP. Deoxyribose
is found in DNA. (Figure 1.10)
Hexose sugars
Figure-1.12: The structure of glucose
These sugars have 6 carbon atoms, for example glucose, fructose and galactose.
They have identical molecular formulas, but their atoms are arranged differently. So
they have different properties, for example fructose tastes sweeter than glucose.
Glucose is found mostly in honey and grapes. Fructose is found in fruit giving
it a sweet taste. Galactose is found in milk. (Figure 1.11).
Glucose, in addition to oxygen, is essential for normal brain function. There are
90 -100 milligrams of glucose in 100 millilitres of the blood of a healthy individ-
ual. This level of glucose within human blood normally remains constant, howev-
er its excess or deficiency results in the disorder known as diabetes mellitus.
(Figure 1.12).

Figure-1.11:
Fructose and
galactose
23
Disaccharides
Two identical or dissimilar monosaccharides associate
to form a disaccharide or double sugar by glycosidic link-
age in a process known as dehydration synthesis or con-
densation.
Sucrose, maltose and lactose are all well known types
of disaccharides. During this process a water molecule is
synthesised.
The reverse of this reaction is known as hydration syn-
thesis or hydrolysis in which water molecules are used to
hydrolyse a large molecule into its subunits.
Maltose
The disaccharide maltose is found in the endosperm of
barley. It is formed from the bonding of two glucose
monosaccharide units. A water molecule is produced dur-
ing its synthesis.
Sucrose
The disaccharide sucrose is found in sugar cane and
sugar beet. In its extracted and refined form, it is known as
table sugar. It is formed from the bonding of a glucose and
a fructose monosaccharide unit. A water molecule is pro-
duced during its synthesis.
Lactose
The disaccharide lactose is found in the milk of mam-
mals. It is formed from the bonding of a glucose and a
galactose monosaccharide unit. A water molecule is pro-
duced during its synthesis.
Polysaccharides
These molecules are formed by chains of monosac-
charides. Well known types of polysaccharides are starch,
cellulose, glycogen and chitin. (Figure 1.13).
Starch
Starch is formed by the combination of many glucose
molecules, previously synthesised in photosynthetic tis-
CYTOLOGY
sues. The individual glucose molecules are transported to

leucoplasts and converted to starch. It has two main forms
which are amylose and amylopectin.
Amylose: This molecule is formed from long,
unbranched chains of glucose units. The first carbon of
24
one glucose molecule bonds with the fourth carbon atom
of another identical molecule, (1-4 glycosidic linkage).
Amylose is helical in structure, variable in molecular
weight and is insoluble in water. On exposure to water it
bonds with hydrogen forming micelles.
Amylopectin: This type of starch is obtained by the
linkage of extraperipherial glucose chains to amylose by (1-
6 glycosidic linkage). The resulting branched structure is
soluble in water and has a high molecular weight.
Excess carbohydrate is stored in plants as starch in the
form of amylose and amylopectin, but in different ratios.
Amylose starch is hydrolysed by the enzyme amylase,
present in human saliva. Starch is a glucose
polymer. Most

Wheat, potatoes, garden peas and nuts are all major
sources of starch. It may be detected using iodine solution starches are
which turns blue-black in colour when reacting with starch. branched and some are
cross-linked. The branching
and cross-linking render the
polymer insoluble and pro-
tect it from degradation.
25
Starch (Amylose)
Potato
Starch (Amylose)
Glycogen
Frog
CYTOLOGY
Cellulose
Common
hemp nettle Figure-1.13: Polysaccharides
26
Glycogen
This molecule resembles amylopectin and is formed by the (1-4) condensation
of many glucose units into a single chain with (1-6) branches. As a carbohydrate,
it provides an immediate energy source for cells.
It has low solubility in water, so does not alter the osmotic potential of the cell.
Glycogen is commonly known as animal starch due to its role as a carbohydrate
storage molecule. It is most abundant in the liver and muscles. In the event of a
decrease in concentration of glucose in the blood, glycogen in the hepatocyte
cells of the liver is broken down into glucose and returned to the blood. (Figure
1.13).
Cellulose
This macromolecule is formed by the (1-4) carbon linkage of individual glucose
units. It is insoluble in water, is unbranched and does not react with iodine solu-
tion. It has a high molecular weight and forms the rigid cell walls of plants due to
its exceptionally strong bonds. Furthermore, it forms 98 % of cotton fibres and
50% of wood fibres.
Cellulose is used commercially in the production of paper, some plastics, syn-
thetic silk, photographic film and some explosives.
Although the human body is incapable of starch digestion, as fibre or roughage
it plays an important role in the movement of undigested food through the colon. Figure-1.14: Mushroom cell walls and insect
Cellulosic bacteria within the stomach of ruminants and the human colon are able skeletons contain chitin.
to digest starch, as are insects that feed on wood since they can synthesise an
enzyme known as cellulase. (Figure 1.13).
Chitin
These types of molecules closely resemble cellulose, but differ due to an acety-
lated amino group instead of a hydroxyl group on their second carbon. Chitin is
an example of this type of polysaccharide and is the main component of the
exoskeleton of insects. Chitin is also the building material of fungi cell walls.
(Figure 1.14).
Other polysaccharides
Other complex polysaccharides are heparin, chondroitin sulphate and
hyaluronic acid. They are all composed of an amino group, a backbone of carbo-
hydrate and an acid.
Chondroitin sulphate is found in cartilage, skin, the cornea of the eye and in
the umbilical cord, whereas hyaluronic acid is present in skin and other animal tis-

sues. In order to carry out their function, they associate with various proteins and
lipids to form glycoproteins and glycolipids in the cell membrane.
Pure chitin is leath-
ery, but the addition
of calcium carbonate
hardens the chitin.
27
Lipids (C , H , O , P , S )
Lipids are made up of C, H, and O atoms but some lipids
contain P and S atoms. Lipids are the one class of large bio-
logical molecules that do not include polymers. They are
insoluble in water, dissolving only in organic solvents such as
benzene, chloroform and ether. Their insoluble nature is the
reason why their digestion is slower than other food types.
Functions of Lipids
1. They are the secondary source of energy for organisms.

They release twice the energy produced by proteins and
carbohydrates when they are completely oxidised or bro-
ken down into their constituent units.
2. They participate in the structure of cell membrane.
Figure-1.15: Lipid is a very important insulation material
3. They help joint movement and gives organisms good
appearance.
4. They are found in the structure of some hormones and
Lipids are an works as chemical messengers.
exception among
macromolecules 5. They also release metabolic water which is of vital impor-
because they do not have tance for hibernating animals since it is their only source
polymers. of water.
6. The seeds of plants for example contain a store of
triglycerides to be utilised during germination.
Figure-1.16: The structure of a triglyceride
7. In vertebrates, triglycerides are stored in specialised cells
known as adipocytes or fat cells. These collectively form
adipose tissue. A layer of adipose tissue under the skin
of arctic animals such as seals and penguins plays an
important role in insulation against extreme cold.
(Figure 1.15)
Classification of Lipids
Neutral Lipids or triglycerides (Fats and oils)

Triglyceride is composed of a molecule of glycerol and
three fatty acids. (Figure 1.16). Neutral lipids are found in ani-
mal, plant and human tissue and are stored in this form. They
CYTOLOGY
have a role as both an energy source and a structural compo-

nent.
The structure of fatty acids: Neutral fatty acids are clas-
sified as saturated or unsaturated according to their bond
structure.
28
FATS contains saturated fatty acids
Saturated fatty acids contain only a single bond between carbon atoms.
They are solid at room temperature. Mostly they are obtained naturally from
animal sources such as butyric acid in butter, palmitic acid in nuts. But they
can also be obtained by the artificial saturation of unsaturated liquid fatty
acids. (Figure 1.17)
OILS contains unsaturated fatty acids

Figure-1.17: Unsaturated and saturated fatty acids
An unsaturated fatty acid such as oleic acid contains one or more dou-
ble or triple C-C bonds. They are liquids at room temperature. They are
found mainly in plant resources such as olive oil and corn oil. (Figure 1.17)
Membrane lipids
Figure-1.18: The structure of a phospholipid
They are found in the structure of membranes (plasma
and other membranous structures in the cell).
Phospholipids
Phospholipids are the main component of cell mem-
brane. Actually their structure is similar to neutral lipids. But
unlike neutral lipids they contain nitrogen and phosphate. A
phospholipid is composed of a glycerol molecule attached
to two fatty acids and one phosphate group linked to an
organic compound such as choline. The fatty acid chains
may be single or branched and saturated or unsaturated.
The greater the number of unsaturated bonds the greater
the fluidity.
The most important features of phospholipids are their
hydrophilic (water love) and hydrophobic (water hate) prop-
erties. A phospholipid has a polar head and nonpolar tails.
In the presence of water they arrange themselves in a dou-
ble layer, as seen in the plasma membrane of cells, which is
surrounded by water (Figure 1.18).
The hydrophobic tails position themselves as a layer as
far from water as possible. The hydrophilic heads line up so
that they are in contact with it. As a result, a double unbro-
ken layer of phospholipid molecules forms with a water- free
space between them. (Figure 1.19)
Phospholipids make excellent cell membranes as they
form an effective barrier preventing the loss of proteina-

ceous structures in the cytoplasm. This means that there
can be no movement of polar substances through the dou-
ble layer of phospholipids, their entrance and exit is restrict-
ed to protein pores. Substances that have no charge such
as lipids pass into the cell by dissolving in the hydrophobic
layer in the middle of the membrane .
29
Other Types of Lipids
Lipids are not only involved in membrane structure and storage, they also
function as messengers and pigments.
Steroids
Steroids are lipids that have an entirely different structures from neutral fats.
These molecules are ring compounds that have a similar backbone but vary
according to the attached groups.
This causes them to have different functions in human and animal bodies.
They are fat soluble but are also polar.
They are involved in the regulation of metabolism, for example, in the control
of the hormones of the adrenal cortex. In the human body steroids also form the
structure of the male sexual hormone testosterone and female sexual hormone
estrogen.
Figure-1.19: Phospholipids have polar heads

ACTH, cholesterol and bile are also made up of steroid.
and nonpolar tails. in the presence of water
Cholesterol, an important steroid, is a component in animal cell membranes.
they arrange themselves in a double layer as is
seen in the plasma membrane of cells, sur- it is also the precursor from which all other steroids are synthesised. While choles-
rounded by water. terol is clearly an essential molecule, high levels of cholesterol in the blood may
contribute to cardiovascular disease such as arteriosclerosis.
arterioscle-
READ ME rosis
This refers to the condition where the blood vessels become narrow and lose
their elasticity. It is seen generally in men and women over the age of 40. The
vessels lose their elasticity due to a poor diet during aging. Fats and Ca+ ions
adhere to the walls of blood vessels causing narrowing.
Subsequent disorders in the brain

and heart then appear. Deposition of
fats (Cholesterol) and calcium may
block the affected vessel and cause
arterial bleeding if the condition
remains untreated and coagulation
of the blood may cause paralysis. A
CYTOLOGY
low cholesterol and low salt diet is

recommended for those suffering
from this condition.
Figure-1.19: Testosterone is a male sex-
ual hormone which controls muscle
development.
30
Carotenoids
They are the accessory pigment, either yellow or orange, in the chloroplasts of
plants. These molecules play a role in the light reactions of photosynthesis.
b-carotene for example is found in the chloroplast together with chlorophyll
and is involved in absorption of different wavelengths of visible light and their
transmission to chlorophyll. B-carotene is converted to vitamin A in the liver of
mammals. (Figure 1.20)
Figure-1.20: Lycopine is a kind of
Waxes carotenoids which give red colour.
In wax a fatty acid with a long chain attaches to an alcohol molecule with a long
chain. Waxes are solid at normal temperatures because their melting point is very
high. Being hydrophobic they are also waterproof and resistant to degradation.
Waxes are secreted by diverse organisms from plants and plankton to bees and
birds. Plankton use waxes for energy storage purposes, bees use it as a structural
component of the honeycomb whereas plants and birds use it as a water repellent
and lubricant. (Figure 1.21)
Humans also produce waxes from sebaceous glands to help protect and lubri-
cate the surface of the skin. Biological waxes have many applications in industries
such as pharmaceuticals and cosmetics. Figure-1.21: Honeycomb contains wax.
READ ME soap production

Most natural fats are made up of triglycerides. Olive oil for example contains
long unsaturated fatty acid chains whereas animal fatty acid chains are satu-
rated and solid. These animal fats can be converted to soap by the process
of saponification.
If animal fats are heated with an alka-
li such as KOH, they become hydrol-
ysed into glycerol and fatty acids. The
KOH is removed, leaving behind
solid fatty acids bonded to potassium.
These are moulded into suitable soap
shapes and used in washing to break
up water insoluble substances.
31
CYTOLOGY
32
PROTEINS (C, H, O, N, S)
Proteins are of vital importance for the body since they per-
form essential biological functions. They differ both chemical-
ly and physically from carbohydrates and lipids due to a nitro-
gen atom within their structure. In addition, some proteins
also contain sulphur atoms. They are the polymers of amino
acids.
Structure of Amino Acids

Proteins are composed of amino acids containing an
amino group (NH2), a carboxyl group, a hydrogen atom and a
radical group. Their structure is amphoteric meaning that they
can function both as an acid and an alkali. The amino group
is alkaline while the carboxyl group is acidic. The chemical
composition of the radical group varies according to the type
of amino acid.
– +
COOH ⎯⎯→ COO + H (an acid)
+
NH2 + H ⎯⎯→ NH3 (an alkali)
Individual amino acids bond to form a protein by the com-

bination of the carboxyl carbon with the nitrogen of the amino
group of another molecule. The peptide bond that is formed
is illustrated in (Figure 1.22).
The combination of two amino acids forms a dipeptide.
Similarly the combination of three amino acids forms a tripep-
tide. A polypeptide results from the bonding of more than ten Figure-1.22: The structure of amino acid and formation of a peptide
bond
amino acids but less than a hundred. A protein is the result of
the bonding of hundreds of amino acids.
Twenty different amino acids are commonly found in living
things, each one with its distinctive radical group. It is the
combination of these amino acids that form a specific protein
to perform a specific function in the body.
Any change to this amino acid sequence results in a
change in the composition of the protein which can cause
malfunction. Sickle cell anaemia for example is a serious

health problem caused by serious distortion of erythrocytes
due to a change in their amino acid configuration. (Figure-
1.23)
Figure-1.23: Little change makes big difference
33
The degree of simi- Functions of Proteins
larity between the All the reactions involved in the continuation of life processes involve the use
proteins of two indi- of proteins. They perform vital roles in structure, transport and defence to name
viduals is directly proportional but a few. The complete range of body functions in which proteins are vital are as
to their genome. Since each follows:
protein is genetically coded,
the proteins of individuals of Structural needs: Proteins form a scaffold for each cell, they play structural
the same family are likely to roles. Cartilage, bones and tendons all contain a structural protein called collagen.
have greater similarity than Keratin, another structural protein, forms the horns of a rhinoceros, the feathers
those who are not blood of a bird. Your hair and finger nails are also made up of this protein.
related. This factor is of great Catalysts: Enzymes are made up of mostly protein. Enzymes increase the rate
importance in organ trans- of a reaction by decreasing its activation energy. Thus they enable metabolic reac-
plantation since the tissues of tions to be carried out at optimum speed at a constant temperature.
the donor and the recipient
must be compatible. Hormone receptors: The proteins on the plasma membrane act as receptors,
recognising and binding to glucose, amino acids etc. and transporting them into
the cell.
Transport: The globular protein haemoglobin provides a vehicle for the trans-
port of oxygen and carbon dioxide throughout the body.
Nutrition: The seeds of plants such as wheat, rice, hazelnuts etc. store the nec-
essary proteins needed for future germination and growth in the early stages of
life. Animal proteins such as albumin in egg white and casein in milk are used for
the same purpose.
Spider silk is made Motion: Proteins such as actin, myosin and tubulin participate in the organs
up of protein. The involved in movement. Tubulin for instance, forms the structure of microtubules
presence of so many and provides cellular movement. Actin and myosin proteins form the structure of
hydrogen bonds makes each muscles.
silk fibre stronger than steel. Hormonal Activities: Hormones are the chemical messengers of the body and
are essential for regulation of body processes long term.
Defence: At any one moment, millions of white blood cells are circulating
around the body on the lookout for invaders that can do potential harm. They pro-
duce antibodies proteinaceous in structure. Without them, even the most simple
bacterium or virus would cause a fatal illness.
Proteins are vital for body growth and repair of damaged tissues. Any deficien-
cy can result in the following disorders;
Edema resulting from a decrease of blood proteins induced by starvation.

Slow recovery of any injury to the body.
CYTOLOGY
Disorders in erythrocyte structure.

Reduction in the resistance of the body to foreign or toxic substances.
34
Three Dimensional Structure of Proteins
Protein structure determines its biological activity. Their unique physical
shape enables them to function as enzymes, receptors and structural compo-
nents in the body. Proteins are three dimensional, high molecular weight macro-
molecules. The 3D structure of a protein results from interaction between its
chemical components at four different levels of complexity.
Primary Structure
An amino acid is linked by a peptide bond to another amino acid which may
either be identical to it or different, according to the information received from
DNA. This results in a linear sequence of amino acids. However, their shape can
alter since each peptide bond allows rotation of the amino acids that it joins.
Their number and order is critical since if one amino acid is lost from the
sequence or if the order alters, the resulting change in shape will cause malfunc-
tion of the finally assembled protein.
Secondary Structure
Secondary structure results from hydrogen bonding involving the backbone.
These bonds are formed between all the N-H and C=O groups of peptide
bonds. There can also be bonding between the radicals of each amino acid. Two
forms of secondary structure are possible: an a-helix and a b-pleated sheet.
a-helix: A polypeptide chain forms a helical structure if bonding occurs only
between N-H and C=O groups of the same chain. Proteins with an a-helical
secondary structure are myosin, actin, fibrogen and keratin.
b-Pleated Sheet: Here hydrogen bonding occurs between the N-H and
C=O groups in different chains of polypeptides. Proteins with a b-pleated sheet
type secondary structure are silk fibrin and b-carotene.
Tertiary Structure
Tertiary structure depends on interactions among side chains. The tertiary
structure of protein is formed by the folding of the a-helix or b-pleated sheets in
different directions to form a dense, complex globular structure. The tertiary
structure is supported by hydrogen, ionic and covalent bonds and also Van der
Waals forces and disulphide bonds.
Quaternary Structure
Quaternary Structure results from the interaction of two or more polypep-
tides. Some globular proteins such as haemoglobin are formed from more than

one chain of amino acids. Hydrogen bonding, Van der Waals forces and other
ionic attractions can all contribute to quaternary protein structure. For instance,
haemoglobin is composed of 2a and 2b subunits. Each a and b unit is a glob-
ular protein at a tertiary level. However, they polymerise to form quaternary pro-
tein structures.
35
Effects of heat on the protein structure
Protein structure is ideally suited to the temperature range and conditions in
which life is possible. Factors such as high pressure, high temperature and acidi-
ty may cause its denaturation or loss of structure. Complete denaturation is gen-
A protein has up to erally an irreversible reaction and the original shape of the protein can never be
4-levels of structures restored. However, if the structure is only partially denatured, the protein may
that account for its return to its original shape.
final 3-D shape. The 3-D
shape of a protein determines Simple and Complex Proteins
its function in the cells.
Proteins can be categorised as either simple or complex according to their
structure. Simple Proteins: These molecules are made up of only amino acid com-
ponents. Albumins, globulins, histones and protamines are examples of this type.
Complex Proteins: These molecules are composed of both amino acid and non-
amino acid components. Nucleoproteins, glycoproteins, lipoproteins and phos-
phoproteins are examples of this type. Proteins may also be classified according
to their shape such as filamentous and globular.
Three Dimensional Structure of Proteins
Level of structure Description Type of bond
Primary Amino acid sequence Covalent (peptide) bonds between amino acids.
CYTOLOGY
Secondary Alfa helix, beta sheet Hydrogen bond between amino acids in the peptide chain.
Covalent (S-S), hydrogen and ionic bonds, hydrophobic interac-
Tertiary Folding and twisting
tions between R groups.
Quaternary Several polypeptides Hydrogen and ionic bonds between polypeptide chains.
36
proteins and organ
READ ME transplantation
The degree of similarity between the proteins of two individuals is directly proportional to their genome. Since
each protein is genetically coded, the proteins of individuals of the same
family are likely to have greater similarity than those who are not blood
related.
This factor is of great importance in organ transplantation since the tissues
of the donor and the recipient must be compatible. Tissue typing of both
individuals gives vital information as to the likely success of a transplant.
Incompatibility results in the rejection of the transplanted organ.
Transplantation between identical twins has been shown to have the lowest
risk of rejection due to the presence of identical proteins in each individual.
READ ME amino acids and kwashiorkor

Kwashiorkor results from prolonged insufficient essential amino acids such as
lysine and tryptophan in the diet and greater digestion of carbohydrate. It is a
disease associated with underdeveloped third world countries. Young children
in areas affected by famine are most at risk. Children continue to grow at a near-
ly normal rate.
Their adipose tissue reserves are decreased as their fat is metabolised. The char-
acteristic symptoms of kwashiorkor are swelling of the abdomen, muscle wast-
ing, hair loss and skin sores. This condition can be rapidly reversed when the

protein component of the diet is improved.
37
VITAMINS
Vitamins are needed for growth, reproduction and survival. They are generally
obtained from both animal and plant sources. The functions of vitamins in main-
taining human health can be summarised as follows;
promotion of body growth
help in maintaining overall health
promotion of the normal functioning of the nervous and digestive system
promotion of body immunity against disease
In the deficiency or absence of a vitamin in the body, dependent reactions slow
down or cease resulting in health disorders. Most vitamins function as coenzymes,
and are required for the activation of an enzyme. Vitamins are divided into two
Vitamins are essen- major groups; water soluble and lipid soluble.
tial to cellular
metabolism, many Water Soluble Vitamins
are protective against illness- Vitamin C and B-complex vitamins are water soluble.
es. Vitamins are required in
CYTOLOGY
the diet in quantities that are Vitamin C: It is found in oranges, lemons, tomatoes, guava and green vegeta-
quite small compared with bles. Its deficiency known as scurvy causes bleeding from the gums and poor heal-
the relatively large quantities ing of wounds. Vitamin C is essential for increased immunity of the body against
of essential amino acids and colds and flu.
fatty acids humans need.
38
Vitamin B-complexes: This group of vitamins is found in many different
forms. Liver, eggs and pulses are all rich sources and are essential for the function
of nerves, muscles and metabolism. Examples of vitamin B are thiamin (B1),
riboflavin (B2), niacin (PP), pyridoxine (B6), biotin (B7), folic acid (B9), vitamin (B12),
and lipolic acid.
Lipid Soluble Vitamins

Vitamins A, D, K and E are lipid soluble.
Vitamin A: It is found in dairy products such as butter cheese and milk, as well
as liver, oil and fresh green vegetables. Its deficiency causes night blindness and
rough dry skin.
Vitamin D: It is found in oil, butter, milk, cheese, egg yolk and liver. The pre-
cursors of vitamin D are located in the skin and are converted into vitamin D using
ultraviolet light from the sun. Deficiency of vitamin D may cause skeletal deforma- Figure-1.23: Deficiency of vitamin D may
cause rickets.
tion called rickets. In this disease the bones of children in particular cannot hard-
en properly resulting in distorted and fragile bones.
Vitamin E: It is found mostly in oils made from cereals, nuts and leafy green
vegetables. Deficiency of vitamin prevent normal growth and anaemia in prema-
ture infants.
Vitamin K: It is found in liver, egg yolk and green vegetables. Deficiency of vita-
min K may cause slow blood clotting and liver problems.
EFFECTS OF
VITAMIN SOURCES
DEFICIENCY
Milk, Butter, Carrots, Night blindness,

A (Retinol)
Fresh vegetables Dry scaling skin
B1 (Thiamine) Legumens, Peanuts,

Beriberi-Nerve disorders
Liver
Figure-1.24: Vitamins, and fresh air are very
B9 (Folacin) Liver, Legumes, important for newborn babies
Anaemia, Birth defects
Orange and Green veg.
Fruit and Vegetables, Scurvy-Teeth, Skin and

C (Ascorbicacid)
Cabbage, Tomatoes Blood vessels disorders
D (Calcipherol) Fish oil, Milk, Egg yolk Rickets-Bone disorders

Vegetable oils, Nuts, Nerve damage,
E (Tocopherol)
Seeds Reduced fertility
Green vegetables, Tea,
K (Phylloquinone) Made by intestinal Slow blood clotting
bacteria
39
NUCLEIC ACIDS
They contain C, O, H, N and P atoms. They are the master molecules of the
cell. Nucleic acids have a unique role in the controlling life activities in the cell.
There are two types of nucleic acid in the cell. They are DNA and RNA.
Deoxyribonucleic acid or DNA is the nucleic acid that directs the synthesis of
all proteins in a cell. RNA helps DNA during cellular activities. They are very large
polymers which consist of many nucleotides. The monomer of all nucleic acids is
the nucleotide. It is the combination of three molecules; a sugar, a phosphate
group and a nitrogenous base . The significant differences between DNA and RNA
are that uracil is used instead of thymine in RNA. Also that DNA contains deoxyri-
bose sugar whereas RNA contains ribose sugar.
DNA ( Deoxyribonucleic Acid)

DNA is the master molecule which directs all metabolic activities of a cell by
the sequence of its nucleotides. It has the following functions:
storage of genetic information
provision of genetic continuity by self replication
regulation of cellular metabolic activity by the control of the synthesis of all
proteins and enzymes
RNA (Ribonucleic Acid)

Ribonucleic acid is a single stranded nucleic acid and is synthesised from DNA
in the nucleus. RNA molecules are incapable of replication since their function is
to carry information for protein synthesis from DNA to the ribosome. There are
three types of RNA; m-RNA, t-RNA and r-RNA.
m-RNA (messenger RNA)

m-RNA is a single stranded molecule and is synthesised from DNA by RNA
polymerase enzyme. Transferring of the genetics information from DNA to m-RNA
is called transcription. After transcription, the m-RNA moves to the cytoplasm
where the information it carries is translated into proteins by the ribosomes. In this
way, the synthesis of proteins is regulated.
t-RNA (transfer RNA)

This type of nucleic acid is also synthesised in the nucleus but remains in the
cytoplasm after its formation. The function of t-RNA is to transfer individual amino
acids to the ribosomes during protein synthesis according to the order determined
by m-RNA.
CYTOLOGY
r-RNA (ribosomal RNA)

This type of nucleic acid is synthesised in the nucleolus where it combines with
proteins to form ribosomal subunits. These then move into the cytoplasm ready
to attach themselves to m-RNA molecules.
40
THE CHEMISTRY OF LIFE
Everything around us is made up of solids, liquids or gases. Despite their obvious differences in physical appear-
ance, they are all made up of matter and share the same basic structure. Matter is anything that has weight and takes
up space. All matter is composed of basic structures called elements. An element is a substance that can not be bro-
ken down to other substances by chemical reactions. Elements are composed of atoms. An atom is the smallest unit
of matter. All atoms are comprised of a nucleus containing protons and neutrons, with electrons spinning around them.
A compound is a substance consisting of two or more elements combined in a fixed ratio. A molecule is the smallest
unit of a compound, just as an atom is the smallest unit of an element.
Ionic Bond is a chemical bond formed between ions as a result of the attraction of opposite electrical charge.
Covalent Bond is a type of strong chemical bond formed by the sharing one or more pairs of electron. Hydrogen Bond
is a type of weak chemical bond formed when the slightly positive hydrogen atom of a polar covalent bond in one
molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule.
A compound is formed when molecules are rearranged or bonds form between atoms. The bonds that form may
be ionic or covalent. The formation of bonds is termed a chemical reaction and may be categorised according to the
charge of the reacting molecules, water uptake or release and synthesis or breakdown of molecules.
Water is essential to life. Three-fourth of the earth's surface is covered by water. About two-third of your body is
water, and you can not survive long without water. A water molecule consists of one oxygen and a pair of hydrogen
atoms. The oxygen atom forms the core of the molecule with the hydrogen atoms attached to it at an angle of 104.5°.
Acid is a substance that increases the hydrogen ion concentration of a solution. Strong acids are corrosive and irri-
tant. Weak acids have a sour taste and are found in many types of food and drink.
Base is a substance that reduces the hydrogen ion concentration of a solution. A salt is the product of a neutrali-
sation reaction of an acid and an alkali.
Although water is the universal medium for life on Earth, most of the chemicals that make up living organisms are
based on the carbon element. Both organic and inorganic forms of carbon occur widely in nature. Compounds which
contain carbon are called organic compounds and the branch of chemistry that specialises in the study of carbon
compounds is called organic chemistry. Some of the organic molecules in organisms are small and simple. They are
called monomers. Monomers are combined to each other to form polymers.
Carbohydrates are made up of C, H and O atoms. Carbohydrates provide the primary energy source for all organ-
isms. Furthermore, they participate in the structure of the plasma membranes and cell walls. They are categorised into
three groups; monosaccharides, disaccharides and polysaccharides.
Lipids are made up of C, H, and O atoms but some lipids contain P and S atoms. Lipids are the one class of large
biological molecules that do not include polymers. They are insoluble in water, dissolving only in organic solvents
such as benzene, chloroform and ether. Their insoluble nature is the reason why their digestion is slower than other
food types.
Proteins are made up of C, H, O, N and S atoms. Proteins are of vital importance for the body since they perform essen-

tial biological functions. They differ both chemically and physically from carbohydrates and lipids due to a nitrogen atom
within their structure. In addition, some proteins also contain sulphur atoms. They are the polymers of amino acids.
Vitamins are needed for growth, reproduction and survival. They are generally obtained from both animal and plant
sources. Vitamins are divided into two major groups: water soluble and lipid soluble.
Nucleic acids contain C, O, H, N and P atoms. They are the master molecules of the cell. Nucleic acids have a unique
role in the controlling life activities in the cell. There are two types of nucleic acids in the cell. They are DNA and RNA.
41
EXPERIMENT: Investigation of starch and sugar in foodstuffs
Purpose: Materials: test tubes, beakers

To confirm the presence of iodine water bath
starch and its monomers in Benedict solution pipette
starch solution starch hot plate
5% glucose solution
Procedure:
Diagnostic test for starch
Discussion:
Explain why the colour of starch changed from brown to blue-black when iodine was added.
Diagnostic test for sugar
Discussion: Explain the colour changes in the sugar and Benedict solution when they are heated together.
42
EXPERIMENT: Investigation of fats and proteins in foodstuffs
Purpose: Materials: test tubes

To confirm the presence of biuret reagent water bath
fats and proteins in differ- ether pipettes
ent foods. egg white white paper
meat and fat
Procedure:
Diagnostic test for fats
Discussion:
Did the drop of fat and ether cause any change to the paper?
Diagnostic test for proteins
Discussion:
Explain the difference in colour between the first and second test tube.
43
Information recall questions
8. Compare the structure and function of organic and
1. 200 water molecules are generated after synthesis of inorganic molecules.
a single protein molecule. Calculate the number of
amino acids involved in this reaction and the number
of bonds formed.
9. Explain the following terms:
a) pH b) acid c) alkali d) neutrality
2. Carbohydrates, proteins and lipids are involved in

energy production and the repair of damaged tis-
sues. For each of these processes, name the type of
10. List the properties of water.
organic compound that is most effective in this role,
then the second least effective.
11. Draw the molecular structure of water, then explain

3. What is the most important property of carbohy- its cohesive properties.
drates?
4. Explain the following processes in proteins.

12. Explain the importance of carbohydrates to living
I. Denaturation things and give examples of its common sources.
II. Renaturation
III. Irreversibility
13. Briefly explain the following terms:
5. The order of amino acids in the structure of a protein a) atom

is very important. Thus if any amino acid is substitut- b) element
ed for another, this results in protein malfunction as
in sickle cell anaemia. Relate this information to the c) molecule
characteristics of the illness sickle cell anaemia. d) chemical bond
6. Explain the primary, secondary, tertiary and quater-

nary structure of proteins. Give an example for each. 14. Explain how polymerised glucose units can give rise
to polysaccharides with different characteristics.
7. Compare the structure of fibrous and globular pro-

teins. 15. Explain why proteins are so vital to living things.
44
Application of knowledge Fill in the blanks
1. A junior school student lives on only potato chips 1. The property of water to move upward against the
and cola. Given that this is not a balanced diet, what force of gravity is known as _______________________.
effects would this have on the general health of the
student ? Devise a program of nutrition that would
restore the student back to health. 2. An atom or molecule with an electrical charge is called
a(n) _____________.
3. Buffers are important because body fluids must be

maintained within a relative narrow range of
____________.
2. On a visit to her local doctor a young teenager com-

plained that she had not had a period for the last six 4. The loss of electrons from a molecule is called
months. The doctor observed that the patient was _____________, while the gain of electrons by a mole-
well below the normal weight for her height. When cule is called ______________________.
questioned she admitted to being on a strict diet.
Explain the biological reasons for the girl’s symp-
toms. 5. _______________ is the most common solvent in cells.
What simple treatment would restore the patient’s

normal menstrual cycle? 6. A solution with a pH of 7 is _______________________.
7. Large carbon compounds are built from smaller mole-

cules called _______________________.
8. If an atom is made up of 6 protons, 7 neutrons, and 6

electrons, then its atomic number is ________________.
3. It is a biological fact that a human being can live
without food for a number of weeks. However, if
deprived of water, a human being will die in approx- 9. Because carbon atoms have ______ electrons in their
imately three days. Explain the large difference in outermost energy level, they tend to form ___________
time between these two facts. covalent bonds with other atoms
10. Animals store glucose-containing fragments in the

form of _______________________________________.
11. Two amino acids bond to form a __________________.
4. Suppose that water molecules behaved differently

and were unable to form a regular lattice arrange- 12. A nucleotide is made of three main components:
ment, what would be the implication for aquatic ani- ________, ___________ and __________________.
mals in polar regions?
13. Animals stored glucose-containing fragments in the

form of ________________________________________.
45
True or false Choose the correct alternative
____ Because water is a polar molecule, it tends to cause 1. Which of the following organic molecules is not
ionic compounds mixed in water to dissociate into ions. synthesised during photosynthesis ?
A) cellulose B) starch C) fructose
____ The angle shape of the water molecule contributes to D) maltose E) glycogen
its property of polarity.
____ Capillarity is apparent when you put a straw in water

and the water level inside the straw rises higher than 2. Which of the following factors does not affect the
the level in the surrounding container. composition of a protein?
A) Number of amino acids
____ Organic compounds are substances produced and B) Sequence of amino acids
found in living things. C) Sequence of nucleotides in DNA
D) Binding of amino acids
____ Amino acids become linked together by peptide E) Number of nucleotides in DNA
bonds during hydrolysis reactions.
____ If the body temperature of a human being reached

112 degrees F, many enzymes would be destroyed
and the individual would die.
3. Which of the following is a trace element,
required only in small amounts by most living
____ Nucleic acids function primarily to carry genetic
things?
instructions and direct cellular activities.
A) oxygen B) magnesium C) nitrogen
D) carbon E) hydrogen
____ NAD+ acts as a cell's "energy currency."
____ The angle shape of the water molecule contributes to

its property of polarity.
4. In a green plant the following molecules are syn-

thesised;
____ Vitamin C and B-complex vitamins are water soluble.
I. Chlorophyll
II. Cellulose
____ An unsaturated fatty acid such as oleic acid contains III. Starch
one or more double or triple C-C bonds. IV. Nucleic acids
V. ATP
In which of these combinations (above) is nitro-
gen not required?
____ Hexose sugars are 6 carbon sugars such as glucose,
A) I and II B) II and III C) III and IV
fructose and galactose.
D) I, IV and V E) III and V
46
5. What are three particles that make up an atom? 9. The amount of energy necessary to raise the tem-
perature of 1 gram of liquid water by 1°C _____.
A) protons, neutrons and isotopes
B) neutrons, isotopes and electrons A) depends on the initial temperature of the water
sample
C) protons, neutrons and electrons
D) positives, negatives and electrons B) is 1 kilocalorie
E) molecules, ions and protons. C) is 1,000 calories
D) is 1 calorie
E) is 10 Calories
6. An example of a compound is…

A) water B) oxygen gas C) hydrogen gas 10. Which one of the following polysaccharides do we
use for storing energy in our muscles and livers?
D) chloride ion E) nitrogen gas
A) glucose B) glycogen C) starch
D) chitin E) cellulose
7. For the three types of RNA in a cell; mRNA, tRNA

and rRNA. Which of the following is a common 11. Which of the following organic molecules is pres-
property of all these types of RNA? ent in all cells ?
A) Their structure contains ribose sugar. A) starch B)cellulose C) glycogen
B) Their nitrogenous base is uracil. D) maltose E) protein
C) They all perform identical functions.
D) They are all synthesised in the nucleus.
E) They are synthesised from DNA.
12. Which is the correct term for compounds that do

not mix with water?
A) phospholipids B) hydrophobic C) hydrophilic
D) protein E) hydrogen bonded
8. Examine the following list of molecules.
I. Sugar
II. Nitrogenous Base
III. Vitamin
IV. Phosphoric acid
Which combination of the molecules above par- 13. Which one of the following is the major energy
ticipates to the structure of nucleotides? storage compound of plant seeds?
A) I and III B) III. IV and V C) I. II and III A) amylose B) glycogen C) cellulose
D) I. II and V E) II. III and V D) fats E) oils
47
14. Examine the list of disorders caused by a lack of a 17. Which of the following chemical groups is/are
particular vitamin and the food source used for its involved in the identification of a particular
treatment. amino acid?
I. Liver – Night Blindness I. Carboxyl group
II. Lemon – Scurvy II. Radical group
III. Rice – Beriberi III. Number of carbons in its structure
IV. Meat, Milk – Pellagra IV. Position of N in its structure
Which of the following combinations of vitamins V. Position of C and N in its structure
correctly describes the vitamin associated with A) I and II B) II and III C) III and IV
the disease?
D) I, IV and V E) III and V
I II III IV
A) A C B K
B) K C B A
C) B C D K
D) A B K C
E) A C D K
18. I.Carbohydrates
II. Proteins
III. Lipids
IV. Enzymes
15. The following table shows the name of a monosaccha-
ride that polymerises to form a disaccharide and then Which of the above molecules is/are coded by
a polysaccharide. DNA and synthesised under its control ?
Monosaccharide Disaccharide Polysaccharide A) I and II B) II and III C) II and IV
I. Glucose Fructose Starch D) I, II and IV E) III and IV

II. Galactose Glucose Glycogen
III. Glucose Fructose Cellulose
IV. Glucose Sucrose Starch
V. Fructose Galactose Glucose
Which of the combinations listed is/are correct?
A) I and III B) III. IV and V C) I. II and III 19. Which of the following molecules forms the main
structural component of cell membranes?
D) I. II and V E) II. III and V
A) Vitamins B) proteins C) cholesterol
D) carbohydrates E) phospholipids
16. Which of the following organic compounds is not

paired with its monomer? 20. Estrogen, progesterone, and testosterone belong
A) protein / amino acid B) starch / glucose to which class of molecules?
C) glycogen / glucose D) cellulose / glucose A) proteins B) amino acids C) lipids
E) maltose / galactose D) carbohydrates E) nucleic acids
48
Cytology
THE CELL
MICROUNIVERSE
Classification
Animal
chapter 2
Figure-2.1: Simple microscope
EXPLORING OF THE CELL
Both living and nonliving things are composed of molecules made from chem-
ical elements such as carbon, hydrogen, oxygen, and nitrogen. The organisation
of these molecules into cells is one feature that distinguishes living things from all
other matter. The cell are the building blocks of organisms that can carry on all
the processes of life.
In the same way that bricks form the structural units of buildings cells form the
structural and functional units of living things. Since cells are so minute in size
In 1665, the English
their existence was not known until magnifying lenses were developed. This
Scientist Robert
Hooke used a micro- enabled Robert Hooke to observe components of living matter in 1665. Because
scope to examine a thin slice of his simple microscope (Figure 2.1), he described the small individual units that
of cork and described it as he observed as small empty rooms, referring to them as cells. These days scien-
consisting of "a great many tists are able to use the latest technological developments in order to observe liv-
little boxes". It was after his ing matter in detail.
observation that Hook called
Their investigations led to the cell theory which was composed of the following
CYTOLOGY
what he saw "cells". They

definitions of cells. Namely that;
looked like "little boxes" and
reminded him of the small Cells are the basic structural and functional units of life on earth.
rooms in which monks lived, All living matter is composed of cells.
so he called them cells.
All cells originate from an identical parent cell by means of cell division.
50
Figure-2.2: An eukaryotic and a prokaryotic cell
Types of cell
Cell are grouped as prokaryotic and eukaryotic according to their cellular
structure. Only organisms in the kingdom Monera have a prokaryotic cell, but
organisms in all other kingdoms, which are Protista, Fungi, Plantae and Animalia
are made up of eukaryotic cells. (Figure 2.2)
A major difference between prokaryotic and eukaryotic cells is that in prokary-

otic cells genetic material (DNA) is not enclosed in a nucleus so it is free in the
cytoplasm. In fact, the term prokaryotic means "before the nucleus" and eukaryot-
ic means "true nucleus".
In the cytoplasm of prokaryotic cells the place where the genetic material
(DNA) is located is called nuclear area (nucleoid). The other differences between
All cells are sur-
prokaryotic and eukaryotic cells are that prokaryotic cells do not have membra-
rounded by a plas-
nous organelle such as mitochondria and lysosome, and also prokaryotic cells are
ma membrane. The
smaller and simpler than eukaryotic cells. semifluid substance within
But in the biosphere, cells called archaea also exist. These unicellular organ- the membrane is the cytosol,
containing the organelles. All
isms have special cells which share some characteristics of prokaryotic and
cells contain chromosomes
eukaryotic cells. They can live in very extreme environments where no others can
which have genes in the form
live. They are named as extremophiles, "lovers" of extreme environments, such as of DNA. All cells also have
the hot water and very salty water. ribosomes, tiny organelles The cell
that make proteins using the
We can summarise the differences between prokaryotic, archea and eukaryot-
instructions coded in genes.
ic cells as follows: (Table 2.1)
51
COMPARISON OF PROKARYOTIC AND EUKARYOTIC CELLS
Characteristics Prokaryotic Cells Archea Eukaryotic Cells
Nucleus Absent Absent Present
Membranous organelles Absent Absent Present

Some branched hydrocar-
Membrane lipids Unbranched hydrocarbons Unbranched hydrocarbons
bons
Cytoskeleton Absent Absent Present
Introns (noncoding DNA seg-
Rare Present Present
ment)
Circular without Histone Circular with Histone pro-
DNA form Linear with Histone protein
protein tein
Initiator amino acid Formyl-methionine Methionine Methionine
Peptidoglycan cell wall Present Absent Absent
Response to antibiotics Growth inhibited Growth not inhibited Growth not inhibited
Ability to grow over at tem-
No Some species No
perature 100 C
Cell size Usually 1-10 micrometer Usually 1-10 micrometer Usually 10-100 micrometer
Some unicellular, most
Cellular organisation Unicellular or colonies Unicellular or colonies
multicellular
Protista, Fungi, Plants,
Organism Bacteria Archea
Animals
Table-2.1: Comparison of a prokaryotic and
an eukaryotic cell
Eukaryotic cells are

generally much big-
ger than prokaryotic
cells. The logistics of carrying
out metabolism set limits on
cell size. At the lower limit,
the smallest bacteria,
mycoplasmas, are between
CYTOLOGY
0.1 to 1.0 micron. Most bac-

teria are 1-10 microns in
diameter. Eukaryotic cells are
typically 10-100 microns in
diameter.
52
Not all cells are
how we
READ ME study cells?
alike. Even cells
within the same
organism show enormous
With the naked eye we can't distinguish objects smaller than 100 micron (0.1 diversity in size, shape, and
mm) in size. Biology laboratories use special tools to magnify such small internal organisation. Your
objects. Those tools are microscopes. Microscopes are a major tool in cytology, body contains at least 200
the study of cell structures. Today, many different types of microscopes are different cell types. A few
used to better identify objects. However, the most commonly used micro- types of cells are large
scopes are compound (light) microscopes. enough to be seen by the
unaided eye. The Female
In a light microscope (LMs) visible light passes through the specimen and
Egg is the largest cell in the
then through glass lenses. The lenses refract light such that the image is mag-
body, and can be seen with-
nified into the eye or a video screen. Microscopes vary in magnification and
out the aid of a microscope.
resolving power. Light microscopes can magnify effectively to about 1,000
Most cells are visible only
times the size of the actual specimen. Light microscopes do not have a high
with a microscope.
resolution, but they can be used to study live cells.
Electron microscope: While a light microscope can resolve individual cells,
it cannot resolve much of the internal anatomy, especially the organelles. To
resolve smaller structures we use an electron microscope (EM. Theoretically,
the resolution of a modern EM could reach 0.1 nanometer (nm), but the prac-
tical limit is closer to about 2 nm. Transmission electron microscopes (TEM)
are used mainly to study the internal ultrastructure of cells.
Scanning electron microscopes (SEM) are useful for studying surface struc-
tures. The SEM has great depth of field, resulting in an image that seems three-
dimensional. Electron microscopes reveal organelles, but they can only be
used on dead cells and they may introduce some artifacts.
The cell
53
NOT in Animal cells
1. Central vacuole
2. Plastids
3. Plasmodesmata
4. Cell wall
Figure-2.3: A typical animal cell

The structure of eukaryotic cell
An eukaryotic cell is composed of three main parts;
Cell membrane
Cytoplasm
Nucleus
Cell membrane
You and all other
organisms are made The Cell Membrane is a complex barrier separating the cell from it's external
up of cells. Cells are environment. The cell membrane functions like a gate, controlling what enters and
CYTOLOGY
the building blocks of organ- leaves the cell. The cell membrane controls the passing of substances into and out
isms. They form the parts of of the cell, some substances easily cross the membrane, while others cannot cross
organisms and carry out all of at all. For this reason, the cell membrane is said to be selectively permeable. A
an organism’s processes and cell cannot survive if it is totally isolated from its environment. Due to its small size,
functions. approximately 75-120 Å in width, its detailed structure is invisible under the light
microscope and can only be distinguished by using an electron microscope.
54
NOT in Plant 3. Flagella
cells (some plant
1. Centrosome cells have)
2. Lysosome
Figure-2.4: A typical plant cell
Structure of the Plasma Membrane
The current accepted model of the plasma membrane is the Fluid Mosaic
Model proposed by Singer and Nicolson in 1972. They suggested that a cell
membrane was composed of a lipid bilayer containing mobile proteins. They also
suggested the presence of carbohydrates in combination with lipids and proteins. The plasma mem-
According to their model, the proteins in the membrane provide gateways or pores brane maintains the
through which substances may actively or passively enter or leave the cell. (Figure integrity of the cell.
2.5) It gives protection against
The plasma membrane differs from the nuclear membrane due to the pres- environmental hazards. It
provides the cell with shape.
ence of branched glycoproteins and glycolipids on its external surface. Their com-
It forms a barrier between the
position and arrangement on the plasma membrane is highly specific to an indi-
cell and its environment. It
vidual cell, this is called glycocalyx. These structures are involved in the recogni-
allows the transport of certain The cell
tion of the cell by hormones and antibodies. The role of these glycoproteins and
substances in and out of the
glycolipids is vital and any distortion or disruption results in cancer or other disor-
cell .
ders.
55
Observations under the electron microscope have revealed that the plasma
membrane is renewed by the exocytosis of material by the golgi apparatus. During
this process, material enclosed within a membrane is released. As the membra-
nous vesicle ruptures its contents are discharged and the membranous coat fuses
with the existing plasma membrane.
The functions of the plasma membrane
It maintains the integrity of the cell.
It gives protection against environmental hazards.
Figure-2.5: Structure of cell membrane It provides the cell with shape.
It forms a barrier between the cell and its environment.
It allows the transport of certain substances in and out of the cell due to
its selectively permeable nature.
Cytoplasm
The aqueous environment between the plasma membrane and the nucleus is
Most of the cytosol termed the cytoplasm. It is viscous, semifluid and jelly-like. It will precipitate if
is composed of water.
The amount however
placed into water.
varies according to the It has two main parts,
type of cell. It may for example
Cytosol
CYTOLOGY
range from 98% in the flesh of a

juicy fruit such as a water melon Organelles
to 5-15% in seeds and spores.
Compare this with a typical The living components of the cytoplasm are the cell organelles, whereas the
human cell which is composed nonliving components of the cytoplasm are composed of organic and inorganic
of 65% water.
compounds.
56
The Cytosol The cytoplasm is
composed of three
Most of the cytosol is composed of water. The amount however varies accord- main regions; the
ing to the type of cell. It may for example range from 98% in the flesh of a juicy ectoplasm, tonoplasm and
fruit such as a water melon to 5-15% in seeds and spores. Compare this with a endoplasm. The region of
typical human cell which is composed of 65% water. interaction between the plas-
The cytosol also contains both organic and inorganic molecules. Organic mol- ma membrane and the cyto-
ecules constitute 90% of the structural components of the cytosol whereas inor- plasm is termed the ecto-
ganic molecules constitute only 10% of it. plasm. The tonoplasm is the
membrane which surrounds
In both animal and plant cells the cytosol is particularly rich in proteins since
cytoplasmic vacuoles and the
all protein synthesis reactions are carried out within it. Furthermore, vitamins,
region between the ecto-
lipids and hormones are present. The cytosol of plant cells is particularly rich in
plasm and tonoplasm is
carbohydrates due to photosynthesis. In addition, their vacuoles may contain a
known as the endoplasm.
variety of substances including organic and inorganic acids.
In both plant and animal cells, Na, Ca, K, P, Mg and Fe are the vital inorganic
molecules found in the cytosol and are involved in the following functions: They
participate in the structure of some molecules. Mg for instance is present in
chlorophyll and Fe is present in haemoglobin. They are involved in the mainte-
nance of osmotic pressure due to differences in their concentration. This affects
the movement of water molecules both in and out of the cell. They function as reg-
ulatory elements in the structure of enzymes and vitamins.
Cytoplasmic movements
The cytosol of a living cell is constantly active. This activity is observable as

movement in the form of either rotation or streaming. This movement enables
food and waste molecules in the cytoplasm to be equally distributed.
Rotation: The aquatic plants elodea and nitella both demonstrate this type of
cytoplasmic movement. The cytoplasmic contents including the chloroplast and
nucleus rotate in a parallel plane to the plasma membrane. (Figure-2.6)
Figure-2.6: Cytoplasmic movements
Streaming: Both terrestrial and aquatic plants show
this type of random cytoplasmic movement. It may be
observed in the hair cells of terrestrial plants, in the com-
panion cells of seed plants and in the anther filaments of
the house-plant tradescantia.
The main causes of cytoplasmic movement are sur-
face tension and changes in viscosity, as well as the
movement of microtubules and microfilaments.
The rate of cytoplasmic movement is also affected by
external factors such as oxygen, light, temperature and
some chemicals. An increase in temperature for exam-
ple, accelerates the rate of cytoplasmic movement while
a decrease decelerates it. If oxygen is deficient, cytoplas- The cell
mic movement ceases completely.
Rotation Streaming
57
Organelles
The cell organelles in the cytoplasm are mitochondria, ribo-
somes, endoplasmic reticulum, golgi apparatus, lysosomes,
peroxisomes, vacuoles, plastids and centrioles. They comprise
the essential machinery that perform all cell activities and are
specialised to perform a variety of specific functions.
1. Mitochondria
A mitochondrion is an oval-shaped organelle composed of

a double membrane. Its size varies from 0.2-0.5 microns and its
number per cell varies from a few to 2500.
A mitochondrion is surrounded by a lipid bilayer which is
structurally similar to the plasma membrane. The outer mem-
brane is smooth but the inner membrane is folded into the
matrix to form cristae. It is here that the enzymes of the ener-
gy generating the electron transport systems (ETS) are located. For this reason,
cristae are abundant in the mitochondria of high energy-requiring cells.
The inner membrane borders an aqueous solution known as the matrix. Within
this solution are minerals and water, ribosomes, proteins, respiratory enzymes,
RNA and DNA.
Mitochondrial DNA is circular and can replicate itself, thus it is not under the
control of the nucleus. A mitochondrion can regulate and perform its own meta-
bolic activities by the synthesis of m-RNA, t-RNA and r-RNA. Despite this, its res-
piratory enzymes are coded for by nuclear DNA since mitochondrial DNA contains
much less information as compared to nuclear DNA. (Figure 2.7)
Figure-2.7: A mitochondrium Functions:
Mitochondria have The function of mitochondria is to produce ATP (Adenosine Triphosphate)

unique characteris- energy for the cell. They are especially abundant in high energy-requiring cells
tic, they are inherited such as muscle cells, nerve cells and cells involved in active transport.
from the mother only. This is Mitochondria are fuelled by organic food molecules, hydrolysed into their sub-
because mitochondria are units by the action of enzymes in the digestive tract. The food molecules diffuse
found in the middle region of into target cells. During cellular respiration they enter the mitochondria in where
the sperm cells not in the they are catabolised step by step until all the available energy has been extracted
head region which is the por- and the end products CO2 and H2O have formed. These serial reactions are
tion that enters the egg to
known as oxidation reactions since oxygen is consumed at each stage.
fertilise. So the mitochondrial
diseases results from abnor- The energy extracted from oxidation reactions is stored in the bonds of ATP.
mal mitochondria are always ATP acts as an intermediate molecule for energy transfer and may be transported
passed from mother to off- to any site of energy consumption.
CYTOLOGY
spring, such as muscle weak- 2. Ribosomes

ness because muscle is a
very active tissue which Ribosomes are essential for almost all prokaryotic and eukaryotic cells as they
needs energy produced by play a key role in protein synthesis. However, they are not found in viruses.
mitochondria. Ribosomes are approximately 150-200 Å in size and consist of a large and a small
58
subunit. Normally these subunits exist independently in dif-
ferent regions of the cell, but associate to perform protein
synthesis.
Unlike most other organelles, ribosomes are not sur-
rounded by a membrane. They are most numerous
organelles in almost all cells. Some are free in the cytoplasm;
others line the membranes of rough endoplasmic reticulum.
They are also found as free floating structures in the chloro-
plasts, mitochondria. (Figure 2.8a.b)
Types of ribosome
There are two forms of ribosomes: prokaryotic and

eukaryotic. Prokaryotic ribosomes have a sedimentation (s)
value of 70 when centrifuged and are found in bacteria, mito-
chondria and chloroplasts. Eukaryotic ribosomes have a value
of 80s and are found in the cytoplasm of eukaryotic cells.
Ribosomes contain both r-RNA and proteins. The pro-
teins needed for ribosomal structure are manufactured in the
cytoplasm. The RNA of ribosomes (r-RNA) is coded from
DNA and stored in the nucleolus.
Functions:
Ribosomes are involved in protein synthesis. The free

amino acids in the cytoplasm are ordered and assembled to
form functional proteins. The type of protein is governed by
the information received by the ribosome from DNA. Protein
synthesis is possible in vitro if the necessary amino acids, m-
RNA, enzymes, t-RNA and energy in the form of ATP are all
Figure-2.8a: Ribosomes types and formation
provided.
3. Endoplasmic Reticulum
The ER is a system of membranous tubules and sacs

located between the plasma membrane and nuclear mem-
brane of mature eukaryotic cells. It is an extensive network of
membranes that connect the nuclear envelope to the cell
membrane.
The cell
Figure-2.8b: Ribosomes on the ER
59
The endoplasmic reticulum of eukaryotes is well
developed whereas embryonic cells possess only poorly
developed endoplasmic reticulum. Erythrocytes may
have none at all. ER seems to disappear during cell divi-
sion and reappears after it has taken place.
Structurally, ER resembles the plasma membrane, it
connects the space between the double membrane of
the nucleus to the inner surface of the plasma mem-
brane. This arrangement provides a direct passage
between the nucleus, the cytoplasm and the pores on the
plasma membrane.
ER is categorised into two groups according to its
structure: rough ER and smooth ER.
Rough ER
The ribosomes on this type of ER are responsible for
its rough or granulated appearance. They are regularly
distributed along the endoplasmic reticulum in cells
where protein synthesis is frequent. Proteins synthesised
at the ribosomes pass through the channels of the endo-
plasmic reticulum to the golgi apparatus where they are
capsulated and secreted
Smooth ER
Its surface has no ribosomes that is why it is called
smooth. It plays a role in phospholipid, steroid and fatty
acid metabolism. Enzymes in smooth ER destroy toxic
chemicals and carcinogens. It is generally found in the
liver, testis, ovaries, adrenal glands, intestinal mucosa,
stomach and skeletal muscles. (Figure 2.9a.b)
Functions of Endoplasmic Reticulum
Support of cellular structures and maintenance of their shape.
Intercellular transport of ions and small molecules.
Transport of protein molecules synthesised by the ribosomes to the golgi
apparatus.
Figure-2.9a: Rough ER
Provision of a medium in which acidic and alkaline reactions can proceed
without affecting each other.
Synthesis of lipid molecules such as steroid hormones by the smooth en-
doplasmic reticulum of endocrine glands. It has also been suggested that
smooth ER plays a role in the relaxation and contraction of skeletal mus-
CYTOLOGY
cle.
Provision of a site where enzymes can detoxify potential carcinogens.
Figure-2.9b: Smooth ER
60
4. Golgi Apparatus
It is composed of a membranous complex of flattened sacs and is found

around the centrioles of all cells except sperm cells and immature blood cells. It
differs from ER due to the complete absence of ribosomes. (Figure 2.10)
Functions:
The golgi complex is involved in the formation of the plasma membrane.
The protein molecules synthesised at the ER are transported into the gol-
gi apparatus through channels and then combine with glucose molecules
to form glycoproteins. They are then packaged into a vesicle by the gol-
gi apparatus and secreted onto the surface of the cell. When the vesicle
reaches the plasma membrane it ruptures, fusing with it and adding to its
structure. Lipoproteins formed by protein synthesis as well as lipid mole-
cules of the golgi apparatus are also secreted, however these molecules
are exported out of the cell.
The formation of contractile vacuoles used in the removal of excess water
from the cell. These vacuoles are common in unicellular fresh water or-
ganisms.
The formation of the cell wall and cell plate.
The regulation of secretion. It is abundant in the cells of the salivary
glands, silk producing cells, aromatic plant cells and the chief cells of the
Figure-2.10: Golgi body
stomach mucosa.
The formation of lysosomes including the enzymes active in the hydroly-
sis and breakdown of food particles after they are phagocytosed. The en-
zymes are first synthesised at the ER and transported into the golgi where
they are packaged. The vesicles together with their enzymes known as
lysosomes, split away from the main complex and fuse with food vac-
uoles. (Figure 2.11) Figure-2.11: Secretion of molecules by ER,
golgi and lysosome
The cell
61
5. Lysosomes
Lysosomes are single layered vesicles 0.5 microns in size and

contain hydrolysing enzymes. The enzymes are synthesised by ribo-
somes on the ER and are packaged by the golgi. Research has shown
that a lysosome may contain as many as forty types of enzymes in its
matrix. Lysosomes are present in all animal cells that are capable of
phagocytosis and pinocytosis. Erythrocytes however are the excep-
tion to this rule. There is no lysosome in plant cells, but all plant cells
have lysosome-like structures. (Figure 2.12)
Functions:
They are involved in the digestion of intracellular and extra-
cellular materials when needed, fusing with food vacuoles
formed within the cell by phagocytosis or pinocytosis. The
lysosome then releases its contents onto the food molecules
in order to digest them. Deformed or aging cell organelles
are hydrolysed by the same mechanism of intracellular di-
gestion.
The contents of lysosomes include many enzymes for the hy-
drolysis of proteins, polysaccharides and nucleic acids.
These enzymes however, are inactive within the lysosome
vesicle itself. If the enzymes of the lysosome penetrate the
cytoplasm, they hydrolyse all the components of the cell, a
process known as autolysis. This system of self destruction
is only normally activated if a cell is deformed or aging. Af-
ter death, all cells of an organism are autolysed.
Lysosomes are involved in the defence of a cell against inva-
Figure-2.12: Formation of lysosomes and intracellular digestion
sion by bacteria and viruses and also against toxic sub-
stances. The cells of leucocytes for example, contain large
numbers of lysosomes.
Lysosomal enzymes are also released into the cytoplasm in
some normal processes. For example some organelles are
destroyed in order to get raw material or to get energy. Pro-
grammed cell death is known as apoptosis, the normal part
of development process of finger formation, during human
development, the hand is webbed but lysosomes destroy the
tissue between the fingers by apoptosis.
Lysosomes play an important role in the fertilisation of an
ovum by a sperm cell. The acrosome at the tip of the head
of the sperm contains lysosomes which hydrolyse the mem-
CYTOLOGY
brane of the ovum. This allows the contents of the sperm

head to penetrate the cell so that fertilisation can take place.
Lysosomes are also vital during the metamorphosis of in-
sects. The body contents are degraded to a protein-rich
soup from which the adult form develops. (Figure 2.13)
62
Figure-2.13: Lysosomes have many functions
lysosomal
READ ME disorders
As explained previously, lysosomes contain many enzymes which have spe-
cific roles. The absence of certain lysosomal enzymes causes disorders such
as Tay-sachs disease. It results from a missing lysosomal enzyme that normal-
ly breaks down lipids in cells surrounding nerve cells. Without the enzyme
lipids accumulates in the nerve cells. Children who have inherited Tay-Sachs
disease soon lose their vision and hearing and later are paralysed finally die
before age 4 years old. Pompe disease results form a missing lysosomal
enzyme which breaks down glycogen into simple sugars. As a result, glyco-
gen builds up in muscle and liver cells. The young patients usually die of
heart failure, because the heart muscle cells swell and no longer function
properly. Another lysosomal storage disease is Hurler disease causes bone
deformities. Affected bone cells contain huge lysosomes swollen with
mucus-like substances called mucopolysaccharides. These disorders are
treatable by addition of the enzymes that are deficient. In addition, the mal-
function of lysosomes may result in mutation. For instance, lysosomal
DNAase can cause defects in the structure of DNA resulting in cancer.
Lysosomes are sin-
gle layered vesicles
0.5 microns in size
LYSOSOMAL DISORDERS
and contain hydrolysing
Disorders Defect enzymes. The enzymes are
Accumulations of lipids in the brain cells, Patients lose synthesised by ribosomes on
Tay-Sachs the ER and are packaged by
their vision and hearing and later are paralysed, finally die
disease the golgi. Research has
before they are 4 years old.
shown that a lysosome may
Accumulation of glycogen in the liver and muscle cells,
Pompe disease contain as many as forty
The patients have heart failure and die
The cell
types of enzymes in its
Hurler disease Accumulation of mucopolysaccharides in the bone cells. matrix.
63
6. Peroxisomes
Peroxisomes are spherical, single layered

organelles. Peroxisomes metabolise H2O2 and
they are found in large numbers in cells that syn-
thesise, store, or degrade lipids. In animals they
are abundant in the cells of the liver, heart, mus-
cle and kidney. (Figure 2.14)
Peroxisomes in human liver and kidney cells
detoxify ethanol, the alcohol in alcoholic bever-
ages. Peroxisomes contain four types of
enzymes. Three of them are involved in the for-
mation of hydrogen peroxide, the other known
as hydrogen peroxidase, is involved in catabo-
lism of hydrogen peroxide (H2O2) into H2O and
1/2 O2.
Figure-2.14: Peroxisome
In plants specialised peroxisomes, called glyoxysome are found in the fat-stor-
ing tissues of plant seeds. Glyoxysomes have enzymes that convert stored fats into
sugar during germination until photosynthesis begins. Animal cells do not have
glyoxysome so they can not convert fats into sugar.
The difference between lysosome and peroxisome is that, unlike lysosomes,
peroxisomes do not bud from the endomembrane system (golgi body and endo-
plasmic reticulum). They grow by incorporating proteins and lipids made in
cytosol. They can increase in number by division when they reach a certain size.
PEROXIMAL DISORDERS
Disorder Cause and Symptoms
No peroxisomes in the cells, enzymes work in the cytoplasm. Symptoms include

Zellweger syndrome
abnormal face, hands, and feet, kidney cysts, damaged liver.
Too few peroxisomes in liver and skin cells, accumulation of very long chain fatty
Infantile Refsums disease acids. Symptoms include mental retardation, abnormal face, defective vision
and hearing, enlarged liver and weak bones.
Lack of some peroxisomal enzymes. A peroxisomal enzyme enters mitochondria

Primary hyperoxaluria instead of peroxisomes. Symptoms include metabolic disorders, toxin accumu-
lation.
CYTOLOGY
Lack of peroxisomal enzyme or too few peroxisomes in the brain cells.

X-linked adrenoleukodystrophy Accumulation of fatty acids in the brain cells. Symptoms are weakness, low
blood sugar, behavioural complications, dark skin, abnormal muscular control.
64
Figure-2.15: Storage vacuole
7. Vacuoles
These structures are sac-like single layered organelles surrounded by a single
membrane known as the tonoplast. They are found in both animal and plant cells
and differ in both size and quantity. They are small but numerous in animal cells
while large but fewer in number in plant cells. Their large size in plant cells is due
to the accumulation of wastes. As the vacuole increases in size, the cell cytoplasm
is confined to a small, band-like area.
The contents of a typical vacuole include salts, alkaloids, carbohydrates,
organic acids and inorganic molecules. Furthermore, some plant cells include an
additional molecule, a pigment known as anthocyanin. This pigment varies its
colour according to pH. In acidic conditions it is red in colour and in alkaline con-
ditions is blue.
Common types of vacuoles:
Storage vacuoles: They are a characteristic feature of aging plant cells. The Figure2.16: Formation of food vacuole
toxic wastes of cell metabolism react with salts and are stored as crystals. These
vacuoles enlarge due to the accumulation of wastes as the plant cells age. This is
accompanied by a decrease in metabolism. (Figure 2.15)
Food vacuoles: They are generally seen in unicellular organisms and leuco-
cytes and are formed by phagocytosis where a giant food molecule is engulfed
into a sac. Under acidic conditions, these giant molecules are then hydrolysed into
small molecules by lysosomes. The small molecules diffuse through the vacuole
membrane into the cytoplasm under alkaline conditions. Any waste molecules
remain in the vacuoles and are excreted by exocytosis. (Figure 2.16)
Contractile vacuoles: Unicellular organisms living in fresh water environments
possess one or two contractile vacuoles in order to regulate the osmotic balance
of the cell. Excess water that has collected in the cell is pumped out through con-
traction and relaxation. (Figure 2.17) The cell
Figure-2.17: Contractile vacuole
65
8. Plastids
Plastids are stained structures unique to the cells of high-

er plants. They are lacking in bacteria, blue-green algae,
fungi and animal cells. There are three types of plastids;
chloroplasts, chromoplasts and leucoplasts.
Chloroplasts
They are green coloured pigments present in the leaves
and other green parts of a plant and each is approximately
4-8 microns in size. Chloroplasts are disc-shaped in appear-
ance and are surrounded by a double membrane. The outer
smooth membrane resembles that of a mitochondrion and
the inner membrane is folded to form lamellae or thylakoid.
In some regions of the chloroplast the lamellae are stacked
in a pile, forming grana. This increases the capacity for light
absorption and provides a site for the enzymes of the elec-
tron transport system and chlorophyll molecules.
The fluid portion of the chloroplast surrounding the
grana is known as the stroma and contains DNA, RNA, ribo-
somes, the enzymes involved in dark phase of photosynthe-
sis, carbohydrates, lipids, proteins, water and minerals.
(Figure 2.18)
Both chloroplasts and mitochondria are structurally sim-
ilar to prokaryotic cells. Their ribosomes are structurally sim-
ilar all have their own DNA, and are capable of replication.
Both chloroplasts and mitochondria have the ability to syn-
Figure-2.18: The structure of chloroplast thesise ATP molecules. They differ however, in how this ener-
gy is utilised. Chloroplasts utilise these molecules within their own structure where-
as mitochondria export most of them to be used in other structures.
Functions:
The main function of chloroplasts is the synthesis of organic molecules and
oxygen from water and carbon dioxide using sunlight. During this process, light
energy is converted to chemical bond energy, a form that can be used by all living
things. This process of photosynthesis has both light dependent and light inde-
Both chloroplasts pendent phases. The light dependent phase occurs in the grana of the chloroplas-
and mitochondria ts while the light independent phase occurs in the stroma.
are structurally simi-
Leucoplasts
lar to prokaryotic cells. Their
ribosomes are structurally They are colourless plastids formed in plant tissue that is not exposed to sun-
similar, they all have their light. If light is provided however, they are converted into chloroplasts. Some leu-
CYTOLOGY
own DNA and are capable of coplasts are involved in the storage of starch and are known as amyloplasts.
replication. Both chloroplasts Starch is deposited in granules in their stroma. Some leucoplasts store proteins
and mitochondria have the but they are deposited in vesicles.
ability to synthesise ATP mol-
ecules.
66
All plastids develop
from proplastids,
they are the precur-
sor organelles found in less
specialised plant cells, espe-
cially in growing, undevel-
oped tissues. During devel-
opment, depending on the
special function cells will
have, their proplastids can
mature into one of the types
of plastids.
Chromoplasts
Plant cells lack cen-
They are plastids formed by the alteration of chloroplasts but are incapable of trioles, but their
photosynthesis. spindle fibres are
They are responsible for the yellow, orange and red pigments of flowers and formed by cytoplasmic struc-
fruits. Xanthophyll for example gives lemons their yellow colour, carotene colours tures during cell division.
carrots orange, and lycopine colours tomatoes red. Furthermore, algae contain
other chromoplasts known as phycoerthyrin and phycocyanin.
All plastids develop from proplastids, they are the precursor organelles found
in less specialised plant cells, especially in growing, undeveloped tissues. During
development, depending on the special function cells will have, their proplastids
can mature into one of the types of plastids. But under some certain conditions
even mature plastids can convert from one type to another.
9. Centrioles
Centrioles are found in pairs adjacent to the nucleus of a cell. Each is formed
from nine groups of microtubules attached to each other by a triple bond and
arranged in a circle. Each of these groups is formed from three microtubules per-
pendicular to each other (9x3). The whole of the centriole structure is surrounded
by a membrane. (Figure 2.19)
Functions:
Centrioles are involved in the formation of spindle fibres in animal cells dur-
ing cell division. The centrioles have ability to replicate themselves, they replicate
before cell division. During prophase of cell division each pair moves to the oppo-
site pole of the cell. Once there they maintain the spindle fibres, position the chro-
mosomes at the equatorial plate and then move them to the poles. Any defect in
the centrioles effectively prevents a cell from dividing. Additionally, the centrioles
located at the base of flagella and cilia regulate the formation of microtubules. The cell
Plant cells lack centrioles, however their spindle fibres are formed by cytoplas-
mic structures during cell division. Figure-2.19: Centrioles
67
10. Nucleus
The nucleus is the control centre (brain) of the cell. It is

vital to the survival of an organism. If you remove the nucle-
us from any cell, death is unavoidable. An amoeba can sur-
vive for a period of time after its nucleus has been removed
but dies unless the nucleus of another amoeba is transplant-
ed.
The nucleus contains a eukaryotic cell's genetic library. It
contains most of the genes in the eukaryotic cell (some
genes are located in mitochondria and chloroplast). All
eukaryotic cells except erythrocytes have an organised
nucleus. (Figure 2.20)
The nucleus is visible under the light microscope and is
either disc or oval-shaped. The size of the nucleus varies
according to the rate of metabolic activity in a cell. A highly
active cell has a large, active nucleus. Generally a cell con-
Figure-2.20: The structure of nucleus tains only one nucleus. However paramecium, liver and
muscle cells have at least two nuclei.
Nuclear Membrane: The hereditary material of a cell is surrounded by a lipid
bilayer known as the nuclear membrane. It is formed from an extension of the
endoplasmic reticulum. The nuclear membrane is structurally similar to the plas-
ma membrane but differs in that it has ribosomes on it and contains pores.
(Figure 2.21) These pores are involved in the transport of materials between the
cytoplasm and nucleoplasm. In the prophase stage of mitosis, the nuclear mem-
brane disappears and the cytoplasm and nucleoplasm mix. Towards the end of
cell division, these structures are repartitioned by the endoplasmic reticulum and
golgi.
Nucleoplasm: The semifluid structure which fills the nucleus is termed as

nucleoplasm. The viscosity of nucleoplasm is higher than cytoplasm.
Nucleolus: The nucleolus is a small coiled structure within the nucleus. It con-
tains DNA, RNA and proteins and is the site where r-RNA accumulates after its
synthesis at the chromosomes. The rRNA is combined with histone proteins and
Figure-2.21: Nuclear membrane and its pore
is moved to the cytoplasm to form ribosomes. It is visible using a light microscope
due to its high light refracting properties. Although the other structures of the
nucleus are stained using a basic dye, the nucleolus is stained using an acidic dye.
A single nucleus may contain one or more nucleoli which disappear during cellu-
lar division.
The nucleus con- Hereditary Material: The nucleus contains hereditary material in the form of
CYTOLOGY
tains most of the DNA, chromatin and chromosomes. The double stranded helical structure of DNA
genes in a eukaryot- is associated with chromatin. During cell division, DNA is wound around histones,
ic cell. Some genes are locat- made of a protein that behaves as a bobbin for the long DNA molecule. During
ed in mitochondria and metabolic activity, the DNA unwinds in order for genetic information to be tran-
chloroplasts. scripted.
68
Cytoskeleton
Just as your body depends on

your skeleton to maintain its
shape and size, so a cell needs
structures to maintain its shape
and size. The cytoskeleton main-
tains the three-dimensional struc-
ture of the cell, participates in the
movement of organelles within
the cytosol and helps the cell
move. The cytoskeleton is made
up of microtubules, microfila-
ments and intermediate filaments.
(Figure 2.22)
Microtubules: They are hollow cylinders assembled from subunits of
tubulin protein. Microtubules grow out from the centrosome in animal
cells. Microtubules shape the cells, guide movement of organelles and
carry chromosomes during cell divisions. Microtubules move past each
other using the motor protein dynein.
Cilia and flagella are motile appendages of cells. Each consists of a
9+2 arrangements of microtubules and each is anchored in the cell by a
basal body that has 9x3 organisation of microtubules. (Figure 2.23)
Microfilaments: They are thin rods built from actin protein. They func-
tion in muscle contraction, amoeboid movement, cytoplasmic movement
and support for microvilli.
Intermediate filaments: They are stable structures formed from differ- Figure-2.22: Members of cytoskeleton
ent types of fibrous proteins. They support cell shape and fix organelles in
place.
THE CYTOSKELETON
Maintenance of cell shape

Microtubules Cell motility (as in cilia or flagella)
(Tubulin protein) Chromosome movements
Organelle movements
Muscle movements
Microfilaments Cytoplasmic streaming
(Actin protein) Cell motility (as in pseudopodia)
Cell division (cleavage furrow formation)
Intermediate Filaments Supporting of nucleus and organelles

The cell
(Keratin family protein) Formation of nuclear lamina
Figure-2.23: The structure of cilia flagellum
69
The extracellular matrix (ECM)
The extracellular matrix of animals cells plays a role in support, adhe-

sion and movement. The components of ECM are mainly glycoproteins
which are secreted by cell. The glycoproteins are made up of protein and
small amounts of carbohydrates. The most abundant glycoprotein found
in ECM is collegen. They form strong fibres outside the cells. The other
types of glycoproteins are proteoglycans and fibronectins.
Proteoglycans form complexes by noncovelantly attaching to long poly-
saccharide molecules. Fibronectins bind the receptor proteins on the cell
membrane and they attach ECM to the plasma membrane of the cell.
Figure-2.24: The extracellular matrix Surface Features of Cells
The outermost layers of a cell act as the interface between its internal environ-
ment and the rest of the organism. It performs functions vital to the survival of the
cell.
Plasma membrane: Eukaryotic animal cells have no cell wall and are bordered
only by the plasma membrane. It is selectively permeable. In both animal and
plant cells it provides material exchanges. The plasma membrane also plays a key
role in identification as the features on the external surface of the membrane
enable the cell to be recognised by hormones and antibodies. The cell membrane
is largely made up of a double layer of lipids in which proteins, carbohydrate-lipid
complexes or glycolipids and glycoproteins are embedded. These glycoproteins
are the receptors for extracellular signals such as hormones. They then transmit
the signal to the rest of the cell in order to generate a response. (Figure 2.24)
Cell wall: The outermost layer of plant and protist cells is the cell wall. Its rigid
structure protects the contents of the cell and prevents the cell membrane from
rupturing when the cell is turgid. The strength of the cell wall in plants, some fungi
and algae is due to two layers of the polysaccharide cellulose with a thin layer of
Figure-2.25: The structure of cell wall pectin between them, holding each layer together. Directly beneath this cell wall is
the fluid bilipid plasma membrane which controls the passage of substances in
and out of the cell. (Figure 2.25)
Microvilli: Microvilli are the microscopic projections of plasma membrane
which increase the surface area of the cells. They are found mostly in cells con-
cerned with absorption or secretion. For example, the epithelial cells of the small
intestine absorbs nutrients. This is made possible by extending their surface area
so that each cell forms part of a long projection known as a villus.
The cells that comprise it contain many minute projections on their upper sur-
face known as microvilli. In this way they increase their surface area 600 times
more than would be possible if the small intestine were merely a smooth surfaced
CYTOLOGY
tube with no villi or microvilli at all. The cytoskeleton within the main cytoplasm of
the villus extends into each projection producing a network of microfilaments. This
network of filaments generates the wave-like movement of each microvillus.
(Figure 2.26)
Figure-2.26: The microvilli
70
Intercellular junctions
The cells of multicellular organisms are
organised into tissues, organs, and organ sys-
tems. As a result of this, neighbouring cells
must interact, and communicate with each
other in order to perform body functions.
Intercellular junctions help integrate cells into
higher level of organisation, structure and
function. There are three types of junction in
animal cells: desmosomes, gap junctions and
tight junctions. All these connections are
especially common in epithelial tissue which
lines internal surface of the body. (Figure 2.27)
Desmosomes (Anchoring junctions)
They act as a rivet, holding the cells

securely together at one point, but still allow-
ing substances to pass through adjacent cell
membranes. Desmosomes are supported by
Intermediate filaments which form the strong
protein keratin. They are found mostly in the
upper layer of skin. Desmosomes are also
present in large numbers in cardiac muscle
and other organs carrying out mechanical
work.
Gap junctions (Nexus)
Gap junction is another method of com-

munication between the cells themselves
through numerous pores that connect adja-
cent cells. Gap junctions provide cytoplasmic
channels between adjacent cells. Special
membrane proteins surround each pore
which is wide enough for salts, sugar, amino
acids and other small molecules to pass. Gap
junctions resemble a desmosome in structure
but differ in that the bridge formed between
two adjacent cells is only 2-4 nm in length thus
providing a closer attachment between cells.
A single gap junction consists of six mem-
brane proteins arranged as the segments of a
hexagon. The central channel bordered by
these proteins enables a chemical or electrical
stimulus to be transferred rapidly in one or The cell
both directions from cell to cell through the Figure-2.27: ( Right) Neighbouring cells communicate with each other through cellu-
lar junctions. (Left ) A longitudinal section through two adjacent cells showing their point
central channel.
of contact through a desmosome.
71
Pancreatic and cardiac cells are the most well known examples of intercellular
The cells of multi-
communication through gap junctions. Cardiac muscle uses gap junctions to
cellular organisms
transmit electrical impulses between neighbouring cells so that their contraction is
are organised into
synchronised.
tissues, organs, and organ
systems. As a result of this, Gap junctions are also involved in cell defence. In the event of any injury to the
neighbouring cells must cell, an increase in calcium ion concentration and the subsequent lowering of pH
interact, and communicate stimulate the gap junctions to close rapidly.
with each other in order to
perform body functions.
Tight Junctions (Zonula occludens)
Intercellular junctions help
These are connections in which the membranes of adjacent cells are very
integrate cells into higher
close. In the tight junction, the two plasma membranes are often fused. There is
level of organisation, struc-
no intercellular space and material can not pass between the cells.
ture and function.
In tissues where intercommunication is vital, a small gap is always present
between adjacent cells bridged by a small, proteinaceous channel through which
substances can pass. Tissues containing potentially toxic substances such as the
small intestine, colon and bladder must have a strategy for isolating their contents
from other parts of the body to prevent contamination. In order to achieve this, the
membranes of adjacent cells are pressed together so tightly that they are even
thought to be fused. This prevents any substance on one side of the cell layer from
seeping through spaces or channels between cells into other parts of the body.
The impermeable nature of tight junctions between cells is also thought to play
an important role at synapses and in the entry of drugs etc. from the blood to the
brain.
Plasmodesmata
The permeability of the plant cellulose cell wall is insufficient to provide a con-
nection between the living contents of neighbouring cells. Plasmodesmata are the
cytoplasmic bridges between the plant cells. They are formed at the same time as
the cell plate and consist of the fused plasma membrane of both cells.
Plasmodesmata contain tubules known as desmotubules connecting the endo-
plasmic reticulum of each cell. In this way, water and its solutes as well as larger mol-
ecules can pass freely from cell to cell according to their osmotic concentration.
Table-2.2: Intercellular junctions
INTERCELLULAR JUNCTION
Type Location Function
Desmosomes Outer skin layer Like rivets, fastening cells together into strong sheets.
Muscle cells in heart and Provide cytoplasmic channels between animal cells, allowing
Gap Junction
CYTOLOGY
digestive tract exchange of substance

Inside lining of small intestine The two plasma membranes are often fused. There is no inter-
Tight Junction
and brain cellular space and material can not pass between the cell.
Weakened areas of plant cell
Plasmadesmata Provides material exchanges between plant cells
walls
72
THE STRUCTURE OF EUKARYOTIC CELL
Structure Description Function
Encloses cellular contents
Membrane composed of protein, lipid and carbohy- Regulates material exchanges
Cell membrane
drates Helps maintain cell shape
Communicates with other cells
The jelly-like (viscous, semi-fluid) Provides environment for biochemi-

Cytoplasm
structure found between nucleus and cell membrane cal reactions and cell organelles
Cell organelles:
Nonmembranous granules composed of RNA and pro-
Ribosome tein, some attached to ER some free in cytoplasm some Synthesise protein
in chloroplast and mitochondria
Endoplasmic Network of internal membranes extending through the

Material production and transport
Reticulum cytoplasm
Lipid synthesise
Smooth ER Lack ribosomes on outer surface
Drug detoxification
Rough ER Ribosomes attached to outer surface Synthesise exportable proteins
Formation, packing and secretion of

Golgi Complex Stacks of flattened membranous sacks
exportable materials
Double membranous organelles, inner membrane is Power house of the cell, produces
Mitochondria
folded to form cristae ATP energy
Found in animal cells, nonmebranous structures com- Help distribute chromosomes to new
Centrosome
posed of two centrioles. cells during cell division
Microbodies Membrane bound sacks containing variety of enzymes Destroys toxic chemicals such as
(Peroxysome) such as hydrogen peroxidase hydrogen peroxide
Microbodies Its enzymes convert stored fats to

Found in the seeds of certain plants sugar to produce energy during ger-
(Glyoxisome) minations
The cell
Contains digestive enzymes respon-
Lysosome Single membrane-bound sacks
sible for cellular digestion
73
THE STRUCTURE OF EUKARYOTIC CELL
Structure Description Function
Vacuole Membrane bound sacks, 3-types Store materials, waste and water
Food Vacuole Contains food obtained by endocytosis Food storage
Contractile
Found in fresh-water protists Removes excess water
Vacuole
Storage
Found in plant cells Stores toxic salts as crystals
Vacuole
Plastids Found in plant cells, double membranous, 3-types Variety of functions
Contains chlorophylls on thylocoid membrane, found in Site of photosynthesis

Chloroplast
green parts of plants and protists gives green colour
Stores proteins, lipids and carbo-

Leucoplast Colourless plastids, found in stem and root
hydrates
Formed from the alternation of chloroplast, contains red,

Chromoplast Gives variety of colour
orange and yellow pigments
Large structure surrounded by double membrane, contains

Nucleus The control centre of the cell
chromosomes and nucleolus
Dense region within the nucleus composed of protein and

Nucleolus The site of ribosome synthesis
RNA
Rod-like structure composed of DNA and protein, contains

Chromosome Controls all cellular activities
genes
Cell wall Found in plants, protista, fungi and some bacteria Protection and structural support
Cilia (9+2) Short projections extending from the surface of the cell Provides cellular movement
CYTOLOGY
Flagella(9+2) Long projections extending from the surface of the cell Cellular locomotion
Table-2.3: Comparison of a prokaryotic and an eukaryotic cell
74
Transport of materials through the
plasma membrane
Cell membranes help organisms maintain homeostasis by

controlling what substances may enter or leave the cells.
Materials are conducted in and out of the cell by two basic
methods which are passive mechanisms and active mecha-
nisms.
Passive mechanisms
Passive mechanisms move molecules from an area of high

concentration to an area of low concentration without the use
or input of energy by the cell. Passive mechanisms can take
place in living or nonliving cells.
There are three forms by which this method of transport is
possible. (Figure 2.28)
Diffusion
Diffusion is the movement of ions, atoms or molecules

from regions of higher concentration to regions of lower con-
centration. Perfume for example diffuses throughout a room
until its concentration is constant, as does a drop of ink when
added to a glass of water. This type of movement occurs in
both living and nonliving material. (Figure 2.28)
Facilitated diffusion
Carrier molecules in the cell membrane accelerate move-

ment of relatively large molecules from regions of higher con-
centration to one of lower concentration. The movement of
glucose molecules through the cell membrane is provided by Figure-2.28: (a) Diffusion through the pore, (b) Diffusion of lipid solu-
carrier molecules. (Figure 2.28) ble materials, (c) Facilitated diffusion.
PERMEABILITY OF THE LIPID BILAYER TO THE DIFFERENT SUBSTANCES
Types of molecules Examples Permeability

Gases N2, CO2, O2 Freely permeable
Hydrophobic Hydrocarbons Freely permeable

Small polar H2O, glycerol, urea Freely permeable
Large polar Glucose, fructose, maltose, starch Not permeable The cell
H+,Na+, HCO3 , K+, Mg+2, etc.

-
Ions Not permeable
75
OSMOTIC TERMINOLOGY
Solute Concentration Solute Concentration Direction of

Tonicity
in Solution A in Solution B Net Movement of Water
A and B are isotonic to
Equal Equal No net movement
each other
B hypertonic to A
Less Equal A to B
A hypotonic to B
A hypertonic to B
Equal Less B to A
B hypotonic to A
Osmosis
This process is the diffusion of water across a semipermeable

membrane. Imagine that two sugar solutions differing in concentra-
tion are separated by a membrane that will allow water through, but
not sugar. The hypertonic solution has a lower water concentration
than the hypotonic solution. Water diffuses across a selectively perme-
able membrane from the hypotonic solution to the hypertonic solution
and continues until the solutions are isotonic. (Figure 2.29)
Osmosis can result in two extreme conditions:
Plasmolysis
When a cell is placed into a hypertonic environment where the

water concentration is lower than that of its own cytoplasm, it conse-
Figure-2.29: Osmosis, water passes from high concentra- quently shrinks. This is due to water loss as a result of the difference
tion(B-Pure water) to low concentration (A Glucose contain-
ing water)
in concentration. The cell wall of plant cells gives some protection
when tissue is placed in a hypertonic environment. The rate of plas-
molysis in plant cells is slower than in animal cells.
Deplasmolysis
When a cell is placed in a hypotonic environment where the water

concentration is higher than that of its own cytoplasm, it absorbs
water and swells. The events during this process are the complete
reverse of those of plasmolysis. If the cell has no cell wall or no mech-
anism for expelling the excess water, it will lyse.
Deplasmolysis and plasmolysis result from the combination of two
important forces: osmotic pressure and turgor pressure. (Figure 2.30)
CYTOLOGY
Osmotic Pressure
Water molecules have a tendency to move from a hypotonic solu-

tion to a hypertonic solution. We define the osmotic pressure of a solu-
Figure-2.30: Plasmolysis and deplasmolysis in RBC tion as the tendency of water to move into hypertonic solution by
76
osmosis. A solution with a higher solute concentra-
tion has low water concentration therefore it has
high osmotic pressure because water always tends
to move toward solution of greater osmotic pres-
sure.
In the roots of plants, the effects of osmotic
pressure are clear. During deplasmolysis, water
molecules move from the soil to the root hairs since
they have a higher concentration of soluble salts
than the soil, and a lower concentration of water.
The osmotic pressure gradually falls as equilibrium
is established.
Turgor Pressure
It is the pressure exerted by water against the

cell membrane and cell wall of plant cell. During
deplasmolysis, the cell absorbs water and the vol-
ume of its cytoplasm increases. As a result, the Figure-2.31: Observation of osmotic pressure
plasma membrane is stretched due to the large vol-

ume of fluid exerting pressure on it.
The membrane of erythrocytes for example is
incapable of tolerating high turgor pressure and
lysis if placed into a dilute solution. This is also
known as haemolysis.
Unicellular organisms living in freshwater envi-
ronments however, pump out the excess water in
their cytoplasm by using their contractile vacuole to
maintain constant osmotic pressure. Plants use
their cell wall to withstand high pressure.
Turgor pressure in fact is used to the advantage
of the plant in the following ways.
As support for herbaceous tissue lacking
the strength of secondary growth.
Regulation of opening and closure of stom-
ata.
Nastic movement of plants such as in the
plant mimosa.
Absorption of water is inversely proportional to

turgor pressure. It is however, directly proportional
to osmotic pressure. If both osmotic and turgor
The cell
pressure are equal, there is no movement of water
within the plant. (Figure 2.31-32) Figure-2.32: Plasmolysis, deplasmolysis and turgor pressure in plant and animal cells
77
Dialysis
Dialysis is a method by which small soluble molecules may be sepa-
rated from larger ones through a selectively-permeable membrane that
only allows the passage of small molecules.
If for example, a mixture of starch and glucose is placed in visking
tubing within a beaker of distilled water, glucose molecules move
through the tubing into the beaker of water. The large starch molecules
remain behind in the tubing together with water that has moved across
from the beaker. Glucose and water molecules continue to move across
until equilibrium is established on both sides of the membrane.
The same principle is used to eliminate nitrogenous waste from the
blood of individuals who suffer from renal insufficiency. The contaminat-
ed blood with its high concentration of urine is circulated through the
dialysis tube of an artificial kidney where the urine diffuses from the
blood into the dialysis fluid. Useful materials remain in the blood, where-
as waste diffuses out into the dialysis tube. Useful substances such as
Figure-2.33: The principle of dialysis. Blood to be serum may also be added using the same principle. (Figure 2.33-34)
cleaned passes the apparatus and toxic substances dif-
fuse through a selectively permeable membrane. Filtration
The movement of molecules from regions of higher pressure to

regions of lower pressure. In the capillary vessels food molecules are
forced into tissue fluid by blood pressure. As it is seen in the figure, near
the vein the blood pressure (filtration) decreases and osmotic pressure
increases enabling tissue fluid to enter back into the circulation. (Figure
2.35)
CYTOLOGY
Figure-2.34: Dialysis machine Figure-2.35: Filtration in capillary vessels
78
Factors Affecting the Rate of Passive Transport
In a living cell, there is a continuous movement of molecules
in both directions across the membrane. Some molecules enter
the cell by means of pores, others enter directly across the cell
membrane. Both the type and rate of transport vary according to
the following factors: (Figure 2.36)
Concentration Level
The rate of collision between molecules at a high concentra-

tion is greater than the rate of those at a lower concentration. It
is this potential energy that assists the movement of materials
from a high concentration to a low concentration level.
Molecular Size Figure-2.36: Molecular size and diffusion rate
Pore diameter limits the transport of molecules through the plasma mem-
brane. The size of a molecule and its rate of diffusion are inversely proportional.
Giant molecules diffuse with great difficulty and may be unable to enter the cell at
all, due to their large size.
Molecular Weight
The rate of diffusion is inversely proportional to the molecular weight and

increases as the molecular mass decreases. Thus the rate of diffusion is fast in
gases and slow in solids. This is due to the greater attractive force between mole-
cules of high molecular weight.
Temperature
The rate of collision between molecules increases as the temperature increases.

Molecules of a gas for example vibrate rapidly at high temperatures.
Molecular Charge
Molecules with a neutral charge pass through the pores easily as compared to
negatively or positively charged ions. For instance, the rate of diffusion of a neu-
tral potassium atom is faster than that of a potassium ion.
Solubility in Lipids
Lipid soluble structures diffuse into the cell easily since their plasma membrane
is composed mainly of phospholipids. These molecules form a barrier to water
and water-soluble substances due to their hydrophobic nature.
Unicellular organ-
Deformation of the Plasma Membrane isms living in fresh-
water environments
The plasma membrane is sensitive to alcohol, ether and chloroform. These pump out the excess water in
molecules may deform the plasma membrane on entering or leaving the cell. their cytoplasm by using their
Pore number on the Plasma Membrane contractile vacuole to main-
tain constant osmotic pres- The cell
Pores are gate-like orifices on the plasma membrane. The higher the number of sure. Plants use their cell wall
pores, the faster the rate of transport. to withstand high pressure.
79
Soluble molecules Active Mechanisms
have a natural ten-
dency to move from In the active mechanisms cells use energy and sometimes use carrier proteins
areas of high concentration to transport materials in or out of the cytoplasm. So cells must be living for mate-
to those of low concentra- rial transport, dead cells can not make active mechanisms.
tion. However in some Active transport
instances, certain soluble
molecules need to be kept Active transport is the movement of molecules from area of low concentration
out of a cell. Also, other solu- to area of high concentration.
ble molecules may be need-
ed at a higher concentration In active transport, a carrier protein on the membrane binds with the molecule
than can be achieved using that will enter the cell. Once inside the cell, the carrier protein detaches the mole-
simple diffusion. This is only cule using energy from ATP as it does so. As the concentration of the target mol-
possible however, at high ecule increases, the difference between conditions inside and outside the cell facil-
energy cost and with the help itates the transport of further molecules.
of carrier proteins. Both energy and carrier proteins are needed for active transport. If the activity
of the carrier slows or ceases, or if ATP cannot be generated, the concentration of
the target molecule on both sides of the membrane equalises and the cell dies.
K+ ions for instance are essential for growth and protein synthesis and their con-
centration inside the cell must be maintained at 40 times that of the outside con-
centration.
Figure shows the active transport of Na+ and K+ ions through the plasma
membrane. Normally, sodium ions are concentrated on the outside of the plasma
membrane while potassium ions are concentrated on the inside. It would be
expected that movement would be from high to low concentration however move-
ment is the reverse from low to high concentration. The carrier protein known as
the sodium-potassium pump combines with Na+ ions on the inside of plasma
membrane, then transports these ions out of the cell. Simultaneously, K+ ions are
pumped in. These serial reactions are carried out by the enzyme Na-K ATPase
Figure-2.37: The mechanism of active
which hydrolyses ATP into ADP and Pi to yield energy. This energy is consumed
transport during ion transport. (Figure 2.37)
CYTOLOGY
80
Endocytosis
Endocytosis is the taking of large molecules into the

cytoplasm. The size of a molecule is an important factor in
its method of movement in or out of a cell. Since large mol-
ecules cannot pass through pores in the membrane, the
plasma membrane alters its shape in order to transport Figure-2.38: Endocytosis (Phagocytosis)
these molecules into the cell. The process is achieved by
endocytosis.
There are three types of endocytosis
Phagocytosis (cell eating)
Phagocytosis is the taking of solid large particles into the

cytoplasm. Well known examples of phagocytosis include
the elimination of microbes in the body by leucocytes and
the type of nutrition shown by amoeba. (Figure 2.38)
Pinocytosis (cell drinking)
Taking of the large dissolved particles by a food vacuole

into the cell is named pinocytosis. Taking of some dissolved
food molecules into the blood in the intestine is the exam-
ple of pinocytosis. Both processes occur only in animal
cells, as plant cells are incapable of phagocytosis due to the
cell wall surrounding them. (Figure 2.39) Figure-2.39: Endocytosis (Pinocytosis)
Receptor mediated endocytosis
Taking of specific molecules into a cell by the inward

budding of membranous vesicles that have receptor pro-
teins specific to the molecules being taken in. For example
cholesterol are taken into the cell by this method.
Exocytosis
The process by which cells remove large particles from

the cytoplasm is called exocytosis. Any waste substances
present after the completion of digestion are excreted by
exocytosis as illustrated in Figure-2.40).
The cell
Figure-2.40: Endocytosis and exocytosis
81
MOVEMENTS THROUGH CELL MEMBRANES
Process Characteristics Energy Source Example
Passive mechanisms
Net movement of ions, atoms, molecules from Exchange of O2 and CO2

Diffusion region of high concentration to region of lower con- Molecular motion
centration in the lungs
Carrier proteins in the cell membrane accelerates

Facilitated movement of relatively large molecules from region Movement of glucose
Molecular motion
Diffusion of high concentration to region of lower concentra- into the cells
tion
The movement of water molecules from region of

Entering of water into the
Osmosis high concentration to a region of lower concentra- Molecular motion
cell
tion through a selectively permeable membrane.
Molecules are forced from region of higher pressure Hydrostatic Food molecules leaving
Filtration
to region of lower pressure pressure blood capillaries
Active mechanisms
Active The movement of molecules from a region of lower

Na-K pump in the nerv-
concentration to a region of higher concentration by Cellular energy
transport ous cell
carrier proteins in membrane
Endocytosis
Taking of solid big particles into the cytoplasm Cellular energy WBC ingest bacteria
(Phagocytosis)
Endocytosis Taking of food droplets in

Taking of fluid droplets into the cytoplasm Cellular energy
(Pinocytosis) the small intestine
Endocytosis Certain kinds of molecules combine with receptors

(Receptor on the plasma membrane and are taken into the Cellular energy Cholesterol uptake
mediated) cytoplasm
CYTOLOGY
The removing of big complex molecules from the

Exocytosis Cellular energy Secretion of mucus
cytoplasm
Table-2.4: Comparison of active and passive transport
82
THE CELL
The cell is the smallest unit of matter that can carry on all the processes of life. Cells contain a variety of internal
structures called organelles. An organelle is a cell component that performs specific functions for the cell. A large
organelle near the centre of the cell is the nucleus. The presence or absence of a nucleus is important for classify-
ing cells. Organisms whose cell contain a nucleus and other membrane-bound organelles are called eukaryotes.
Organisms whose cells never contain (or lack) a nucleus and other membrane-bound organelles are called prokary-
otes. The structures that make up a eukaryotic cell are determined by the specific functions carried out by the cell.
Three main components: a cell membrane, a nucleus, and other organelles.
The cell membrane controls the ease with which substances pass into and out of the cell. Some substances eas-
ily cross the membrane, while others cannot cross at all. For this reason, the cell membrane is said to be selective-
ly permeable. Cell membranes are made mostly of phospholipid molecules. Everything between the cell membrane
and the nucleus is the cytoplasm. The cytoplasm consists of two main components: cytosol and organelles.
Cytosol is a jelly-like mixture that consists mostly of water, along with proteins, carbohydrates, salts, minerals and
organic molecules. Organelles are structures that work like miniature organs, They carry out specific functions in
the cell. The organelles plus the cytosol make up the cytoplasm. Ribosomes are the site of protein synthesis (pro-
duction or construction) in a cell. They are most numerous organelles in almost all cells. Mitochondria are the sites
of chemical reactions that transfer energy from organic compounds to ATP. Energy contained in food is released and
converted to ATP, the molecule that most cells use as their main energy currency. Endoplasmic reticulum is a sys-
tem of membranous tubules and sacks. The ER functions primarily as an intracellular highway, a path along which
molecules move from one part of the cell to another. The golgi apparatus is the processing, packaging and secret-
ing organelle of the cell. Lysosomes are small spherical organelles that enclose hydrolytic enzymes within a single
membrane. Lysosomes are the site of food digestion in the cell. Peroxisomes are spherical, single layered organelles.
Peroxisomes metabolise H2O2 and they are found in large numbers in cells that synthesise, store, or degrade lipids.
In plants, specialised peroxisomes, called glyoxysome are found in the fat-storing tissues of plant seeds.
Gyloxysomes have enzymes that convert stored fats into sugar during germination until photosynthesis begins.
Animal cells do not have glyoxysome so they can not convert fats into sugar. Centrioles are involved in the forma-
tion of spindle fibres in animal cells during cell division. The vacuole is a large membrane-bound sack that takes up
a large amount of space in most plant cells. The vacuole serves as a storage area, and may contain stored proteins,
ions, wastes, or other cell products. A distinguishing feature of plant cells is the presence of structures called plastids
that make or store food. A common kind of plastid is the chloroplast, an organelle that converts sunlight, carbon
dioxide, and water into sugars. This process is called photosynthesis. The nucleus is the control centre (brain) of the
cell. Most cells have a single nucleus some cells have more than one.
In animal cells an internal framework called the cytoskeleton maintains the shape of the cell. The cytoskeleton
maintains the three-dimensional structure of the cell, participates in the movement of organelles within the cytosol,
and helps the cell move. Cilia and flagella are hairlike organelles that extend from the surface of the cell where they
assist in movement. The outermost layer of plant and protist cells is the cell wall. Its rigid structure protects the con-
tents of the cell and prevents the cell membrane from rupturing when the cell is turgid. Microvilli are the microscop-
ic projections of plasma membrane which increase the surface area of the cells. They are found mostly in cells con-
cerned with absorption or secretion.
Materials are conducted in and out of the cell by two basic methods which are Passive mechanisms and Active
mechanisms. Passive mechanisms move molecules from an area of high concentration to an area of low concen- The cell
tration without the use or input of energy by the cell. Passive mechanisms can take place in living or nonliving envi-
ronments. In active mechanisms cells use energy and sometimes use carrier proteins to transport materials in or out
of the cytoplasm. So cells must be living for material transport, dead cells can not make active mechanisms.
83
EXPERIMENT: Observation of the transport of materials across a cell membrane.
Purpose of experiment: Materials Distilled water

To observe the transport of Microscope A branch of Elodea or
water across the membrane of Slide onion membrane
an onion cell or Elodea. Cover slip Blotting paper
Teat pipette
Procedure:
1. Place some drops of water on a slide.

Add a young leaf taken from the actively growing
region of Elodea or a piece of onion membrane.
Observe one of the cells under high magnification
and draw a typical cell from a part of the leaf near
the middle of your field of view.
2. Remove the extra water from one side of the cover
slip with blotting paper and add some salt solution
to the other side. Observe any changes to the cells
after one or two minutes in salt solution.
3. Using the same method, flood the slide with dis-
tilled water instead of salt solution. Repeat the pro-
cedure using distilled water to ensure that the salt
solution has been replaced. Wait for 4 –5 minutes to
view any further changes.
Discussion:
Describe the cells in salt solution. Explain what you
observed. Use the words “transport of water” and
“plasmolysis” in your answer.
Explain what happens to the cells if they are left in
salt solution for a few hours?
Explain why spraying weeds with salt solution is a
successful method of eradicating them.
The sugar concentration in strawberry jam is high.
Give another possible reason for putting sugar in
jam in addition to enhancing the taste.
84
EXPERIMENT: Investigation into the general structure of a nonphotosynthetic plant cell.
Purpose of experiment: Materials Scalpel

To identify the basic parts of Microscope Needle
plant cells by observing onion Slide Methylene blue
epidermal cells. Cover slip Iodine solution
Teat pipette Blotting paper
Pins Onion bulb
Procedure:
1. Take an onion and cut it into four parts. Observe the rings of fleshy leaves.
Part the leaves. Peel off the thin transparent
membrane from one of the fleshy leaves
using a pin.
Place it on a slide, add a drop of water and
then a cover slip.
Observe first under low then high magnifica-
tion.
2. Prepare a second slide in the same way. Add
a drop of methylene blue or iodine solution
before adding the cover slip.
Compare the two slides under low and high
magnification.
Discussion:
Describe the general appearance of the cells

of the onion cell membrane.
Identify and describe the cell wall.
Suggest possible factors that might affect the
speed of chloroplast movement.
How can you confirm that the cells you
observed are living?
Describe the shape and position of the nucle-
us in the stained preparation
Describe the location of the cytoplasm. What
proportion of the cell does it fill?
In all living things, water is abundant.
According to your observations, define the
area of the onion cells where water is most
abundant.
85
11. Explain the structure and function of mitochondria.
Information Recall Questions
1. Explain how important contributions made by scien- 12. List the different types of endoplasmic reticulum and
tists led to developments in cell theory. explain how each is adapted for its particular func-
tion.
2. Label the structures of the plasma membrane in the
figure below. 13. Explain the structure and function of the following:
golgi apparatus
lysosome.
14. Label the parts of the chloroplast shown in the figure

below.
3. List the main functions of the plasma membrane.
4. Explain the different types of passive transport.
5. Compare plasmolysis and deplasmolysis.
6. Explain turgor pressure and describe how and why

plants use it.
7. Explain the events of active transport. 15. Compare and contrast the structure, location and
function of chloroplasts, chromoplasts and leucoplas-
8. Use the information given in this unit to compare and ts.
contrast endocytosis and exocytosis.
16. Compare and contrast the structure and function of a
9. List the organelles found in a eukaryotic cell and mitochondrion and a chloroplast.
explain how they contribute to the cell as a whole.
17. Label the parts of the nucleus shown in the figure
10. Label the parts of the mitochondrion shown in the below.
figure below .
18. List the components of the cytoskeleton and explain

the functions of each.
86
13. Where are poisons and wastes detoxified in a cell?
Fill in the blanks _________.
1. The first person to describe microscopic organisms
and living cells was _____________________________. 14. The mitochondria of a cell contain an inner mem-
brane called _____________________________.
2. The maximum size to which a cell may grow is limit-

ed mainly by the cell's ________________________. 15. What are the membrane-bound sacks that package
and secrete cell products? _______________________.
3. Some ribosomes are free in the cytoplasm, while oth-

ers line the membrane of the ________________. 16. The organelle that digests molecules, old organelles,
and foreign substances in the cell ________________.
4. Everything between the cell membrane and the

nucleus is the cell's ___________________________. 17. The organelle that prepares proteins for export and
synthesises steroids is ________________________.
5. The organelle that processes and packages sub- 18. The "powerhouse" of the cell ________________.
stances produced by the cell ____________________.
19. Short, hairlike organelles that can move and may
6. The ____________________________ is the control cen- cover a unicellular organism or line the respiratory
tre of the cell. tract are called _______________________________.
20. What word means "Water Fearing"? _______________.

7. The DNA in the form of a long strand is called
______________________________. 21. A pigment that absorbs energy in sunlight
________________________________.
8. Cytoplasm consists of two main components: 22. In what type of cells would you expect to find large
_________________ and _______________________. numbers of mitochondria?________ ______________.
23. The cell membrane functions like a ______________,

controlling what _______ and ______________ the cell.
9. The nucleus is surrounded by a double layer mem-
brane called the ________________________________.
24. The nucleus is surrounded by a double layer mem-
brane called the _______________________________.
10. The nucleoli make ______. Which in turn build pro-

teins.
25. Unlike animal cells, plant cells have ______________.
11. Organisms whose cells never contain a membrane-
bound nucleus are called __________________.
26. Short, hair-like organelles that can move and may
12. Organisms whose cells always or usually contain a cover a unicellular organism are called ____________.
nucleus or nuclei are called ______________________.
87
5. Which of the following organelles and their con-
Choose the correct alternative tents are incorrectly paired?
1. I. Osmotic Pressure > Turgor Pressure A) Ribosome - RNA
II. Osmotic Pressure = Turgor Pressure B) Mitochondrion - DNA
III. Osmotic Pressure < Turgor Pressure C) Lysosome - Digestive enzymes
In a plant cell, in which of the above conditions D) Chloroplast - Chlorophyll
would water uptake be expected to increase ? E) Nucleolus - Nucleus
A) I B) II C) III D) I and III E) II and III
6. What is the function of the chloroplast?

A) To digest sugar to provide ATP energy for the cell
B) To convert one kind of chemical energy to another
2. Which of the following clues would tell you C) To produce digestive enzymes
whether a cell is prokaryotic or eukaryotic? D) To convert light energy to chemical energy
A) the presence or absence of a rigid cell wall E) To convert light energy to heat
B) whether or not the cell is partitioned by internal
membranes
C) the presence or absence of ribosomes
7. Which of the following correctly matches an
D) whether or not the cell carries out cellular metabo- organelle with its function?
lism
A) mitochondrion ... photosynthesis
E) whether or not the cell contains DNA
B) nucleus ... cellular respiration
C) ribosome ... manufacture of lipids
D) lysosome ... movement
E) central vacuole ... storage
3. What is the genetic centre of the cell?

A) the nucleolus
B) the nucleus 8. I. Enzymic activity
C) the Golgi apparatus II. Chloroplasts
D) the lysosomes III. Nucleotides
E) the rough endoplasmic reticulum IV. Mitochondria
Which of the items above are present in all living
things ?
A) I and II B) I and III C) II and III
D) II and IV E) III and IV
4. What are the primary sites of protein production
in a living cell?
A) the Golgi apparatus
B) ribosomes 9. Which of the following structures cannot be found
C) microbodies in prokaryotic cells?
D) mitochondria A) flagella B) cell membranes C) mitochondria
E) lysosomes D) ribosomes E) RNA
88
10. Microfilaments and microtubules… 15. Which of the following maintains the three-
A) contain digestive enzymes dimension structure of animal cells?
B) are sites of protein synthesis A) Centrioles B) Cytoskeleton C) A cell membrane
C) function in cell structure and movement D) Cell wall E) Nucleus
D) are sites of photosynthesis
E) are the site of ATP synthesis
16. Examine the list of cellular structures.

I. Chloroplast
11. The part of the cell that regulates movement of II. Ribosome
substances into and out of the cell is the…
III. Mitochondria
A) Nucleus B) Cell membrane C) Golgi apparatus
IV. Cytoplasm
D) Mitochondrion E) Lysosome
Which are present in both prokaryotic and
eukaryotic cells ?
A) I-II B) I-III C) II-III D) II-IV E) III-IV
12. I. Chloroplast
II. Leucoplast
III. Chromoplast
17. Which of the following cell organelles cause a
The plastids found in plants are listed above. decrease in the concentration of organic material
Which form the origin of other plastids ?
in the cytoplasm?
A) I B) II C) III D) I - III E) II- III
A) Golgi bodies B) Chloroplast
C) Ribosome D) Mitochondrion
E) Endoplasmic Reticulum
13. Which of the following properties is incorrect for

both mitochondria and chloroplasts ?
A) Both have an electron transport system.
B) ATP is synthesised 18. Which one of the following includes the members
C) Both are present in all cells of the cytoskeleton?
D) Both contain their own DNA A) Cell wall and intermediate filaments
E) Both are structurally similar to bacteria B) Cell wall, microtubules, and centrioles
C) Microfilaments
D) Microtubules, intermediate filaments, and microfila-
ments
E) Microfilaments and cellulose
14. Examine the list of structures that may be present
on the typical surface of a cell.
I. Microvilli
II. Cilia
III. Flagella
IV. Desmosomes 19. The cell organelle that digests molecules, old
Which of them are structurally and functionally organelles, and foreign substances is…
identical ? A) ER B) Golgi apparatus C) Lysosomes
A) I-II B) I-III C) II-III D) II-IV E) III-IV D) Mitochondria E) Chloroplast
89
20. Which of the structures and their functions listed er concentration to an area of lower concentration
below are incorrectly paired ? is called _____.
A) Ribosome- Protein synthesis A) diffusion
B) Chloroplast- Photosynthesis
B) endocytosis
C) Mitochondria- Fermentation
C) phagocytosis
D) Nucleus- Mitosis
D) active transport
E) Plasma membrane- Osmosis
E) osmosis
21. Which of the following cell organelles is present in 27. Not all substances can cross the cell membrane,
both animal and plant cells ? for this reason, the cell membrane is said to be...
A) Chlorophyll B) Plasma membrane A) Selectively permeable
C) Large vacuole D) Cell wall B) Membrane bound
E) Plastid C) A cell wall
D) A barrier
22. Which of the following cell organelles is not
E) Full permeable
involved in the sequence of events from synthesis
of an enzyme to its excretion ?
A) Ribosome 28. A magnified picture of the detailed architecture of
B) Lysosome cell surfaces can best be obtained from a(n) _____.
C) Golgi apparatus A) scanning electron microscope
D) Endoplasmic Reticulum B) transmission electron microscope
E) Plasma Membrane
C) light microscope
D) magnifying glass
23. What is the ultimate function of contractile vacuoles E) none of the above
of unicellular organisms living in freshwater ?
A) Excretion of CO2
B) Movement of the organism in water
C) Excretion of excess water 29. A normal size range for a typical eukaryotic cell is
D) Excretion of minerals _____.
E) Excretion of digestive wastes A) 0.1 nanometers
B) 10 nanometers
24. Which is not a principle of the cell theory? C) 100 nanometers
A) Cells are the basic units of life. D) 1-10 micrometers
B) All cells arise from preexisting cells. E) 10-100 micrometers
C) All organisms are made of one or more cells.
D) All of above is true
E) All matter consists of at least one cell.
30. Cholesterol enters cells by means of _____.
A) active transport
25. What is the membrane-bound sack that packages
and secretes cell products? B) osmosis
A) ATP B) Mitochondria C) Lysosomes C) receptor-mediated endocytosis
D) Vacuole E) Golgi apparatus D) protein-mediated exocytosis
26. The movement of molecules from an area of high- E) passive transport
90
Cytology
chapter
METABOLISM
3
Animal Classification
METABOLISM
Metabolism is the sum of all the biochemical processes that occur within a cell
or organism. Cell metabolism describes the chemical reactions performed by a
cell to extract energy and synthesise organic molecules.
Metabolism involves two categories of reactions: anabolism and catabolism.
Anabolism is metabolic reactions in which complex molecules are synthesised
from simple ones.
Energy is funda-
mental to all meta- Anabolic pathways consume energy to build complicated molecules from sim-
bolic processes, and pler compounds. All synthesis reactions of a cell are classified as anabolic reac-
therefore to understanding tions. A well-known example is photosynthesis, where CO2 and H2O molecules are
how the living cell works. The
utilised in the synthesis of organic molecules such as glucose in the presence of
principles that govern energy
CYTOLOGY
resources in chemistry, sunlight.

physics, and engineering also Catabolism is a kind of metabolic reaction in which complex molecules are
apply to bioenergetics, the degraded to simple ones. Catabolic pathways release energy by breaking down
study of how organisms man- complex molecules to simpler compounds. This energy is stored in organic mol-
age their energy resources. ecules until needed to do work in the cell.
92
Organic molecules such as carbohydrates, lipids and proteins are
catabolised to yield energy during both anaerobic and aerobic respi-
ration. These reactions extract the energy stored within the bonds of
these molecules. The energy released by catabolic pathways is used
to drive anabolic pathways.
The major metabolic activities in an organism result in the following:
Biosynthesis of organic molecules
Degradation of ingested materials
Formation of storage molecules
Detoxification of ingested or synthesised toxic mole-

cules
Removal of waste molecules from the body

Energy
Energy is the capacity to perform work, to bring about change,
to make things happen. All cells use energy, such as a growing leaf
or a running human. It can exist in many forms, such as chemical
energy, light energy, electric energy, heat energy, nuclear energy and
mechanical energy (potential and kinetic energy).
There are many ways to measure energy but the most convenient
way is in terms of heat energy, because all other forms of energy can
be converted into heat energy. The science which studies heat is
called thermodynamics, meaning heat changes. The unit of heat is
the calorie.
A single calorie is the amount of heat required to increase the
temperature of 1 g of water from 14.5°C to 15.5 °C. The unit of heat
in biology is the kilocalorie (kcal), 1 kilocalorie is equal to 1000 calo-
rie. The food calorie is written as Calorie (with a capital C), which is
actually another form of kilocalorie.
Chemical reactions can be classified as either exergonic or ender-
gonic based on free energy. Free energy is the amount of energy
available to do work under the conditions of a biochemical reaction.
An exergonic reaction is a spontaneous chemical reaction in
which there is a net release of free energy. For example cellular res-
piration releases ATP energy.
An endergonic reaction is a nonspontaneous chemical reaction
Metabolism
in which free energy is absorbed from the surroundings. For exam-
ple photosynthesis absorbs sunlight energy. Endergonic reactions
store energy.
93
Energy transformations
Energy
Cell Type Energy can be changed from one form to another form in
transformation
nature. There is a flow of energy through all living things. Much
Nerve, brain Chemical to electrical of the work carried out by living orgasms involves the transforma-
tion of potential energy into kinetic energy.
Kidney Chemical to mechanical For example, during running, your body changes chemical
energy (which is a form of potential energy) stored in your mus-
Muscle Chemical to mechanical cle into kinetic energy.
Heat, radiant, chemical, electrical and nuclear energy are all
Inner ear Mechanical to electrical present in the natural world. In a biological system, mitochondria,
chloroplasts and leucoplasts are the functional organelles involved
Retina Light to electrical in energy transfer either to or between chemical bonds. Some
forms of energy in the natural world are in fact hazardous to organ-
Tongue and nose Chemical to electrical isms. In photosynthesis, light energy is converted into chemical
energy and is stored in the bonds of carbohydrates.
the law of thermodynamics

READ ME and energy changes
Thermodynamics is the study of energy
transformations. In most energy transforma-
tions, ordered forms of energy are converted
at least partly to heat.
The first law of thermodynamics states that
total energy in the universe is constant. It can
not be created or destroyed; it can only
undergo change from one form to another.
Life converts energy from the sun to other
forms of energy that drive life processes. The
energy is never lost, but as it ýs used, more
and more of it is converted to heat. Heat is the
energy of random molecular motion.
The second law of thermodynamics states
that disorder (entropy) in the universe is
increasing. Entropy is the measure of the dis-
order of a system. While order can increase locally, there is an unstoppable trend toward randomisation of the uni-
verse. Much of the increased entropy of the universe takes the form of increasing heat, which is the energy of ran-
dom molecular motion. In most energy transformations, ordered forms of energy are converted at least partly to
heat. Automobiles convert only 25% of the energy in gasoline into motion; the rest is lost as heat. Living cells
CYTOLOGY
unavoidably convert organised forms of energy to heat. The metabolic breakdown of food ultimately is released
as heat even if some of it is diverted temporarily to perform work for the organism. Heat is energy in its most ran-
dom state. Combining the two laws, the quantity of energy is constant, but the quality is not. The most important
energy in the universe is free energy, the energy that is able to perform work when temperature is uniform through-
out the system. Not all the energy in a system is available for work.
94
Enzymes
Enzymes are biological catalysts. A catalyst is a chemical
agent that changes the rate of a reaction without being con-
sumed in the reaction. Catalysts reduce the activation energy
and so increase the rate of reactions. They do not enter into the
reaction themselves and exit from the reaction without undergo-
ing any change. Cells employ proteins as catalysts to regulate
the movement of molecules through metabolic pathways.
(Figure 3.1)
For example: Enzyme Catalase catalyses the decomposition
of hydrogen peroxide into water and oxygen. One molecule of
catalase can break 40 million molecules of hydrogen peroxide
each second. As this same amount of H2O2 is catalysed by iron
atoms in 300 years, the high level of efficiency of enzymes is
obvious. Figure-3.1: Enzyme action
Enzyme Structure
Enzymes are categorised as either simple or complex according to their chem-
ical composition. Simple enzymes are composed of only amino acid compo-
nents such as pepsin. Complex enzymes are composed of amino acid and non Many enzymes
amino acid components such as catalase, which has two subunits: an apoenzyme require nonprotein
(protein) and a prosthetic group (iron). helpers, cofactors,
for catalytic activity. They bind
Apoenzyme and prosthetic group permanently or reversibly to
The protein component of a complex enzyme is known as an apoenzyme. The the enzyme. Some inorganic
specificity of an enzyme is provided by the variety of forms that the apoenzyme cofactors include zinc, iron,
component may take. Each is unique to a particular substrate and has the ability and copper. Organic cofac-
to recognise it. In order for an apoenzyme to become functional, it must bind with tors, coenzymes, include vita-
a prosthetic group. This may be organic or inorganic. mins or molecules derived
from vitamins. The manners
Cofactors: Prosthetic groups made up of inorganic molecules are called in which cofactors assist
cofactors, for example minerals such as Ca++, Mg++ and K+ ions. They partici- catalysis are diverse.
pate in the structure of enzymes.
Coenzymes: Prosthetic groups containing organic molecules are called coen-
zymes. For example, vitamins can participate in the enzyme structure as coen-
zymes. (Figure 3.2)
Prosthetic groups (cofactors and coenzymes) are essential to
the function of most enzymes and target the bonds of the sub-
strate. The apoenzyme recognises the substrate, after which the
prosthetic group modifies its structure. Neither component is
capable of functioning separately. The structure formed by the
fusion of the apoenzyme and prosthetic group is known as a
holoenzyme. A specific apoenzyme is only functional with one Metabolism
type of prosthetic group. However, a particular type of prosthet-
ic group may function with more than one type of apoenzyme.
Figure-3.2: Apoenzyme and prosthetic group
95
Mechanisms of enzyme actions
Enzyme 1 Substrate
substrate binds to Enzymes are globular proteins. Their molecules are round
Substrate complex enzyme in shape.
(maltose)
An enzyme has an active site where the substrates and
Enzyme enzyme fit together in such a way that the substrates are ori-
(maltase) ented to react. Following the reaction the products are
+ H2O released and the enzyme is free to react again. Some
4 enzymes carry out catabolic reactions in which the substrate
Active site is is broken down into smaller molecules, other enzymes carry
available for
another out anabolic reactions in which the substrates are joined to
molecule 2 form a larger molecules.
of substrate
Substrate is Some enzymes are found inside cells (intracellular
converted to
products enzymes), and some, especially digestive enzymes, are
Glucose released so they have their effects outside the cell (extracellu-
lar enzymes).
Products are Glucose
3 released
Properties of Enzymes
Figure-3.3:Mechanism of enzyme actions
Enzymes cannot initiate reactions themselves, their role is to accelerate those
reactions already initiated. They also reduce the activation energy needed to ini-
tiate a particular reaction.
An enzyme is named by adding the suffix ‘ase’ to either the name of the sub-
strate or to the type of reaction catalysed by it. Chitin for instance, is catalysed
by the enzyme chitinase.
Enzymes are synthesised under the control of DNA in the cell, but they are func-
tional under both intracellular and extracellular conditions.
As enzymes are proteinaceous in structure, they can operate only within a nar-
row range of temperature and pH. Conditions above this range destroy or dena-
ture their protein structure.
Enzymes work in a team. Enzymes catalysing a series of reactions function
cooperatively since the product of one reaction is the substrate of the next. For
instance, the enzyme amylase breaks its substrate, starch, into maltose. The
enzyme maltase then breaks maltose into glucose units. A series of eleven
enzymes then cooperate to catabolise glucose into lactic acid.
The surface area of the substrate available for enzyme action also affects the
Binding by some speed at which a reaction can take place. Thus the rate of enzymatic reaction is
molecules, inhibi- directly proportional to the total surface area of the substrate. For example, pepsin
tors, prevents is considerably more effective on minced meat than on one large piece of steak.
enzymes from catalyzing
reactions. Enzymes may occur either free in the cytoplasm or attached to a cellular com-
ponent.
CYTOLOGY
If binding involves covalent Enzymatic reactions are reversible. The equilibrium point, the direction of a
bonds, then inhibition is reaction, is determined according to the laws of thermodynamics.
often irreversible.
Enzymes are very specific. They can only act on their own substrate.
If binding is weak, inhibition Enzymatic reactions are very fast. Enzymes are extremely efficient, catalysing
may be reversible. many molecules in a single second.
96
Regulation of Enzyme Activity
Enzymes are the regulators of all chemical reactions in living
things. However, their activities are coordinated according to the
needs of the cells of an organism. Their self-regulating mechanism
reduces to a minimum both the energy needed to perform a reac-
tion and the materials required. The method by which enzymes are
regulated is summarised as follows:
As it is proteinaceous, an enzyme is coded for by a segment of

DNA known as a gene. Switching this gene on or off by hormones
or cell products regulates the concentration and activity of the
enzyme.
The speed of an enzyme-driven reaction is influenced by various
physical and chemical factors. For example, the reaction rate is
proportional to the substrate concentration if the temperature, pH
and enzyme concentration are kept constant.
Some reactions in the body are performed by a series of enzymes.
Each step is catalysed by a specific enzyme.
Figure-3.4: Feedback inhibition
E1 E2 E3 E4
X ⎯→ Y ⎯→ Z ⎯→ Q ⎯→ P
In the example shown above, the product P is produced at the end of the
reaction sequence. A high concentration of P then inhibits the activities of E1,
causing a deceleration of the reactions that follow. This type of regulation of
enzymatic activity is called increased negative feedback inhibition. By this
method, overproduction of P and overconsumption of the substrate X is pre-
vented. If the concentration of P decreases, enzymatic activity increases. This
is termed decreasing positive feedback, resulting in the acceleration of the
overall reactions.
The activity of enzymes is decreased by some chemicals, called inhibitors.
Inhibitors bind the enzyme and prevent enzymes from catalysing reactions.
Binding by the inhibitor causes the enzyme to change shape. Enzyme inhibition
can occur in one of two ways, competitive or noncompetitive.
If the inhibitor binds to the same site as the substrate, blocking substrate bind-
ing, it is called competitive inhibition If the inhibitor binds somewhere other than
the active site, but blocks substrate binding, it is called noncompetitive inhibi-
tion.
Most noncompetitive inhibitors bind to a specific place on an enzyme called an
allosteric site. Some molecules, called activators, increase enzyme activity by
binding to allosteric sites to keep the enzymes in their active configurations.
(Figure 3.4-5-6)
Metabolism
Figure-3.5: Allosteric inhibition
97
Factors Affecting Enzyme Activity
Enzyme Concentration
In the presence of sufficient substrate, the rate of reaction is directly propor-
tional to enzyme concentration. (Figure 3.6)
Substrate Concentration
Figure-3.6: Effects of enzyme concentration If sufficient enzyme is present, the rate of reaction increases proportionally as
on an enzymatic reation. the concentration of substrate increases. The rate of reaction remains constant,
however, when all the active sites available have become saturated by the sub-
strate. (Figure 3.7)
Temperature
Enzymatic reactions are dependent on temperature, operating most rapidly at
normal body temperature. This is also referred to as the optimum temperature of
an enzyme. A decrease in temperature slows the rate of reaction, but has no effect
on the structure of the enzyme or of the product. An increase in temperature slows
the rate of reaction and may stop it altogether if the proteinaceous enzyme struc-
ture is irreversibly damaged. The relationship between temperature and enzyme
Figure-3.7: Effects of substrate concentration
on an enzymatic reaction.
activity is almost identical for all reactions. (Figure 3.8)
pH
A pH value between 1 and 14 indicates the concentration of hydrogen ions in
a medium as acidic, neutral or alkaline. A pH value from 1 - 6.9 is acidic, 7 is neu-
tral and 7.1 - 14 is alkaline. The pH of the environment affects enzyme activity.
Each enzyme has an optimum pH value at which it is most effective.
Pepsin, for instance, has an optimum pH of between 1 and 2. Generally, how-
ever, enzymes operate optimally at neutral pH since high or low values of pH dam-
age their proteinaceous structure. (Figure 3.8)
Figure-3.11: Effects of temperature on the Water Concentration

activity of enzymes
The presence of water is a prerequisite for enzyme function. If the concentra-
tion of water is less than 18%, an enzyme becomes inactive. This means that con-
centrated substances such as honey or jam must be diluted before an enzyme can
act upon them.
Inhibitors
An inhibitor either decelerates enzymatic activity or causes it to cease entirely.
Examples of enzymatic inhibitors are drugs, heavy metals, pesticides and animal
CYTOLOGY
venom such as that from a snake or scorpion.
Activators
Figure-3.9: Effects of pH on the activity of Enzyme activators are organic or inorganic substances that stimulate enzymat-
pepsin enzyme. ic activity. Cysteine and H2S are enzyme activators.
98
READ ME classification of enzymes
In the early days of enzyme discovery, new enzymes were named by

adding the suffix ‘ase’ to the name of the substrate. This system became pro-
gressively unworkable due to the huge number of enzymes discovered. Since
the structure and function of more then 2000 enzymes have been identified
to date, it is difficult to categorise enzymes only according to their name. As
an alternative and improved system of classification, scientists developed an
international system. Enzymes were divided into six main groups and
assigned a classification number composed of four digits. For instance, the
enzyme classification number (ECS) of glucose transferase is 2.7.1.1.
(2) denotes a transferase
(7) denotes phosphotransferase
(1) denotes a hydroxyl group as an acceptor
(1) denotes D-glucose as a phosphate group acceptor.
IUBMB CLASSIFICATION OF ENZYMES
Class IUBMB Example Involved in Functions
Glycerol-3-phosphate
Oxidoreductases EC 1.1.1.8 Cellular respiration Transfer of electrons
dehydrogenase
Transferases EC 2.1.1.127 Ribusco Photosynthesis Group transfer reactions
Hydrolases EC 3.4.25.1 Proteasome Protein digestion Transfer of functional groups to water
Addition of groups to double

Lyases EC 4.1.1.1 Pyruvate decarboxylase Cellular respiration bonds, or formation of double
bonds
Phosphoglycerate Transfer of groups within molecules

Isomerases EC 5.4.2.1 Cellular respiration
mutase to yield isomeric groups
Metabolism
Formation of C-C, C-S, C-O and C-
Ligases EC 6.1.1.1 Tyrosine—tRNA ligase Protein synthesis`
N bonds by condensation reactions
99
ATP (Adenosine Triphosphate)
ATP is the universal energy currency, which means all organisms
can use ATP as their energy source. ATP holds readily available ener-
gy for very short periods of time. Like cash in your wallet ready to be
spent, ATP is ready to be used in the cell. (Figure 3.12)
If you have extra money, you may deposit some in the bank.
Similarly, a cell might deposit the energy in the chemical bonds of
nutrients, such as lipids, proteins and carbohydrates.
Structure of ATP
An ATP molecule is composed of an adenine base, a ribose sugar
and three phosphoric acid molecules.
The structure formed by the combination of adenine and ribose
sugar is known as adenosine. If a phosphate group is added to
adenosine, AMP or adenosine monophosphate results. Adenosine
diphosphate, ADP is obtained by addition of a phosphate group to
AMP. Adenosine triphosphate is formed by the addition of another
phosphate group to ADP.
Reactions in cells are categorised as exothermic or endothermic
according to whether energy is produced or required. Exothermic
reactions are catabolic reactions which release energy into the envi-
ronment.
Enzyme
ATP + H2O ⎯⎯⎯⎯⎯⎯→ ADP + Pi+ Energy
CYTOLOGY
The phosphate bonds of ATP are extremely energetic and have

the capacity to yield energy in a highly exothermic reaction. They are
known as high energy phosphate bonds and are signified by (~).
Breaking the bond between the second and third phosphate releas-
es 7300 cal of energy, This is then consumed in cellular reactions.
ATP provides a unique form of energy for all organisms.
100
Metabolic reactions
A complex organism would be unable to carry out
any of its life processes without performing thousands
of chemical reactions. Each of the catabolic or anabol-
ic reactions of the body serves a specific purpose, con-
tributing to a larger and vital process. Just the function-
ing of these reactions is insufficient to sustain life.
The rate and concentration of products are all criti-
cal and must be carefully regulated. A complex organ-
ism is able to maintain the reactions of its metabolism
Figure-3.12: The central role of ATP
by using biological catalysts (enzymes), and provide
them with optimum conditions of pH and temperature in which to function. The
constant round of chemical reactions occurring in your body as you read this are
also under the control of other factors such as hormones. The combined effect of
enzymes, coenzymes and cofactors, hormones, pH and temperature all contribute
to a healthy body. Many reactions are involved in the metabolism of an organism. In a working muscle
These are categorised into five different groups: cell the entire pool
of ATP is recycled
Hydrolysis once each minute. Over 10
Condensation ( Dehydration) million ATP are consumed
and regenerated per second
Oxidation-Reduction per cell.
Transphosphorylation, and Other Reactions
R E A D M E the universal energy currency

In all living cells, energy is temporarily packaged within
a remarkable chemical compound called adenosine triphos-
phate (ATP), which holds readily available energy for very
short periods of time.
We may think of ATP as the energy currency of the cell.
While you work to earn money, you might say that your
energy is symbolically stored in the money you earn. The
energy the cell requires for immediate use is temporarily
stored in ATP, which is like cash. When you earn extra
money, you might deposit some in the bank. Similarly, a cell
might deposit energy in the chemical bonds of lipids, starch,
or glycogen. Moreover, just as you dare not make less
money than you spend, so too the cell must avoid energy
bankruptcy, which would mean its death. Finally, just as you
(alas) do not keep what you make very long, so too the cell Metabolism
continuously spends its ATP, which must be replaced imme-
diately.
101
Hydrolysis
Hydrolysis is a chemical process that lysis, or splits, molecules by the addition
of water. It is an essential process in digestion.
In hydrolysis, the cleavage of a complex molecule into its subunits is provided
by the addition of water across a bond. This addition of H+and OH- ions to the
bonds between subunits is primarily carried out in the alimentary tract. Here gly-
cosidic, esteric and peptide bonds of carbohydrates, lipids and proteins are hydrol-
ysed by specific enzymes into their subunits and absorbed.
Condensation (Dehydration)
Condensation is a chemical reaction in which two molecules covalently bond
When threatened, a to each other with the removal of a water molecule.
bombardier beetle
uses the enzyme This results when two molecules bond in the synthesis of a larger molecule.
catalase to decompose Condensation reactions are endothermic, energy-demanding reactions. The
hydrogen peroxide. The oxy- strength of the esteric, glycosidic and peptide bonds between molecules is direct-
gen gas formed in the decom- ly proportional to the energy required to form them. Condensation or dehydration
position ejects water and reactions are responsible for the formation of energy-rich macromolecules such
other chemicals with explosive as polysaccharides.
force. Because the reaction
releases a great deal of heat, Transphosphorylation
the water comes out as
The transfer of the terminal phosphate group from ATP to another molecule is
steam. (The beetle is immo-
phosphorylation.
bilised by a wire attached to its
back by a drop of adhesive. All metabolic activities in cells require energy. This energy is obtained from the
His leg was just prodded with degradation of ATP molecules into ADP + Pi. The high-energy-containing phos-
the dissecting needle on the phate bonds of ATP break down and release energy.
right to trigger the ejection.)
Types of Transphosphorylation
The main types of energy transformation involving phosphorylation reaction of
A cell does three
ATP synthesis are explained below. Four distinct pathways are possible.
main kinds of work:
a. Substrate Level Phosphorylation (SLP): The formation of ATP by directly
Mechanical work: transferring a phosphate group to ADP from an intermediate substrate in catabo-
beating of cilia, contraction lism. In this pathway, the substrate from which energy is to be extracted is phos-
of muscle cells, and move- phorylated by soluble enzymes. SLP can be seen both in glycolysis and in the
ment of chromosomes Krebs cycle.
Transport work: pumping b. Oxidative Phosphorylation: The production of ATP using energy derived
substances across mem- from the redox reactions of an electron transport chain. Oxidative phosphorylation
branes against the direction is performed both in the chloroplast and mitochondria.
of spontaneous movement
CYTOLOGY
c. Photophosphorylation: The process of generating ATP from ADP and

Chemical work: driving phosphate by means of a proton-motive force generated by the thylakoid mem-
endergonic reactions such as brane of the chloroplast during the light reactions of photosynthesis.
the synthesis of polymers
d. Chemosynthetic Phosphorylation: In this pathway, energy is released dur-
from monomers
ing chemical oxidation. This energy can be utilised in the synthesis of ATP.
102
Oxidation-reduction reactions
Reactions that result in the transfer of one or more elec-
trons from one reactant to another are oxidation-reduction
reactions, or redox reactions. The loss of electrons is called
oxidation. The addition of electrons is called reduction.
(Figure 3.13). Redox reactions release energy when elec-
trons move closer to electronegative atoms
+ –
Oxidation: K ⎯→ K + e
A potassium atom releases an electron and is oxidised to

a positively charged ion.
– –
Reduction: Cl2 + 2e ⎯→ 2 Cl
A chlorine molecule gains two electrons and is reduced to

two negatively charged ions.
In an oxidation – reduction (redox) reaction:
+ –
K + Cl ⎯⎯→ KCl
oxidising reducing
agent agent
In the compound potassium chloride, potassium is oxi- Figure-3.13: Oxidation reduction reactions.
dised while chlorine is reduced.
Catabolic pathways relocate the electrons stored in food molecules, releasing
energy that is used to synthesise ATP.
In the catabolism of glucose, for example, electrons are transferred from glu-
cose to oxygen molecules by redox reactions, finally forming water molecules.
C6H12O6 + 6O2 → 6CO2 + 6H2O + Energy (Oxidation)

ATP is the vital mol-
ecule in cellular
The reverse of this reaction is seen in the anabolic reactions of photosynthesis, energetics.
where the electrons of water molecules are transferred to CO2 by redox reac- The price of most cellular
work is the conversion of ATP
tions, finally forming glucose molecules.
to ADP and inorganic phos-
phate (Pi).
Sunlight An animal cell regenerates
6CO2 + 6H2O ⎯⎯⎯⎯⎯→ C6H12O6 + 6O2 (Reduction)
Chlorophyll ATP from ADP and Pi by the Metabolism
catabolism of organic mole-
cules.
103
Electron Acceptors (Coenzymes)
Photosynthesis and cellular respiration include a redox reaction.
In cellular respiration, glucose and other fuel molecules are oxi-
dised, releasing energy. Photosynthesis reverses the direction of
electron flow in respiration. Water is split and electrons transferred
with H+ from water to CO2, reducing it to sugar. In the cells, the
redox reactions are very complicated and use some other mole-
cules to perform their task. They use many biochemical steps, elec-
tron acceptors and enzymes.
The most important electron acceptors are the coenzymes.
NAD, FAD and Coenzyme A are all well-known types of coenzymes
involved in respiration.
NAD (Nicotinamide Adenine Dinucleotide)

Nicotinamide adenine dinucleotide, a coenzyme present in all
cells that helps enzymes transfer electrons during the redox reac-
tions of metabolism.
It comprises an adenine base, a phosphate group and nicoti-
namide and is involved in the transport of electrons extracted from
substrate molecules by oxidation.
This enzyme picks up hydrogen from the substrate, passing it
to NAD. The substrate is subsequently oxidised and the coenzyme
reduced by this process.
NADP is another acceptor that temporarily stores energised
electrons produced during the light reactions of photosynthesis.
NADP has a structure identical to NAD, except for its extra phos-
Figure-3.14-15: The structure of NADP (top)
phate group, (Figure 3.14)
and coenzyme A (bottom).
FAD (Flavine Adenine Dinucleotide)
It is functionally identical to NAD and is involved in redox reac-
tions. It contains the enzyme riboflavin within its structure and func-
tions in the collection of hydrogen from the substrate during the
Krebs cycle.
CoA (Coenzyme-A)
It is a derivative of vitamin B and is involved in the transport of
acetic acid formed by the degradation of proteins, lipids and car-
CYTOLOGY
bohydrates in the mitochondria. The combination of acetic acid

and coenzyme A forms the molecule acetyl coenzyme A, or CoA.
This coenzyme then returns to the cytoplasm where the same pro-
cedure is repeated. The acetic acid then initiates the Krebs cycle by
fusing with oxaloacetate to form citric acid. (Figure 3.15)
104
Other metabolic reactions
Transamination
It describes the transfer of an amino group from a donor
molecule to a recipient molecule without the release of any
NH3. The donor molecule may be an amino acid, however
the main types of recipient molecules are 2-oxoglutaric acid,
oxaloacetic acid and pyruvic acid.
Transacetylation
It describes the transfer of the acetyl group of acetate or
succinate from one molecule to another, by the activity of
the enzyme transacetylase. The cofactor of transacetylase
enzyme is coenzyme A. The acetyl group binds to Co-A and
forms Acetyl-CoA.
Transmethylation
It describes the transfer of a methyl group (-CH3) from a
methyl donor to a recipient. In animal metabolism, the main
methyl donors are choline and the amino acid methionine.
Transpeptidation
It describes the transfer of amino acids, peptides and
amines to other amino acids or peptides.
Carboxylation and Decarboxylation

The attachment of a molecule of CO2 to an organic molecule is termed car- Vitamins are organic
molecules that func-
boxylation. The enzyme involved in this reaction is carboxylase. The reverse of car-
tion in a wide variety
boxylation is termed decarboxylation and is carried out by decarboxylase enzyme.
of capacities within
the body. The most promi-
nent function is as cofactors
for enzymatic reactions. The
Detoxification distinguishing feature of vita-
It describes the elimination of synthesised or ingested toxic materials from the mins is that they generally
body. cannot be synthesized by
mammalian cells and, there- Metabolism
fore, must be supplied in the
diet.
105
READ ME basal metabolism
The amount of energy required for an organism to survive at normal room temperature with minimal energy
expenditure is known as the basal metabolism. This energy requirement is calculated 12-14 hours after the last
meal when the body is at rest. A normal individual needs a minimum of 1500 Kcal of energy per day for the nor-
mal function of all body systems.
Basal metabolism is determined by the measurement of oxygen consumption over a given time period and the
heat released by the body into the environment.
The basal metabolism of children and adolescents is high compared to adults. Babies have the highest basal
metabolism of all, in order to maintain a constant body temperature despite the heat loss from their body due to
their high surface area-to-volume ratio. This increased rate of metabolism generates extra heat energy from brown
fat cells located directly below the skin of their back. After the first year of life, as the surface area-to-volume ratio
falls, these brown fat cells are gradually lost.
Generally, organisms with a high basal metabolism are physically active. Domestic animals that assist man, such
as horses, huskies and sheep dogs, have a high basal metabolism. Domestic animals that are used solely for their
food products are generally physically inactive and have a low basal metabolism.
The basal metabolism of an organism is affected by a number of factors. The environmental temperature, for
example, has the greatest effect. Movement at low external temperatures activates the body to mobilise energy by
cellular respiration. Under such conditions, most of the energy is released in the form of heat, rather than in the
formation of ATP. In conditions above those of normal room temperature, the body loses heat by both transpira-
tion and dilation of capillaries beneath the surface of the skin. In addition, the rate of ATP synthesis exceeds that
of heat release.
The energy consumption of an organism is
directly related to its physical activities. For
instance, an individual at complete rest consumes
1500-1800 Kcal energy per day, whereas a normal-
ly active individual requires between 2500 to 2700
Kcal of energy per day. A manual worker expends
the most energy--4500-5500 Kcal per day.
The rate of metabolism is also influenced by the
chemical constituents of food. Proteins require a
great deal of energy for their digestion and accel-
erate the body’s metabolism by 30%, while carbo-
hydrates and lipids accelerate it by 6% and 4%
respectively.
Both muscular and mental activity require
energy. Muscular activity demands a great deal of
CYTOLOGY
energy and increases the rate of metabolism pro-

portionally to its intensity. Mental activity however
has no effect on the rate of metabolism.
106
METABOLISM
Metabolism is the sum of all the biochemical processes that occur within a cell or organism. Cell metabolism
describes the chemical reactions performed by a cell to extract energy and synthesize organic molecules. Metabolism
involves two categories of reactions, anabolism and catabolism.
Energy is the capacity to perform work, to bring about change, to make things happen. All cells use energy such
as a growing leaf or a running human. It can exist in many forms, such as chemical energy, light energy, electric
energy, heat energy, nuclear energy and mechanical energy (potential and kinetic energy). There are many ways to
measure energy but the most convenient way is in terms of heat energy, because all other forms of energy can be
converted into heat energy. The science which studies heat is called thermodynamics, meaning heat changes. The
unit of heat is the calorie.
Chemical reactions can be classified as either exergonic or endergonic based on free energy. Free energy is the
amount of energy available to do work under the conditions of a biochemical reaction. An exergonic reaction is a
spontaneous chemical reaction in which there is a net release of free energy. For example, cellular respiration releas-
es ATP energy. An endergonic reaction is a nonspontaneous chemical reaction in which free energy is absorbed from
the surroundings. For example, photosynthesis absorbs sunlight energy. Endergonic reactions store energy.
Enzymes are biological catalysts. A catalyst is a chemical agent that changes the rate of a reaction without being
consumed by the reaction. Catalysts reduce the activation energy and so increase the rate of reactions. They do not
enter into the reaction themselves and exit from the reaction without undergoing any change. Cells employ proteins
as catalysts that regulate the movement of molecules through metabolic pathways. Enzymes are categorized as
either simple or complex according to their chemical composition. Simple enzymes are composed only of amino acid
components such as pepsin. Complex enzymes are composed of amino acid and non amino acid components such
as catalase, which has two subunits, an apoenzyme (protein) and a prosthetic group (iron). Cofactors: If the pros-
thetic group is made up of inorganic molecules, it is called a cofactor, for example minerals such as Ca++, Mg++
and K+ ions. They participate in the structure of the enzyme. Coenzymes: If the prosthetic group contains organic
molecules, it is called a coenzyme, for example vitamins can participate in the enzyme structure of a coenzyme.
Enzymes are the regulators of all chemical reactions in living things. However, their activities are coordinated
according to the needs of the cells of an organism. Their self-regulating mechanism reduces to a minimum both the
energy needed to perform a reaction and the materials required.
ATP is the universal energy currency. That means all organisms can use ATP as their energy source. ATP holds
readily available energy for very short periods of time. Like cash in your wallet ready to be spent, ATP is ready to be
used in the cell’s metabolic reactions. The rate and concentration of products are all critical and must be carefully
regulated. A complex organism is able to maintain the reactions of its metabolism by using biological enzymes or
catalysts, and provide them with optimum conditions of pH and temperature in which to function. The constant
round of chemical reactions occurring in your body as you read this are also under the control of other factors, such
as hormones. The combined effect of enzymes, coenzymes and cofactors, hormones, pH and temperature all con-
tribute to a healthy body. Many reactions are involved in the metabolism of an organism.
Photosynthesis and cellular respiration include a redox reaction. In cellular respiration, glucose and other fuel
molecules are oxidized, releasing energy. Photosynthesis reverses the direction of electron flow in respiration. Water
is split and electrons transferred with H+ from water to CO2, reducing it to sugar. In the cells the redox reactions are Metabolism
very complicated and use some other molecules to perform their task. They use many biochemical steps, electron
acceptors and enzymes. The most important electron acceptors are the coenzymes. NAD, FAD and Coenzyme A are
all well-known types of coenzymes involved in respiration.
107
EXPERIMENT: Investigation of salivary amylase
Purpose of experiment: Materials: 3 teat pipettes

To observe the effects of temper- test tubes iodine solution
ature on salivary amylase. beakers of different sizes starch solution
thermometer
timer
water bath
Procedure:
Discussion:
Explain the purpose of
varying the temperature
of the experiment ?
108
Information Recall Questions Fill in the blanks
1. State the primary energy source in ATP synthesis. 1. Most enzymes are _________________________.
2. Which of the following factors is not involved in the 2. A reactant being catalyzed is known as the
formation of a peptide bond? Explain why. _________________________.
I. enzyme activity
II. synthesis of water
3. In a condensation reaction, two molecules
III. consumption of energy
become linked together and a molecule of
IV. release of NH2 ________________________ is produced.
3.
4. Large carbon compounds are built from smaller
molecules called ___________________________.
5. What kind of reaction allows amino acids to

become linked together? ___________________.
6. What is the by-product of a condensation reac-

tion? ____________________
Which of the following describes the metabolic
reaction illustrated above.
( ) anabolic reaction
( ) polysaccharide synthesis True or false
( ) lipid synthesis
( ) glycosidic linkage between molecules ___ Enzymes speed up a chemical reaction by
increasing the activation energy of the reaction.
Application of Knowledge ___ In a triple bond, three pairs of electrons are

shared between two atoms.
4. Despite the large number of high-energy trans- ___ Without enzymes, chemical reactions necessary
formations performed inside a cell, there is no for life would not occur at a rate sufficient to
damage to it. Explain why. sustain life.
___ Amino acids become linked together by peptide
5. The following reactions were all detected in cell bonds during hydrolysis reactions.
A. Categorize the type of cell and explain your
reasons. Explain how you would detect each ___ If the body temperature of a human being
synthesis. reached 43 degrees C, many enzymes would be
destroyed and the individual would die.
I. glycogen synthesis
II. starch synthesis ___ Nucleic acids function primarily to carry genetic
III. ATP synthesis from glucose
instructions and direct cellular activities.
___ NAD+ acts as a cell's "energy currency."
109
6. A correlation exists between the metabolic rate
Choose the correct alternative of an organ and its concentration of capillaries.
Which of the organs listed below has the fastest
1. ATP releases energy when ____________. metabolic rate?
A) it undergoes a condensation reaction I. Lung
B) a hydroxyl group is added to it II. Brain
C) a phosphate group is added to it III. Kidney
D) a phosphate group is removed from it IV. Heart
E) none of the above is correct V. Large intestine
A) I B) II C) III D) IV E) V
2. Energy is most commonly stored in plants as
____________.
A) electrical energy 7. Which of the following environments or actions
B) chemical energy does not affect enzyme activity?
C) mechanical energy A) heating the enzyme
D) electromagnetic energy B) pH
E) kinetic energy C) cooling the enzyme
D) salt concentration
E) All of the above can affect enzyme activity.
3. Cellular respiration is an example of _____.
A) a catabolic pathway
B) an anabolic pathway
C) entropy
8. Special proteins that speed up the chemical
D) bioenergetics reactions in a cell are called...
E) thermodynamics
A) Enzymes B) Ions C) ATP
D) Glycogen E) Nucleic acid
4. The list below shows various metabolic processes.
I. Degradation of glycogen into glucose
II. Degradation of starch into glucose
III. Storage of glucose as fat droplets 9. Which of the following molecules has no role in
IV. Energy extraction from amino acids cell metabolism?
V. Energy extraction from glucose A) Enzymes B) Coenzymes C) Vitamins
Which of those listed above is not performed by D) ATP E) Cellulose
a human cell ?
A) I B) II C) III D) IV E) V
10. Which of the following is an example of poten-

tial energy?
5. Which of the following cell organelles is capable A) a hot cup of coffee
of dehydration synthesis? B) a biology book placed on the top shelf
A) Chloroplast B) Leucoplast C) the mercury rising within a thermometer
C) Golgi body D) Ribosome D) a car rolling downhill
E) Lysosome E) a car moving on the road
110
11. The optimum pH of enzymes is illustrated in the 15. In which of the following processes is energy
graph below. from organic molecules directly utilized?
A) active transport
B) respiration
C) lipid synthesis
D) protein synthesis
E) ATP synthesis
16. Which monomer could be most easily modified

to form ATP?
A) the RNA nucleotide adenosine
Which is the only correct statement about the B) cholesterol
enzymes shown above ? C) the amino acid alanine
A) They are not affected by changes in pH D) the DNA nucleotide adenosine
B) They generally function in acidic conditions E) the monosaccharide fructose
C) They generally function in alkaline conditions
D) They have an optimum pH
E) They are less active in conditions of neutral pH 17. A competitive inhibitor competes with the
__________ at the __________ of an enzyme.
A) product ... active site
12. What is energy?
B) product ... allosteric site
A) the capacity to perform work
C) substrate ... active site
B) the amount of food eaten
D) substrate ... allosteric site
C) movement
E) substrate ... active site and allosteric site
D) the rearrangement of chemical molecules within
matter
E) the capacity to produce heat
18. The reaction A --> B + C + heat (released) is
a(n) _____ reaction.
13. Which of the following properties are shared by
both coenzymes and cofactors ? A) endergonic
B) dehydration synthesis
A) composed of organic molecules
C) exergonic
B) synthesized in cells
D) exchange
C) composed of metal ions
E) anabolic
D) function as enzyme activators
E) participate in the structure of proteins
19. Which of the following reactions occurs sponta-

14. Enzymes are made up of mostly_____. neously?
A) carbohydrates A) anabolic
B) minerals B) endergonic
C) lipids C) chemical
D) nucleic acids D) exergonic
E) proteins E) kinetic
111
20. Which of the following molecules is most direct- 25. What type of reaction breaks the bonds that join
ly involved in energy transfer within cells? the phosphate groups in an ATP molecule?
A) ATP B) O2 C) CO2 D) NH3 E) CH4 A) anabolism
B) hydrolysis
C) dehydration decomposition
D) dehydration synthesis
E) entropic
21.Which of the following molecules is most directly
involved in energy transfer between cells?
A) ATP B) O2 C) CO2 D) NH3 E) CH4 26.Which of the following is the incorrect associa-
tion?
A) enzyme ... protein
B) potential energy ... positional energy
C) exothermic ... uphill
22. Enzymes are described as catalysts, which
D) endothermic ... downhill
means that they _____.
E) kinetic energy ... motion
A) are proteins
B) provide activation energy for the reactions they
facilitate
27. Which one of the following has the most free
C) change the rate of a reaction without being con-
energy per molecule?
sumed by the reaction
D) can make an endothermic reaction exothermic A) a glucose molecule
E) are lipids B) a vitamin molecule
C) an amino acid molecule
D) a starch molecule
E) a fatty acid molecule
23. Which of these exhibits kinetic energy?
A) a rock on a mountain ledge
B) the high-energy phosphate bonds of a molecule 28.The process of stabilising the quaternary struc-
of ATP ture of an enzyme in its active form by the bind-
ing of a molecule is an example of _____.
C) a person sitting on a couch while watching TV
D) an archer with a flexed bow A) allosteric regulation
E) a space station orbiting Earth B) feedback regulation
C) competitive inhibition
D) the participation of a co-factor
E) all of the above
24. Chemical energy is a form of _____ energy. 29. A molecule is oxidized when it _____.
A) kinetic energy A) changes shape
B) heat energy B) gains a hydrogen (H+) ion
C) potential C) loses a hydrogen (H+) ion
D) motion D) gains an electron
E) entropic E) loses an electron
112
Cytology
PHOTOSYNTHESIS
CAPTURING ENERGY
chapter 4
PHOTOSYNTHESIS
The sun is the ultimate source of energy for all living things. Without the sun,
Photosynthesis is life as we know it would be impossible. The light energy on which all life on earth
the process by depends is obtained by the conversion of hydrogen into helium atoms inside the
which plants, some sun. Only a fraction of this energy reaches the earth and less than 2% is utilised
bacteria, and some by photosynthesising autotrophs to form the chemical bonds of complex mole-
protists use the energy in cules. The radiant energy from the sun is used in the production of both the
sunlight to produce sugar, structural and energy-producing components of cells. It cannot, however, be used
which is used in cellular res- directly to fuel the life functions of an organism. It must first be transformed into
piration to produce ATP, the another usable form of energy. Photosynthesis is the most important energy trans-
“fuel” used by all living formation in the natural world, upon which all organisms depend. It involves the
things. The conversion of conversion of radiant energy into chemical bond energy.
unusable sunlight energy into
usable chemical energy is Photosynthesis is the production of organic compounds and O2 from water
associated with the actions of and CO2. Energy from sunlight is used in the presence of chlorophyll.
the green pigment chloro- Approximately 200 billion tons of organic molecules are synthesised by photosyn-
phyll. Most of the time, the thetic organisms every year. Only one tenth of this amount is produced by terres-
CYTOLOGY
photosynthetic process uses trial plants, the bulk being produced by aquatic autotrophs such as algae and uni-
water and releases the oxy- cellular autotrophs.
gen that we absolutely must
have to stay alive. Oh yes, we Sunlight
6H2O + 6CO2 ⎯⎯⎯⎯→ C6H12O6 + 6O2
need the food as well! Chlorophyll
114
Photosynthesis nourishes almost the entire living world direct-
ly or indirectly. All organisms require organic compounds for
energy and for carbon structures. Autotrophs produce their own
food from CO2 and other inorganic raw materials obtained from
the environment. Autotrophs are the producers of the biosphere
and they are the ultimate source of food for all nonautotrophic
organisms.
Photosynthesis and respiration

Photosynthesis and cellular respiration are reversible reactions
and are closely interrelated. The products of photosynthesis,
namely organic compounds and O2, are used by both the plant
and its consumers during respiration. During this reaction CO2,
H2O and energy in the form of ATP are released. Both CO2 and
H2O then become available for further photosynthetic reactions.
Photosynthesis
(Figure 4. 1)
Photosynthesis
6H2O + 6CO2 +Energy ⎯⎯⎯⎯→ C6H12O6 + 6O2
Respiration
Figure-4.1: The interrelation between photosynthesis and respiration
115
Necessary factors for photosynthesis
1. Light
Light is a radiant form of energy and can be thought of as consisting of many
particles or photons. The photon theory states that a photon carries a unit of ener-
gy known as a quantum. The energy that each photon carries together with the
A wavelength is the number of photons per unit area per second determines the intensity of light.
distance from one
wave peak to the next. Photons are, therefore, accepted as having a physical nature similar to protons
At one end of the electro- or electrons. According to the photon theory, light energy resembles the waves
magnetic spectrum are gamma generated in water by a drop falling into it. Light exists in both visible and invisible
rays, which have very short
phases. These are categorised according to their wavelength on the electromag-
wavelengths. At the other end of
the spectrum are radio waves netic spectrum. X- rays have a short wavelength, ultra violet light has a slightly
with wavelengths so long they longer wavelength, as has visible light, between 380-400 nm and 700-760 nm.
can be measured in kilometres. The visible phases of light are violet, indigo, blue, green, yellow, orange and red.
The portion of the electromag-
netic spectrum from 380 The energy of a quantum of light is inversely proportional to its wavelength.
nanometers to 760 nanometers Thus, if the wavelength is long, the energy carried is small. In contrast to quanta
is called the visible spectrum of long wavelength, those of short wavelength carry considerable energy. Violet
because humans can see it. The light, for example, contains twice the energy of red light. When a light wave hits
CYTOLOGY
visible spectrum includes all the

matter, it produces one or a combination of three results:
colours of the rainbow; violet has
the shortest wavelength, and red it may be transmitted if the matter is transparent.
has the longest.The energy from
visible light is used in photosyn- it may be reflected.
thesis.
it may be absorbed.
116
A combination of the last two possibilities is seen in
green plants. The leaf colour is due to the absorption of all
wavelengths of the spectrum except for green, which is
mostly reflected. Of the phases of light absorbed, particu-
larly red and violet are used in photosynthesis.
When a molecule absorbs a photon of light energy, one
of its electrons is energised. One of two things then hap-
pens, depending on the atom and its surroundings.
The electron may return to its ground state. If this hap-
pens, its energy is dissipated as heat or as light of a longer
wavelength than the wavelength of the absorbed light.
This emission of light is called fluorescence.
Alternatively, the energised electron may leave the Figure-4.2: The lowest energy state an
atom and be accepted by an electron acceptor molecule; this is what occurs in atom possesses is called the ground
photosynthesis. Now that we have an understanding of some of the properties of state. Energy can be added to an electron
so that it attains a higher energy level.
light, we will consider the cellular location where light is used for photosynthesis. When an electron is raised to a higher
energy level than its ground state, the
atom is said to be excited, or energised.
engelman
READ ME experiment
Most of the energy used in photosynthesis is absorbed in the blue, violet and
red phases of the light spectrum. This fact was proved by Thedor Engelman in
1883 by the following experiment.
There are several
Engelman directed light onto a prism and split it into its phases. He then direct-
kinds of chlorophyll.
ed the individual phases of light (red, orange, yellow, green, blue, indigo and
The most important
violet) at a suspension of algae together with aerobic bacteria in the hope of
is chlorophyll a, the pigment
detecting different rates of photosynthesis. At the end of the experiment, he
that initiates the light-depend-
observed that the bacteria had congregated in the regions of blue, violet and
ent reactions. Chlorophyll b is
red light phases of light.
an accessory pigment that
There were also high
also participates in photosyn-
levels of oxygen in the
thesis. It differs from chloro-
blue, violet and red
phyll a only in a functional
phases. This showed
group on the porphyrin ring.
that the algae had
This difference shifts the
selected light phases
wavelengths of light absorbed
Photosynthesis
that contained the high-
and reflected by chlorophyll b,
est amount of energy for
making it yellow-green,
photosynthesis.
whereas chlorophyll a is
bright green.
117
2. Chloroplasts and chlorophylls
Chloroplasts are the sites of photosynthesis in plants. They are found mainly
in mesophyll cells forming the tissues in the interior of the leaf. A typical meso-
phyll cell has 30-100 chloroplasts.
Chloroplasts are disc-shaped and are composed of two portions, the stroma
and grana. The stroma is the fluid portion of the chloroplast and contains ribo-
somes, DNA, RNA and enzymes. Within each chloroplast is a system of internal
membranes. In some regions, these membranes form thylakoids or lamellae,
formed from lipids and proteins and surrounded by the thylakoid membrane.
A stack of thylakoids is known as a granum. The grana are interrelated by
interlamellar structures. Thylakoid membranes contain several kinds of pigments,
which are substances that absorb visible light.
Different pigments absorb light of different wavelengths. Chlorophyll is the
main pigment of photosynthesis and is found in the thylakoid membrane. The
colour of a leaf comes from chlorophyll, the green pigment in the chloroplasts.
Chlorophyll
Chlorophyll plays an important role in the absorption of light energy during
photosynthesis. Its role is to catalyse the transference of radiant energy into
chemical energy in a molecular form.
Chlorophyll absorbs light primarily in the blue and red regions of the visible
spectrum. Green light is not appreciably absorbed by chlorophyll. Plants usually
appear green because most of the green light that strikes them is scattered or
reflected.
Plants contain two types of chlorophyll, chlorophyll a and b, which differ only
in their number of oxygen and hydrogen atoms. Chlorophyll a, has one oxygen
molecule less than chlorophyll b, and two extra hydrogen molecules.
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118
The structure of chlorophyll
Each chlorophyll molecule is composed of four rings containing carbon

(C), hydrogen (H), oxygen (O) and nitrogen (N). Each forms a complex with
a central magnesium (Mg).
Chlorophyll a: C55H72O5N4Mg
Chlorophyll b: C55H70O6N4Mg
Chlorophyll a is the main pigment that initiates the light-dependent reac-

tions. Chlorophyll b is an accessory pigment that also participates in photo-
synthesis. Furthermore, chlorophyll a is blue-green in colour while chloro-
phyll b is yellow-green.
Chloroplasts also have other accessory photosynthetic pigments, such as
carotenoids. They can funnel the energy from other wavelengths to chloro-
phyll a and also participate in photoprotection against excessive light.
Some give colour to flowers and fruits. Examples of these pigments
include carotene (orange), xanthophyll (yellow) and licopine (red). Other
pigments include phycoerthyrin of red algae and phycocyanin of blue-green
algae.
These last two pigments are found in the cytoplasm and carry out photo-
synthesis with greater efficiency than a chloroplast.
Photosynthesis
119
Photosynthetic reactions
During photosynthesis, light energy is captured and converted to the chemical
energy of sugars and other organic compounds. Water and carbon dioxide are
used and oxygen released as a byproduct into the atmosphere.
We can summarise the equation of photosynthesis as,
Photosynthesis con-
sists of two process-
Sunlight
es, each with multi- 6H2O + 6CO2 ⎯⎯⎯⎯→ C6H12O6 + 6O2
ple stages. The light reac- Chlorophyll
tions convert solar energy to
chemical energy. The Calvin Photosynthesis involves a series of chemical reactions. Photosynthesis trans-
cycle incorporates CO2 from fers electrons from H2O to CO2 molecules, forming sugar molecules (C6H12O6).
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the atmosphere into an This electron transfer is an oxidation-reduction process: the water is oxidised
organic molecule and uses (loses electrons) and the CO2 is reduced (gains electrons). It consists of two main
energy from the light reaction stages, light phase and dark phase. In the light phase, light energy is converted
to reduce the new carbon
into chemical energy in the form of ATP. In the dark phase, products of the light
piece to sugar.
phase are used to combine carbon dioxide to produce sugar molecules.
120
Light reactions Electron Primary
transfer electron
acceptor Reaction
The reactions of the light phase begin with the absorption of light by chloro- Photon
Reaction-center
center
phyll. As it does so, it gains energy, releasing highly energised electrons into the chlorophyll
electron transport system (ETS). The ETS is made up of ferrodoxin, plasto-

quinone, cytochromes and plastocyanin, an important molecule in chlorophyll
synthesis and in oxidation-reduction reactions. It plays a key role in photosynthe- Transfer of
energy Antenna
pigment
sis. These component molecules of the ETS are arranged according to their abil- Photosystem
molecules
ity to transfer electrons. The electrons released from chlorophyll flow through the
system, transferring their energy to ATP molecules.
ATP synthesis by light is a photophosphorylation reaction. There are two
types of phosphorylation in photosynthesis and the reactions involved occur with-
in two systems of linked chlorophyll molecules known as photosystem I and pho-
tosystem II.
Pigment systems: In the thylakoid membrane, chlorophyll is organised along
with proteins and smaller organic molecules into photosystems. Each photosyn-
thetic unit includes a light-gathering antenna complex and a reaction centre.
Chlorophyll molecules and accessory pigments are organised into antenna com-
plexes. Only a special chlorophyll a in the reaction centre actually gives up its ener-
gised electrons to a nearby electron acceptor.
When any antenna molecule absorbs a photon, it is transmitted from molecule
to molecule until it reaches a particular chlorophyll a molecule, the reaction cen-
tre. At the reaction centre is a primary electron acceptor which removes an excit-
ed electron from the reaction centre chlorophyll a. This starts the light reactions.
Photosystems I and II are the two types of photosynthetic units involved in pho-
tosynthesis. Photosystem I has an absorption peak at 700 nanometers, referred to
as P700. Photosystem II has a reaction centre with a peak at 680nm. These two
photosystems work together to use light energy to generate
ATP and NADPH.
a. Cyclic Photophosphorylation
Only PS-I is functional in cyclic photophosphorylation, in
which light energy is converted to chemical energy in the
form of ATP. The energised electrons that leave PS-I pass
along a series of acceptor molecules back to the chlorophyll
molecules in the reaction centre of PS-I.
As electrons are passed along this Electron Transport
System, the energy of electrons is released and is used to
make ATP. Electrons are removed from chlorophyll within
photosystem I by radiant energy. They then flow via ferro-
doxin, plastoquinone, cytochromes b and c, finally returning
Photosynthesis
to chlorophyll. The electrons are returned to the same
chlorophyll from which they were removed, resulting in the
synthesis of ATP molecules. As chlorophyll is oxidised due
to electron displacement, ferredoxin attracts electrons and it
is subsequently reduced.
121
During the cyclic b. Noncyclic Photophosphorylation
light-dependent In noncyclic photophosphorylation the energised electrons that originate from
reactions, known as PS-I are not returned to PS-I, but are passed to the NADP+ and form NADPH. The
cyclic photophosphorylation, missing electrons of PS-I are replaced from the PS-II, while PS-II gets electrons
electrons from Photosystem I from water.
are eventually returned to
Photosystem I. Cyclic pho- In the process of photolysis (light splitting), water is split into two protons, two
tophosphorylation produces electrons and oxygen. Electrons are given to PS-II, and the protons are released to
ATP but no NADPH. the thylocoid space. Oxygen does not exist in atomic form. The oxygen produced
from one H2O molecule is written ½ O2, so two H2O molecules are used to make
one oxygen molecule (O2) which is released into the atmosphere.
In contrast to cyclic photophosphorylation, two pigment systems are present:

pigment system I (PS-I) and pigment system II (PS-II). PS-I absorbs sunlight, the
two energised electrons moving from chlorophyll to ferrodoxin. The reduced fer-
rodoxin transmits these electrons to NADP+, forming NADPH for oxidation during
the dark phase. PS-I replaces its missing electron from PS-II. PS-II obtains its elec-
trons from water. The electrons of PS-II then flow from plastoquinone to the
cytochromes, plastocyanin and PS-I. During this flow, the energy of the electrons
is converted to ATP.
As a result of noncyclic photophosphorylation,
ATP, NADPH and O2 are produced.
The products of the light phase, namely ATP and NADPH, are transferred to
the dark phase of photosynthesis, known as the Calvin cycle. The dark phase is
therefore indirectly dependent on the light phase.
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122
2. Dark Phase Noncyclic pho-
All the reactions of photosynthesis that are not directly dependent upon light tophosphorylation
are known as the dark reactions. The dark reactions occur whether there is light produces ATP and
present or not. The dark reactions occur in the part of the chloroplast known as NADPH.
the stroma. Both Photosystems I and II
The purpose of the dark reactions is to take the energy from ATP and energised are used in noncyclic pho-
electrons and hydrogen ions from NADPH and add them to CO2 to make glucose tophosphorylation, which is
or sugar. the more common light-
dependent reaction.
The dark reactions are commonly referred to as the Calvin-Benson cycle after
the pioneering work of its discovery. Melvin Calvin won a Nobel prize in biochem-
istry for elucidating the pathway of carbon fixation in plants. The reactions of the
Calvin cycle can be thought of as occurring in 3 stages:
Carboxylation - fixation of CO2 into an organic intermediate.
Reduction - reduction of this intermediate to the level of carbohydrate

Regeneration - regeneration of the CO2 acceptor
Leaves look green

because chlorophyll,
the dominant pig-
ment, absorbs red and blue
light, while transmitting and
reflecting green light.
The carbon fixation

reactions require
ATP and NADPH. In
Photosynthesis
carbon fixation, the energy of
ATP and NADPH is used in
the formation of organic mol-
ecules from CO2.
123
Carboxylation
Carboxylation involves the addition of one molecule of CO2 to a
5-carbon “acceptor” molecule, ribulose bisphosphate (RuBP). This
reaction is catalysed by the enzyme RUBISCO. The resulting 6-car-
bon product splits into 2 identical 3-carbon products. This product
is 3-phosphoglyceric acid or simply PGA. At this point in the cycle,
CO2 has been “fixed” into an organic product but no energy has
been added to the molecule.
Reduction
The second step in the Calvin cycle is the reduction of PGA to
the level of carbohydrate. This reaction occurs in two steps: (1)
phosphorylation of PGA by ATP to form a “DiPGA”; (2) reduction of
di-PGA by NADPH to form PGAL (triose phosphate, a simple 3-car-
bon carbohydrate). This reaction requires both ATP and NADPH,
the high-energy chemical intermediates formed in the light reac-
tions. The overall equation can be written as follows:
PGA + ATP + NADPH → PGAL + NADP + ADP+ Pi
Note that the basis for the term “C3 photosynthesis” comes from
the fact that the initial product is the 3-carbon acid, PGA. The
NADP+ and ADP formed in this process return to the thylakoids to
Figure-4.3: PGAL is a key intermediate mole- regenerate NADPH and ATP in the light reactions.
cule from which all other organic molecules can
be synthesised.
Regeneration
The final stage in the Calvin cycle is the regeneration of the CO2 acceptor,
RuBP. This involves a series of reactions that convert triose phosphate (PGAL) first
to the 5-carbon intermediate Ru5P (ribulose 5-phosphate), then phosphorylation
of Ru5P to regenerate RuBP (ribulose-bisphosphate). This final step requires ATP
formed in the light reactions.
The triose phosphate formed in the Calvin cycle can remain in the chloroplast
where it is converted to starch. Alternatively, triose phosphate can be exported from
the chloroplast where it is converted to sucrose in the cytosol. Both reactions involve
the release of phosphate. In the case of sucrose , this phosphate must be returned
to the chloroplast to support continued photophosphorylation (ATP formation).
Finally, 3 molecules of ATP and 2 of NADPH+H+ are used in the reduction of
Plants invest a huge a CO2 molecule. 18 molecules of ATP and 12 of NADPH+H+ are used in the pro-
amount of their duction of one 6-carbon glucose molecule. Six molecules of CO2 are required for
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available nitrogen the synthesis of a single molecule of glucose. The carbon fixation reactions may
into making this one protein. be summarised as follows,
As a result, Rubisco is the
most abundant protein in the 12NADPH+18ATP+6CO2⎯→C6H12O6+12NADP++18ADP+18P +6H2O
biosphere.
124
atp production by
READ ME c h e m i o s m ot i c m o d e l
Chemiosmotic theory is the theory of proton electrochemical coupling: that a
proton gradient is established across a membrane by the action of a primary
proton pump and that this proton gradient drives ATP synthesis through a sec-
ondary proton pump (ATP synthase or proton-translocating ATPase).
1. In noncyclic pho-
tophosphorylation,
water molecules are
split into hydrogen ions and
electrons. The oxygen is
released as a gas and the elec-
trons enter the first electron
transport system.
It has been proved that ATP synthesis is driven by oxidative and photophos- 2. The hydrogen ions obtained
phorylation. However the mechanism of ATP synthesis itself was unknown from splitting water are
until Peter Mitchell proposed the chemiosmotic model of synthesis in 1961. His released into the lumen of the
work earned him the Nobel Prize in 1978. thylakoid. The concentration
of hydrogen ions increases,
Chloroplasts and mitochondria generate ATP by the same mechanism, creating a potential difference
chemiosmosis. across the thylakoid mem-
An electron transport chain pumps protons across a membrane as electrons brane.
are passed along a series of more electronegative carriers. This builds the pro- 3. As the potential difference
and concentration increases,
ton-motive force in the form of an H+ gradient across the membrane.
hydrogen ions flow across the
ATP synthase molecules harness the proton-motive force to generate ATP as thylakoid membrane into the
H+ diffuses back across the membrane. stroma through special chan-
nels known as ATP synthase.
Mitochondria transfer chemical energy from food molecules to ATP, and The flow of ions provides the
chloroplasts transform light energy into the chemical energy of ATP. The pro- energy for ATP formation.
ton gradient, or pH gradient, across the thylakoid membrane is substantial.
When illuminated, the pH in the thylakoid space drops to about 5 and the pH
in the stroma increases to about 8, a thousandfold difference in H+ concentra-
tion. The light-reaction “machinery” produces ATP and NADPH on the stroma
side of the thylakoid. Noncyclic electron flow pushes electrons from water,
where they are at low potential energy, to NADPH, where they have high
potential energy.
Photosynthesis
This process also produces ATP. Oxygen is a byproduct. Cyclic electron flow
converts light energy to chemical energy in the form of ATP.
125
Factors affecting the rate of photosynthesis
1. Environmental Factors
CO2 Concentration
The concentration of CO2 is most likely to be the limiting factor under
natural field conditions. At low concentrations of CO2, the rate of photosyn-
thesis is slow but increases proportionally as the concentration increases.
Since the atmospheric concentration of CO2 is low, a saturation point is
unlikely to be reached. (Figure 4. 4)
Figure-4.4: The effect of CO2 concentration on the rate of Light
photosynthesis
Light Intensity: As photosynthesis is a light-dependent process, the
intensity of light has a direct effect on its rate. Given that sufficient CO2 is
present, the rate of photosynthesis increases proportionally as the intensity of
light increases. For this reason, the growth of shade-tolerant plants is slow as
compared to other plants.
Light colour: The quality of light also affects the rate and products of
photosynthesis. Red light alone, for example, reduces the rate of photosyn-
thesis. However, when red light is mixed with weak blue light, the rate of pho-
tosynthesis increases greatly. The quantity of ATP and NADPH+H+ pro-
duced during the light reaction dictates the amount of glucose produced in
the dark reaction and is therefore affected by light intensity. (Figure 4. 5)
Temperature
Temperature affect the dark phase of photosynthesis most since its reac-
tions are catalysed by enzymes. Any increase in temperature up to approxi-
mately 40°C accelerates the rate of photosynthesis. Above this temperature,
Figure-4.5: The effect of light intensity on the rate of
photosynthesis reactions slow as proteinaceous enzymes denature. (Figure 4. 6)
Water concentration
Water is used as a source of hydrogen and oxygen and as an electron
acceptor. It is therefore a fundamental prerequisite for photosynthesis.
2. Additional Factors
Photosynthesis is also affected by the following factors;
Structure of the plant
Number and distribution of stomata
Thickness of the epidermal layer
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Air spaces between the cells of the leaf

Surface area of the leaf
The structure of root and stem
Figure-4.6: The effect of temperature on the rate of pho-
tosynthesis The genetic make up of the plant
126
Photosynthesis uses
light energy to drive
the electrons from
water to their more energetic
states in the sugar products,
thus converting solar energy
to chemical energy. In the
light reactions, light is
absorbed by chlorophyll mol-
ecules. Light energy is trans-
ferred to their electrons. The
energy of excited electrons is
then used to join ADP and
phosphate to form ATP.
NADP+ joins with excited
electrons to form NADPH,
which temporarily stores the
energised electrons. In the
Minerals: Fe, Mg, Ca, Na, P, N, etc. process called photolysis,
Magnesium is well-known for its structural role in the chlorophyll molecule and water is split and oxygen is
also as a cofactor or activator in enzyme driven reactions. Its deficiency affects the released.
quantity of chlorophyll molecules and subsequently the extent to which photosyn-
thesis is possible. (Figure 4. 7)
Iron is a component of ferrodoxin which plays a role in the Electron Transport
System and the synthesis of chlorophyll.
Phosphorus is essential to the structure of ATP and nucleic acids.
Nitrogen is essential for the structure of amino acids, nucleic acids and vita-
mins formed in subsequent reactions using the products of the Calvin cycle.
Figure-4.7: A deficiency of ions affects the
growth of plants. The plants at far left and far right
are nutritionally satisfied. Compare them with the
others, where some important ion is missing.
Photosynthesis
127
CO2 fixation and photorespiration
All plants share a common feature, the fixation of CO2. But the method by which this is achieved varies with the type
of plant and its habitat. Green plants are categorised according to their strategy of CO2 fixation as C3, C4 and CAM
plants.
C3 Synthesis
C3 plants are suited to temperate climates where water is plentiful and sufficient
CO2 can enter the leaf through the stomata without the risk of irreplaceable water
loss. C3 plants therefore are able to use the enzyme RBP carboxylase (Rubisco),
which is only functional at high concentrations of CO2. The most well known C3
plants are legumes and cereals such as wheat, oats, barley, soybean, rice and
bluegrass.
Mechanism of CO2 Fixation in C3 Plants: Plants that undergo photosynthe-
sis as described above are called C3 plants because the end result of CO2 fixation
is two 3-carbon molecules (PGA). In C3 plants, CO2 is fixed to RuBP to form a 6-
carbon compound by the enzyme Rubisco. When the concentration of CO2 is low,
oxygen will bind to the active site of Rubisco. When oxygen is bound to Rubisco,
RuBP is broken down and CO2 is released. This wastes energy and is of no use
to the plant. It is called photorespiration because oxygen is taken up and CO2 is
released. Normally, photosynthesis reduces CO2 to carbohydrate.
C4 Synthesis
This method of CO2 fixation is seen in plants living in dry climates. Well-known
examples of C4 plant species include sugar cane, corn, sorghum and crabgrass.
C4 plants differ slightly morphologically from C3 and CAM plants. For instance,
photosynthesis in C3 and CAM plants is carried out within the chloroplasts of the
mesophyll cells. There are no chloroplasts in the bundle sheath cells surrounding
the leaf veins. In C4 plants however, the bundle sheath cells contain chloroplasts
and are photosynthetic. The C4 plants have less or no photorespiration so they are
high-productive agricultural plants.
Mechanism of CO2 Fixation in C4 Plants: C4 plants have an enzyme, PEP
carboxylase, that is capable of adding CO2 to a 3-carbon compound to produce
a 4-carbon compound. This process is called C4 photosynthesis because the prod-
uct of carbon fixation is a 4-carbon compound. This enzyme functions well even
at extremely low CO2 concentrations because it is unaffected by oxygen. This CO2
CYTOLOGY
fixation occurs within the mesophyll cells that surround the bundle sheath cells.
Efficiency of C4 Photosynthesis: This mechanism requires extra ATP but
under hot, dry conditions C4 plants are two to three times more efficient than C3
plants. In moderate weather, C3 plants are at an advantage.
128
129
Photosynthesis
CAM Synthesis
Plants that fix CO2 by Crassulacean Acid Metabolism generally live in very hot
and dry conditions where water is seldom available. Well-known examples include
cacti, agave and pineapple. The Calvin cycle occurs in mesophyll cells of these
plants but the stomata open only at night when it is cool and more humid. CO2
fixation occurs when the stomata are open at night. CO2 is stored as a 4-carbon
compound and is released to the cells during the day.
One of the main differences between CAM plants and C4 plants is that CO2 fix-
ation occurs in the mesophyll cells and the Calvin cycle in the bundle sheath cells
in C4 plants. All of these reactions occur in the mesophyll cells in CAM plants. In
C3 and C4 plants, CO2 is taken into the plant during the day in order to store ATP
and NADPH for the dark phase. A CAM plant would dessicate rapidly if it used the
CYTOLOGY
same method, even for a short period of time. Instead, CAM plants economise on
water consumption by opening their stomata at night to take in CO2 by combina-
tion with PEP to form oxaloacetic acid.
Efficiency of CAM Photosynthesis: CAM plants are 5 to 7 times more effi-
cient than C4 plants.
130
Photorespiration
Photorespiration is the energy-wasting process
that consumes oxygen, produces carbon dioxide,
generates no ATP, and decreases photosynthetic
output. This usually occurs on hot, dry days when
stomata are closed and the O2 concentration in the
leaf exceeds that of CO2, thereby competing for a
common active site.
Under optimum conditions of light, water and
carbon dioxide, C3 plants fix carbon dioxide using
ribulose diphosphate, PGA, NADPH+H+ and ATP
to produce carbohydrate from the Calvin cycle. If,
however, the environmental temperature increases
and the water available decreases, C3 plants are
obliged to close their stomata in order to conserve
water. In doing so it is impossible for CO2 to enter
the leaf and for O2 to leave it.
Since the stomata are closed, the O2 is trapped

inside the leaf. Under normal conditions, CO2 binds
with ribulose biphosphate in a reaction catalysed by
the enzyme RBP carboxylase. When the concentra-
tion of oxygen is high however, it competes for the
binding site of RBP carboxylase enzyme, preventing
CO2 from binding. The product of the combination
of oxygen with the five-carbon ribulose biphosphate
is the three-carbon compound phosphoglycerate
and the two-carbon compound phosphoglycolate.
The Calvin cycle requires two molecules of the
three-carbon 3-phosphoglycerate, normally
obtained from the splitting of a six-carbon com-
pound formed from ribulose diphosphate and CO2.
If they are unavailable, the cycle can no longer

function and halts until the level of carbon dioxide
rises sufficiently. During this time, the phosphoglycolate is converted into glycolate. The glycolate is transferred to a per-
oxisome where it is converted to glycoxate with the formation of hydrogen peroxide. During this process an O2 molecule
is consumed. The hydrogen peroxide formed then dissociates into a water molecule and half a molecule of oxygen.
For C4 and CAM plants, photorespiration is an inefficient process since PEP carboxylase has a higher affinity for CO2.
This enables it to be fixed at lower concentrations, allowing the Calvin cycle to continue uninterrupted.
Photosynthesis
C4 plants such as sugar cane and corn are more productive, generating carbohydrate under conditions where water
is less available and the temperature is high.
131
THE SUMMARY OF PHOTOSYNTHESIS
Reaction series Summary of process Needed materials End products
Light reactions Light energy is converted

(Grana of chloroplast) into chemical energy.
Photochemical Cholorophyll-activated energised electron Light energy, pigments

Electrons
reactions goes to an acceptor molecule (chlorophyll)
energised electrons are transported along

the chain electron acceptor in thylocoid Electrons, NADP, NADPH,
Electron transport membrane, electron reduces NADP+, pho-
H2O, Electron acceptor Oxygen
tolysis provides H+ that accumulates inside
the thylocoid space.
H+ are moved down their potential gradient Proton gradient

Chemiosmosis into the stroma, Energy released is used to ATP
produce ATP. ADP+Pi
Chemical energy is stored in the bond of

Dark reactions
organic molecules.
Rubisco, CO2, ATP, Carbohydrates,

Calvin Cycle CO2 is used to make carbohydrate.
NADPH, other enzymes ADP, NADP+
A COMPARISON OF CYCLIC AND NONCYCLIC PHOTOPHOSPHORYLATION
Features Cyclic photophosphorylation Noncyclic photophosphorylation
Photosystem involved PS-I only PS-I and PS-II
Final electron acceptor None: electrons cycle through the system NADP+
Photolysis No Yes
Chlorophyll: electrons cycle through the H O

Electron source 2
system
ADP+Pi, light, chlorophyll
Needed materials ADP+Pi, light, chlorophyll
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NADP+, H2O
End products ATP ATP, NADPH, O2
Oxygen production No Yes (by photolysis)
132
Bacterial photosynthesis
You know that bacteria are prokaryotic organisms. Like plants, some of them
are photoautotrophs and undergo photosynthesis. In some ways, bacterial pho-
tosynthesis is different from plant photosynthesis because some bacteria do not
use chlorophyll molecules to capture sunlight energy, but may use another pig-
ments instead. There are three major groups of photosynthetic bacteria:
cyanobacteria, purple bacteria, and green bacteria.
The cyanobacteria carry out oxygenic photosynthesis. That is, they use
water as an electron donor and generate oxygen during photosynthesis.The pho-
tosynthetic system is located in an extensive thylakoid membrane system that is
lined with particles called phycobilisomes.
The green bacteria carry out anoxygenic photosynthesis. They use reduced
molecules such as H2, H2S, S, and organic molecules as an electron source and
generate NADH and NADPH. The photosynthetic system is located in ellipoidal
vessicles called chlorosomes that are independent of the cytoplasmic membrane.
The purple bacteria carry out anoxygenic photosynthesis. They use
reduced molecules such as H2, H2S, S, and organic molecules as an electron
source and generate NADH and NADPH. The photosynthetic system is located in
spherical or lamellar membrane systems that are continuous with the cytoplasmic
membrane. The differences between plant and bacterial photosynthesis are sum-
marised in the table below.
Sunlight
2H2O+H2S+ CO2 ⎯⎯⎯⎯⎯→ C6H12O6 +H2SO4
Differences between plant Plant Bacterial

and bacterial photosynthesis photosynthesis photosynthesis
plants, algae, purple and green bac-

Organisms
cyanobacteria teria
chlorophyll a bacteriochlorophyll
Type of chlorophyll
absorbs 650-750nm absorbs 800-1000nm
Photosystem I
present present
(cyclic photophosphorylation)
All animals, fungi,
Photosystem II (noncyclic and most bacteria
present absent
photophosphorylation) are chemoheterot-
rophs and use preformed
Photosynthesis
Produces O2 yes no organic molecules as a
H2S, other sulfur com- source of both energy and
Photosynthetic electron H2O carbon. A few plants are
donor pounds or certain
chemoheterotrophs as well.
organic compounds
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Chemosynthesis
Inorganic O Inorganic
matter intermediary matter Some bacteria use chemosynthesis as another means of
food production. Chemosynthesis is a kind of autotrophic
Energy
O nutrition process in which carbohydrates are manufactured
from carbon dioxide and water using chemical nutrients as
H2O the energy source, rather than the sunlight used for energy in
photosynthesis. Chemosynthetic bacteria such as sulfolobus
H2
do not have chlorophyll so they can not use sunlight energy;
Carbohydrates the energy is taken from chemical reactions. Most life on
CO2 earth is fuelled directly or indirectly by sunlight. There are,
Organic
compounds however, certain groups of bacteria, referred to as chemosyn-
thetic autotrophs, that are fuelled not by the sun but by the
oxidation of simple inorganic chemicals, such as sulfates or
ammonia. Chemosynthetic autotrophs are a necessary part of the nitrogen cycle.
The energy is then used for food production. We can show an example of
chemosynthetic reaction as follows,
2S+3O2+2H2O ⎯→ 2H2SO4+energy
The energy is used to produce food from carbon dioxide, as in the dark reac-
tion of photosynthesis.
READ ME nutrition and metabolic diversity
Autotrophic bacteria can be divided into two categories according to their source of energy for ATP formation
namely: phototrophs and chemotrophs.
Phototrophs: Phototrophs utilise light energy and in turn are divided into two categories, photolithotrophs and
photoorganotrophs. Photolithotrophs use inorganic compounds to generate the electrons needed for ATP forma-
tion. These compounds may be hydrogen sulphide, in the case of Chromatium okenii, or water, in the case of
cyanobacteria. Bacteria that utilise hydrogen sulphide can not produce oxygen as a by-product. Cyanobacteria,
in contrast, are capable of the same photosynthetic reactions as those in the chloroplasts of eukaryotic cells.
Photoorganotrophs use organic compounds to generate the electrons needed for ATP formation. These com-
pounds may be fatty acids or alcohols. Rhodospirillium rubrum, for example, uses succinate as an electron donor.
Chemotrophs: Chemotrophs utilise energy from chemical com-
pounds to generate energy for ATP. They in turn are divided into
two categories: chemolithotrophs and chemoorganotrophs.
Nitrosomonas europaea is an example of a chemolithotroph. It
uses inorganic ammonia as its electron source, oxidising it to
nitrate. This reaction plays a key role in the nitrogen cycle.
CYTOLOGY
Pseudomonas pseudoflava is an example of a chemoorganotroph.

It uses organic glucose as its electron source. Other members of
the family Pseudomonadacae also use organic compounds and
are responsible for mineralisation or breakdown of organic mate-
rials to inorganic compounds in the environment.
134
PHOTOSYNTHESIS
The sun is the ultimate source of energy for all living things. Without the sun, life as we know it would be impos-
sible. The light energy on which all life on earth depends is obtained by the conversion of hydrogen into helium
atoms inside the sun. Photosynthesis and cellular respiration are reversible reactions and are closely interrelated.
Light is a radiant form of energy and can be thought of as consisting of many particles, or photons. The photon
theory states that a photon carries a unit of energy known as a quantum. The energy that each photon carries togeth-
er with the number of photons per unit area per second determines the intensity of light.
Chloroplasts are the sites of photosynthesis in plants. They are found mainly in mesophyll cells forming the tis-
sues in the interior of the leaf. Chloroplasts are disc-shaped and are composed of two portions: the stroma and grana.
Chlorophyll is the main pigment of photosynthesis and is found in the thylakoid membrane. The colour of a leaf
comes from chlorophyll, the green pigment in the chloroplasts. Chlorophyll plays an important role in the absorption
of light energy during photosynthesis. Their role is to catalyse the transference of radiant energy into chemical ener-
gy in a molecular form.
Photosynthesis involves a series of chemical reactions. Photosynthesis transfers electrons from H2O to CO2 mol-
ecules, forming sugar molecules (C6H12O6). This electron transfer is an example of an oxidation-reduction process:
the water is oxidised (loses electrons) and the CO2 is reduced (gains electrons). During photosynthesis, light energy
is captured and converted to the chemical energy of sugars and other organic compounds; H2O and CO2 are used,
and O2 is released as a byproduct into the atmosphere. Photosynthesis involves a series of chemical reactions. It con-
sists of two main stages, the light phase and the dark phase. In the light phase light energy is converted into chem-
ical energy in ATP. In the dark phase, products of the light phase are used to combine carbon dioxide.
Chemiosmotic theory is the theory of proton electrochemical coupling. A proton gradient is established across a
membrane by the action of a primary proton pump, and this proton gradient drives ATP synthesis through a second-
ary proton pump (ATP synthase or proton-translocating ATPase).
Environmental and other factors affect the rate of photosynthesis. The concentration of CO2 is most likely to be
the limiting factor under natural field conditions. As photosynthesis is a light-dependent process, the intensity of light
has a direct effect on its rate. Temperature affects the dark phase of photosynthesis most since its reactions are catal-
ysed by enzymes. Water is used as a source of hydrogen and oxygen and as an electron acceptor. It is therefore a
fundamental prerequisite for photosynthesis. Plant structure affects the rate of photosynthesis
All plants share a common feature, the fixation of CO2. But the method by which this is achieved varies with the
type of plant and its habitat. Green plants are categorised according to their strategy of CO2 fixation as C3, C4 and
CAM plants. Photorespiration is the energy-wasting process that consumes oxygen, produces carbon dioxide, gen-
erates no ATP, and decreases photosynthetic output. This usually occurs on hot, dry days when stomata are closed
and the O2 concentration in the leaf exceeds that of CO2, thereby competing for a common active site.
In some ways, bacterial photosynthesis is different from plant photosynthesis because some bacteria do not use
Photosynthesis
chlorophyll molecules to capture sunlight energy, but may use another pigments instead. There are three major
groups of photosynthetic bacteria: cyanobacteria, purple bacteria, and green bacteria.Some bacteria use chemosyn-
thesis as another means of food production. Chemosynthesis is a kind of autotrophic nutrition process in which car-
bohydrates are manufactured from carbon dioxide and water using chemical nutrients as the energy source, rather
than the sunlight used for energy in photosynthesis.
135
EXPERIMENT: Investigation into photosynthetic gases
Purpose of experiment: Materials Pond weed such as Elodea

To investigate the gas pro- 2 tall beakers Sodium Bicarbonate
duced during photosynthesis. 2 glass funnels (NaHCO3)
2 test tubes Teaspoon
Wooden splint
Lamp
Procedure:
Discussion:
Which factor is the variable in
this experiment ?
Putting a glowing splint into
each tube is a test for which
gas ?
Explain why you would expect
this test to be positive in only
one tube ?
136
EXPERIMENT: Investigation into photosynthesis
Purpose of experiment: Materials: Forceps

To investigate the conditions Conical flask Scissors
required for photosynthesis. Polythene bag Methylated spirits
KOH or NaOH Iodine solution
Aluminum foil Pipette
Three petri dishes
Procedure:
Discussion:
Give reasons for the differences in
staining in each leaf and between differ-
ent leaves.
Explain the role of potassium hydrox-

ide in the results of the experiment.
Explain why the periphery of the varie-
gated leaf stained differently than the
rest of the leaf.
137
9. Name the type of pigments involved in photosynthe-
Information Recall Questions sis and explain their purpose.
1. I. iron
II. nitrogen
III. magnesium
IV. carbon
10. Explain the term photorespiration and give examples
V. oxygen of the conditions in which it might be observed.
Select the element required in the synthesis of a
chlorophyll molecule even though it does not partici-
pate in its structure.
11. Discuss the role of light in photosynthesis and state

the most effective light phase(s) needed for this
process.
3. Which molecules provide an electron source in pho-

tosynthesis?
12. Describe exactly where the dark phase of photosyn-

thesis would occur in a plant lacking chloroplasts, but
containing chlorophyll.
4. In the atmosphere, what is the source of the oxygen
that you breathe?
5. State the kind of bacteria used by Engelman in his

experiment. 13. Compare the pathway of photosynthesis in bacteria
and green plants.
6. Calculate the amount of ATP and NADPH2 needed to

synthesise 3 mol of glucose during photosynthesis.
14. Give reasons why most plants are green.
7. Compare and contrast the structure of Chlorophyll-a

and Chlorophyll-b. 15. Compare and contrast the similarities and differences
between cyclic and noncyclic photophosphorylation.
8. Compare and contrast the photosynthetic pathway of

C3 and C4 plants. 16. Calculate how many molecules of RBP are involved in
dark phase reactions in order to synthesise one mol-
ecule of glucose.
138
17. Examine the list of factors and explain their role dur-
ing the dark phase of photosynthesis. Application of knowledge
I. CO2 concentration
1. Suggest crops that a farmer should grow on nitrogen-
II. enzyme concentration poor soil. Explain the reasons for your choice.
III. light intensity
IV. temperature
2. A number of tropical grass seeds were taken from a
farm in Brazil. In an experiment, they were planted on
a farm in southwest England. Despite good soil and
18. Compare and contrast the structure of chloroplasts sufficient water, the grass grew poorly.
and mitochondria. Suggest reasons why the species of grass was unsuc-
cessful in its new environment.
19. A chloroplast contains pigments other than chloro-

3. Half the surface area of a leaf is covered by carbon
phylls. What is the function of these pigments in pho-
paper in the morning and is kept covered during the
tosynthesis?
day. The leaf is broken off from its stem at night and
is boiled in a water bath. The chlorophyll is extracted
from the leaf and lugol solution is added. What colour
20. Calculate the amount of ATP and NADPH2 required changes would you expect to observe in the leaf when
to synthesise a molecule of maltose during the dark lugol solution is rubbed onto the leaf? Explain.
phase of photosynthesis.
Fill in the blanks Choose the correct alternative

to complete each statement
1. Which of the following molecules is/are involved
1. During noncyclic photophosphorylation, the electrons in the oxidation-reduction reactions of photosyn-
of photosystem I originate from .................... while thesis?
those of photosystem II originate from I. NAD
....................................
II. NADP
III. Plastoquinone
A) Only I B) Only II C) I and II
D) I and III E) II and III
2. List the end product(s) of the light phase of photosyn-
thesis.
-............................ 2. What is the ultimate source of energy to support
-............................ most life on Earth?
-............................ A) photosynthetic organisms
B) chemosynthetic organisms
3. In C3 plants, CO2 is captured by C) sunlight
................................. In contrast, it is captured by D) geothermal heat
........................... in C4 plants. E) the nitrogen cycle
139
3. When light strikes chlorophyll molecules, they 8. C4 plants occur more commonly in desert condi-
lose electrons, which are ultimately replaced by _. tions because _____.
A) splitting water A) they store CO2 into the vacuole
B) breaking down ATP B) they can fix carbon at the lower CO2 concentra-
C) removing them from NADPH tions
D) fixing carbon C) they produce water as a product of their photo-
E) oxidising glucose synthetic pathways
D) they produce carbon dioxide internally via pho-
torespiration
4. Which of the following is produced by the light
E) the stomata open at night and close in the day
reactions of photosynthesis and consumed by
the Calvin cycle?
A) oxygen
B) NADPH 9. Which of the following would not be capable of
performing photosynthesis?
C) water
D) sugar A) green algae
E) CO2 B) bacteria
C) an oak tree
D) a mushroom
5. In the electromagnetic spectrum, the type of E) euglena
radiation that we call visible light occurs
between __.
A) ultraviolet radiation and infrared radiation
B) radio waves and microwaves 10. The interaction between the light and dark phases of
photosynthesis is shown in the figure below.
C) infrared radiation and microwaves
D) infrared radiation and radio waves
Light Phase ⎯→ Dark Phase
E) X-rays and ultraviolet radiation
Which of the following combinations of mole-
cules correctly describes the involvement
6. Which of the following is not a product of the between these phases?
light reactions of photosynthesis? + +
A) ATP – NADPH+H – NADP – ADP
A) NADPH + +
B) ADP – FAD – NADH+H – ATP
B) oxygen + + +
C) NADPH+H – FADH2 – FAD – NAD
C) sugar
+ +
D) ATP D) ATP – ADP – FAD – FADH+H
+ +
E) All of above E) ATP – ADP – NADH+H – NAD
7. In photosynthesis, plants use carbon from ____

to make sugar and other organic molecules. 11. How does carbon dioxide enter the leaf?
A) soil A) through the chloroplasts
B) water B) through the mesophyll
C) carbon dioxide C) through the thylakoids
D) chlorophyll-a D) through the stomata
E) the sun E) through the vascular system
140
12. Molecular oxygen is produced during _____. 17. Where do the electrons needed by photosystem
II originate?
A) glycolysis
B) cyclic photophosphorylation A) chlorophyll-a molecules
C) the Calvin cycle B) ATP
D) noncyclic photophosphorylation C) the ETS
E) ETS D) light
E) water
13. Which of these wavelengths is least useful for

photosynthesis?
A) red 18. During photosynthesis in a eukaryotic cell, a
B) green high proton concentration accumulates in the
C) yellow ___________.
D) blue A) matrix
E) orange B) thylakoid membrane
C) (inner) thylakoid space (lumen)
D) stroma
14. A photon of which of these colours would carry E) Cristae

the most energy?
A) red 19. Examine the following list of molecules.
B) green I. Glucose
C) yellow II. O2
D) blue
III. ATP
E) orange +
IV. NADPH+H
Which are the product of noncyclic photophos-
phorylation?
15. The most important role of pigments in photo- A) I–II B) II–IV C) III–IV D) II–III–IV E) I–II–III
synthesis is to _____.
A) capture light energy
B) screen out harmful ultraviolet rays
20. Which of the following would prove conclusively
C) store energy in glucose molecules
that a nonphotosynthetic cell was a plant cell ?
D) release energy from glucose molecules
A) Cellular respiration
E) store energy in ATP
B) Starch synthesis
C) Protein synthesis
16. Rubisco is _____.
D) Conversion of starch into glucose
A) the 5-carbon sugar molecule
E) Lipid biosynthesis
B) the enzyme in C3 plants that first captures CO2
C) the enzyme responsible for photolysis in photo-
synthesis 21. Which of the following cell organelles converts
radiant energy to chemical bond energy ?
D) the enzyme that forms a 4-carbon compound in
CAM metabolism A) chloroplast B) mitochondrion C) ribosome
E) the first stable intermediate in CAM metabolism D) chromoplast E) leucoplast
141
22. In which of the following plant organs is photo- 26. Which of the following molecules is obtained
synthesis fastest ? from phosphoglyceraldehyde in the dark phase
of photosynthesis ?
A) Spongy parenchyma
B) Cuticle A) Ribulose phosphate
C) Epidermis B) Ferrodoxin
D) Palisade parenchyma C) Plastoquinone
E) Phloem vessels D) Phosphoglyceric acid
E) Carbon dioxide
23. I. ATP
II. NADPH+H
III. Glucose
IV. Amino acid 27. According to the diagram, which of the following
Which of the molecules above require sunlight factors does not affect the amount of oxygen
for their biosynthesis ? released in a given period of time?
A) I and II B) I and III C) I and IV
D) II and III E) III and IV
24. Examine the following list of molecules.

I. ATP
A) Volume of container
II. Vitamins
B) Intensity of light
III. ADP
C) Number of leaves
IV. CO2
D) Temperature of water
V. NADPH+H E) CO2 concentration dissolved in water
Which of the molecules listed above are pro-
duced during the dark phase of photosynthesis ?
A) I and IV B) I and V C) II and III
D) II and IV E) IV and V
28. The following types of phosphorylation take
place inside a cell
25. Some reactions of the light phase are given I. Substrate level
below. II. Oxidative
I. Electron trapping by NADP for PS–I III. Cyclic
II. Recovery of electron loss from PS–II by PS–I IV. Noncyclic
III. Recovery of electron loss from water by PS–II V. Chemosynthetic
Which combination is the correct order for these Which of these reactions involve/s the ETS in ATP
reactions? synthesis ?
A) I–II–III B) II–I–III C) III–II–I A) Only I B) I and II C) I and V
D) III–I–II E) I–III–II D) III and V E)II, III and IV
142
Cytology
CELLULAR RESPIRATION
HARVESTING ENERGY
Classification
Animal
chapter 5
CELLULAR RESPIRATION HARVESTS ENERGY
All organisms use energy to carry out the functions of life. Some organisms
obtain this energy directly from sunlight. They capture part of the energy in light
and store it within organic compounds (food). The source of energy for all organ-
isms is food. Cells obtain this energy by catabolising complex organic molecules.
The bodies of organisms contain many enzymes that are employed in harvest-
ing energy from food. Most foods contain a variety of carbohydrates, proteins, and
fats, all rich in energy. The job of extracting energy from these food molecules is
Living is work. To cellular respiration.
perform their many
tasks, cells require Cellular respiration is a kind of catabolic reaction by which chemical bond
transfusions of energy from energy of organic molecules is released as ATP, the “fuel” used by all living things,
outside sources. In most and heat energy. The aim of cellular respiration is to produce ATP.
ecosystems, energy enters as
CYTOLOGY
ATP molecules are used for cellular activities such as the synthesis of organic
sunlight. Light energy
end-products. The energy in the bonds of these complex molecules may be
trapped in organic molecules
extracted by two methods, dependent on whether oxygen is available. Aerobic res-
is available to both photosyn-
piration utilises oxygen whereas anaerobic respiration is possible without it. Of the
thetic organisms and others
two methods, aerobic respiration is more efficient and generates a greater num-
that eat them.
ber of ATP molecules.
144
Aerobic Respiration
Oxygen is essential for the continuation of life on earth since it is utilised by
most living things during respiration. It is produced by green plants during the
process of photosynthesis. Most remains in a gaseous form and diffuses through
the atmosphere. Some is dissolved in water and some participates in the structur-
al organic elements of living things and is chemically and physically utilized in the
process of oxidation of natural compound. Additionally some oxygen contributes Most eukaryotes and
to the structure of many of the minerals in the earth's crust. prokaryotes use a
form of cellular res-
Aerobic respiration is a kind of catabolism in which the energy of organic mol- piration requiring oxygen and
ecules is released by using oxygen. It involves an electron transport system in hence carry out aerobic res-
which molecular oxygen is the final electron acceptor. Most eukaryotes and piration. During aerobic res-
prokaryotes use aerobic respiration to obtain energy from glucose. piration, nutrients are
The overall reaction pathway for aerobic respiration of glucose is summarised catabolised to carbon dioxide
Cellular respiration
as follows. and water. Most cells of
plants, animals, protists,
Glucose + 6O2 ⎯⎯⎯⎯⎯→ 6CO2 + 6H2O + Energy fungi, and bacteria use aero-
bic respiration to obtain ener-
gy from glucose.
145
The release of ener-
gy from a glucose
molecule is analo-
gous to the liberation of ener-
gy by a falling object. The
total energy released is the
same whether it occurs all at
once or in a series of steps.
The metabolic path-

ways of respiration
also play a role in the
anabolic pathways of the cell.
Not all of the organic mole-
cules of food are completely
oxidized to make ATP.
Intermediaries in glycolysis
and the Krebs cycle can be
diverted to anabolic path-
ways. For example, a human
cell can synthesize about half
the 20 different amino acids
CYTOLOGY
by modifying compounds
from the Krebs cycle.
Glucose can be synthesized
from pyruvate, and fatty
acids from acetyl CoA.
146
Aerobic Respiration (An Overview) Have you noticed
The energy stored within a glucose molecule is yielded step by step in a series that when a car runs
out of gasoline, it
of reactions. If this energy were released at once, the heat suddenly generated
stops; that when there is no
would destroy the cell. The stages of energy extraction from glucose are in order electricity, television does not
as follows. (Figure 5. 1) work? So organisms are
Glycolysis - in the cytoplasm unable to carry out their daily
activities if they stop eating,
Pyruvate oxidation in mitochondria since all that gasoline, elec-
tric energy, and food do is
Krebs cycle - in the matrix of mitochondria provide energy.
ETS - on the inner mitochondrial membrane
1. Glycolysis
Glycolysis is a series of enzyme-catalysed reactions by which a glucose mole-
cule (a six-carbon compound) is converted to two molecules of pyruvate (a three-
carbon compound). Glycolysis occurs in the cytoplasm and is common to both
aerobic and anaerobic respiration. As a result of glycolysis, 2 molecules of ATP
and 2 of NADPH + H+ are produced.
2. Pyruvate oxidation
The pyruvic acid that is produced in glycolysis diffuses across the double mem-
brane of a mitochondrion and enters the mitochondrial matrix, the space inside
the inner membrane of a mitochondrion. When pyruvic acid enters the mitochon-
drial matrix, it reacts with a molecule called coenzyme A to form acetyl coenzyme
A, abbreviated acetyl CoA. Carbon dioxide, NADH, and H+ are produced in this
reaction.
3. Krebs Cycle
The Krebs cycle is a series of biochemical reactions by which the acetyl por-
tion of acetyl-CoA is degraded to carbon dioxide and water with the release of
metabolic energy, which is used to produce ATP. The Krebs cycle occurs in the
matrix of mitochondria, because the enzymes required for the reactions of the Glycolysis and the
Krebs cycle are anchored on the inner membrane and matrix of the mitochondria. Krebs cycle function
There are two cycles and each cycle produces one ATP by substrate-level phos- as metabolic inter-
phorylation, three NADH, and one FADH2 per acetyl CoA. changes that enable cells to
convert one kind of molecule
to another as needed. For
4. Electron Transport System (ETS) example, excess carbohy-
drates and proteins can be
It is a series of chemical reactions during which hydrogens or their electrons
converted to fats through
are passed along from one acceptor molecule to another with the release of ener-
intermediaries of glycolysis
gy. In the electron transport chain, the electrons move from molecule to molecule and the Krebs cycle.
until they combine with oxygen and hydrogen ions to form water.
147
Aerobic respiration (A closer look)
1. Glycolysis (Reactions)
Glycolysis is a series of enzyme-catalyzed reactions initiated by
the activation of a hexose molecule and terminating in the produc-
tion of two molecules of pyruvate. The energy released during these
reactions is stored in the form of ATP.
Glycolysis was first discovered by Hans and Eduard Buchner in
1897 while manufacturing cell-free extracts of yeast. When they
added sucrose to the extracts, it was rapidly converted to alcohol,
despite the absence of any cell. Further investigations by Fritz
Lipmann and Herman Kalckar determined the role of ATP in
metabolism, and by 1940 all the steps of glycolysis and their asso-
ciated enzymes had been determined. Two phases were discovered,
a preparatory and a payoff phase.
1. Preparatory Phase
A hexose sugar is first activated, a process requiring two mol-
ecules of ATP and occurring in five distinct stages. By the end of
the preparatory phase of glycolysis, two molecules of ATP have
been consumed in the production of 2 molecules of PGAL from
one glucose molecule.
1. Phosphorylation of Glucose: The addition of a phosphate

group to the 6th carbon by the enzyme hexokinase energis-
es the 6C glucose molecule and converts it to glucose-6-
phosphate.
2. Conversion of Glucose-6-Phosphate to Fructose-6-
Phosphate: Glucose-6-Phosphate is converted to fructose-
6-phosphate by the enzyme phosphohexose isomerase.
3. Phosphorylation of Fructose-6-Phosphate to Fructose
1,6-Diphosphate: Fructose-6-Phosphate is phosphorylated
by the addition of a second phosphate group, this time to
the 1st carbon of the fructose molecule by the enzyme phos-
phofructokinase. Another molecule of ATP is consumed in
this reaction.
4. Cleavage of Fructose-1,6-Diphosphate: Fructose-1,6-
Diphosphate is cleaved by the enzyme aldase to produce
two molecules containing three carbons and one phos-
CYTOLOGY
phate. One is glyceraldehyde-3-phosphate (PGAL), the other

is dihydroxyacetone phosphate.
5. Conversion of Dihydroxyacetone Phosphate:
Dihydroxyacetone phosphate is converted into PGAL by the
enzyme triose phosphate isomerase.
148
2. Payoff Phase
The 3-carbon glyceraldehyde phosphate molecules enter the energy-payoff

phase. Chemical bonds are broken, and NAD+ picks up electrons and hydro-
gen ions, forming NADH. The energy released is used to produce ATP. This way
of making ATP is called substrate-level phosphorylation. During this phase a
small amount of energy is released and converted to ATP in five distinct stages.
Most of the energy available is preserved in end products
6. Oxidation of Glyceraldehyde-3-Phosphate to 1,3-Diphosphoglycerate:

Glyceraldehyde-3-phosphate is converted to 1,3-diphosphoglycerate by the
+
addition of inorganic phosphate and the removal of hydrogen (H ). The
source of phosphate is not ATP. The hydrogen molecules are then accepted
+
by NAD and 2 molecules of NADH + H are synthesised. The inorganic
phosphate molecules of 1,3-diphosphoglycerate are then used in the synthe-
sis of ATP. The reaction is controlled by the enzyme glyceraldehyde-3-phos-
phate dehydrogenase.
7. Synthesis of ATP from 1,3-Diphosphoglycerate: The phosphate on the 1st
carbon of the 1,3-diphosphoglycerate molecule is transferred to ADP by the
enzyme phosphoglycerate kinase. Thus from one hexose sugar, 2 mole-
cules of ATP are synthesized and 2 molecules of 3-phosphoglycerate remain.
8. Conversion of 3-Phosphoglycerate to 2-Phosphoglycerate: According to
the system of nomenclature developed by the international Union of Pure
and Applied Chemistry (IUPAC), the number prefix before the name of the
molecule indicates the position of the phosphate group. For example, the 3-
phosphoglycerate at this stage of glycolysis has a phosphate group attached
to the 3rd carbon of the molecule.
The enzyme phosphoglycerate mutase transfers the phosphate group from
the 3rd to the 2nd carbon. As a result, two molecules of 2-phosphoglycerate
are obtained.
9. Removal of Water from 2-Phosphoglycerate: Two water molecules are syn-
thesized from two molecules of phosphoglycerate by the enzyme enolase
with the gain of two molecules of phosphoenolpyruvate.
10. Synthesis of ATP from Phosphoenolpyruvate: The remaining high ener-
gy-containing phosphate groups of the molecule are transferred from phos-
phoenol pyruvate to ADP by the enzyme pyruvate kinase in the synthesis of
Glycolysis is the
2 ATP molecules. The product of this reaction is pyruvate, and it acts as the
splitting of glucose
substrate for the aerobic or anaerobic pathways that follow.
into pyruvate.
Finally: As a result of gycolysis, 2 ATP molecules are used to activate glucose, Glycolysis is the one meta-
2 molecules of NAD+ are reduced to obtain 2 molecules of NADH + H+, bolic pathway that occurs in
and 4 molecules of ATP are synthesized in the conversion of PGAL to pyru- all living cells, serving as the
starting point for fermenta-
vate. In total 2 molecules of ATP and 2 of NADPH + H+ are produced.
tion or aerobic respiration.
149
2. Pyruvate Oxidation
The pyruvic acid produced in glycolysis diffuses
across the double membrane of a mitochondrion
and enters the mitochondrial matrix, the space
inside the inner membrane of a mitochondrion.
Pyruvate is an important molecule and can be
catabolized by different enzymes to form lactic acid
or ethyl alcohol under anaerobic conditions.
However, under aerobic conditions, pyruvate is
converted into acetyl Co-A in a process yielding
NADH+H+ and CO2. In total 2 molecules of
NADH+H+ and 2 of CO2 are gained from the con-
version of pyruvate to acetyl CoA. The acetyl CoA
then enters the Krebs cycle in the mitochondria.
3. Krebs Cycle
The Krebs cycle is a series of biochemical reac-
tions by which the acetyl portion of acetyl-CoA is
degraded to carbon dioxide and water with the
release of metabolic energy, which is used to pro-
duce ATP.
The Krebs cycle occurs in the matrix of mito-
chondria, because the enzymes required for the
reactions of the Krebs cycle are anchored on the
inner membrane and matrix of the mitochondria.
The cycle is initiated by the fusion of acetyl CoA
and oxaloacetate to form citrate. This part of the
cycle explains why the Krebs cycle is also known as
the Citric Acid cycle.
Two acetyl groups
enter the Krebs The citrate is first isomerised to isocitrate, then oxidised and decarboxylated to
cycle for every glu- form a-ketoglutarate (5C), yielding NADH+H+ and CO2.
cose. Each 2-carbon
The a-ketoglutarate is converted to succinate (4C) in a process yielding
acetyl group combines with
the 4-carbon compound NADH+H+, a molecule of ATP and one of CO2.
oxaloacetate to form the 6- Succinate is converted into fumarate (4C), and a molecule of FADH2 is pro-
carbon compound citrate.
duced. The addition of water to fumarate produces malate (4C) and a molecule of
Two CO2 molecules are
NADH+H+.
removed to regenerate
CYTOLOGY
oxaloacetate, and in the Finally malate is converted to oxaloacetate (4C) by yielding a molecule of
process, energy is captured NADH+H+. The cycle is now ready to begin again with the condensation of
as one ATP, three NADH, and oxaloacetate and acetyl coenzyme A.
one FADH2 per acetyl group
(or two ATPs, six NADH, and
two FADH2 per glucose).
150
In one complete cycle, 3 molecules of NADH+H+, 1 molecule of FADH2, 1 of
If a cell has an
ATP and 2 of CO2 are produced. NADH+H+ and FADH2 are utilized in the ETS
excess of a certain
to release energy in the form of ATP. The waste product CO2 is removed from the amino acid, it typi-
cell. cally uses feedback inhibition
A single glucose molecule completes two full circuits of the Krebs cycle since to prevent the diversion of
from one glucose molecule, two molecules of acetyl CoA are produced. In total, 6 more intermediary molecules
from the Krebs cycle to the
molecules of NADH+H+, 2 molecules of FADH2 and 2 of ATP are gained from
synthesis pathway of that
the Krebs cycle. amino acid.
151
4. Electron Transport Chain (ETC) and Chemiosmosis
The ETC makes up the final stage of aerobic respiration. In eukaryotic cells the
electron transport chain lines the inner membrane of the mitochondrion; the inner
membrane has many long folds called cristae. In prokaryotes, the electron trans-
port chain lines the cell membrane.
The electron transport “chain” is a series of electron carriers in the membrane
of the mitochondria. Through a series of reactions, the “high energy” electrons are
passed to oxygen. In the process, a gradient is formed, and ultimately ATP is pro-
duced. Electrons are finally gained by oxygen, which is why Electron Transport
requires oxygen directly.
Oxidative Phosphorylation
ATP synthesis is termed phosphorylation. Two types of phosphorylation occur
in glucose catabolism: substrate level and oxidative phosphorylation. Oxidative
phosphorylation is the synthesis of ATP by the transfer of electrons through the
ETS to oxygen.
CYTOLOGY
152
These energised electrons are released during glycolysis and
the Krebs cycle and are transported through the ETS in the form
of NADH+H+ and FADH2. They undergo a series of redox reac-
tions to extract energy and synthesize ATP.
The electron transport chain generates no ATP directly. Its
function is to break the large free energy drop from food to oxy-
gen into a series of smaller steps that release energy in manage-
able amounts. The electrons in the hydrogen atoms from NADH
and FADH2 are at a high energy level.
These high energy electrons are passed along a series of mol-

ecules. As they move from molecule to molecule, the electrons
lose some of their energy.
The energy they lose is used to pump protons of the hydrogen
atoms from the mitochondrial matrix to the other side of the inner
mitochondrial membrane. The pumping builds up a high concen-
tration (a concentration gradient) of protons in the space between
the inner and outer mitochondrial membranes. The concentration
gradient of protons drives the synthesis of ATP by chemiosmosis.
ATP synthase (enzyme) molecules are located in the inner
mitochondrial membrane. The ATP synthase makes ATP from
ADP as protons move down their concentration gradient into the
mitochondrial matrix.
ATP can be synthesised by chemiosmosis only if elec-

trons continue to move from molecule to molecule in
the Electron Transport Chain. Oxygen serves as the
final acceptor of electrons. By accepting electrons from the last
molecule in the Electron Transport Chain, oxygen allows addi-
tional electrons to pass along the chain, allowing ATP to con-
tinue to be synthesized. Oxygen also accepts protons that were
once part of the hydrogen atoms supplied by NADH and
FADH2. By combining with both electrons and protons, oxygen
forms water.
153
Chemiosmotic Mechanism (A closer look)
The chemiosmotic theory explains the functioning of electron transport chains. According to this theory, the tranfer
of electrons down an electron transport system through a series of oxidation-reduction reactions releases energy. This
energy allows certain carriers in the chain to transport hydrogen ions (H+, or protons) across a membrane.
Depending on the type of cell, the electron transport chain may be found in the cytoplasmic membrane or the inner
membrane of mitochondria. As the hydrogen ions accumulate on one side of a membrane, the concentration of hydro-
gen ions creates an electrochemical gradient or potential difference (voltage) across the membrane. (The fluid on the
side of the membrane where the protons accumulate acquires a positive charge; the fluid on the opposite side of the
membrane is left with a negative charge.) The energized state of the membrane as a result of this charge separation is
called proton motive force, or PMF. This proton motive force provides the energy necessary for enzymes called ATP syn-
thases, also located in the membranes mentioned above, to catalyse the synthesis of ATP from ADP and phosphate.
This generation of ATP occurs as the protons cross the membrane through the ATP synthase complexes and re-enter
CYTOLOGY
either the bacterial cytoplasm or the matrix of the mitochondria. (Proton motive force is also used to transport sub-
stances across membranes during active transport and to rotate bacterial flagella.) At the end of the electron transport
chain involved in aerobic respiration, the last electron carrier in the membrane transfers 2 electrons to half an oxygen
molecule (an oxygen atom) that simultaneously combines with 2 protons from the surrounding medium to produce
water as an end product.
154
Calculation of ATP production:
Aerobic Respiration in Eukaryotes
In the catabolism of a glucose molecule, Substrate level
2 ATP and 2 NADH+H+ molecules are Phosphorylation ETS (Oxidative Phosphorylation)
gained from glycolysis. The 2 NADH+H+ Processes ATP FADH2 +

Net Gain
NADH+H
from glycolysis are transferred from the
cytosol to the mitochondria and are subse- Glycolysis 2 — 2 x 2-3 6 ATP
quently utilized in the ETS with a gain of 4
ATP. During their transfer across the mito- Pyruvate - Acetyl CoA — — 2x3 6 ATP
chondrial membrane, some of their energy is
Krebs cycle 2 2x2 6x3 24 ATP
lost. Instead of each NADH+H+ yielding 3
ATP molecules, during this stage they only Total 4 ATP 4 ATP 28-30 ATP 36-38 ATP
produce 2 ATP molecules.
In total, 6 molecules of ATP are generat-
ed from glycolysis. Another 2 NADH+H+ are gained from the conversion of pyru-
vate to acetyl-CoA. They are also utilized in ETS and yield 6 ATP molecules. The
most efficient stage of glucose catabolism is the Kreb's cycle. It yields 6 molecules
of NADH+H+, 2 of FADH2 and 2 of ATP. In total 18 ATP molecules are generat-
ed from NADH+H+, 4 from FADH2 and 2 from ATP conversion. The total energy
production from glucose catabolism is listed in the table.
Efficiency of respiration:
When a glucose molecule is broken down into its subunits CO2 and H2O dur-
ing aerobic respiration, the energy stored within it from photosynthesis is released
completely .
Although the breakdown is total, it is impossible to achieve a high level of effi-
ciency. The catabolism of a single glucose molecule yields 36 ATP. By simple cal-
culation, it is possible to assess the quantity of energy transferred to ATP.
The synthesis of an ATP molecule from ADP+Pi requires 7300 cal of energy.
Thus theoretically, 262800 cal (36 x 7300) of energy is stored in ATP. This howev-
er is less than half that is available in the bonds of the molecule. Using a bomb
calorimeter it is possible to obtain 686000 cal of energy from the catabolism of
one glucose molecule. Thus the efficiency of aerobic respiration may be calculat-
Cellular respiration is
ed as follows:
remarkably efficient in
7.3 kcal/mole x 38 ATP/glucose/686 kcal/mole glucose = 40% energy conversion.
Complete oxidation of
The calculations show that 40% of the energy is captured in the form of ATP, glucose releases 686 kcal per
while 60% is lost as heat. The heat energy produced, however, is of great impor- mole. Formation of each ATP
tance to the body as it provides the heat necessary for the metabolism of the body requires at least 7.3 kcal/mole.
to work at the optimum temperature of 37°C. Efficiency of respiration is 7.3
kcal/mole x 38 ATP/glucose/686
kcal/mole glucose = 40%. The
other approximately 60% is lost
as heat.
155
electron transport system
READ ME (a closer look)
The majority of the energy conserved during catabolism reactions occurs near the end of the metabolic series of
reactions in the electron transport chain. The electron transport or respiratory chain gets its name from the fact
that electrons are transported to meet up with oxygen from respiration at the end of the chain. The overall elec-
tron chain transport reaction is:
2H+ + 2e– + 1/2 O2 ⎯⎯⎯⎯⎯→ H2O + Energy
Notice that 2 hydrogen ions, 2 electrons, and an oxygen molecule react to form as a product water with energy
released in an exothermic reaction. This relatively straightforward reaction actually requires eight or more steps.
The energy released is coupled with the formation of three ATP molecules per every use of the electron transport
chain. The oxidation of carbon-containing nutrients is coupled with reduction of cofactor molecules NAD+ and
FAD to produce NADH and FADH2. The electron transport chain oxidises (i.e. “burns”) the NADH and FADH2
cofactors, using molecular oxygen as the final electron acceptor. The energy released in this oxidation is captured
in the form of ATP. This is enough energy to drive the formation of several ATP molecules (DG0' = -31.5 kJ/mol).
On average, each NADH can produce 3 ATP molecules in the electron transport chain. The electrons from NADH
are not used to directly reduce molecular oxygen. Instead they are passed along a series of electron transport com-
plexes. These molecular complexes have reduction potentials greater than NADH and less than molecular oxygen.
Thus, they can accept electrons from NADH and ultimately donate to oxygen. The electron transport is sequen-
tial along these complexes, thus, each complex in the sequence has a slightly higher reduction potential than the
preceding complex. The electron transport chain includes molecular components with redox potentials interme-
diate between NAD+ and oxygen including:
Flavoproteins. Have FMN or FAD as a prosthetic group, and can participate in one- and two-electron transfers
Coenzyme Q (Ubiquinone). Can also participate in one- and two-electron transfers
Cytochromes. Contain a heme (iron) prosthetic group. The
iron can exist in either Fe2+ or Fe3+ oxidation states, and there-
fore can participate in one-electron transfers
Iron-sulfur proteins. Also involve iron(II) and (III) oxidation
states and one-electron transfers
Copper (protein bound). Copper can exist as Cu+ or Cu2+ and
can therefore participate in one-electron transfers
All of these functional groups are part of molecular complexes
that are membrane associated. There are four complexes in
the electron transport chain
Complex I: NADH-coenzyme Q reductase
CYTOLOGY
Complex II: Succinate-coenzyme Q reductase

Complex III: Coenzyme Q-cytochrome C reductase
Complex IV: Cytochrome C oxidase
156
Electrons from food
contain high levels of
free energy. It is not
released at once since it
would generate a lot of heat.
Instead, this energy is released
gradually using specialized elec-
tron carriers. Each occupies a
fixed position in the chain and
can only accept electrons with
the levels of free energy shown
in the diagram. The transfer of
energy from NAD to FP releases
12.2 kcal energy which is suffi-
cient to generate a molecule of
ATP at that level. All the steps
except for FP to B and C to A
generate ATP.
157
Catabolism of lipids
The ultimate source of energy in living things is carbohydrate, as these mole-
cules are simple in structure and can be used without major modifications to their
structure. Lipids and proteins can be utilized in energy production as secondary
sources. Proteins are only utilized in emergencies since their main role is in the
structural components of a cell. In contrast lipids are used readily by cells. The
potential energy of a lipid molecule is 9 kcal/g and is considerably higher than that
of a protein or carbohydrate molecule, 4 kcal/g. However, this concentrated ener-
gy can be extracted only after the cell has expended energy in breaking the mole-
cule down to a usable form.
A lipid molecule is composed of a glycerol molecule bonded to fatty acids.
Before its catabolism, it must be hydrolysed by a lipase into these units.
Fats must be digest-
ed to glycerol and Excess lipid is stored in the body in adipose tissue. In order to mobilize these
fatty acids. Glycerol resources, hormones such as glucagon and epinephrine stimulate cyclic AMP,
can be converted to glycer- which in turn stimulates a protein kinase to activate and phosphorylase lipase.
aldehyde phosphate, an After the action of lipase, the glycerol is converted to PGAL and can be transport-
intermediate of glycolysis. ed immediately into the glycolysis pathway to participate in the Krebs cycle.
The rich energy of fatty acids
The fatty acid component is too large to pass into the mitochondria. It is first
is accessed as fatty acids are
therefore degraded by the following steps:
split into two-carbon frag-
ments via beta oxidation. A fatty acid first reacts with the 2C compound acetyl-CoA in a reaction cat-
These molecules enter the alyzed by acetyl-Co A synthetase to form acyl-Co A. Depending on the length of
Krebs cycle as acetyl CoA. In the fatty acid chain and its number of carbon atoms, it is acted upon by a specif-
fact, a gram of fat will gener- ic form of synthetase enzyme. Thus a fatty acid composed of 16 carbons would
ate twice as much ATP as a be acted on 8 times by synthetase enzyme to form 8 molecules of acyl-CoA.
gram of carbohydrate via aer- During each reaction, a molecule of water is added as the target molecule is
obic respiration. cleaved. During the b-oxidation of a 16 C fatty acid, the following molecules are
synthesized:
7 NADH+H+, 7 FADH2
8 Acetyl-CoA which participate to the Krebs cycle and release 24

NADH+H+, 8 FADH2 and 8 ATP.
Totally 31 NADH+H+ and 15 FADH2 are produced from the breakdown of this
fatty acid molecule. This provides a total of 131 ATP molecules from one fatty acid
chain when NADH and FADH2 are used in the electron transfer chain.
In a lipid containing three fatty acid chains linked to glycerol, 3 X 131 ATP plus
19 ATP molecules from glycerol gives the huge total of 412 ATP molecules from
the catabolism of a single lipid molecule. This total either increases or decreases
according to the number of carbons in the fatty acid chain.
CYTOLOGY
158
159
Catabolism of proteins
In conditions where the human body has to cope with increased demands for
energy, the catabolism of first glucose and then lipid may be insufficient. In such
a case, the third and final energy fuel is protein.
Marathon runners in particular may find themselves depleted of energy
reserves at the end of a long race and consequently start to utilise their body pro-
tein. Obviously using body protein runs the risk of damaging vital organs and
processes, hence the reason why proteins are only used as a last resort.
If a protein is to be catabolized, first proteases break the peptide bonds at spe-
cific points on the amino acid chain. This produces a potential range of twenty
amino acids, each with its specific radical. For each amino acid, there is a differ-
ent process of catabolism.
As illustrated in the figure, 10 amino acids are degraded to acetyl coenzyme
A, 5 are degraded to a-ketoglutarate, 4 are degraded to succinyl coenzyme A and
2 each to oxaloacetate and fumarate. Once degraded, they can then enter the cit-
ric acid cycle and be used to form ATP.
Proteins must first

be digested to indi-
vidual amino acids.
Amino acids that will be
catabolized must have their
amino groups removed via
deamination. The nitroge-
nous waste is excreted as
ammonia, urea, or another
waste products. The carbon
skeletons are modified by
enzymes and enter as inter-
mediaries into glycolysis or
the Krebs cycle depending
on their structure.
CYTOLOGY
160
161
Anaerobic respiration (Fermentation)
Anaerobic respiration releases the energy of organic mol-
ecules in the cell without oxygen. Some lower organisms
such as bacteria or fungi live in habitats where oxygen is
either deficient or absent: for example, deep in the soil or at
the bottom of a swamp. These organisms have the ability to
produce ATP in the absence of oxygen, a process known as
anaerobic respiration or fermentation.
Anaerobic respiration occurs in the cytoplasm as a series
of enzyme-controlled stages known as glycolysis and fer-
mentation.
Glycolysis
As explained in aerobic respiration, glycolysis breaks
down glucose into two pyruvate molecules. At the end of
gycolysis 2 ATP and 2 NADH are released as byproduct.
Fermentation (Post-glycolytic reactions)

Two molecules of pyruvate are produced from one hex-
ose sugar at the end of glycolysis. Pyruvate is a key sub-
stance which can be catabolized under either anaerobic or
aerobic conditions.
After glycolysis, three different pathways are possible.
Alcoholic fermentation
Lactic acid fermentation
Pyruvate oxidation (in aerobic conditions)
These vary according to the type of organism.
Alcoholic fermentation
Alcoholic fermentation occurs in the cytoplasm of some
anaerobic bacteria, in fungi, algae and protozoa. In this path-
way, pyruvate is decarboxylated to acetaldehyde with the
release of CO2. The acetaldehyde is then reduced to ethanol
by the enzyme alcohol dehydrogenase which utilizes the
NADH synthesized at the stage of glycolysis.
CYTOLOGY
Alcoholic fermentation is used in the production of wine,

beer and other alcoholic beverages. Yeast cells are used in
baking to produce the carbon dioxide which causes dough
to rise, but alcohol evaporates during baking. As a result of
alcoholic fermentation, 2 ATP molecules and 2 molecules of
ethyl alcohol are produced.
162
Lactic acid fermentation
Pyruvate can also be catabolized by lactic acid under
anaerobic conditions. Some bacteria, water molds, algae
and protozoa use this pathway. Pyruvate is reduced to lactic
acid by the enzyme lactate dehydrogenase utilising the
NADH synthesized during the stage of glycolysis.
This pathway is also used in the muscles of mammals
when the demand for oxygen exceeds that of the supply. In
such cases, glucose can be catabolized by fermentation and
can produce energy without the need for oxygen.
The disadvantage of anaerobic respiration in muscle is
the accumulation of lactic acid in the intercellular matrix,
leading to muscle hardening or cramp. This condition is
reversible in a living organism when a sufficient amount of
oxygen becomes available. The accumulated lactic acid is
converted first to pyruvate, then acetyl-CoA and finally enters
the Krebs cycle. In a mammal that has just died, rigor mor-
tis occurs by the same mechanism.
During heavy exercise, muscle cells switch from aerobic
respiration to lactic acid fermentation to generate ATP when
O2 is scarce. The waste product, lactate, may cause muscle
fatigue, but ultimately it is converted back to pyruvate in the
liver.
But the end product of fermentation can be harmful for
organisms. High concentrations of lactic acid in the blood
stimulate the brain to make you feel tired, which is why eat-
ing yogurt, which contains lactic acid made by Lactobacillus
vulgaris, makes you sleepy.
Efficiency of fermentation
Fermentation is far less efficient as compared to aerobic
respiration since its substrate is incompletely catabolized. A
molecule of glucose releases 2840 kJ/mol energy if it is fully
oxidised into CO2 and H2O.
However, if it is broken down anaerobically, it releases

only 146 kJ/mol. The efficiency of fermentation is only
5.14% as compared to aerobic respiration.
Most of the energy from the substrate in anaerobic respi-
ration is stored in the large organic molecules lactate
(C3H6O3), ethanol (C2H5OH) and, rarely, acetaldehyde
(CH3CHO). Fermentation may not be an efficient method of
extracting energy for an organism, but it is of great impor-
tance in industry.
163
The industrial importance of fermentation
Fermentation is a fundamental process in both the food and chemical indus-
In alcohol fermenta- tries. Most of the foods that constitute our staple diet are obtained using a process
tion, pyruvate is
that has changed little for thousands of years. Many years ago, as human settle-
converted to ethanol
in two steps. First, pyruvate is ments developed, so cows, sheep and goats became domesticated. When the
converted to a two-carbon supply of dairy products from these animals exceeded the demand, a way was
compound, acetaldehyde, by needed to prevent these products from spoiling. It was discovered that exposing
the removal of CO2. Second, milk to certain bacteria caused changes in both its texture and flavour, and the new
acetaldehyde is reduced by product could be stored for longer periods. Yogurt, for example, is still made today
NADH to ethanol. Alcohol from cultures of Streptococcus thermophilus and Lactobacillus bulgaricus using
fermentation by yeast is used milk as a growth medium. Varieties of cheese are produced from lactic acid fer-
in brewing and winemaking.
mentation using different species of either Streptococcus or Lactobacillus in the
early stage of production. The coagulated milk known as curd is heated and
pressed. This procedure removes a watery component known as whey. The
cheese then ripens and the flavor is developed by the addition of other microor-
During lactic acid ganisms such as Penicillium and Brevibacterium, producing soft cheeses such as
fermentation, pyru-
Brie and Roquefort. Inoculation with varieties of Lactobacillus produces hard-tex-
vate is reduced
directly by NADH to form lac- tured cheeses such as Cheddar, Edam and Parmesan.
tate (ionised form of lactic Bread has formed a major part of the human diet for thousands of years.
acid). Lactic acid fermenta-
Leavened or risen bread is possible due to the growth of the yeast Saccharomyces
tion by some fungi and bac-
teria is used to make cheese cerevisiae on the starchy food medium flour. During its growth and division, it
and yogurt. Muscle cells releases enzymes that act on maltose and sucrose in the dough. Bubbles of CO2
switch from aerobic respira- are produced and become trapped in the mixture. This results in the bread rising.
tion to lactic acid fermenta-
tion to generate ATP when Wine and beer have formed part of the human diet in many cultures for thou-
CYTOLOGY
O2 is scarce. The waste prod- sands of years. In the production of wine, grapes are first pressed and the liquid
uct, lactate, may cause mus- produced sterilised. Any material likely to contaminate the wine is removed. Yeast
cle fatigue, but ultimately it is such as Saccharomyces cerevisiae is then added. The juice is then allowed to fer-
converted back to pyruvate in ment for approximately four days. The excess yeast is removed and the wine is left
the liver. to age so that the flavor and aroma, or bouquet, can develop.
164
READ ME THE REGULATiON OF RESPIRATION
Basic principles of supply and demand

regulate the metabolic economy.
If a cell has an excess of a certain
amino acid, it typically uses feedback
inhibition to prevent the diversion of
more intermediary molecules from
the Krebs cycle to the synthesis path-
way of that amino acid.
The rate of catabolism is also regulat-
ed, typically by the level of ATP in the
cell. If ATP levels drop, catabolism
speeds up to produce more ATP.
Control of catabolism is based mainly
on regulating the activity of enzymes
at strategic points in the catabolic
pathway.
One strategic point occurs in the third
step of glycolysis, catalyzed by phos-
phofructokinase. Allosteric regulation
of phosphofructokinase sets the pace
of respiration. This enzyme is inhibit-
ed by ATP and stimulated by AMP
(derived from ADP). It responds to
shifts in balance between production
and degradation of ATP:
ATP ⇔ ADP + Pi ⇔ AMP + Pi.
Thus, when ATP levels are high, inhi-
bition of this enzyme slows glycolysis.
When ATP levels drop and ADP and
AMP levels rise, the enzyme is active
again and glycolysis speeds up.
Citrate, the first product of the Krebs
cycle, is also an inhibitor of phospho-
fructokinase. This synchronises the
rate of glycolysis and the Krebs cycle.
Also, if intermediaries from the Krebs cycle are diverted to other uses (e. g. , amino acid synthesis), glycolysis
speeds up to replace these molecules. Metabolic balance is augmented by the control of other enzymes at other
key locations in glycolysis and the Krebs cycle. Cells are thrifty, expedient, and responsive in their metabolism.
165
CELLULAR RESPIRATION
The bodies of organisms contain many enzymes that are employed in harvesting energy from food. Most foods
contain a variety of carbohydrates, proteins, and fats, all rich in energy. The job of extracting energy from these food
molecules is cellular respiration. Cellular respiration is a kind of catabolic reaction by which the chemical bond
energy of organic molecules is released as ATP, the “fuel” used by all living things, and heat energy. The aim of cel-
lular respiration is to produce ATP. The energy in the bonds of these complex molecules may be extracted by two
methods, dependent on whether oxygen is available. Aerobic respiration utilizes oxygen, whereas anaerobic res-
piration is possible without it. Of the two methods, aerobic respiration is more efficient and generates a greater num-
ber of ATP molecules. Aerobic respiration is a kind of catabolism in which the energy of organic molecules is released
by using oxygen. In aerobic respiration, the energy stored within a glucose molecule is released step by step in a
series of reactions. If this energy were released at once, the heat suddenly generated would destroy the cell. The
stages of energy extraction from glucose are in order, as follows.
1. Glycolysis is a series of enzyme-catalyzed reactions by which a glucose molecule is converted to two mole-
cules of pyruvate. Glycolysis occurs in the cytoplasm and is common to both aerobic and anaerobic respiration. As
a result of gycolysis, 2 molecules of ATP and 2 of NADPH + H+ are produced.
2. Pyruvate oxidation. The pyruvic acid that is produced in glycolysis diffuses across the double membrane of a
mitochondrion and enters the mitochondrial matrix. When pyruvic acid enters the mitochondrial matrix, it reacts with
a molecule called coenzyme A to form acetyl coenzyme A. CO2, NADH, and H+ are produced in this reaction.
3. Krebs Cycle is a series of biochemical reactions by which the acetyl portion of acetyl-CoA is degraded to car-
bon dioxide and water with the release of metabolic energy, which is used to produce ATP. The Krebs cycle occurs in
the matrix of mitochondria, because the enzymes required for the reactions of the Krebs cycle are anchored on the
inner membrane and matrix of the mitochondria.
4. Electron Transport System (ETS) is a series of chemical reactions during which hydrogens or their electrons
are passed along from one acceptor molecule to another with the release of energy. In the electron transport chain,
the electrons move from molecule to molecule until they combine with oxygen and hydrogen ions to form water.
When a glucose molecule is broken down into its subunits CO2 and H2O during aerobic respiration, the energy
stored within it from photosynthesis is released completely . Although the breakdown is total, it is impossible to
achieve a high level of efficiency. The catabolism of a single glucose molecule yields 36-38 ATP. Calculations show
that 40% of the energy is captured in the form of ATP, while 60% is lost as heat.
Anaerobic respiration releases the energy of organic molecules without oxygen in the cell. Some lower organisms
such as bacteria or fungi live in habitats where oxygen is either deficient or absent: for example, deep in the soil or
at the bottom of a swamp. These organisms have the ability to produce ATP in the absence of oxygen, a process
known as anaerobic respiration, or fermentation. Anaerobic respiration occurs in the cytoplasm as a series of
enzyme-controlled stages known as glycolysis and fermentation.
Alcoholic fermentation occurs in the cytoplasm of some anaerobic bacteria, in fungi, algae and protozoa. In this
pathway, pyruvate is decarboxylated to acetaldehyde with the release of CO2. As a result of alcoholic fermentation,
CYTOLOGY
2 ATP molecules and 2 molecules ethyl alcohol are produced.

Lactic acid fermentation: Some bacteria, water molds, algae and protozoa use this pathway. Pyruvate is reduced
to lactic acid by the enzyme lactate dehydrogenase utilizing the NADH synthesized during the stage of glycolysis.
This pathway is also used in the muscles of mammals when the demand for oxygen exceeds that of the supply. In
such cases, glucose can be catabolized by fermentation and can produce energy without the need for oxygen.
166
EXPERIMENT: Investigation of the gas produced during respiration
Purpose of experiment: Materials a funnel

To determine the gas pro- 2 large conical flasks, 1 rubber tubing
small flask, 2 test tubes lime water
duced during respiration.
glass tubing and tube clips equipment for boiling peas
2 rubber bungs with two germinating peas
holes through them
Procedure:
Discussion:
Explain the purpose of boiling
one set of peas
Explain the differences in the
lime water in both tubes.
167
6. Explain the reactions of the postglycolytic phase.
Information Recall Questions
1. Explain the functions and basic events of respiration.

7. Make a list of different foods that involve fermenta-
tion in their production. Explain how fermentation is
involved in each case.
2. Explain why two molecules of ATP are consumed at

the beginning of glycolysis.
8. Explain the differences between ethyl alcohol and lac-

tic acid fermentation.
3. Compare the preparatory and payoff stages of glycol-

ysis.
9. Explain the events illustrated in the figure below.
4. Label the sites of ATP consumption and release on the

diagram below.
10. List the components of the Electron Transport System.
+
5. Label the sites of NADH+H release on the diagram
below.
11. List two examples of environments where you would
expect to find
i. aerobic organisms
ii. anaerobic organisms
Comment on the size and type of organisms that you
might find and give reasons. Make sure that you
include details on the energy efficiency of aerobic and
anaerobic respiration in your answer.
168
12. Explain the chemiosmotic theory.
Choose the correct alternative
1. I. Enzyme
II. CO2 consumption
III. ATP synthesis
IV. O2 release
Which of the above properties is/are shared by
fermentation, photosynthesis and aerobic respi-
13. Compare the energy efficiency of carbohydrate and ration?
lipid catabolism.
A) I-II B) I-III C) I-IV D) II-III E) III-IV
2. The concentration of glycogen, lactic acid and oxygen

continuously changes in the cells of a marathon run-
ner. Which of the following combinations
14. Account for the fact that if glucose is burned in a
describes these changes?
bomb calorimeter, considerably more energy is
obtained than when it is used in the mitochondria of Glycogen Oxygen Lactic acid
a cell. A) decrease increase decrease
B) decrease decrease increase
C) increase increase increase
D) decrease decrease decrease
E) increase decrease decrease
15. Explain the events of β-oxidation.
3. The steps of aerobic respiration are listed below.

Glycolysis
Krebs
ETS
Which of the following is not a common charac-
16. Explain the importance of oxygen for life. teristic of the steps above?
A) ATP synthesis
B) Coenzyme utilisation
C) Material consumption
D) Enzyme activity
E) Substrate level phosphorylation
17. Explain the following terms:

Oxidative phosphorylation
4. Which of the following does not move from the
Substrate level phosphorylation cytoplasm to the mitochondria during respira-
Electron acceptor tion?
Fermentation A) O2 B) 2H2 C) Glycerol
Electron Transport System D) ADP E) Phosphate
169
5. I. ATP synthesis 10. What is the name of the process in which pyru-
II. NAD reduction vate is converted to lactate?
III. FAD reduction A) fermentation
IV. Oxygen consumption B) photolysis
Which of the events listed above is performed in C) glycolysis
glycolysis, the Krebs cycle and ETS?
D) Krebs cycle
A) I and II B) I and III C) II and III
E) none of the above
D) II and IV E) III and IV
11. In glycolysis, ATP molecules are produced by ___.

6. The main function of cellular respiration is _____.
A) photosynthesis
A) breaking down toxic molecules B) photophosphorylation
B) making ATP C) substrate-level phosphorylation
C) making food D) cellular respiration
D) using light energy E) oxidative phosphorylation
E) consuming ATP
12. Which of these is not a product of glycolysis?

7. Which of the following describes glycolysis? A) pyruvate
A) It generates NADH. B) water
B) It produces CO2. C) NADH + H+
C) It produces a small amount of ATP. D) ATP
D) It splits glucose to form two molecules of pyruvate. E) FADH2
E) It uses oxygen.
13. Which of these enters the Krebs cycle?

8. A glucose molecule is completely broken down in
A) glucose
glycolysis and the Krebs cycle, but these two
processes yield only a few ATPs. Where is the B) NADH + H+
rest of the energy that the cell obtains from the C) acetyl CoA
glucose molecule? D) PGAL
A) in the malate E) pyruvate
B) in the oxygen
C) in the succinate molecule
D) in NADH and FADH2
14. In the Krebs cycle, ATP molecules are produced
E) in the carbon dioxide by _____.
A) photosynthesis
B) photophosphorylation
9. The net gain of ATP for each glucose molecule in C) substrate-level phosphorylation
alcoholic fermentation is_____. D) fermentation
A) 2 B) 4 C) 6 D) 8 E) 38 E) oxidative phosphorylation
170
15. Which of these is not a product of the Krebs 20. Which of the following are products of fermenta-
cycle? tion occurring in muscle cells?
A) acetyl CoA A) Pyruvate
B) ATP B) CO2, ethanol, NAD+, and ATP
C) NADH + H+ C) O2, ethanol, NADH, and ATP
D) FADH2 D) CO2, lactate, NAD+, and ATP
E) CO2 E) CO2, lactate, NADH, and ATP
16. How many NADH molecules are produced for 21. In lactic acid fermentation, _____ is reduced and
each glucose that enters the Krebs cycle? _____ is oxidized.
A) 0 A) lactate ... NADH
B) 2 B) NAD+ ... pyruvate
C) 3 C) pyruvate ... NADH
D) 6 D) lactate ... ethanol
E) 3 to 6 E) NADH ... lactate
17. In cellular respiration, most ATP molecules are 22. Which of the metabolic pathways listed below is
produced by _____. the only pathway found in all organisms?
A) Krebs cycle A) glycolysis

B) photophosphorylation B) aerobic respiration
C) pyruvate oxidation C) the Krebs cycle
D) glycolysis D) the photophosphorylation
E) ETS E) fermentation
18. Which of the following is the final electron accep-

tor of cellular respiration? 23. During respiration in a eukaryotic cell, reactions
of glycolysis occur in or on__________.
A) NADH
B) water A) the cytosol
C) oxygen B) the matrix of the mitochondrion
D) FADH2 C) the cristae of the mitochondrion
D) the stroma of the chloroplast
E) CO2
E) the grana of the chloroplast
19. During electron transport, energy from _____ is 24. Which of the following molecules, if any, is not a
used to pump hydrogen ions into the _____. reactant or product in glycolysis?
A) acetyl CoA ... intermembrane space A) ATP
B) NADH and FADH2 ... intermembrane space B) malate
C) NADH and FADH2 ... mitochondrial matrix C) NADH
D) NADH ... intermembrane space D) ADP
E) NADH ... mitochondrial matrix E) PGAL.
171
25. The overall efficiency of aerobic respiration is 30. The structure and function of a mitochondrion is
approximately _____. illustrated.
A) 0.5%
B) 2%
C) 40%
D) 94%
E) 100%
26. When protein molecules are used as fuel for

aerobic respiration, _____ are produced as
waste. Which of the following combinations is in the
A) ethanol and CO2 correct order ?
B) amino groups I II III IV V

C) fatty acids A) CO2 DNA ETS Krebs H2O
D) amino acids B) RNA ATP ETS H 2O Krebs
E) lactic acid molecules C) Krebs ATP ETS H 2O DNA
+
D) Ribosome ATP NADP+H H 2O CO2
+
E) CO2 NADPH+H H 2O ETS CO2
27. A gram of fat oxidized by respiration produces
approximately _____ as much ATP as a gram of
carbohydrate. 31. Samples were taken from different depths of a lake.
A) half Analysis of these samples showed that bacteria K, L
and M could survive at these depths.
B) twice
C) 4 times
D) 10 times
E) 100 times
28. Which of the following molecules is not involved

in either fermentation or aerobic respiration?
+
A) NADH+H B) ATP C) PGAL
D) CO2 E) FADH2 Taking this information into account, which of
the following combinations correctly describes
the oxygen requirements of these bacteria?
Aerobic Anaerobic Facultative
29. Which of the following molecules is the last elec-
tron acceptor in anaerobically respiring animal A) K L M
tissue? B) K M L
A) Lactic acid B) Amino acid C) L M K
C) Ethyl alcohol D) Acid aldehyde D) M K L
E) Phosphoglyceraldehyde E) M L K
172
Cytology
MASTER MOLECULES
THE SECRET OF LIFE
Classification
Animal
chapter 6
THE SECRET OF LIFE
There are many kinds of organic and inorganic molecules in the cells. They
have different structures and functions. In this chapter you will study the director
or master molecules which control all life activities in the cell. Commonly they are
Why was the alpha- called nucleic acids, and are divided into two types, DNA and RNA.
bet one of the first
things you learned Nucleic acids
when you started school?
Letters are a code that you Nucleic acids are the master molecules of cells since they play such vital roles
need to know before you in the continuation of all life processes. They have two main functions:
learn to read. regulation of all metabolic activities within the cell
A cell also uses a code that is
stored in its hereditary mate- maintenance of genetic continuity between generations.
CYTOLOGY
rial. The code is a chemical Nucleic acids were first discovered in the nucleus of leucocytes and sperm by
called deoxyribonucleic acid, the Swiss biochemist Friedrich Miesher in 1868. Miesher found an unusual mate-
or DNA. It contains informa- rial containing phosphorus in the nuclei of pus cells from used bandages. He
tion for an organism's growth
called this new substance nuclein. It was later given the name nucleic acid since,
and function.
at that time, this substance was found only in the nucleus.
174
Structure of nucleic acids
Both DNA and RNA are composed of a chain of nucleotides. Nucleotides are
the building blocks of nucleic acids. Each nucleotide molecule is composed of a
base, a pentose sugar and a phosphate group. (Figure 6. 1)
Nitrogenous Base: The base of a nucleotide is composed of a combination of

nitrogen, hydrogen, carbon, and oxygen atoms. Bases are categorised as
purines or pyrimidines according to the number of rings in their structure.
Pyrimidines are bases with a single ring. Three different forms exist in living
things: cytosine (C), thymine (T) and uracil (U). Purines are bases with double
rings. The two different forms are adenine (A) and guanine (G). (Figure 6. 2)
Figure-6.1: A Nucleotide
Sugar: Each nucleotide includes a 5-carbon, or pentose, sugar which may
be either in the form of deoxyribose or ribose. Each differs from the other
only in the presence or absence of an oxygen atom. Ribose participates
only in the structure of RNA while deoxyribose participates in the structure
of DNA. (Figure 6. 3)
Phosphate Group: The third molecule in the structure of a nucleotide is

phosphoric acid (H3PO4).
The pentose sugar forms the middle of the nucleotide. It is attached to the
purine or pyrimidine base by glycosidic linkage and to the phosphate group by an
ester bond. Each nucleotide is attached to the next by a phosphodiester bond, a
linkage between the pentose sugar of the first nucleotide and the phosphate group
of the next.
The types of nucleotides

They are classified as either DNA and RNA nucleotides not only because of
Figure-6.2: A purine base
their type of sugar, but according to their type of base.
1. Adenine deoxyribose mono phosphate

2. Guanine deoxyribose mono phosphate
3. Cytosine deoxyribose mono phosphate
4. Thymine deoxyribose mono phosphate
5. Adenine ribose mono phosphate
6. Guanine ribose mono phosphate
The secret of life

7. Cytosine ribose mono phosphate
8. Uracil ribose mono phosphate
Figure-6.3: A ribose sugar
175
DNA (Deoxyribonucleic Acid)
DNA is the master molecule which directs all metabolic activities of a cell by
the sequence of its nucleotides. It has the following functions:
Storage of genetic information
Provision of genetic continuity by self-replication
Regulation of cellular metabolic activity by the control of the synthesis of
all proteins and enzymes
The Distinctive Base Composition of DNA

The studies of Erwin Chargaff in 1940 provided the first comprehensive infor-
mation on the structure of DNA. He found that the ratio of the four different
nucleotide bases varies, however the numbers of some nucleotides have a close
relationship. He proposed the following rules based on his investigations.
The base composition of DNA differs from one species to another.
DNA samples obtained from different tissues of the same species have the
same base composition.
The base composition of DNA in an organism is unrelated to the age,
nutritional state or its environmental conditions.
The number of pyrimidines and purines in a molecule of DNA is equal,
since adenine (A) pairs with thymine (T), and guanine (G) pairs with cyto-
sine (C). Thus,
A+G = T+C A+G / T+C = 1
The Double Helix Model of Watson and Crick

The first clear model of the structure of DNA was proposed by an American
biologist James Watson and a British biophysicist Francis Crick in 1953. For this
achievement they received the Nobel Prize in 1962. Using X-ray crystallography
developed by Rosalind Franklin, they proved that the structure of DNA is com-
posed of two right-handed helical polynucleotide chains forming a double helix
around a single central axis. The bases form a ladder with each rung facing
inwards while the sugar-phosphate forms an external backbone or sides of the lad-
der. Free electrons on each base enable hydrogen bonds to be established
between each pair. These bonds are of great importance since they allow the dou-
ble helix to be unzipped and the inner nucleotides exposed.
CYTOLOGY
The positioning of each pair is not at random and there is a clear rule in the
association of nucleotides. For instance, adenine nucleotides of one chain or
strand can only bind to thymine nucleotides of the opposite strand. Moreover, gua-
nine nucleotides can only pair with neighbouring cytosine molecules of the oppo-
site strand. Cytosine associates with guanine by a triple bond, while adenine asso-
ciates with thymine by a double bond.
176
The number of bonds between each component of a pair is determined by the
chemical nature of nucleotides. As explained previously, DNA is composed of two
strands.
The first strand is termed the sense strand while the second is termed the
nonsense or complementary strand. Since nucleotide pairing is so specific, the
sequence of bases on one strand can be determined if the sequence of the other
strand is known.
The main points of the Watson-Crick model of DNA can be listed as follows
(Figure 6. 4):
DNA is a double-stranded helical structure
Each strand comprises a chain of nucleotide residues
A nucleotide is composed of a base, a sugar and a phosphate group
Figure-6.4: Watson and Crick
The nucleotides of a strand are linked by phosphodiester bonds
The pyrimidine bases of one strand pair with the purines of the other strand
by hydrogen bonds
The sequence of nucleotides on one strand can be identified by the
sequence of the other strand
The length of DNA
The Location of DNA in Cells varies according to
the number of
Cells are categorised as prokaryotic or eukaryotic. The single, circular DNA nucleotides it contains. The
chromosome of prokaryotic cells is located in a cytoplasmic region known as the average approximate weight
nucleoid. However, in eukaryotic cells, the DNA is in the form of compacted chro- of DNA of a microorganism
The secret of life

mosomes. It is particularly condensed in some regions of each chromosome is 10 daltons. That of a chro-
known chromomeres. Giant chromosomes are characterised by horizontal bands, mosome of human DNA is
or striations. Mitochondria and chloroplasts contain their own DNA within their approximately 3.8x1010 dal-
matrix and can synthesise their own protein. These DNA molecules differ physical- tons and its total length is
ly and chemically from chromosomal DNA in that they are less dense. approximately 92 cm.
177
DNA Replication
DNA provides a complete set of information for all activities of each cell of an
organism. When a cell divides, its DNA is copied and passed from one cell gener-
ation to the next generation. As we have explored before, DNA contains the “pro-
grammatic instructions” for cellular activities. When organisms produce offspring,
these instructions, in the form of DNA, are passed down.
DNA replication is the process by which DNA is duplicated, ordinarily a semi-

conservative process in which a double-helix gives rise to two double-helices, each
with an “old” strand and a newly synthesised strand.
At the first the two complementary DNA strands separate, then each strand
can be used as a template to build a new complementary strand, producing two
DNA molecules because each nucleotide can only pair with its complement, i.e.
adenine pairs with thymine, and cytosine pairs with guanine.
DNA replication is simple in principle, but the actual process requires some
complicated molecular maneuvers. The replication of a DNA molecule begins at
special sites, called origins of replication. Many enzymes are necessary to success-
fully replicate DNA. Let's now look at the process of DNA replication more close-
ly, starting at an origin of replication. The DNA opens up there to form a small
bubble. (Figure 6. 5)
1. DNA helicase: unwinds DNA in front of opening replication fork (otherwise

DNA would quickly tangle). Uses ATP, makes single-stranded cut, allows one
strand to swivel freely around the other.
2. DNA gyrase catalyses the formation of a negative supercoil that removes the
torsional strain introduced by opening the double helix.
3. The two strands would naturally tend to rewind, but single-stranded DNA
binding proteins bind to separated DNA strands, and prevent them from
base-pairing back together.
4. The synthesis of a new strand begins when an enzyme called primase

attaches and synthesises a short RNA strand that is complementary to one
of the DNA strands, because DNA polymerase-III cannot start growing a
chain from scratch.
DNA replication:
The process by 5. DNA polymerase-III then adds DNA nucleotides to the 3' end of the RNA primer.
which DNA is dupli- It continues to lengthen the new DNA strand by adding nucleotides complemen-
cated; ordinarily a semicon- tary to the template strand. DNA polymerase-I removes the RNA primer and
CYTOLOGY
servative process in which a then replaces this with DNA. Notice that DNA synthesis always proceeds in a 5'
double helix gives rise to two to 3' direction. The strand just made here is called the leading strand.
double helices, each with an
“old” strand and a newly syn- 6. The other new strand is called the lagging strand. Unlike the leading strand,
thesised strand. the lagging strand cannot be made continuously because DNA polymerase
can only add nucleotides at the 3' end. The replication fork moves in one
178
Figure-6.5: DNA replication
Before mitosis, the

direction, but DNA replication only goes in the 5' to 3' direction. This para- DNA of the chromo-
dox is resolved by the use of Okazaki fragments. These are short, discontin- somes replicates.
uous replication products that are produced off the lagging strand. The hydrogen bonds
between opposite bases
First, the enzyme primase removes the single-strand binding proteins, and break, and the double helix
makes an RNA primer to begin an Okazaki fragment. The enzyme DNA poly- unwinds. Each sugar phos-
merase then adds the complementary DNA nucleotides to synthesise the phate backbone and its sin-
rest of the fragment. The assembly process continues, as primase makes gle chain of bases forms a
new RNA primers and DNA polymerase adds DNA nucleotides to create template for a second chain.
more Okazaki fragments. The result, two identical dou-
ble helices both containing
The secret of life

one strand from the original
7. After the fragments are made, the DNA polymerase-I removes the RNA
DNA molecule, and one
primers and then replaces this with DNA. Next, the enzyme DNA ligase links
newly synthesised. This type
the Okazaki fragments to form the lagging strand. of replication is known as
semiconservative.
179
RNA (Ribonucleic Acid)
A type of nucleic acid consisting of nucleotide monomers with a ribose sugar
and the nitrogenous bases adenine (A), cytosine (C), guanine (G), and uracil (U).
RNA is usually single-stranded and it plays a role in protein synthesis and as the
genome of some viruses. Three types of RNA may be synthesised from DNA,
namely, m-RNA, t-RNA and r-RNA. All of them are structurally and functionally
different.
Figure-6.6: mRNA Messenger RNA (m-RNA)

M-RNA is synthesised from DNA by RNA polymerase enzyme. The RNA poly-
merase unzips the relevant part of the DNA molecule and transcription begins.
The complementary RNA molecule is synthesised according to base-pairing rules,
except that uracil is the complementary base to adenine.
After pairing has been completed, the RNA polymerase enzyme moves along
the molecule rezipping it. The synthesis of m-RNA ceases when RNA polymerase
reaches a signal for it to stop. This signal takes the form of three adjacent
nucleotides and is called a stop codon. After completion, the strand moves out of
the nucleus through the nuclear pores into the cytoplasm. During protein synthe-
sis, m-RNA is involved in the transmission of genetic information from DNA in the
nucleus to the ribosome in the cytoplasm. Once there, ribosomes bind to m-RNA
in order to assemble the sequence of amino acids coded by DNA. (Figure 6. 6)
Transfer RNA (t-RNA)

T-RNA is transcribed from DNA by the same method as m-RNA. The single
strand of nucleotides leaves the nucleus and enters the cytoplasm. Weak hydro-
gen-bonding between base pairs of the nucleotide string give it a clover leaf shape,
formed by three hairpin loops at right angles to each other. The ends of the
Figure-6.7: tRNA nucleotide form the site of attachment of an amino acid. This double-stranded
structure of t-RNA in the cytoplasm maintains its structure. As its name suggests,
t-RNA is involved in the transfer of free amino acids to the ribosomes where they
participate in protein structure. There are 45 types of t-RNA which code for 20
types of amino acids. One end of the t-RNA nucleotide strand forms an amino
acid-specific anticodon region. This region is made up of a specific order of three
nucleotide bases known as a triplet, or codon, and determines the type of amino
acid which will bind to t-RNA. A t-RNA molecule can only donate an amino acid
to a protein if the anticodon and codon are correctly paired. (Figure 6. 7)
Ribosomal RNA (r-RNA)

CYTOLOGY
R-RNA is the abundant type of RNA, which together with proteins, forms the
structure of ribosomes. Ribosomes coordinate the sequential coupling of tRNA
molecules to mRNA codons. This type of RNA is transcribed in the nucleus and
forms the structure of ribosomes, the sites of protein synthesis. The nucleotide
sequence of ribosomal RNA also enhances the attachment of t-RNA and m-RNA
Figure-6.8: rRNA to the ribosomes. In the absence of r-RNA, ribosome function ceases. (Figure 6. 8)
180
DNA RNA
ª double-stranded ª single-stranded
ª found in the nucleus ª found in the nucleus and cytoplasm
ª replicates itself by DNA polymerase ª synthesised from DNA by RNA polymerase
ª nucleotides are A, T, G, C ª nucleotides are A, U, G, C
ª contains the sugar deoxyribose ª contains the sugar ribose
ª functions to store information and to regulate meta- ª function is to transfer genetic information and to synthe-
bolic activity sise proteins
Table-6.1: Comparation of DNA and RNA
THE MESELSON-STAhl
READ ME EXPERiMENT
The semiconservative replication of DNA was proved in
1958 by Meselson and Stahl in an experiment using nitro-
gen isotopes. Nitrogen exists in two forms, the isotope N15
and its normal form, N14.
E. coli bacteria were grown in a medium containing N15.
The bacteria used the isotope to synthesise nucleotide
bases which were then used in DNA replication.
Subsequently new strands of DNA were produced con-
sisting purely of N15-containing nucleotides. The first gen-
eration of bacteria grown on the medium contained
hybrid DNA (N14N15), namely one strand of each type.
The second generation, however, contained bacteria
containing only either heavy DNA (N15N15) or hybrid
DNA (N14 N15). When a suspension of the bacteria were
centrifuged, Meselson and Stahl observed that the heavy
DNA precipitated out first, then the hybrid DNA and final-
ly the light DNA (N14N14).
A reverse form of their experiment is possible if E. coli
containing heavy DNA (N15N15) are grown in a normal
(N14) nitrogen-containing medium. The initial colony
contains heavy DNA, the first generation contains the
hybrid (N14N15) while the second generation contains equal proportions of light (N14N14) DNA and hybrid DNA.
The secret of life

If a suspension of all generations is centrifuged, the initial colony forms a band at the bottom of the tube, the first
or hybrid generation collects in the middle of the tube, and the second generation containing light DNA forms a
band at the top. Observation of these DNA bands is possible since N15 is a radioactive isotope. Meselson and
Stahl’s experiment and adaptations of it prove conclusively that DNA replicates semiconservatively since a hybrid
DNA (N14N15) is obtained in the first generation.
181
Chromatin and chromosome
From the simplest virus to the most complex human, every organism con-
tains a massive amount of information in the form of DNA. The DNA is organised
into informational units called genes that ultimately control all aspects of the life
of the organism. A eukaryotic nucleus contains multiple DNA molecules, each of
which is packaged with histone and nonhistone proteins and assembled into a
structure called a chromosome. This organisation is essential to the highly organ-
ised processes by which DNA is distributed during cell division.
Chromosomes are made up of chromatin, a complex of DNA and proteins
that makes up a eukaryotic chromosome. When the cell is not dividing, chromatin
exists as a mass of very long, thin fibres that are not visible with a light microscope.
At the time of cell division, the chromatin fibres condense and the chromosomes
become visible as distinct structures
CYTOLOGY
Chromatin arranges itself into pieces known as nucleosomes. Each nucleo-

some is composed of approximately 200 base pairs of DNA and two sets of his-
tone proteins (2 H2A, 2 H2B, 2 H3 and 2 H4). The double strand of DNA is coiled
around the core of the nucleosome, as shown, like cotton thread on a spool. The
formation of nucleosomes makes possible a 6-fold reduction in the length of DNA.
182
The nucleosomes themselves form coils to form a structure known as a sole-
noid. The formation of this structure makes a further six- to seven-fold decrease
in length possible. H1 proteins are active in the combination or attraction of nucle-
osomes to form a solenoid. By the formation of many of these structures, a 105
cm molecule of DNA is shortened 40-fold to fit into a cell nucleus approximately
5 to 10 nm in diameter. The condensed form of this structure is termed a chro-
mosome.
Properties of Chromosomes
Chromosomes vary in their reaction to a specific stain such as acetic orcein.
Some regions stain darkly and are referred to as heterochromatic regions. The het-
erochromatic regions consist of introns, inactive genes composed of DNA and RNA.
The slightly stained or unstained regions of chromosomes are known as euchromat-
ic regions. They consist of exons, areas in between genes, and histone proteins.
They contain the code for all metabolic activities of the cell.
A normal chromosome contains a special node known as a centromere, locat-
ed in the area of the chromosome known as the primary constriction. It is the last
structure to replicate before cell division and is connected to the spindle fibres dur-
ing metaphase and anaphase. It also facilitates the separation of chromosomes into
chromatids during metaphase. Any chromosome lacking centromeres is eliminated
from successive divisions since it can not participate in cell division. (Figure 6.10)
Chromosomes are categorised according to the position of their centromere.
Metacentric Chromosomes: The centromere is located at the mid-point
and each chromosome arm is of equal length.
Submetacentric Chromosomes: The arms of submetacentric chromo-
Figure-6.9: Nucleosome and histone proteins
somes are unequal.
Telocentric Chromosomes: The centromere is located at the tip of one
end of the chromosome.
Acrocentric Chromosomes: The centromere is located in the region of
the chromosome tip but a short distance from the very end.
The secret of life

Figure-6.10: Before mitotic division, the DNA
of each chromosome coils itself into specific
shapes. (Left) A metacentric chromatid
(Middle) A submetacentric chromatid (Right)
An acrocentric chromatid. Notice the satellite
at the end of each long arm, marking the
region of repeated nucleotide sequences.
183
Cell Karyotype
Diploid Chromosomes (2n): Diploid cells con-
tain two sets of chromosomes and are abbreviat-
ed as 2n.
Homologous Chromosomes: A diploid cell con-
tains two sets of chromosomes. These chromo-
somes are termed homologous to each other
since a particular character is controlled by two
genes located at the same position on both.
These genes are known as alleles. One homolo-
gous chromosome is inherited from the mother
while the other is inherited from the father. Each is
genetically different but actively controls the same
characteristics.
Haploid Chromosomes (n): Some cells contain
only a single set of chromosomes.
Sister Chromosomes: During metaphase, chro-
mosomes arrange themselves into homologous
or sister chromosomes. Their separation is the
main event in mitotic cell division.
Human Karyotype
Figure-6.11: A diagrammatic view of a normal female human karyotype A diploid human cell contains 46 chromosomes,
of 23 unique chromosomes.
namely 23 pairs. Of these, 44 form 22 pairs and are auto-
somic. The remaining two are known as sex or gonoso-
mal chromosomes. (Figure 6. 11)
Female cells are identified by their pair of X sex chro-
mosomes, while males are identified by their single short
Y sex chromosome and single X chromosome.
The generative cells of a female produce a haploid
ovum symbolised as 22+X. Those of a male produce
haploid sperm symbolised as 22+X and 22+Y.
Both types of haploid cells are termed gametes and
are responsible for the variation of traits in an offspring as
compared with its parents.
Thus an ovum fertilised by a male gamete produces a
genetically different offspring. The sex of the offspring is
CYTOLOGY
determined by the presence or absence of the Y chromo-

some.
Figure-6.12: The replicated form of chromosome
184
The cell cycle
It is an ordered sequence of events in the life of a dividing eukaryotic cell, from
its origin in the division of a parent cell until its own division into two. In cells capa-
ble of dividing, the cell cycle is the period from the beginning of one division to
the beginning of the next division. The time to complete one cycle is the gener-
ation time. The generation time can vary in the cell, but in actively growing plant
and animal cells, it takes about 8 to 20 hours. It consists of two main stages, inter-
phase and mitosis (or meiosis). (Figure 6. 13)
Figure-6.13: The cell cycle
Why cells divide

All cells have a self-imposed limit on their size. When this limit is exceeded, the
cell divides. The point at which the cell divides is determined by the ratio of cell
surface to its volume. If the cell is considered as a box, the volume / surface ratio
can be calculated by the relationship r3/r2 . Thus an increase in surface area of the
square of this figure results in a three-fold increase in volume. As the cell increas-
es in size, the rate of gas exchange, food uptake, waste removal and transport in
the cytoplasm decelerates. Finally a point is reached when the plasma membrane
of a mature cell is insufficient to perform all the vital life functions. This triggers
division, increasing the available surface area for absorption and separating the
original cytoplasm into two, thereby reducing its volume.
Cell division is also triggered when the amount of nuclear activity in a mature
cell decreases due to an increase in the volume of cytoplasm. Failure to divide
results in cell death. The surface-to-volume ratio of cells is an important factor in
cell division, but is not the only factor. The command for cell division is given by
the nucleus and is initiated by the replication of its DNA. Thus, once the signal is
given, division occurs irrespective of the volume of cytoplasm in the cell.
Additional Factors Affecting Cell Division

Environmental Factors: The cells of multicellular organisms are suscepti-
ble to touch and divide immediately if stimulated in this way. Cell division is funda-
Intracellular Calcium Concentration: Some cells expel calcium ions into mental to the repro-
their environment before cell division. ductive process.
Fertilisation results in the for-
Hormones: The plant hormone cytokinin stimulates mitotic cell division in mation of a zygote, the first
roots, stems and leaves. In animals, growth and cell division is controlled diploid cell of a multicellular
by growth hormone, insulin and epidermal hormones. Additionally, animal organism. Subsequent divi-
cells possess a growth inhibitor known as chalones. sions produce approximately
cAMP and cGMP: cGMP stimulates cell division in a culture, while it is 1013 cells in a fully grown
The secret of life

inhibited by cAMP. adult human. Cell division and
differentiation form the
organs and systems of the
body, including the reproduc-
tive glands.
185
Mitosis
Recall that all cells are formed by the division of pre-
existing cells. When a cell divides, the information con-
tained in the DNA must first be exactly duplicated and the
copies then transmitted to each daughter cell through a
complex series of processes. Most cell divisions in the
body cells of eukaryotes involve a process called mitosis,
which is a kind of cell division in which a parent cell is
divided into two daughter cells.
The genetic make-up of both parent and daughter
cells are identical. A parent human body cell, for instance,
has the same number of chromosomes as both its daugh-
ter cells. The whole process of mitotic cell division is com-
plete in approximately an hour, and the number of chro-
mosomes remains fixed in all cells. (Figure-6. 14-16)
Figure-6.14.: Cell cycle and mitosis
1. Interphase
The cell is carrying out its normal life activities. The chromosomes become
duplicated.
G1 Phase: The length of this phase varies from a few minutes, hours or days
to a few weeks, according to the type of cell. In the G1 phase, the protein required
for cell division, ATP and other cell structures are synthesised. Spindle fibres are
formed in this stage (Figure-6. 10).
S Phase: Following the G1 phase, it occurs within 6 hours in normal cells.
During the S phase, chromosomal DNA is replicated and identical copies of each
of its two halves, or chromatids, are assembled. For instance, a diploid cell con-
taining two sets of eight chromosomes, or 16 chromatids (2n: 16) replicates dur-
ing the S phase to produce a total of 32 chromatids. Since the S phase initiates
division, a cell can not divide without passing through this phase. (Figure-6. 15)
G2 Phase: It follows the S phase, and is completed within 4-5 hours. The
replicated DNA condenses, shortens and is visible if stained.
Nerve and muscle cells are incapable of dividing and remain in a phase
Figure-6.15: Interphase and mitosis known as G0.
2. Karyokinesis
Karyokinesis occurs in four distinct phases; (Figure-6. 11)
prophase
CYTOLOGY
Since mitotic cell

division produces a metaphase
pair of genetically
identical cells, all traits from anaphase
the parent cell are transferred telophase
to each daughter cell.
186
Prophase
In early prophase, the nuclear envelope and nucleolus begin to disappear.
Long threadlike bodies of chromatin begin to shorten and condense as visible.
Toward the end of prophase, chromosomes continue to shorten and thicken.
Spindles form between the centrioles, which have moved to the poles of the cell.
Metaphase
The formation of spindle fibres is complete by the beginning of metaphase.
Spindle fibres attach to the kinetochores of the chromosomes. Chromosomes
line up along the equatorial plane of the cell.
The metaphase chromosomes orient themselves on the equatorial plate and
are clearly visible with a stain. Each metaphase chromosome is composed of two
sister chromatids attached to the spindle fibres of opposite poles. The chro-
matids are now ready to separate.
Anaphase
The unique feature of anaphase is chromatid separation. Chromatids sepa-
rate at their centromeres, and one group of chromosomes moves toward each
pole. The microtubules of the spindle shorten considerably, pulling the chromo-
somes towards the poles.
Telophase
The events of telophase are almost the reverse of those of prophase. This
phase begins as chromosome movement ceases. A new nuclear membrane is
formed at each pole which surrounds the daughter chromosomes. Each chro-
mosome begins to uncoil, becoming less condensed. Chromatin fibres are
formed and metabolic activities are initiated.
Finally, a nucleolus appears within each nucleus. When karyokinesis or divi-
sion of nuclear material is complete, the result is two identical nuclei.
Cytokinesis The secret of life

Cytokinesis is the division of cytoplasm which follows nuclear division or
telophase. Cytokinesis differs in plant and animal cells. Figure-6.16.: Mitosis in plant and animal cells
187
Cytokinesis in animal and plant cells
The animal cell cytoplasm is subdivided into two by a furrow
that forms at the equatorial plate.
In plant cells however, this is impossible as the rigid cell wall is
too rigid. Instead, the cytoplasm is separated into two by the for-
mation of a cell plate at the equator of the cell.
Vesicles produced by the Golgi apparatus accumulate at the
equatorial plate and form a barrier between both sides, separating
the cytoplasm. (Figure-6. 17)
CYTOLOGY
Figure-6.17.: Animal and plant cells differ in the events of cytokinesis. Notice the for-
mation of the cell plate in plant cells.
188
Meiosis
Meiosis is a kind of cell division in which the chromosome number is reduced
by half. As you know, most multicellular organisms reproduce sexually. In sexual
reproduction, each parent produces a specific type of sex cell, or gamete, known
as a sperm or an egg. These fuse to form a zygote, the first cell of the new off-
spring. In higher plants and animals, the gametes are the eggs and sperm. Each
gamete contains only half the number of parental chromosomes, thereby prevent-
ing the zygotes from having twice as many chromosomes as the parents. For this
reason, sexual life cycles require a mechanism to reduce the chromosome num-
ber. Meiosis is a special type of cell division which reduces the chromosome num-
ber by half. This reduction division ensures a constant number of chromosomes
in a species from one generation to the next. Meiosis produces haploid cells with Figure-6.18.: Cell at interphase
unique gene combinations. (Figure-6. 18)
The steps of meiosis
Meiosis–I
During meiosis-I, each of the double set of chromosomes is replicated to pro-
duce a complete copy of every gene in the nucleus. These sets are passed on to
the two daughter cells.
Prophase-I
During prophase-1 the members of homologous pairs of chromosomes under-
go synapsis and crossing over, during which segments of DNA strands are
exchanged between homologous (nonsister) chromatids. (Figure 6. 19-20)
Prophase I begins with condensation of the chromosomes. Homologous chro-
mosomes, each made up of two sister chromatids, come together in pairs. This
pairing is called synapsis. Each chromosome pair is called a tetrad, a complex of
four chromatids. Chromatids of homologous chromosomes cross over at chias-
mata.
Figure-6.19.: Crossing over
The secret of life
189
Crossing over is the exchange of genetic material between nonsister chro-
matids during synapsis of meiosis I. After crossing over, the centrosomes move
away from each other, and spindle microtubules form between them. The nuclear
envelope and nucleoli disappear. Finally, spindle microtubules capture the kineto-
chores that form on the chromosomes, and the chromosomes begin to move to
the cell plate.
Metaphase I
Tetrads line up on the equatorial plane of the cell. Tetrads are held together at
chiasmata. The centromere of each chromosome attaches itself to a separate
spindle fibre extending from one of the poles of the cell (Figure-6. 21).
Figure-6.20.: Prophase-I
Anaphase I
In anaphase I, the homologous chromosomes separate and are pulled toward
opposite poles. Note that sister chromatids remain attached at their centromeres.
(Figure-6. 22).
Telophase I
In telophase I, movement of homologous chromosomes continues until there
is a haploid set at each pole. Each chromosome consists of linked sister chro-
matids. Cytokinesis occurs simultaneously. (Figure-6. 23).
Interkinesis
Otherwise known as meiotic interphase, the daughter cells prepare for a sec-
Figure-6.21.: Metaphase-1
ond division.
No replication of DNA occurs so the cell passes directly from the G1 to the G2
phase (Figure-6. 24).
CYTOLOGY
Figure-6.22.: Anaphase-1 Figure-6.23.: Telophase-1 Figure-6.24.: Interkinesis
190
2. Meiosis–II
Meiosis II is very similar to mitosis. During prophase II a spindle apparatus
forms, attaches to kinetochores of each sister chromatids, and moves them
around.
Prophase II
During second prophase, the chromosomes continue to coil and thicken. By
the end of this short phase, the chromosomes are once more fully visible. (Figure-
6. 25).
Metaphase II
A new metaphase plate forms in the middle of each daughter cell and the two
chromosome sets align themselves centrally on it. (Figure-6. 26).
Anaphase II
The centromere of each chromosome divides, giving each of the two sister
chromatids of each chromosome its own centromere. Each attaches itself to a
spindle extending from one of the poles.
The centromeres are pulled apart, effectively splitting the chromosome into
two complete sets of genes. (Figure-6. 27).
Telophase II
The nuclear membrane reforms and is followed by cytokinesis to give a total of
four cells from one parent cell. The ploidy of the cells has been reduced from two
to one and a unique assortment of genetic information is now present in each full Figure-6.28.: Telophase-2
set. At least one of these haploid cells is now ready to fertilise or be fertilised
(Figure-6. 28).
The secret of life
Figure-6.25.: Prophase-2 Figure-6.26.: Metaphase-2 Figure-6.27.: Anaphase-2
191
CYTOLOGY
Figure-6.29.: Meiotic division is a two stage process. Replication and crossing over produce two daughter cells with a unique diploid genotype.
These cells then divide once more to produce a total of four haploid cells from the original parent cell.
192
THE SUMMARY OF MITOSIS AND MEIOSIS
EVENT MITOSIS MEIOSIS
DNA replication Occurs during interphase Occurs during interphase
Synapsis and crossing over Does NOT occur It occurs during prophase-I
Number of daughter cells Two Four
Diploid (2N) and genetically identical Haploid (N) and genetically nonidenti-
Genetic composition
to the parent cell cal to the parent cell
Growth and development, tissue Reproduction, produce gametes,
Role in the animal body
repair increases genetic variability
Number of divisions One Two, meiosis-I and meiosis-II
READ ME cracking the genome
The Human Genome Project is a worldwide research effort with the goal of analysing the structure of human DNA
and determining the location of the estimated 30,000 human genes. In addition to this effort, the DNA of a set of
model organisms will be studied to provide the comparative information necessary for understanding the func-
tion of the human genome.
The information generated by the human genome project is expected to be the source book for biomedical sci-
ence in the 21st century and will be of immense benefit to the field of medicine. It will help us to understand and
eventually treat many of the more than 4000 genetic diseases that afflict mankind, as well as the many multifacto-
rial diseases in which genetic predisposition plays an important role.
Five year goals have been identified for the following areas which together encompass the human genome proj-
ect:
Mapping and Sequencing the Human Genome
Mapping and Sequencing the Genomes of Model
Organisms
Data Collection and Distribution
Ethical, Legal, and Social Considerations
Research Training
The secret of life

Technology Development
Technology Transfer
193
Protein synthesis
The information content of DNA, the genetic material, is
T A
in the form of specific sequences of nucleotides along the
Alanine
Codon 7
G C DNA strands. But how is this information related to an
organism’s inherited traits? Put another way, what does a
C G
gene actually say? And how is its message translated by cells
into a specific trait, such as blood type A, blue eyes, brown
T A
hair, and etc.
Alanine
Codon 6
G C
The gene is the fundamental unit of hereditary. That is, a
C G
gene determines a particular trait. At the molecular level, a
gene is a particular segment of DNA molecule that codes for
G C a cellular product, usually a polypeptide. In the cells, DNA
contain the information needed to make all of the proteins
Glycine
Codon 5
C G
that the cells use. Eye colour, hair color, and other such traits
C G
are visible because of protein synthesis. At the same time
other aspects of body structure and function more difficult
G C to observe directly are also under the control of genes.
A U
Isoleucine The messages in an organism's genes control everything
Codon 4
about it by governing its production of protein.

T A
DNA does not control protein synthesis directly. It uses
G C RNA. The flow of genetic information from DNA to RNA to
protein is called central dogma.
G C
RNA is a nucleic acid made up of a single chain of
Serine
Codon 3
A U nucleotides (differs from DNA by having ribose sugar and

uracil base).
A U
Recall that there are 3 types of RNA:

G C
mRNA carries the information from DNA to ribosome.

Codon 2
Glycine
C G
tRNA carries amino acid to the ribosome during protein
C G synthesis. They are found in the cytoplasm of cells.
DNA coding strand
Messenger RNA
C G
rRNA participates in the structure of ribosome.
Methionine
Transcription and translation are the two main processes

Codon 1
A U
linking gene to protein.
T A Transcription: The passing of genetic information from
DNA to RNA
DNA Double Helix Transcription Translation
Translation: The process of translating a message from
one language (nucleic acid language--sequence of
nucleotides) to another language (protein language--
CYTOLOGY
sequence of amino acids)
194
The genetic code Each of the amino
In the genetic code, nucleotide triplets specify amino acids. There are only 4 acids in the body is
nucleotides in DNA to specify 20 amino acids. So the genetic code can not be a coded for by a
language like Chinese, where each written symbol corresponds to a single word. sequence of three bases
If each nucleotide base were translated into an amino acid, only 4 of the 20 amino known as a codon. The table
acid could be specified. Would a language with two-letter code words suffice? The shows the codon sequences
base sequence AG, for example, could code one amino acid, and GT code anoth- for all 64 amino acids in the
er. Since there are 4-bases, this would give us 16 (that is 42) possible arrange- body by using the arrows as
ments--still not enough to code for all amino acids. shown above. For example
the base sequence for serine
The genetic instructions for a polypeptide chain are written in the DNA as a is UCA The sequence for
series of 3-nucleotide words, a triplet code (43 = 64 possible codes, enough to valine is GUC Notice that
code for all amino acids). For example, the base triplet AGT codes for serine. The amino acids such as leucine
mRNA base triplets are called codons. For example, UGG is the codon for the and arginine are coded for by
amino acid tryptophan. (Figure-6.30). six different base sequences.
The secret of life
Figure-6.30: The genetic code
195
The gene is the fun- Steps of protein synthesis
damental unit of The first stage in the process of protein synthesis is the transcription or copy-
hereditary; that is, a ing of the gene coding only for the molecule concerned onto a length of m-RNA.
gene determines a particular Transcription is initiated by the uncoiling of DNA by RNA polymerase. The
trait. At the molecular level, a nucleotide sequence of the sense strand determines the type of nucleotides that
gene is a particular segment form the RNA strand.
of DNA molecule that codes
for a cellular product, usually This means that the code of RNA is given by the sense strand of DNA. The
a polypeptide. In the cells, nucleotide sequence of m-RNA is identical to the antisense strand, also called the
DNA contains the information complementary strand, only differing in thymine-urasil substitution. Every three
needed to make all of the pro- nucleotides in the m-RNA is termed a codon. The number of codons in the m-
teins that the cells use. RNA is the same as the amino acid which is going to be used.
The m-RNA then moves to the cytoplasm and is translated to protein by the
activities of ribosomes and t-RNA. It forms a complex with an amino acid and then
transports it to the ribosome, translating codes of m-RNA. The amino acid on t-
RNA binds to the polypeptide sequence of the codon of m-RNA and anticodon of
t-RNA pairs. The free t-RNA leaves the ribosome and combines with a new amino
acid. t-RNA can transfer only one type of amino acid and can be reused after it
does so. The polypeptide sequence lengthens as amino acids transferred by t-RNA
Figure-6.31: The genetic code are bound to it (Figure, next page).
CYTOLOGY
196
197
The secret of life
READ ME gene regulation
Gene Regulation in Prokaryotes

Gene regulation in prokaryotes primarily involves control of transcription. Cells control
metabolism by regulating enzyme activity or by regulating enzyme synthesis through
activation or inactivating genes. In bacteria, coordinately regulated genes are often clus-
tered into operons. In 1965, a Nobel Prize was awarded to 3 biochemists: F. Jacob, J.
Monod, and A. Lwoff. They explained how genes control enzymes.
Operons are the units of gene expression in prokaryotes, which consist of 3-parts. They
are promoter, operator and structural genes. Regulator gene is outside of the operon.
The operator is the on-off switch of an operon.
Regulator gene: A gene that codes for a protein (repressor), which controls the expres-
sion of another gene. This gene codes for the production of a protein that can bind to
the operator. When this repressor binds to an operator, it prevents RNA polymerase
from binding to the promoter region of the operon. So the repressor prevents the
expression of structural genes.
Repressor is the protein coded by regulatory gene. Repressor can bind to the operator.
Promoter is the part of the operon where RNA polymerase binds to begin transcription
of the structural genes. The structural gene and operon all share a single promoter site.
When RNA polymerase binds to this site, it transcripts all of the structural genes onto
one mRNA strand, which may go on to be translated into the individual proteins
(enzymes).
Operator is the part of DNA that controls expression of structural genes. It acts as a con-
trol switch on or off by allowing or preventing RNA polymerase enzyme on the promot-
er.
Structural genes are the part of DNA that code synthesis of a group of enzymes that
are involved in the same function (for example the digestion of lactose).
Two type of operons:
1. The lactose-operon (Inducible system)
2. The tryptophan operon (Repressible system)
The Lactose-operon (Inducible system)
The lactose operon is activated by the presence of lactose. It controls the produc-
tion of enzymes, which digest lactose. It is regulated by synthesis of inducible enzyme.
CYTOLOGY
Lactose (allolactose, an isomer of lactose) is an inducer. An inducible operon is normal-

ly turned off because the repressor is normally bound to the operator. The presence of
substrate (lactose) inactivates the repressor protein (lactose binds repressor and inacti-
vates). As a result, the repressor protein cannot bind to the operator, and the structural
genes are transcribed.
198
199
The secret of life
The tryptophan operon (Repressible system)
The tryptophan operon is activated by the absence of tryptophan. The tryptophan operon
includes 5 structural genes that code for the 5 enzymes needed to produce tryptophan amino acid.
The tryptophan operon is regulated by synthesis of repressible enzymes. A repressible system is
normally turned on.
The repressor protein is synthesized in an inactive form that can not bind to the operator. The
presence of end product (that is tryptophan) of biosynthesis binds to the inactive repressor and acti-
vates it. As a result, RNA polymerase can no longer bind to the promoter, and transcription of the
genes cannot occur.
CYTOLOGY
200
Gene Regulation in Eukaryotes
A typical eukaryotic cell, such as a human liver cell, contains more than
1000 times the amount of DNA found in E. coli. So gene regulation mecha-
nism is more complex than in prokaryotes.
Their DNA is in the form of chromosomes, which affects regulation. The
signal which has first effect can be a hormone (rennin, thyroxin, adrenaline
etc.) or a neurotransmitter (acetylcholine, dopamine, serotonin etc). Gene
regulation in eukaryotes occurs at the level of the following steps.
1. Transcription: by turning genes ON and OFF. Histones play an
essential role.
2. mRNA processing: gene regulation can occur as a result of mRNA
processing in which introns (noncoding segment) are removed and
exons (coding segment) are bound together.
3. Translation: eukaryotes also regulate gene expression at the level of
translation by regulating the stability of mRNA. When mRNA is more
stable, more polypeptides can be formed per mRNA molecule.
4. Post-translational processing: gene regulation can occur after pro-
teins have been synthesized and feed back inhibition.
A BIOLOGICAL IDENTITY CARD FOR

READ ME EVERYONE
The DNA stored in the somatic cells in human beings contains approximately 30,000 genes for an equal number
of characteristics. In France at the end of 1994, researchers finally succeeded in constructing a map or karyotype
of these genes, so revealing the genetic structure of human beings. This map provides the means of identifying
serious hereditary diseases caused by mutations at the gene level. Genes responsible for a disease or disorder can
be pinpointed and the DNA of members of fami-
lies at risk scanned for certain sequences. The
applications of the knowledge that DNA mapping
provides can be used to the advantage of individ-
uals. Some of us would prefer to know if we are
at risk from a disorder or disease such as heart
infarctus or cancer so that we can change our
lifestyle accordingly. On the other hand, those in
high risk groups can expect to find great difficul-
ties in finding a job and taking out health or life
The secret of life

insurance if their karyotype becomes public
knowledge. For these reasons, they would obvi-
ously prefer to keep their health status secret. Any
plans to use the human karyotype as a form of
identity card are likely to be opposed.
201
THE SECRET OF LIFE
Nucleic acids are the master molecules of cells since they play such vital roles in the continuation of all life
processes. Both DNA and RNA are composed of a chain of nucleotides.
Nucleotides are the building blocks of nucleic acids. Each nucleotide molecule is composed of a base, a pentose
sugar and a phosphate group.
DNA is the master molecule which directs all metabolic activities of a cell by the sequence of its nucleotides. Cells
are categorized as prokaryotic or eukaryotic. The single circular DNA chromosome of prokaryotic cells is located in
a cytoplasmic region known as the nucleoid.
The structure of DNA is composed of two right-handed helical polynucleotide chains forming a double helix
around a single central axis. The bases form a ladder with each rung facing inwards while the sugar-phosphate forms
an external backbone or sides of the ladder. Free electrons on each base enable hydrogen bonds to be established
between each pair. These bonds are of great importance since they allow the double helix to be unzipped and the
inner nucleotides exposed.
DNA replication: The process by which DNA is duplicated; ordinarily a semiconservative process in which a dou-
ble-helix gives rise to two double-helices, each with an “old” strand and a newly synthesized strand.
RNA (Ribonucleic Acid) is a type of nucleic acid consisting of nucleotide monomers with a ribose sugar and the
nitrogenous bases adenine (A), cytosine (C), guanine (G), and uracil (U). RNA is usually single-stranded and it plays
a role in protein synthesis and as the genome of some viruses. Three types of RNA may be synthesized from DNA;
namely m-RNA, t-RNA and r-RNA. All of them are structurally and functionally different.
Chromatin and chromosome: From the simplest virus to the most complex human, every organism contains a
massive amount of information in the form of DNA. The DNA is organized into informational units called genes that
ultimately control all aspects of the life of the organism. Chromosomes are made up of chromatin, a complex of DNA
and proteins that makes up a eukaryotic chromosome. like cotton thread on a spool. The formation of nucleosomes
makes possible a 6-fold reduction in the length of DNA.
The cell cycle is the period from the beginning of one division to the beginning of the next division.
Mitosis is a kind of cell division in which a parent cell is divided into two daughter cells. The genetic make up of
both parent and daughter cells are identical.
Meiosis is a special type of cell division which reduces the chromosome number by half. This reduction division
ensures a constant number of chromosomes in a species from one generation to the next. Meiosis produces haploid
CYTOLOGY
cells with unique gene combinations. (Figure-6.18)
The genetic code: In the genetics code nucleotide triplets specify amino acids. There are only 4 nucleotides in
DNA to specify 20 amino acids. Each of the amino acids in the body is coded for by a sequence of three bases known
as a codon.
202
EXPERIMENT: Investigation into the stages of mitosis
Purpose of experiment: Materials onion

To observe onion root meris- microscope orcein stain
tematic cells at different razor hot plate
stages of mitosis teat pipette beaker
slide and cover slip
watch glass
Procedure:
Discussion:
Explain why the onion
roots were left in water for a
few days.
Explain why samples were
taken from the tip of the
roots.
Comment on the number
of dividing cells that you
observed.
203
8. Explain the sequence of events that resulted in the
Information Recall Questions ratios in question 7. You should include the term
semiconservative replication in your answer.
1. What are the main functions of nucleic acids?
2. Where would you expect to find nucleic acids in

eukaryotic cells?
9. Using what you have learned about chromosomes
and their structure and function, complete the table.
Phase Physical state Its significance
3. How would you distinguish DNA from an RNA mole- G1
cule?
DNA replication
Prophase
4. Explain why the presence of DNA replication can be
used to define a living thing.
10. Discuss the importance of meiosis for the variety of life.

5. Explain how the differences in structure between m-
RNA, t-RNA and r-RNA make them suitable for their
functions in a cell. You should also state each function
clearly while answering this question.
11. Explain why all animal cells synthesize their own pro-
6. Explain the following terms clearly teins even though they ingest ready-made protein as
Chromatin food.
Chromosome
Nucleosome
Euchromatin
Heterochromatin
Exon
Intron
12. Correct these incorrect statements and explain them.
A cell can continue to increase its volume indefi-

nitely.
7. According to Meselson and Stahl’s experiment, what A bacteria such as Escherichia coli is capable of
15 15 15 14 reduction division.
is the ratio of heavy (N N ), hybrid (N N ) and
14 14
light DNA (N N ) in a third generation colony of The genome of Escherichia coli is fixed and never
bacteria? changes.
204
3. Which of the following combinations correctly
Application of knowledge describes the structures involved in heredity in
ascending order of size?
13. Sections of root tips from a variety of plants were
A) nucleotide – codon – gene – chromosomes
taken. A high school biology student was asked to try
to identify from which species each root tip was B) codon – nucleotide – gene – chromosomes
taken. A microscope, stains and the usual laboratory C) codon – gene – nucleotide – chromosomes
equipment were provided, as well as a book of D) chromosomes – gene – nucleotide –codon
botanical genetic information. E) codon – chromosomes – gene – nucleotide
Using the items provided, suggest a way of determin-
ing each species.
14. In an observation of some plant cells, many were 4. Examine the list of molecules below.
seen to be filled with homologous chromosomes I. Pentose sugar
attached to each other.
II. Nitrogenous base
III. Amino acid
Explain the significance of this for an organism wish-
ing to exploit new niches. IV. Vitamin
V. Phosphoric acid
Suggest the location of the plant from which the cells Which of these molecules participates in the
were taken. structure of nucleotides?
A) I and III B) I, II and III C) I, II and V
D) II, III and V E) III, IV and V
Choose the correct alternative

1. A DNA molecule is found to contain a total of
2400 nucleotides. If there are 300 adenine 5. In a meiotically dividing cell, the amount of DNA at
nucleotides, how many cytosine nucleotides the G1 stage is labelled as X.
would be expected?
How much DNA would be found in metaphase I
A) 300 B) 900 C) 750 D) 1000 E) 1800 and metaphase II of this cell?
A) X, 0.5 X B) 2X, 0.5X C) 2X, X
D) 2X, 4X E) 4X, 2X
2. Which of the following is not a common charac-

teristic of DNA , RNA and ATP?
A) presence of pentose (5C) sugar within their struc- 6. Which of the following correctly matches a
ture phase of the cell cycle with its description?
B) effects of any mutation seen in subsequent gener-
A) M: duplication of DNA
ations
B) S: DNA replication
C) presence of a phosphate group within their struc-
ture C) G2: cell division
D) presence of adenine within their structure D) G1: follows cell division

E) presence of phosphodiester bonds E) All of the above are correctly matched.
205
7. During _____ the cell grows and replicates both 12. “Cytokinesis” refers to _____.
its organelles and its chromosomes.
A) duplication of the DNA
A) S B) division of the cytoplasm
B) cytokinesis C) division of the nucleus
C) G1 D) division of the mitochondria
D) interphase E) cell movement
E) mitosis
13. The phase of mitosis during which the chromo-

8. During prophase-I a homologous pair of chro- somes move toward separate poles of the cell is
mosomes consists of _____. _____.
A) four chromosomes and two chromatids A) telophase
B) two chromosomes and two chromatids B) anaphase
C) two chromosomes and four chromatids C) metaphase
D) one chromosome and two chromatids D) prophase
E) one chromosome and four chromatids E) cytokinesis
9. Mitosis results in the formation of ______; meio-

sis result in the formation of ________.
14. Which of the following is not needed for DNA
A) four haploid cells ... two diploid cells
replication?
B) four diploid cells ... four haploid cells
A) ribosomes
C) two diploid cells ... two haploid cells
B) DNA
D) two diploid cells ... four haploid cells
E) two diploid cells ... two diploid cells C) nucleotides
D) enzymes
E) all of the above are needed
10. The complex of DNA and protein that makes up
a chromosome is properly called _____.
A) a histone
B) a chromatid 15. DNA replication is said to be semiconservative.
C) a nucleotide This means that _____.
D) chromatin A) half of the old strand is degraded and half is used
E) a chromoplast as a template for the replication of a new strand
B) one of the two resulting double-helixes is made of
two old strands, and the other is made of two new
11. The region of a chromosome holding the two
strands
double strands of replicated DNA together is
called _____. C) the old double-helix is degraded and half of its
nucleotides are used in the construction of two
A) a matrix new double-helices
B) chromatin D) one strand of the new double-helix is made of
C) a centriole DNA and the other strand is made of RNA
D) a centromere E) each new double-helix consists of one old and
E) a chromatid one new strand
206
16. Which of these is a difference between a DNA 20. Short segments of newly synthesized DNA are
and an RNA molecule? joined into a continuous strand by _____.
A) DNA contains uracil, whereas RNA contains A) helicase
thymine. B) DNA polymerase
B) DNA is a polymer composed of nucleotides, C) ligase
whereas RNA is a polymer composed of nucleic
acids. D) primase
C) DNA is double-stranded, whereas RNA is single- E) single-strand binding protein
stranded.
D) DNA contains five-carbon sugars, whereas RNA 21. One strand of a DNA molecule has the base
contains six-carbon sugars. sequence ATAGGT. The complementary base
E) DNA contains nitrogenous bases, whereas RNA sequence on the other strand of DNA will be ___.
contains phosphate groups.
A) TATCCA B) TGGATA C) TGGAUA
D) UAUCCA E) ATAGGT
17. Which of these nitrogenous bases is found in 22. Who is generally credited with discovering that
DNA but not in RNA? the DNA molecule is constructed as a double-
A) adenine helix?
B) cytosine A) Melvin Calvin
C) guanine B) Watson and Crick
D) thymine C) Singer and Nicolson
E) uracil D) Davson and Danieli
E) Hershey and Chase
18. In a nucleotide, the nitrogenous base is

attached to the sugar's _____ carbon and the
phosphate group is attached to the sugar's _____ 23. Which one of the following accurately reflects
carbon. complementary base pairing in the DNA mole-
cule?
A) 1' ... 2'
A) adenine-cytosine
B) 1' ... 5'
B) guanine-cytosine
C) 2' ... 3'
C) guanine-adenine
D) 1' ... 3'
D) cytosine-hemanine
E) 2' ... 1'
E) uracil-thymine
24. One strand of DNA has the following sequence

of nucleotides: 3'-ATTCGCTAT-5' The base
19. Nucleic acids are assembled in the _____ direc- sequence on the other strand of DNA would be
tion. _____.
A) 1' to 5' A) 5'-ATTCGCTAT-3'
B) 2' to 3' B) 3'-ATTCGCTAT-5'
C) 5' to 3' C) 5'-TAAGCGATA-3'
D) 4' to 5' D) 3'-TAAGCGATA-5'
E) 5' to 1' E) 5'-GCCTATCGG-3'
207
25. Which enzyme joins Okazaki fragments? 30. What enzyme catalyzes the attachment of an
amino acid to tRNA?
A) DNA polymerase
B) DNA ligase A) nuclease
C) topoisomerase B) aminoacyl-tRNA synthetase
D) helicase C) rubisco
E) primase D) dextrinase
E) argininosuccinate lyase
31. The tRNA anticodon, GUC, is complementary to

26. Monomers for the synthesis of DNA are called
the mRNA codon with the sequence _____.
_____.
A) GAG
A) amino acids
B) CAC
B) fatty acids
C) GAC
C) nucleotides
D) CAG
D) monosaccharides
E) TAG
E) disaccharides
32. Which of the following is a difference between

mitotic division in animal and plant cells?
27. The flow of information in a cell proceeds _____.
A) Thickening of chromosomes
A) from DNA to RNA to protein B) Replication of DNA
B) from RNA to DNA to protein C) Cytokinesis
C) from protein to RNA to DNA D) Segregation of chromatids
D) from DNA to protein to RNA E) Arrangement of chromosomes
E) from RNA to protein to DNA
33. What number of chromosomes would be expect-

ed in the nerve cells of an animal whose
28. Which of the following processes occurs in the gametes have 16 chromosomes?
cytoplasm of a eukaryotic cell?
A) 8 B) 12 C) 16 D) 32 E) 64
A) translation and transcription
B) DNA replication
C) translation
D) transcription 34. The figure shown below shows the various stages of
E) DNA replication and translation protein synthesis, also known as the central dogma.
– DNA – mRNA – Protein
Which of the following combinations correctly
describes the order of events of protein synthe-
29. Which one of the following is true of tRNAs? sis?
A) Each tRNA binds a particular amino acid. A) replication–transcription–translation
B) tRNAs are produced by ribosomes. B) translation–replication–transcription
C) tRNAs carry special sequences known as codons. C) replication–translation–transcription
D) They carry messages from the DNA D) transcription–translation–replication
E) They have thymine base. E) transcription–replication–translation
208
Cytology
APPENDIX
Animal Classification
BIOLOGICAL ABBREVIATIONS
A Adenine mtDNA Mitochondrial DNA
ADP Adenosine diphosphate NAD/NADH Nicotinamide adenine dinucleotide (oxi-

dized and reduced forms, respectively)
AMP Adenosine monophosphate
ATP Adenosine triphosphate NADP/NADPH Nicotinamide adenine dinucleotide

phosphate (oxidized and reduced forms, respectively)
BMR Basal metabolic rate
P680 Reaction centre of photosystem II
C Cytosine
P700 Reaction centre of photosystem I
C3 Three-carbon pathway for carbon fixation (Calvin cycle)
PEP Phosphoenolpyruvate
C4 Four-carbon pathway for carbon fixation
PGA Phosphoglycerate
CAM Crassulacean acid metabolism
pre-mRNA Precursor messenger RNA (in eukaryotes)
cAMP Cyclic adenosine monophosphate
RNA Ribonucleic acid
CoA Coenzyme A
rRNA Ribosomal RNA
DNA Deoxyribonucleic acid
Rubisco Ribulose bisphosphate carboxylase/oxygenase
EA Activation energy (of an enzyme)
RuBP Ribulose bisphosphate
EM Electron microscope or micrograph
S phase DNA synthetic phase (of the cell cycle)
ER Endoplasmic reticulum
SEM Scanning electron microscope or micrograph
FAD/FADH2 Flavin adenine dinucleotide (oxidised
and reduced forms, respectively) snRNP Small nuclear ribonucleoprotein complex
G Guanine T Thymine
G1 phase First gap phase (of the cell cycle) TEM Transmission electron microscope or micrograph
G2 phase Second gap phase (of the cell cycle) tRNA Transfer RNA
CYTOLOGY
G3P Glyceraldehyde-3-phosphate U Uracil
GTP Guanosine triphosphate UV light Ultraviolet light
mRNA Messenger RNA WBC White blood cell (leukocyte)
210
UNDERSTANDING BIOLOGICAL TERMS
PREFIXES AND SUFFIXES
a-, an-, unless, lack, not (asymmetrical, not symmetrical) one cotyledon, or seed leaf, in the seed)
anti- against (antibody, proteins that have the capacity to photo- light (phototropism, growth of a plant in response
react against foreign substances in the body) to the direction of light)
auto- self (autotroph, organism that manufactures its own
poly- many, much, multiple, complex (polysaccharide, a
food)
carbohydrate composed of many simple sugars)
bi- two (biennial, a plant that takes two years to complete
its life cycle) semi- half (semilunar, half-moon)
bio- life (biology, the study of life) trans- across, beyond (transport, carry across)
cyt- cell (cytology, the study of cells) -logy, study or science of (cytology, study of cells)
-phyll, leaf (mesophyll, the middle tissue of the leaf )
di- two (disaccharide, a compound made of two sugar
molecules chemically combined) -scope, instrument for viewing or observing (microscope,
instrument for viewing small objects)
end-, endo- within, inner (endoplasmic reticulum, a net-
bi-, bio- life (biology, study of life)
work of membranes found within the cytoplasm)
chlor- green (chlorophyll, a green pigment found in plants)
epi- on, upon (epidermis, upon the dermis)
chrom colour (chromosome, deeply staining body in nucleus)
ex-, e-, ef- out from, out of (extension, a straightening out)
cili- small hair (cilium, a short, fine cytoplasmic hair pro-
homo-, hom- same (homologous, corresponding in struc- jecting from the surface of a cell)
ture; homozygous, having identical members of a gene pair) cyt- cell (cytology, study of cells)
hyper- excessive, above normal (hypersecretion, excessive glyc, glyco sweet, sugar (glycogen, storage form of glucose)
secretion) hem blood (haemoglobin, the pigment of red blood cells)
hist- tissue (histology, study of tissues)
hypo- under, below, deficient (hypotonic, a solution
hom, homeo same, unchanging, steady (homeostasis,
whose osmotic pressure is less than that of a solution with
reaching a steady state)
which it is compared)
hydr water (hydrolysis, a breakdown reaction involving water)
inter- between, intra- within (intracellular, within the cell) leuk- white (leukocyte, white blood cell)
iso- equal, like (isotonic, equal osmotic concentration) phag- eat (phagocytosis, process by which certain cells
ingest particles and foreign matter)
macro- large (macronucleus, a large, polyploid nucleus
phil- love (hydrophilic, a substance that attracts, i.e.,
found in ciliates)
“loves,” water)
meso- middle (mesoderm, middle tissue layer of the ani- som body (chromosome, deeply staining body in the nucleus)
mal embryo) stom- a mouth (stoma, a small pore, i.e., “mouth,” in the
meta- after, beyond (metaphase, the stage of mitosis after epidermis of plants)
prophase) xanth- yellow (xanthophyll, a yellowish pigment found in
plants)
micro-small (microscope, instrument for viewing small
xyl- wood (xylem, water-conducting tissue in plant, the
Glossary
objects) “wood” of woody plants)
mono- one (monocot, a group of flowering plants with zoo- an animal (zoology, the science of animals)
211
SCIENTIFIC MEASUREMENT
The relationship between mass Some Common Units of Length

and volume of water Unit Abbreviation Equivalent
(at 20°C)
meter m 39 inches
1 g = 1 cm3 = 1 mL
centimeter cm 0.01 meter
millimeter mm 0.001 meter
micrometer μm 10-6(one-millionth) of a meter
nanometer nm 10-9 (one-billionth) of a meter
angstrom A 10-10 (one-trillionth) of a meter
Some Common Units of Mass

dalton or atomic mass unit
(amu) the approximate mass of Unit Abbreviation Equivalent
a proton or neutron
kilogram kg 1000 gram
mole the formula weight of a
substance expressed in grams gram g 10-3 kg
milligram mg 10-3 gram
Avogadro’s number (N)
microgram μg 10-6gram
6.02 x 1023 the number of par-
ticles in one mole of any sub- nanogram ng 10-9 (one-billionth) of a gram
stance
picogram pg 10-12 (one-trillionth) of a gram
Some Common Units of Volume

Energy Conversions
Unit Abbreviation Equivalent
calorie (cal) energy required to
raise the temperature of 1 g of
liter L 1000 milliliter
CYTOLOGY
water (at 16°C) by 1°C

1 calorie = 4.184 joules millilitre mL 10-3 L (1 mL = 1 cm3 = 1 cc)
1 kilocalorie (kcal) = 1000 cal
microlitre μL 10-6 Liter
212
A substances are combined to form more complex sub-
stances, resulting in the storage of energy, the produc-
absorption: The uptake of small nutrient molecules by
tion of new cellular materials, and growth.
an organism's own body.
Anaerobic respiration: The use of inorganic molecules
acetyl coenzyme (acetyl CoA): A key intermediate
other than oxygen to accept electrons at the “downhill”
compound in metabolism; consists of a two-carbon
end of electron transport chains
acetyl group covalently bonded to coenzyme A.
anticodon: A sequence of three nucleotides in transfer
acid: A substance that increases the hydrogen ion con-
RNA that is complementary to, and combines with, the
centration of a solution.
three nucleotide codon on messenger RNA, thus help-
actin: The protein of which microfilaments are com- ing to specify the addition of a particular amino acid to
posed. Actin, together with the protein myosin, is the end of a growing polypeptide.
responsible for muscle contraction.
apoenzyme: Protein portion of an enzyme; requires the
activation energy (EA): The kinetic energy required to presence of a specific coenzyme to become a complete
initiate a chemical reaction.The amount of energy that functional enzyme.
reactants must absorb before a chemical reaction will atom: The smallest quantity of an element that can
start. retain the chemical properties of that element.
active site: Specific region of an enzyme that accepts atmosphere: The envelope of gases that surrounds the
one or more substrates and catalyses a chemical reac- Earth; consists largely of nitrogen (78%) and oxygen
tion. (21%).
active transport: Transport of molecules against a con- ATP synthase: Large enzyme complex that catalyzes
centration gradient (from regions of low concentration the formation of ATP from ADP and inorganic phos-
to regions of high concentration) with the aid of pro- phate by chemiosmosis; contains a transmembrane
teins in the cell membrane and energy from ATP.
channel through which protons diffuse down a concen-
adenosine triphosphate (ATP): A common form in tration gradient; located in the inner mitochondrial
which energy is stored in living systems; The energy membrane, the thylakoid membrane of chloroplasts,
coin of the cell. and the plasma membrane of bacteria.
allosteric regulators: Substances that affect protein autosome: A chromosome other than the sex (X and Y)
function by binding to allosteric sites. chromosomes.
amino acids: The subunits (monomers) from which autotrophs: Organisms that synthesise their own nutri-
proteins (polymers) are assembled. Each amino acid ents; include some bacteria that are able to synthesize
consists of an amino functional group, and a carboxyl organic molecules from simpler inorganic compounds.
acid group, and differs from other amino acids by the
composition of an R group. B
basal metabolic rate (BMR): The amount of energy
aminoacyl-tRNA: Molecule consisting of an amino acid
expended by the body at resting conditions, when no
covalently linked to a transfer RNA.
food is being digested and no voluntary muscular work
aminoacyl-tRNA synthetase: An enzyme that joins is being performed.
each amino acid to the correct tRNA.
base: A substance that is a hydrogen ion (proton)
anabolism: The aspect of metabolism in which simpler acceptor; bases unite with acids to form salts.
213
beta oxidation: Process by which fatty acids are convert- catabolism: The type of metabolism in which complex
ed to acetyl CoA before entry into the citric acid cycle. substances are broken down to form simpler sub-
stances; catabolic reactions are particularly important in
beta pleated sheet: A regular, folded, sheetlike struc-
releasing chemical energy stored by the cell.
ture resulting from hydrogen bonding between two dif-
ferent polypeptide chains or two regions of the same catalyst: A substance that increases the speed at which
polypeptide chain. a chemical reaction occurs without being used up in the
reaction. Enzymes are biological catalysts.
biochemistry: Chemical processes associated with liv-
ing things. cell: The smallest structural units of living matter capa-
ble of functioning independently.
buffer: A substance in a solution that tends to lessen
the change in hydrogen ion concentration (pH) that cell cycle: The sequence of events from one division of
otherwise would be produced by adding an acid or a cell to the next; consists of mitosis (or division) and
base. interphase.
bundle sheath cells: Tightly packed cells that form a cellular respiration The transfer of energy from various
sheath around the veins of a leaf. molecules to produce ATP; occurs in the mitochondria
of eukaryotes, the cytoplasm of prokaryotes. In the
C process, oxygen is consumed and carbon dioxide is
C3 plant: Plant that carries out carbon fixation solely by generated.
the Calvin cycle. cell plate: Structure that forms during cytokinesis in
C4 plant: Plant that fixes carbon initially by the Hatch- plants, separating the two daughter cells produced by
mitosis.
Slack pathway, in which the reaction of CO2 with phos-
phoenolpyruvate is catalyzed by PEP carboxylase in leaf cell wall: Structure outside the plasma membrane of
mesophyll cells; the products are transferred to the bun- certain cells; may contain cellulose (plant cells), chitin
dle sheath cells, where the Calvin cycle takes place. (most fungal cells), peptidoglycan and/or lipopolysac-
charide (most bacterial cells), or other material.
calorie: The amount of heat energy required to raise
the temperature of 1 g of water 1°C; equivalent to 4.184 cellulose: A structural polysaccharide composed of
joules. beta glucose subunits; the main constituent of plant pri-
mary cell walls.
Calvin cycle: Cyclic series of reactions in the chloro-
plast stroma in photosynthesis; fixes carbon dioxide and centriole: One of a pair of small, cylindrical organelles
produces carbohydrate. lying at right angles to each other near the nucleus in
the cytoplasm of animal cells and certain protist and
CAM plant: Plant that carries out crassulacean acid plant cells; each centriole is in the form of a cylinder
metabolism; carbon is initially fixed into organic acids at composed of nine triplets of microtubules (9_3 structure).
night in the reaction of CO2 and phosphoenolpyruvate,
catalyzed by PEP carboxylase; during the day the acids chemiosmosis: Process by which phosphorylation of
break down to yield CO2, which enters the Calvin cycle. ADP to form ATP is coupled to the transfer of electrons
down an electron transport chain; the electron transport
carbohydrates: Organic molecules composed of car- chain powers proton pumps that produce a proton gra-
bon, hydrogen, and oxygen that serve as energy dient across the membrane; ATP is formed as protons
sources and structural materials for cells of all organ- diffuse through transmembrane channels in ATP syn-
isms. thase.
carotenoids: A group of yellow to orange plant pig- chitin: A nitrogen-containing structural polysaccharide
ments synthesised from isoprene subunits; include that forms the exoskeleton of insects and the cell walls
carotenes and xanthophylls. of many fungi.
214
chlorophyll: The pigment in green plants that absorbs D
solar energy.
dehydrogenation: A form of oxidation in which hydro-
chloroplasts: Disc-like organelles with a double mem- gen atoms are removed from a molecule.
brane found in eukaryotic plant cells; contain thylakoids
desmosomes: Button-like plaques, present on two oppos-
and are the site of photosynthesis.
ing cell surfaces, that hold the cells together by means of
chromatid: One of the two identical halves of a dupli- protein filaments that span the intercellular space.
cated chromosome; the two chromatids that make up a
deoxyribonucleic acid (DNA): A nucleic acid com-
chromosome are referred to as sister chromatids.
posed of two polynucleotide strands wound around a
chromatin: The complex of DNA and protein that central axis to form a double helix; the repository of
makes up eukaryotic chromosomes. genetic information.
chromosomes: Structures in the nucleus of a eukaryotic dialysis: The diffusion of certain solutes across a selec-
cell that consist of DNA molecules that contain the genes. tively permeable membrane.
codon: A triplet of mRNA bases that specifies an amino diffusion: Net movement of particles (atoms, mole-
acid, a start signal, or a signal to terminate the polypeptide. cules, or ions) from a region of higher concentration to
a region of lower concentration.
coenzyme: An organic cofactor for an enzyme; gener-
ally participates in the reaction by transferring some com- digestion: The process of breaking down food into its
ponent, such as electrons or part of a substrate molecule. molecular and chemical components so that these
nutrient molecules can cross plasma membranes.
cofactor: A nonprotein substance needed by an enzyme
for normal activity; some cofactors are inorganic (usu- disaccharide: A sugar produced by covalently linking
ally metal ions); others are organic (coenzymes). two monosaccharides.
competitive inhibitor: A substance that binds to the DNA ligase: Enzyme that catalyzes the joining two DNA
active site of an enzyme, thus lowering the rate of the fragments; essential in DNA replication and used in
reaction catalyzed by the enzyme. Compare with non- recombinant DNA technology.
competitive inhibitor. DNA polymerases: Family of enzymes that catalyse the
cristae: Finger-like inward projections of the inner synthesis of DNA from a DNA template, by adding
membrane of a mitochondrion. nucleotides to a growing 3’ end.
cytochromes: Iron-containing heme proteins of an DNA replication: The process by which DNA is dupli-
electron transport system. cated; ordinarily a semiconservative process in which a
double helix gives rise to two double helices, each with
cytokinesis: Stage of cell division in which the cyto- an "old" strand and a newly synthesized strand
plasm divides to form two daughter cells.
E
cytology: The branch of biology dealing with cell structure.
electron transport system: A series of chemical reac-
cytoplasm: The viscous semiliquid inside the plasma tions during which hydrogens or their electrons are
membrane of a cell; contains various macromolecules passed along an electron transport chain from one
and organelles in solution and suspension. acceptor molecule to another, with the release of energy.
cytoskeleton: Dynamic internal network of protein element: A substance composed of atoms with the
fibers that includes microfilaments, intermediate fila- same atomic number; cannot be broken down in ordi-
ments, and microtubules. nary chemical reactions.
cytosol: Fluid component of the cytoplasm in which the endergonic reaction: Nonspontaneous reaction; a
organelles are suspended. reaction requiring a net input of free energy.
215
endocytosis: The active transport of substances into compounds serve both as electron donors and terminal
the cell by the formation of invaginated regions of the electron acceptors.
plasma membrane that pinch off and become cytoplas-
mic vesicles. fertilisation: The fusion of two gametes (sperm and
ovum) to produce a zygote that develops into a new indi-
endoplasmic reticulum (ER): A network of membra- vidual with a genetic heritage derived from both parents.
nous tubules in the cytoplasm of a cell; involved in the
production of phospholipids, proteins, and other func- flagellum: Long, whiplike, movable structure extending
tions. Rough ER is studded with ribosomes; smooth ER from the cell and used in locomotion.
is not. free energy: The maximum amount of energy available
energy: The ability to bring about changes or to do work. to do work under the conditions of a biochemical reaction.
enzyme: An organic catalyst (usually a protein) that G

accelerates a specific chemical reaction by lowering the gamete: Haploid reproductive cells (ovum and sperm).
activation energy required for that reaction.
gene: A segment of DNA that serves as a unit of hered-
ethyl alcohol: A two-carbon alcohol. itary information.
eukaryote: A type of cell found in many organisms gene therapy: The insertion of normal or genetically
including single-celled protists and multicellular fungi, altered genes into cells through the use of recombinant
plants, and animals; characterised by a membrane- DNA technology; usually done to replace defective
bounded nucleus and other membranous organelles; genes as part of the treatment of genetic disorders.
an organism composed of such cells.
genetics: The study of the structure and function of genes
exocytosis: The active transport of materials out of the and the transmission of genes from parents to offspring.
cell by fusion of cytoplasmic vesicles with the plasma
membrane. genome: The set of genes carried by an individual.
F generation time: The time required for the completion

of one cell cycle.
facilitated diffusion: The passive transport of ions or
molecules by a specific carrier protein in a membrane. glycocalyx: A coating on the outside of an animal cell,
As in simple diffusion, net transport is down a concen- formed by the polysaccharide portions of glycoproteins
tration gradient, and no additional energy has to be and glycolipids associated with the plasma membrane.
supplied.
glycogen: The principal storage polysaccharide in ani-
NAD/FADH2: Oxidized and reduced forms, respective- mal cells; formed from glucose and stored primarily in
ly, of flavin adenine dinucleotide; coenzyme that trans- the liver and, to a lesser extent, in muscle cells.
fers electrons (as hydrogen) in metabolism, including
glycolipid: A lipid with covalently attached carbohydrates.
cellular respiration.
glycolysis: The first stage of cellular respiration, literal-
fats: Triglycerides that are solid at room temperature.
ly the “splitting of sugar.” The metabolic conversion of
fatty acid: An organic acid containing a long hydrocar- glucose into pyruvate, accompanied by the production
bon chain. of ATP.
feedback inhibition: Type of enzyme regulation in glycoprotein: A protein with covalently attached carbo-
which the accumulation of the product of a reaction hydrates.
inhibits an earlier reaction in the sequence.
glycosidic linkage: Covalent linkage joining two sug-
fermentation: Anaerobic process by which ATP is pro- ars; includes an oxygen atom bonded to a carbon of
duced by a series of redox reactions in which organic each sugar.
216
glyoxysomes: Membrane-bounded structures in cells equivalent of a water molecule; a hydrogen atom is
of certain plant seeds; contain a large array of enzymes added to one subunit and a hydroxyl group to the other.
that convert stored fat to sugar.
hydrophilic: Attracted to water.
Golgi complex: Organelles in animal cells composed
hydrophobic: Repelled by water.
of a series of flattened sacs that sort, chemically modi-
fy, and package proteins produced on the rough endo- hypertonic solution: In comparing two solutions, refer-
plasmic reticulum. ring to the one with a greater solute concentration.
granum: A stack of thylakoids within a chloroplast. hypotonic solution: In comparing two solutions, the
one with a lower solute concentration
greenhouse effect: The heating that occurs when
gases such as carbon dioxide trap heat escaping from I-J
the Earth and radiate it back to the surface; so-called
interphase: The period in the cell cycle when the cell is
because the gases are transparent to sunlight but not to
not dividing. During interphase, cellular metabolic activ-
heat and thus act like the glass in a greenhouse.
ity is high, chromosomes and organelles are duplicated,
H and cell size may increase. Interphase accounts for 90%
of the cell cycle.
haploid: The condition of having one set of chromo-
somes per nucleus. intron: A noncoding, intervening sequence within a
eukaryotic gene.
helicases: Enzymes that unwind the two strands of a
DNA double helix. ion: An atom that has gained or lost electrons, thus
acquiring a charge.
histones: Small, positively charged (basic) proteins in
the cell nucleus that bind to the negatively charged DNA. ionic bond: A chemical bond resulting from the attrac-
tion between oppositely charged ions.
homeostasis: The ability to maintain a relatively con-
stant internal environment. isotonic Having the same solute concentration as
another solution.
homologous chromosomes: Chromosome pairs of
the same length, centromere position, and staining pat- isotope: One of several atomic forms of an element,
tern that possess genes for the same characters at corre- each containing a different number of neutrons and
sponding loci. One homologous chromosome is inherited thus differing in atomic mass.
from the organism's father, the other from the mother.
joule (J): A unit of energy: 1 J 50.239 cal.
hormone: An organic chemical messenger in multicel-
lular organisms that is produced in one part of the body K
and transported to another part where it signals cells to karyokinesis: The division of nucleus in mitosis
alter some aspect of metabolism.
karyotype: The chromosomal constitution of an indi-
Human Genome Project: Federally funded project to vidual. Representations of the karyotype are generally
determine the DNA base sequence of every gene in the prepared by photographing the chromosomes and
human genome. arranging the homologous pairs according to size, cen-
tromere position, and pattern of bands.
hydrogen bond: A weak attractive force existing
between a hydrogen atom with a partial positive charge keratin: A horny, water-insoluble protein found in the
and an electronegative atom (usually oxygen or nitro- epidermis of vertebrates and in nails, feathers, hair, and
gen) with a partial negative charge. horns.
hydrolysis: Reaction in which a covalent bond between kilocalorie: The energy needed to heat 1000 grams of
two subunits is broken through the addition of the water from 14.5 to 15.5 degrees C.
kinetic energy: The energy of motion, which is directly matrix: The interior of the compartment enclosed by
related to the speed of that motion. Moving matter does the inner mitochondrial membrane.
work by imparting motion to other matter.
matter: Anything that has mass and takes up space.
kinetochore: A specialised region on the centromere
meiosis: Process in which a 2n cell undergoes two suc-
that links each sister chromatid to the mitotic spindle.
cessive nuclear divisions (meiosis I and meiosis II),
Krebs cycle: Series of chemical reactions in aerobic potentially producing four n nuclei; leads to the forma-
respiration in which acetyl coenzyme A is completely tion of gametes in animals and spores in plants.
degraded to carbon dioxide and water with the release
mesophyll cell: A loosely arranged photosynthetic cell
of metabolic energy that is used to produce ATP; also
located between the bundle sheath and the leaf surface.
known as the Krebs cycle and the tricarboxylic acid
(TCA) cycle. messenger RNA (mRNA): RNA that specifies the
amino acid sequence of a protein; transcribed from
L DNA.
lactic acid fermentation: The conversion of pyruvate to metabolism: The sum of all the chemical processes
lactate with no release of carbon dioxide. that occur within a cell or organism: the transforma-
lagging strand: Strand of DNA that is synthesized as a tions by which energy and matter are made available for
series of short segments, called Okazaki fragments, use by the organism.
which are then covalently joined by DNA ligase. A discon- microfilament: A solid rod of actin protein in the cyto-
tinuously synthesized DNA strand that elongates in a direc- plasm of almost all eukaryotic cells, making up part of
tion away from the replication fork. the cytoskeleton and acting alone or with myosin to
leading strand: The new continuous complementary cause cell contraction.
DNA strand synthesized along the template strand in micronutrient: An element that an organism needs in
the mandatory 5' 3' direction. very small amounts and that functions as a component
light reactions: The steps in photosynthesis that occur or cofactor of enzymes.
on the thylakoid membranes of the chloroplast and that microtubule: A hollow rod of tubulin protein in the
convert solar energy to the chemical energy of ATP and cytoplasm of all eukaryotic cells and in cilia, flagella,
NADPH, evolving oxygen in the process. and the cytoskeleton.
lipids: One of the classes of organic macromolecules. microvillus: (plural, microvilli) One of many fine, finger-
Lipids function in the long-term storage of biochemical like projections of the epithelial cells in the lumen of the
energy, insulation, structure and control. Examples of small intestine that increase its surface area.
lipids include the fats, waxes, oils and steroids (e.g.
testosterone, cholesterol). mitochondria: Spherical or elongate intracellular
organelles that are the sites of oxidative phosphorylation
lysosomes: Membrane-enclosed organelles containing in eukaryotes; include an outer membrane and an inner
digestive enzymes. The lysosomes fuse with food vac- membrane.
uoles and enzymes contained within the lysosome
chemically breakdown and/or digest the food vacuole's mitosis: Division of the cell resulting in two daughter
contents. nuclei, each with the same number of chromosomes as
the parent nucleus; mitosis consists of four phases:
M prophase, metaphase, anaphase, and telophase.
Cytokinesis usually overlaps the telophase stage.
macronutrients: 1. Elements needed by plants in rela-
tively large (primary) or smaller (secondary) quantities. molecule: The smallest particle of a covalently bonded
2. Foods needed by animals daily or on a fairly regular element or compound that has the composition and
basis. properties of a larger part of the substance.
218
monomer: The subunit that serves as the building otes that contains the DNA and serves as the control
block of a polymer. center of the cell.
monosaccharide: A simple sugar that cannot be O
degraded by hydrolysis to a simpler sugar.
Okazaki fragment: One of many short segments of
N DNA, each 100 to 1000 nucleotides long, that must be
joined by DNA ligase to form the lagging strand in DNA
NAD+/NADH: Oxidized and reduced forms, respective-
replication.
ly, of nicotinamide adenine dinucleotide; coenzyme that
transfers electrons (as hydrogen), particularly in cata- operator: In prokaryotic DNA, a sequence of
bolic pathways, including cellular respiration. nucleotides near the start of an operon to which an
active repressor can attach. The binding of the repres-
NADP+/NADPH: Oxidized and reduced forms, respec-
sor prevents RNA polymerase from attaching to the pro-
tively, of nicotinamide adenine dinucleotide phosphate;
moter and transcribing the genes of the operon.
coenzyme that acts as an electron (hydrogen) transfer
agent, particularly in anabolic pathways, including pho- operon: A unit of genetic function common in bacteria
tosynthesis. and phages, consisting of coordinately regulated clus-
ters of genes with related functions.
negative feedback: A primary mechanism of home-
ostasis, whereby a change in a physiological variable organelle: One of the specialized structures within the
that is being monitored triggers a response that coun- cell, such as the mitochondria, Golgi complex, ribo-
teracts the initial fluctuation. somes, or contractile vacuole; most organelles are
noncompetitive inhibitor: A substance that reduces the membrane-bounded.
activity of an enzyme by binding to a location remote osmosis: Net movement of water (the principal solvent
from the active site, changing its conformation so that in biological systems) by diffusion through a selectively
it no longer binds to the substrate. permeable membrane from a region of higher concen-
noncyclic photophosphorylation: The production of tration of water (a hypotonic solution) to a region of
ATP by noncyclic electron flow. lower concentration of water (a hypertonic solution).
nuclear envelope: The membrane in eukaryotes that osmotic pressure: The pressure that must be exerted
encloses the nucleus, separating it from the cytoplasm. on the hypertonic side of a selectively permeable mem-
brane to prevent diffusion of water (by osmosis) from
nucleic acid: A polymer (polynucleotide) consisting of the side containing pure water.
many nucleotide monomers; serves as a blueprint for
proteins and, through the actions of proteins, for all cel- oxidation: The loss of one or more electrons (or hydro-
lular activities. The two types are DNA and RNA. gen atoms) by an atom, ion, or molecule.
nucleolus: Specialized structure in the cell nucleus oxidative phosphorylation: The production of ATP
formed from regions of several chromosomes; site of using energy derived from the transfer of electrons in
assembly of the ribosomal subunits. the electron transport system of mitochondria; occurs
by chemiosmosis.
nucleotide: A molecule composed of one or more phos-
phate groups, a five-carbon sugar (ribose or deoxyri- P
bose), and a nitrogenous base (purine or pyrimidine).
PEP carboxylase: An enzyme that adds carbon dioxide
nucleoside: An organic molecule consisting of a to phosphoenolpyruvate (PEP) to form oxaloacetate.
nitrogenous base joined to a five-carbon sugar.
peptide bond: A distinctive covalent carbon-to-nitro-
nucleus: The central region of an atom, containing the gen bond that links amino acids in peptides and pro-
protons and neutrons; (2) A cellular organelle in eukary- teins.
peroxisomes: Membrane-bounded organelles in pigments: Colouring matter in animals and plants,
eukaryotic cells containing enzymes that produce or especially in a cell or tissue.
degrade hydrogen peroxide.
plasmodesmata: Cytoplasmic channels connecting
pH: The negative logarithm of the hydrogen ion con- adjacent plant cells and allowing for the movement of
centration of a solution (expressed as moles per litre). molecules and ions between cells.
Neutral pH is 7, values less than 7 are acidic, and those
plasmolysis: The shrinkage of cytoplasm and the
greater than 7 are basic.
pulling away of the plasma membrane from the cell wall
phagocytosis: Literally, "cell eating"; a type of endocy- when a plant cell (or other walled cell) loses water, usu-
tosis by which certain cells engulf food particles, ally in a hypertonic environment.
microorganisms, foreign matter, or other cells.
polysaccharide: A carbohydrate consisting of many mono-
photolysis: The photochemical splitting of water in the saccharide subunits, e.g., starch, glycogen, and cellulose.
light-dependent reactions of photosynthesis, catalyzed
potential energy: Stored energy; energy that can do
by a specific enzyme.
work as a consequence of its position or state.
photon: A particle of electromagnetic radiation; one
pre-mRNA: RNA precursor to mRNA in eukaryotes;
quantum of radiant energy.
contains both introns and exons.
photophosphorylation: The production of ATP in pho-
primase: An enzyme that joins RNA nucleotides to
tosynthesis.
make the primer
photorespiration: A metabolic pathway that consumes
prokaryote: Type of cell that lacks a membrane-bound
oxygen, releases carbon dioxide, generates no ATP, and
nucleus and has no membrane organelles; a bacterium
decreases photosynthetic output; generally occurs on
lacking membrane-bound organelles and having a sin-
hot, dry, bright days, when stomata close and the oxygen
gle circular chromosome, and ribosomes surrounded
concentration in the leaf exceeds that of carbon dioxide. by a cell membrane.
photosynthesis: The biological process that captures protein: A large, complex organic compound com-
light energy and transforms it into the chemical energy posed of covalently linked amino acid subunits; con-
of organic molecules (such as carbohydrates), which tains carbon, hydrogen, oxygen, nitrogen, and sulfur.
are manufactured from carbon dioxide and water; per-
formed by plants, algae, and certain bacteria. protists: Single-celled organisms; a type of eukaryote.
photosystem I: One of two complexes, consisting of purine: One of two families of nitrogenous bases found
chlorophyll molecules, accessory pigments, proteins, and in nucleotides. Adenine (A) and guanine (G) are purines.
associated electron acceptors, responsible for capturing
pyrimidine: One of two families of nitrogenous bases
light energy and transferring excited electrons; photosys-
found in nucleotides. Cytosine (C), thymine (T), and
tem I best absorbs and uses light of about 700 nm.
uracil (U) are pyrimidines.
photosystem II: One of two complexes, consisting of
quaternary structure: The particular shape of a com-
chlorophyll molecules, accessory pigments, proteins, and
plex, aggregate protein, defined by the characteristic
associated electron acceptors; responsible for capturing
three-dimensional arrangement of its constituent sub-
light energy and transferring excited electrons; photosys-
units, each a polypeptide.
tem II best absorbs and uses light of about 680 nm.
phycocyanin: A blue pigment found in cyanobacteria R
and red algae. radiation: Energy emitted from the unstable nuclei of
radioactive isotopes.
phycoerythrin: A red pigment found in cyanobacteria
and red algae. reactant: A starting material in a chemical reaction.
220
reaction center: The chlorophyll-a molecule and the RNA primer: Sequence of about five RNA nucleotides
primary electron acceptor in a photosystem; they trig- that are synthesized during DNA replication to provide a
ger the light reactions of photosynthesis. The chloro- 3' end to which DNA polymerase can add nucleotides.
phyll donates an electron, excited by light energy, to the The RNA primer is later degraded and replaced with
primary electron acceptor, which passes an electron to DNA.
an electron transport chain.
RNA processing: Modification of RNA before it leaves
receptor-mediated endocytosis: The movement of the nucleus, a process unique to eukaryotes.
specific molecules into a cell by the inward budding of
membranous vesicles containing proteins with receptor RNA polymerase: An enzyme that links together the
sites specific to the molecules being taken in; enables a growing chain of ribonucleotides during transcription.
cell to acquire bulk quantities of specific substances. Rubisco: Common name of ribulose bisphosphate car-
recombinant DNA technology: A series of techniques boxylase, the enzyme that catalyzes the reaction of car-
in which DNA fragments are linked to self-replicating bon dioxide with ribulose bisphosphate in the Calvin
forms of DNA to create recombinant DNA molecules. cycle.
These molecules in turn are replicated in a host cell to
create clones of the inserted segments. S
saturated fatty acid: A fatty acid in which all carbons in
reaction center: Portion of an antenna complex within
the hydrocarbon tail are connected by single bonds,
a photosystem that includes chlorophyll a molecules
thus maximising the number of hydrogen atoms that
capable of transferring electrons to a primary acceptor;
can attach to the carbon skeleton.
the reaction center of Photosystem I is P700 and of
Photosystem II is P680. scanning electron microscope (SEM): A microscope
that uses an electron beam to scan the surface of a
redox reaction: Chemical reaction in which one or
more electrons are transferred from one substance (the sample to study details of its topography.
substance that becomes oxidized) to another (the sub- selective permeability: A property of biological mem-
stance that becomes reduced). branes that allows some substances to cross more eas-
reduction: The gain of one or more electrons. ily than others.
replication fork: Y-shaped region on a replicating DNA semiconservative replication: Type of DNA replication
molecule where new strands are growing. in which the replicated double helix consists of one old
strand, derived from the old molecule, and one newly
repressor: A protein that suppresses the transcription made strand.
of a gene.
sickle-cell disease: A human genetic disease of red
ribonucleic acid (RNA): Nucleic acid containing ribose blood cells caused by the substitution of a single amino
sugar and the base Uracil; RNA functions in protein syn- acid in the hemoglobin protein; it is the most common
thesis. The single stranded molecule transcribed from one inherited disease among African Americans.
strand of the DNA. There are three types of RNA, each is
involved in protein synthesis. RNA is made up nucleotides single-strand binding protein: During DNA replica-
containing the sugar ribose, a phosphate group, and one of tion, molecules that line up along the unpaired DNA
four nitrogenous bases (adenine, uracil, cytosine or guanine). strands, holding them apart while the DNA strands
serve as templates for the synthesis of complimentary
ribosomes: Small organelles made of rRNA and protein strands of DNA.
in the cytoplasm of prokaryotic and eukaryotic cells.
The site of protein synthesis. The ribosome is com- small nuclear ribonucleoprotein complexes (snRNP):
posed of two subunits that attach to the mRNA at the Aggregations of RNA and protein responsible for bind-
beginning of protein synthesis and detach when the ing to premRNA in eukaryotes and catalysing the exci-
polypeptide has been translated. sion of introns and the splicing of exons.
sodium-potassium pump: A special transport protein tissue: A group of closely associated, similar cells that
in the plasma membrane of animal cells that transports work together to carry out specific functions.
sodium out of the cell and potassium into the cell
transcription: The synthesis of RNA from a DNA tem-
against their concentration gradients.
plate.
solute: A substance that is dissolved in a solution
translation: Conversion of information provided by
solution: A homogeneous, liquid mixture of two or mRNA into a specific sequence of amino acids in a
more substances. polypeptide chain; process also requires transfer RNA
and ribosomes.
solvent:The dissolving agent of a solution. Water is the
most versatile solvent known. transmission electron microscope (TEM): A micro-
scope that passes an electron beam through very thin
steroids: Complex molecules containing carbon atoms sections, primarily used to study the internal ultrastruc-
arranged in four attached rings, three of which contain ture of cells.
six carbon atoms each and the fourth of which contains
five; e.g., cholesterol and certain hormones, including U-V-W-X-Z
the male and female sex hormones of vertebrates.
unsaturated fatty acid: A fatty acid possessing one or
stomata: Small pores located in the epidermis of more double bonds between the carbons in the hydro-
plants that provide for gas exchange for photosynthesis; carbon tail. Such bonding reduces the number of
each stoma is flanked by two guard cells, which are hydrogen atoms attached to the carbon skeleton.
responsible for its opening and closing.
uracil: A nitrogenous pyrimidine base found in RNA.
stroma: A fluid space of the chloroplast, enclosed by
the chloroplast inner membrane and surrounding the valence electron: The electrons in the outermost elec-
thylakoids; site of the reactions of the Calvin cycle. tron shell.
substrate: A substance on which an enzyme acts; a vitamin: A complex organic molecule required in very
reactant in an enzymatically catalyzed reaction. small amounts for normal metabolic functioning.
substrate-level phosphorylation: The formation of wavelength: The distance from one wave peak to the
ATP by directly transferring a phosphate group to ADP next; the energy of electromagnetic radiation is inverse-
from an intermediate substrate in catabolism. ly proportional to its wavelength.
synapsis: The pairing of replicated homologous chro- X-chromosome: One of the sex chromosomes.
mosomes during prophase I of meiosis. xylem: Tissue in the vascular system of plants that
moves water and dissolved nutrients from the roots to
T the leaves;
tetrad: Chromosome complex formed by the synapsis zygote: A fertilised egg. A diploid cell resulting from
of a pair of homologous chromosomes (i.e., four chro- fertilisation of an egg by a sperm cell.
matids) during meiotic prophase I; also known as a
bivalent.
thermodynamics: Principles governing energy transfer
(often expressed in terms of heat transfer).
tight junctions: Specialized structures that form
between some animal cells, producing a tight seal that
prevents materials from passing through the spaces
between the cells.
222
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223

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I also wish to acknowledge the experts Cengiz ARAS, Bakhytzhan

The chemistry of life . . . . . . . . . . . . . . . . .8 Water soluble vitamins . . . . . . . . . . . . . .38

Bioelements . . . . . . . . . . . . . . . . . . . . . . .9 Lipid soluble vitamins . . . . . . . . . . . . . . .39

Organisation of matter . . . . . . . . . . . . . . .9 Nucleic acids . . . . . . . . . . . . . . . . . . . . .40

Atomic number, Summary . . . . . . . . . . . . . . . . . . . . . . .41

Hydrolysis - Dehydration synthesis . . . . .16

Read me . . . . . . . . . . . . . . . . . . . . . . . .21 Structure of the plasma membrane . . . .55

Carbon and life . . . . . . . . . . . . . . . . . . . .22 The cytosol . . . . . . . . . . . . . . . . . . . . . .57

Carbohydrates (C,H,O) . . . . . . . . . . . . . .23 Organelles . . . . . . . . . . . . . . . . . . . . . . .58

Lipids (C, H, O, P, S) . . . . . . . . . . . . . . . .28 Read me . . . . . . . . . . . . . . . . . . . . . . . .63

Read me . . . . . . . . . . . . . . . . . . . . . . . .30 Cytosceleton . . . . . . . . . . . . . . . . . . . . .69

Read me . . . . . . . . . . . . . . . . . . . . . . . .31 Surface features of cells . . . . . . . . . . . .70

Proteins (C, H, O, N, S) . . . . . . . . . . . . . .33 Transport of materials through the

Functions of proteins . . . . . . . . . . . . . . .34 plasma membrane . . . . . . . . . . . . . . . . .75

Three dimensional structure of proteins . .35 Passive mechanisms . . . . . . . . . . . . . . .75

Read me . . . . . . . . . . . . . . . . . . . . . . . .37 Active mechanisms . . . . . . . . . . . . . . . .80

Exocytosis . . . . . . . . . . . . . . . . . . . . . . .81 Factors affecting the rate of

Read me . . . . . . . . . . . . . . . . . . . . . . .117 Read me . . . . . . . . . . . . . . . . . . . . . . .156

Photosynthetic reactions . . . . . . . . . . . .120 Catabolism of lipids . . . . . . . . . . . . . . .158

Anaerobic respiration (Fermentation) . . .162 Information recall questions . . . . . . . . .204

The industrial importance of Appendix . . . . . . . . . . . . . . . . . . . . . . . . .209

6. The Secret Of Life . . . . . . . . . . . . . . . . .174

Nucleic acids . . . . . . . . . . . . . . . . . . . .174

DNA (Deoxyribonucleic Acid) . . . . . . . . .176

RNA (Ribonucleic Acid) . . . . . . . . . . . . .180

Chromatin and chromosome . . . . . . . . .182

The cell cycle . . . . . . . . . . . . . . . . . . . .185

Protein synthesis . . . . . . . . . . . . . . . . .194

sequently unstable. (Figure-1.1)

The chemistry of life

Figure-1.1: The structure of atom

Electrons and energy

Figure-1.2: Electrons have different energy level.

Particle Symbol Function Location Mass Charge

The chemistry of life

Proton p Identity Nucleus 1 +

Neutron n Isotope Nucleus 1 0

Compounds and molecules

Formation of Chemical Bonds

When atoms share their CH4

The chemistry of life

When negative charged

Element A pure chemical substance

Atom The smallest unit of element

A pure substance formed from the atoms of different ele-

Molecule The smallest unit of compound

C6H12O6 + 6O2 ⎯→ 6CO2 + 6H2O + Energy (38 ATP/686 Kcal/mol)

The chemistry of life

6CO2 + 6H2O + Light energy (686 Kcal/mol) ⎯⎯→ C6H12O6 + 6O2

C12H22O11 + H2O ⎯→ 2 C6H12O6 (hydrolysis)

Anabolic reactions, the condensation of two amino acids or carbohydrates for

An exothermic reaction is one that releases energy as the bonds of a com-

C6H12O6+6O2 → 6CO2+6H2O+38 ATP (686.4 kcal)

Structure of Water Molecules

The chemistry of life

Water is the principle solvent of life

High melting point regulates body temperature

Water has low density at solid state making ice float

Metabolic reactions need enough water concentration

Water is essential to life

High heat capacity Water regulates constant body temperature.

The chemistry of life

NaOH + HCl ⎯⎯→ NaCl + H2O

Edema resulting from a decrease of blood proteins induced by starvation.

Disorders in erythrocyte structure.

Purpose: Materials: test tubes, beakers

Purpose: Materials: test tubes