INTRODUCTION

Levels of Organization of Life

The approach used in this course is based on the levels of organization concept, that “life in
the universe is made up of a series of levels of organization so constructed that the units of one level
of complexity form the building blocks for the units of the next higher level”. The primary levels of
organization are:

1. Sub-atoms – electrons, neutrons, protons, positrons, etc.

2. Atoms ( chemical elements) – of the 92 naturally occurring chemical elements, 16 are
commonly used in forming the chemical compounds from which living organisms are
made. These bioelements include: C, H, O, P, K, I, N, S, Ca, Fe, Mg, Na, Cl, Zn, Mn and
Cu. In the human body, only the following six bioelements account for 99% of the total
mass:

Oxygen 65%
Carbon 18%
Hydrogen 10%
Nitrogen 3%
Calcium 2%
Phosphorus 1%

The other bioelements (about 1%) which are found in the body in small amounts but which
are vital to life are generally referred to as trace elements, including potassium (0.35%), sulphur
(0.25%), chlorine (0.15%), sodium (0.15%), magnesium (0.05%), iron (0.004%), while there are only
minute traces of copper, manganese, zinc and iodine.
3. Molecules/compounds – these are formed from the combination of two or more atoms,
such as H2O, CO2 and many others. There are two kinds of molecules found in the cell:
A. inorganic molecules – those that do not contain the element C
B. organic molecules or C-containing molecules – in which the element C always
forms important part of the molecule
4. Cells – composed of molecules, both organic and inorganic
5. Organisms – composed of millions of cells
6. Population – a group of organisms belonging to the same species
7. Community – a group of populations occupying an area in any given time
8. Ecosystem - composed of a community interacting with the physical factors of the
environment
9. Biosphere – made up of all the ecosystems on earth; also referred to as global ecosystem.
All portions of air, water and land occupied by life make up the biosphere.

The primary levels of organization are capable of independent existence while the so-called
secondary levels of organization ( tissue, organ, and organ system) are not. They remain alive only
when they are intact in the organism. A tissue is made up of a group of similar cells; an organ is made
up of different tissues that perform a specific function; and an organ system is composed of various
organs that perform a specific/definite function.

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Definition of Terms

Biology is the study of life or living things. It is divided into two:

1. Botany – the scientific study of plant life; their structure and function,
classification, reproduction and development, heredity and variations as well as
interaction with the environment
2. Zoology – the scientific study of animal life. It studies the fundamental properties
of living animals, both invertebrates and vertebrates, giving emphasis on their
structure and function, reproduction, development, heredity and variations,
diversity and interaction with the environment.

Branches of Zoology
1. Morphoanatomy – the study of forms and structures of animals
a. microscopic anatomy – the parts studied are so small that it requires the use
of the microscope. Examples are:
cytology – the study of cells
histology – the study of tissues
b. gross anatomy – the study of large parts/structures of animals
2. Physiology - the study of functions
3. Embryology/Developmental Biology – the study of the development of animals
from the egg stage up to the adult stage
4. Taxonomy – the study of the classification, identification and nomenclature of
animals
5. Genetics – the study of heredity and variations or the transmission of
heritable characteristics from parents to offprings
6. Ecology – the study of the interactions/relationships between organisms (animals)
and the environment
7. Evolution – the study of changes occurring in animals through time
8. Paleontology – the study of fossils
9. Zoogeography – the study of the distribution of animals on the surface of the earth
10. Ethology – the study of animal behavior

Areas of zoology based on specific groups of animals studied:

1. Parasitology – the study of parasites (ectoparasites and endoparasites)
2. Microbiology – the study of microorganisms, including bacteria and fungi
3. Helminthology – the study of worms
4. Protozoology – the study of one-celled organisms (protozoans)
5. Ornithology – the study of birds
6. Ichthyology – the study of fishes
7. Herpetology – the study of amphibians and reptiles
8. Entomology – the study of insects
9. Malacology – the study of mollusks
10. Conchology – the study of shells

Manifestations/Properties of Life
The term “life” is so broad that it cannot be defined in just one statement. However, living
systems can be described by the following manifestations / properties:

1 Chemical uniqueness. Living systems demonstrate a unique and complex molecular organization.
Biological macromolecules (proteins, lipids, carbohydrates and nucleic acids) are composed of the
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same atoms and chemical bonds that occur in non-living matter and they obey all fundamental laws
of chemistry. It is only the complex organizational structure of these macromolecules that make them
unique. They differ in their component parts, the kinds of chemical bonds that link their subunits
together and their functions in living systems. This organization gives living systems both a
biochemical unity and a great potential for diversity.

2. Complexity and hierarchical organization. The living system consists of a hierarchy of levels:
macromolecules, cells, organisms, population and species. Within the cell, the macromolecules are
compounded into structures, such as ribosomes, chromosomes and membranes which are likewise
combined in various ways to form more complex sub-cellular structures (organelles), such as
mitochondria, Golgi bodies, lysosomes, endoplasmic reticulum, etc. Cells are then organized into
tissues, organs and organ systems.

Cells are the basic units of living systems and the smallest units of the biological hierarchy
that are semiautonomous in their ability to conduct basic functions, including reproduction and gene
replication. One important characteristic of this biological hierarchy is that the properties of any
given level cannot be obtained from knowledge of the properties of its component parts. For
example: it is impossible to predict someone’s blood pressure (a property of the organism level)
simply by knowing the physical characteristics of the individual cells of the body.

The appearance of new characteristics at a given level of organization is called emergence and
the characteristics are known as emergent properties. Emergent properties expressed at a particular
level are influenced and restricted by properties of the lower-level components. Nonetheless,
properties of parts of a living system do not rigidly determine the properties of the whole. Different
levels of the biological hierarchy and their particular emergent properties are products of evolution.

3. Reproduction. Living systems can reproduce themselves. Life does not arise spontaneously but
comes only from prior life through a process of reproduction. At each level of the biological
hierarchy, living forms reproduce to generate others like themselves. Genes replicate to produce new
genes; cells divide to produce new cells; organisms reproduce sexually or asexually to produce new
organisms; populations can be fragmented to give rise to new populations; and species gives rise to
new species through a process known as speciation. Reproduction thus increases the number of
genes, cells, organisms, populations and species.

Reproduction features the complementary phenomena of heredity and variation. Heredity is

the faithful transmission of traits from parents to offsprings. Variation is the production of differences
among the traits of different individuals. In the reproductive process, the properties of descendants
resemble those of their parents to varying degrees but are usually not identical to them.

4. Possession of a genetic program. A genetic program provides fidelity of inheritance. For animals
and most organisms, the genetic information is contained in the DNA. The structures of the protein
molecules that are needed for the development and functioning of organisms are encoded in nucleic
acids (DNA). The sequence of nucleotide bases (genetic code) represents the order of amino acids in
the protein specified by the DNA molecule.

5. Metabolism. This is defined as the sum total of all chemical processes that occur inside the cell. It
consists of two phases: 1) catabolism or breakdown process and 2) anabolism or synthesis or building
up process. Living systems obtain nutrients from their environments and break them down to yield
chemical energy and molecular components for use in building and maintaining themselves through
the chemical process called metabolism. Therefore, metabolism includes digestion, respiration
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(breakdown of nutrients to obtain chemical energy) and protein synthesis (for synthesis of molecules
and structures).

6. Development. All organisms pass through a characteristic life cycle. Development describes the
characteristic changes that an organism undergoes from its origin (usually, the zygote) to its final
adult form. It usually features changes in size and shape and the differentiation of structures within
the organism. The stages of development are: zygote, embryo, juvenile and adult. In insects: egg,
larva, pupa and metamorphosed adult. The transformation that occurs from one stage to another is
called metamorphosis.

7. Environmental interaction. All organisms interact with their environment. (This is the scope of
ecology.) Life and environment are inseparable. All organisms respond to environmental stimuli in
appropriate ways by adjusting its metabolism and physiology.
The ability to respond to stimuli is known as irritability which is one of the important attributes of
life.

The Scientific Method or Hypothetico-deductive Method. This is the systematic method used by
scientists in solving scientific problems. However, this can also be used by any layman in solving
daily problems. The steps are:

1) Formulation / Statement of the problem. This may take the form of a question.
2) Generation of hypothesis. A hypothesis is a tentative or potential answer to the question being
asked. It is usually based on prior observations of nature or they may be derived from theories based
on such observations.
3) Experimentation or observation. Here, data are collected to support the hypothesis; they are
arranged, sorted out and then analyzed. An experiment must consist of a) the experimental group and
b) the control group.
4) Testing of hypothesis by further experimentation and/or observation
5) Drawing of conclusion
6) Formulation of a theory. A theory is a scientifically acceptable body of principles offered to
explain a phenomenon.

CHEMICAL BASIS OF LIFE

What is life? This is a perennial question whose answer has somehow eluded the most
brilliant of human minds. For even if scientists have identified many years ago, the right combination
of atoms and molecules that make up the protoplasm, the substance or ‘stuff’ of life, they have not
succeeded in ‘switching it on’ or ‘breathing life’ into it.

The Origin and Chemistry of Life

All living organisms share a common ancestor, most likely a population of colonial
microorganisms that lived almost 4 billion years ago. This common ancestor was itself the product of
a long period of prebiotic assembly of non-living matter, including organic molecules and water, to
form self-replicating units. All living organisms retain a fundamental chemical composition inherited
from their ancient common ancestor. This is the secret of life, the so-called chemical basis of life.

Prebiotic Chemical Evolution

The term protoplasm refers to the ‘stuff’ of life or the living substance of the cell. It is entirely
made up of chemical compounds or molecules formed from about 105 elements known today, four of
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which constitute about 97% of the living matter: hydrogen, oxygen, carbon and nitrogen. These “big
4” elements are among the highest and most abundant elements of the early Earth. Hydrogen is the
most reactive that it probably combined with oxygen to form water (H2O), nitrogen to form ammonia
(NH3) and carbon to form methane (CH4).

In the laboratory, a mixture of water, ammonia and methane, heated with hydrogen and
carbon dioxide and energized with electrical discharges or UV radiation, generated several chemical
compounds, including amino acids, sugars, fatty acids and nucleotides. These are the same chemical
compounds that make up the protoplasm of cells. The simple organic molecules may have formed
more complex ones, such as polysaccharides from sugars, protein from amino acids, fats from fatty
acids and nucleic acids from nucleotides. In the absence of ozone in the primitive Earth, UV may
have provided the energy for the synthesis of the different organic molecules. Although laboratory
experiments cannot simulate exactly the early conditions of the earth, however, they prove the
possibility of forming organic compounds from inorganic elements.

Living cells may have arisen by the assembly of these organic compounds. The incipient
nucleus of the prokaryotic cell may have formed from the assembly of nucleic acids (DNA and RNA)
and the first cytoplasm may have formed from proteins and water that became organized into a
gelatinous mass. It has also been postulated that the first cell membrane formed from the spontaneous
arrangement of phospholipids and proteins into an envelope that enclosed the gelatinous mass, the
cytoplasm.

The Chemical Composition of Cells and Organisms

Organisms are composed of two kinds of compounds — organic and inorganic. Inorganic
compounds rarely contains the element carbon, however, there are inorganic compounds that contain
carbon; examples are CO2 and the carbonates, including Na2CO3, CaCO3, etc. On the other hand,
organic compounds always contain carbon, hence they are called carbon compounds. They
characteristically contain hydrocarbon bonds which directly attach H atoms to C atoms. Any
compound that has at least one hydrocarbon bond is most likely an organic compound, except urea
which does not have a hydrocarbon bond.

The Inorganic Compounds

There are four main types of inorganic compounds in living systems, namely acids, bases,
salts and water.

1. Water is the most abundant inorganic compound, constituting about 60% to 90% of the organism,
depending on the species. It serves as the medium in which other substances are dissolved,
dispersed or suspended. Water is often called a ‘universal’ solvent but which is a misnomer
because it cannot dissolve fats.

The origin and maintenance of life on earth depends critically on water. It has several
extraordinary properties that explain its essential role in living systems. These properties are as
follows:

a. Water has a high specific heat. This means that organisms gain and lose heat slowly which
is helpful in temperature control. Its high thermal capacity greatly moderates
environmental temperature changes, thereby protecting living organisms from extreme
temperature fluctuation.

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 b. Water has a high heat of vaporization. For terrestrial animals cooling produced by
evaporation of water is important for expelling excess heat. This explains why the body
feels cold as sweat evaporates.
c. Water has unique density behavior during changes of temperature. It reaches its maximum
density at 4 0C then becomes less dense with further cooling. When displaced, water gives
good support for aquatic organisms.
d. Water has high surface tension, exceeding that of any other liquid, except mercury. H
bonding among H2O molecules produces a cohesiveness that is important for maintaining
protoplasmic form and movement. The resulting surface tension creates an ecological
niche for insects that skate on the surfaces of ponds.
e. Water has low viscosity permitting movement of blood through minute capillaries and of
cytoplasm inside cellular boundaries.
f. Pure water has low conductivity but dissolved ions make the cytoplasm quite a good
conductor. This is important for the functioning of many cells, such as nerve cells.
g. Water is incompressible. This is important in transport systems and as a means of support
in organisms with a hydrostatic skeleton, like the earthworms.
h. Water also participates in many chemical reactions in living organisms. For example,
many large compounds are split into smaller pieces by the addition of a molecule of water,
a process called hydrolysis. Likewise, larger compounds may be synthesized from smaller
components by the reverse of hydrolysis, called condensation reaction.

2. Acids, Bases and pH

In a given volume of water, a small but definite proportion of water molecules split or
dissociate to form ions. This occurs when a hydrogen atom from one water molecule is transferred to
the oxygen atom of a second. The reaction yields hydroxyl ions (OH −) and hydroxonium ions (H3O+).
Each hydroxonium ion is a hydrogen ion (H +) which do not exist separately but always in combined
form in water.

Pure water contains an exactly equal number of H+ and OH- ions, in addition to many
undissociated water molecules. However, substances dissolved in water often affect the balance of H +
and OH- ions. For example, an acid substance increases the H + ions in solution while a base or alkali
combines with H+ ions and, in effect, removes them from the solution. pH refers to the acidity or
alkalinity of a solution. Practical values of pH range from 0-14. At 250C, pure water has a pH = 7,
called neutral pH, acid solutions have a pH less than 7 while an alkaline solution has a pH greater
than 7.

Certain solutions called pH buffers, resist changes in pH so that the pH of the solution tends
to remain constant. For example, hydrogencarbonate ions can combine with H + ions to form carbonic
acid:

HCO3- + H+ → H2CO3

Or with OH- ions:

HCO3- + OH- → H2O + CO3 2-

In this way, H+ and OH- ions added to a solution containing hydrogencarbonate ions are
absorbed and do not affect the overall pH level. In living systems, the pH buffers include phosphate
ions (H2PO4 -), amino acids and proteins.

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The Organic Compounds
The organic compounds in organisms are carbohydrates, fats or lipids, proteins and nucleic
acids. They may form part of the organism or they are cell products.

Carbohydrates. They are chemically composed of C, H and O (1:2:1 ratio). They are otherwise
known as hydrated carbons (CH2O). There are three types of carbohydrates:

1) Monosaccharide or simple sugar – the backbone chain of the molecule consists of 3

to 6 C atoms. It is simple because it can no longer be broken down to smaller forms.
Monosaccharides include triose (3 – C), tetrose (4 – C), pentose (5 – C) and hexose
(6 – C) sugars, the most common of which are the hexoses (C 6H12O6). The three hexose sugars,
glucose, fructose and galactose, are called isomers because they have the same structural formula but
they differ in the arrangement of the atoms. They serve as the building blocks for the formation of
disaccharides. The sweetest of the hexoses is fructose or fruit sugar while the most biologically
important form of hexose is glucose. There are two important pentose (5-C) sugars, deoxyribose and
ribose; they form part of the nucleotides, the building blocks of nucleic acids. Deoxyribose sugar
forms part of DNA while ribose sugar forms part of RNA.

2) Disaccharide or double sugar – formed out of two simple sugars through condensation reaction
with the formation of glycoside bonds. The three common disaccharides (C12H22O11) are: 1)
maltose or malt sugar for brewing beer, 2) lactose or milk sugar and sucrose or cane sugar.

Glucose + Glucose → Maltose + H2O

Glucose + Fructose → Sucrose + H2O
Glucose + Galactose → Lactose + H2O

3) Polysaccharide - a macromolecule or giant molecule formed out of a chain of simple sugars

linked together through condensation reaction and the formation of glycoside bonds. The four
common examples are starch, glycogen, cellulose and chitin. A polymer is a molecule made up of
many similar units (monomers) linked together by dehydration synthesis. Usually, the
monosaccharide units used are glucose molecules bonded together by glycoside bonds. Starch
serves as the main stored food in plants, like rice and cassava. Glycogen, also called “animal
starch”, is especially present in high concentrations in the muscles and livers of animals.
Cellulose is an important structural component of plant cell walls.

Biochemical Functions of Carbohydrates:

1.They supply about 1/2 of the total energy requirements of an organism.
2.Glucose is the main energy source of living cells.
3.Starch serves as food storage material in plants and utilized as source of energy by organisms.
4.Carbohydrates serve as structural components of cells/organisms:
a. Cellulose in plant cells and chitin in the external skeletons of insects, shrimps and crabs
which protect the cells or the whole organism.
b. Deoxyribose sugar forms part of the genetic material (DNA) and ribose sugar forms part of
RNA which plays important role in protein synthesis.

 Lipids. These organic molecules are chemically composed of C, H and O but in a ratio that is
greater than that of carbohydrates. They are not soluble in water but soluble in organic solvents
like alcohol, acetone and ether. The best known examples are fats, oils, waxes and phospholipids.

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 A true fat or neutral fat or triglyceride molecule is synthesized from one molecule of
glycerol (an alcohol) and three molecules of fatty acid by condensation reaction.
Glycerol + 3 fatty acids → fat + 3 H2O

A phospholipid molecule is formed from one molecule of glycerol to which are attached two
molecules of fatty acids and one phosphate group.

Waxes are lipid molecules in which the alcohol group is larger than glycerol.

Cholesterol is a steroid; it is only lipid-like, being insoluble in water but it is not chemically
composed of glycerol and fatty acids.

There are two kinds of fats:

1)Saturated fat – in which all C – C bonds of the fatty acid chains are single bonds; solid
at room temperature. Examples: lard and butter
2)Unsaturated fat – contains double C – C bond or bonds in any of the fatty acid chains;
usually liquid at room temperature, also referred to as oils. Examples: plant and fish
oils

Biochemical Functions of Lipids

1. They serve as structural components of cells and organisms:
All cell membranes consist of a phospholipid bilayer with associated proteins.
The cutinized outer cell walls of leaves and young stems contain a waxy cutin.
The suberized cell walls of cork cells in plants contain the waxy suberin.
2. Lipids, such as fats and oils, serve as concentrated source of energy among organisms. A gram
of fat provides more than twice as much energy as a gram of starch.
3. Some hormones are lipids (steroids), including testosterone, estrogen and estradiol which are
known as metabolic regulators.

 Proteins. A protein molecule contains the elements C, H, O, and N, sometimes with S and P. It is
a macromolecule made up of a polymer of amino acids linked together through condensation
reaction with the formation of peptide bonds. Amino acids are known as the building blocks of
protein.

An amino acid molecule consists of an amino group (NH 2) and an acid group (COOH)
attached to a central C atom. There are about 20 different kinds of amino acids that constitute the
structure of all proteins found in plants and animals (Table 1). Amino acids are often analogized
to the 26 letters of the alphabet that form all the words in the dictionary. While letters form words,
amino acids form proteins. Or, amino acids are the letters that form proteins, the words.

Table 1. The twenty amino acids in proteins.

Essential Non-essential
Amino Acids Amino Acids
Histidine (His) Alanine (Ala)
Isoleucine (Iso) Arginine (Arg)
Leucine (Leu) Asparagine (Asn)
Lysine (Lys) Aspartic acid (Asp)

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 Methionine (Met) Cysteine (Cys)
Phenylalanine (Phe) Glutamic acid (Glu)
Threonine (Thr) Glutamine (Gln)
Tryptophan (Trp) Glycine (Gly)
Valine (Val) Proline (Pro)
Serine (Ser)
Tyrosine (Tyr)

Eleven out of the 20 amino acids are called non-essential amino acids because they can be
synthesized by the cells while the other nine which cannot be synthesized by the cells are called
essential amino acids. The latter must therefore be supplied by the diet. The 20 amino acids differ
from each other by the R group of atoms that is attached to one end of the central C atom.

A protein molecule is formed by linking together the amino acids end to end through
condensation reaction. The bonds formed between amino acids in a protein molecule are called
peptide bonds. One peptide bond is formed between every two amino acids bonded together.
Amino acid + amino acid → dipeptide
Amino acid + amino acid + amino acid → tripeptide
If four or more amino acids are bonded together, a polypeptide or protein molecule is
formed.

Structures of Protein
Every protein molecule is unique because it has a) specific number of amino acids b) specific
types of amino acids, c) specific sequence of amino acids and d) shape (pattern of coiling and folding
of the polypeptide chain). These are the characteristics that determine the biological functions of
proteins.

1. Primary structure – refers to the specific number, types and sequence of amino acids in the
polypeptide chain. The bonds formed are all peptide bonds. Any change in the number, type and
sequence of the amino acids in the protein molecule will alter/destroy the properties and
function(s) of the molecule.

2. Secondary structure – refers to the alpha helix shape of the protein molecule. This results from
the coiling of the polypeptide chain with the formation of additional bonds, the hydrogen bonds,
to stabilize the helical shape. When the H bonds are broken down by heating and other means, the
helix collapses and the physical as well as chemical properties of the protein are destroyed. The
protein is said to be denatured.

3. Tertiary structure – refers to the globular shape of the protein molecule which is formed by
further coiling of the helix and the formation of additional ionic bonds and disulfide bonds.
Example: most enzymes

4. Quaternary structure – is formed by the interaction of two or more polypeptide chains. Example:
hemoglobin

Biochemical Functions of Proteins

1. They serve as the main structural components of cells and organs.
2. Proteins are the most abundant organic compounds in the cell constituting about 50% of the dry
weight of most cells.

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3. All enzymes are either totally or partly protein. Enzymes catalyze various biochemical processes
that are important to life; they are called organic catalysts.
4. Most hormones are protein in chemical composition.
5. Antibodies which defend the body against various types of infection are also protein in nature.
6. Some proteins function in the transport of materials, like hemoglobin of red blood cells which
carries free oxygen from the lungs to the different parts of the body. Transport proteins also
operate across cell membranes.
7. Proteins serve as source of energy. At times of starvation, organisms meet their energy
requirements by using up first, their own carbohydrates, then their own fats and finally, their own
proteins.

Enzymes. As catalysts of living systems, an enzyme reduces the amount of activation energy
required for a reaction. It affects only the rate of reaction and does not take part nor change the
proportions of reactants and products of a reaction.

Chemical Nature of Enzymes

They are complex molecules that vary in size from small, simple proteins to highly complex
molecules. Many enzymes are pure proteins; others contain small non-protein groups called
cofactors to perform their enzymatic function. Some cofactors are metallic ions – Fe, Cu, Zn, Mg, K,
Ca – that form a functional part of the enzyme. Examples: carbonic anhydrase contains Zn
cytochrome contains Fe
troponin (muscle contraction enzyme) contains Ca

Another class of cofactors, the coenzymes, is organic. In this case, an enzyme molecule is
composed of a larger protein group, about 90% (called apoenzyme) and a smaller (about 10%) non-
protein or prosthetic group (called coenzyme). All coenzymes contain groups derived from vitamins
that must be supplied in the diet. The B complex vitamins are coenzymatic compounds. Examples of
coenzymes that contain vitamins:
1) NAD (nicotinamide adenine dinucleotide) – contains nicotinic acid or niacin
(vitamin B6)
2) FAD (flavin adenine dinucleotide) – contains riboflavin (vitamin B2)
3) Coenzyme A – contains pantothenic acid

Action of Enzymes
The molecule catalyzed by an enzyme is called substrate. The enzyme bears an active site
located within a cleft or pocket containing a unique molecular configuration. The active site has a
flexible surface that enfolds and conforms to the substrate.

When an enzyme binds to a substrate, an enzyme-substrate complex (ES complex) is formed.

The substrate is secured by covalent bonds to one or more points in the active site of the enzyme. The
ES complex then quickly dissociates but during this fleeting moment, the enzyme provides a unique
chemical environment that stresses certain chemical bonds in the substrate so that much less energy is
required to complete the reaction.

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 Figure 1. Enzyme – substrate relationship

Specificity of Enzymes
Enzymes are highly specific; this is due to the exact molecular fit that is required between
enzyme and substrate. This is clearly demonstrated by the lock-and-key pattern of enzyme function.
Moreover, an enzyme catalyzes only one reaction ( one enzyme – one substrate relationship).

Enzyme-catalyzed reactions may be reversible, example:

Fumaric acid + H2O ←→ Malic acid

Or, irreversible in the case of:

Proteins + pepsin → Amino acids

The above catalyzed reaction proceeds in one direction only (catabolic); it does not accelerate the
rebuilding of amino acids into protein (anabolic). The same is true to the breakdown of nucleic acids,
polysaccharides, lipids and proteins wherein they must be re-synthesized by a different set of
reactions that are catalyzed by different enzymes. This irreversibility exists because the chemical
equilibrium usually favors the formation of smaller degradation products.

 Nucleic Acids. These are polymers of nucleotides. A nucleotide is an organic molecule made up
of three components, namely, a 5-C sugar, a nitrogenous base and a phosphate group. The
composition of a nucleotide is diagrammed below:

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 Figure 2. Structure of a nucleotide

The 5-C sugar is deoxyribose in DNA and ribose in RNA Deoxyribose sugar has one
oxygen atom less than in ribose sugar. Ribose sugar has an oxygen atom attached to carbon 2
(Figure 2).

Figure 3. Structure of ribose and deoxyribose sugar

The nitrogenous base may be a purine or a pyrimidine. Purine bases (adenine and
guanine) are larger molecules consisting of two rings of carbon and nitrogen atoms while the
pyrimidine bases (thymine, cytosine and uracil) consist of only one ring each, hence smaller
(Figure 5).
The third component of a nucleotide is the phosphate group (PO 4-3) below derived from
phosphoric acid (H3PO4).

Figure 4. Structure of a phosphate group

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 Figure 5. Comparative structures of purine and pyrimidine bases
There are two kinds of nucleic acids found in living cells, DNA (deoxyribonucleic acid)
and RNA (ribonucleic acid). There are three types of RNA: 1) messenger RNA, 2) ribosomal
RNA and 3) transfer RNA. Following are some of the differences between DNA and RNA:

DNA RNA
Deoxyribose sugar Ribose sugar
Nitrogenous bases: A, T, C, G Nitrogenous bases: A, U, C, G
Double-stranded Single-stranded
Mostly found inside the nucleus Mostly found in the cytoplasm
Functions as primary carriers of Act as intermediate agents of
genetic information protein synthesis

Biochemical Functions of Nucleic Acids

1. DNA makes up the genes which are the carriers of hereditary traits. In eukaryotic cells, DNA
forms part of the chromosomes. DNA is considered as the genetic or hereditary material for two
reasons:
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 a) It is the material that is handed down unchanged from parents to offspring.
b) It controls all cellular activities by controlling protein synthesis.
2. RNA act as intermediate agents in protein synthesis under the direction of the DNA.

DNA (Deoxyribonucleic Acid)

DNA (deoxyribonucleic acid) is otherwise known as the genetic material or the chemical
basis of heredity. It carries the genetic information that is transmitted from parents to offspring from
generation to generation. Structurally, a DNA molecule is composed of a linear sequence of base
pairs which is colinear with the sequence of amino acids that make up a protein molecule.

The synthesis of proteins in the cell is exclusively controlled by DNA. According to the
central dogma of molecular genetics, the genetic information is transferred from DNA to RNA and
from RNA to proteins.

Chemical Structure of DNA

To recall, DNA is a nucleic acid just like RNA. Both macromolecules are polymers of units
called nucleotides. A nucleotide consists of three component molecules: a 5-carbon sugar, a
phosphate group and a nitrogenous base. In all DNA molecules, the sugar is always deoxyribose
while the phosphate group is constant. There are four types of nitrogenous bases that can be found in
DNA molecules: adenine (A), guanine (G), cytosine (C) and thymine (T). Adenine and guanine are
larger molecules called purines while the smaller molecules, cytosine and thymine, are pyrimidines.

The Watson-Crick Model of DNA

In 1950, Francis H.C. Crick and James D. Watson determined the structure of the DNA
molecule, using the technique of X-ray crystallography. Their work was widely acclaimed as the
single most important biological discovery of the 20th century for which they won a Nobel prize.
According to the Watson-Crick model, DNA is double-stranded. The two strands run in opposite
directions, that is, they are anti-parallel.

Figure 6. Double helix (left) and ladder (right) structures of DNA

14
 The two strands are complementary, that is, the sequence of bases along one strand specifies
the sequence of bases along the other strand. The backbone of the molecule is built of phosphoric
acid and deoxyribose sugar and attached to this backbone are the nitrogenous bases. The result is a
ladder structure with the sugar-phosphate backbones serving as the banisters and the paired
nitrogenous bases as the rungs. The two strands are held together by the formation of hydrogen bonds
between the nitrogenous bases; two H bonds are formed between A and T while three H bonds are
formed between C and G. However, the ladder is twisted into a double helix with approximately 10
base pairs for each complete turn of the helix (Figure 5).

DNA and Chromosomes

The total length of the DNA molecules in a typical mammalian cell has been calculated to be
about 2 m, giving a staggering total of more than 10 billion DNA in the whole human body. Each
chromosome in an individual cell is believed to contain just one single long molecule of DNA so that
the 46 chromosomes of a human cell correspond to 46 individual molecules of DNA, each about 4
cm long. To prevent the interior of the nucleus from becoming a hopeless tangle, the DNA threads of
the individual chromosomes are coiled in some organized way. This is the function of the specialized
histone proteins which are associated with DNA to form chromatin. Chromatin refers to the state of
the chromosomes during interphase or when the cell is not dividing.

In an actively growing cell, the chromosomes in the nucleus are mainly present as long chains
of nucleosomes (DNA + histones). When the cell is preparing to divide, the chromosomes coil up
much more tightly and become visible by a process called condensation. Eukaryotic cells carry out
cell division with the chromosomes in this densely packed form. It is the chromosomes that transmit
the hereditary or ‘genetic’ information to the daughter cells during sexual reproduction. The
chromosomes are also
considered as the repository of the genes that determine the traits of an individual.

DNA fulfills three fundamental requirements of a genetic material. The molecule is extremely
stable so that the coded instructions it contains normally remain intact from one generation to the
next. It can replicate, thus it is able to provide new copies of the genetic instructions for each new
cell. DNA is able to control the activities of the cell by directing the synthesis of proteins aided by the
three types of RNA.

Figure 7. Structure of nucleosomes

15
 The Genetic Codes
It has been emphasized that protein synthesis in the cell is directed by DNA. Therefore, in
order to understand better the process of protein synthesis, let us begin by considering how molecules
of DNA are able to carry information. The DNA uses a remarkable molecular code language or
genetic code in which the nucleotides in an individual strand represent a sequence of ‘code words’
following one after another. The genetic code is thereby known as the ‘language’ of protein synthesis.

Table 4. The genetic codes (codons) and the amino acids that they specify during protein synthesis.
AMINO ACID mRNA codons used to AMINO mRNA codons used to
specify the position of this ACID specify the position of this
amino acid amino acid
Alanine GCA, GCC, GCG, GCU lysine AAA, AAG
4 2
Arginine AGA, AGG, CGA, CGC, methionine AUG (initiation codon)
CGG, CGU 6 1
Asparagines AAC, AAU phenylalanine UUC, UUU
2 2
aspartic acid GAC, GAU proline CCA, CCC, CCG, CCU
2 4
Cysteine UGC, UGU serine AGC, AGU, UCA, UCC,
2 UCG, UCU 6
glutamic acid GAA, GAG threonine ACA, ACC, ACG, ACU
2 4
Glutamine CAA, CAG tryptophan UGG
2 1
Glycine GGA, GGC, GGG, GGU tyrosine UAC, UAU
4 2
Histidine CAC, CAU valine GUA, GUC, GUG, GUU
2 4
Isoleucine AUA, AUC, AUU ‘stop’ codons UAA, UAG, UGA
3 3
Leucine CUA, CUC, CUG, CUU,
UUA, UUG 6 total number of different mRNA codons ─ 64

Each genetic code is composed of three letters (triplet) formed out of the four letters
corresponding to the four nitrogenous bases of the RNA molecule. Each triplet codes for one amino
acid. Actually, there are 64 triplets (3-letter combinations) that can be formed from the four
nitrogenous bases, more than enough to specify each of the 20 amino acids in any protein chain.
However, some triplets are used as “start” or “stop” signals for protein synthesis as has been
indicated in the table.

THE CELL: ITS STRUCTURE AND FUNCTION

16
 The field of biology that studies the structure and function of the cell is called cytology (from
the Greek word cyto, meaning cell and logos, study). It is through this study that you will realize and
appreciate the wonderful world of living things; that despite their great diversity, all organisms share
a common basic pattern of structure and function.

The Cell Theory

This is one of the great unifying concepts of biology. The Cell theory can be summarized into
two statements:
. 1. All living things are composed of fundamental units called cells; and
2. New cells come from the division of pre-existing cells.
The cell theory was the product of the work of many biologists from different parts of the
world within roughly three centuries.

 Anton van Leeuwenhoek (1632 – 1723), a Dutch naturalist who discovered bacteria and
other microscopic organisms in rainwater; he also studied the structure of plant and animal
cells.

 Robert Hooke (1635 – 1703), an Englishman who coined the term cell; he introduced the
subdiscipline in biology known as cytology.
 Lazzaro Spallanzani (1729 -1799) and Francesco Redi (1627 – 1697), Italian biologist and
physician, respectively, who proposed the Theory of Spontaneous Generation which
postulated that living things arose from non-living material.

 Robert Brown (1773 – 1858), a Scottish botanist who discovered the presence of nucleus
inside the cell.

 Johannes Purkinje (1787 – 1869), a Czechoslovakian who coined the term ‘protoplasm’ to
refer to the living substance of the cell.

 Matthias Schleiden (1804 – 1881) and Theodore Schwann (1810 – 1882), German botanist
and zoologist, respectively, who introduced the concept that plants and animals are made up
of cells.

 Rudolf Virchow (1821 – 1902), a German physician who found that cells divide to form new
cells; he concluded that cells come from pre-existing cells (“omnies cellula e cellula”) which
negate the Theory of Abiogenesis.

 Louis Pasteur (1822 – 1895), a French chemist who supplied proof for the Biogenetic
Theory of Virchow.

Parts and Function of the Cell

The cell is regarded as the basic unit of life. It is composed of organic and inorganic
molecules. Irregardless of their shape, size or function, virtually all cells share three basic structural
features:

17
 1. All cells are surrounded by cell membrane which acts as a selective barrier between the inside
and outside of the cell; it also helps regulate its internal composition.
2. All cells have a nucleus or nuclear material which contains the genetic information and
ultimately controls all cellular activities.
3. All cells contain a fluid or jelly-like medium, the cytoplasm, where the chemical reactions of
metabolism take place; it is also where the enzymes, proteins and other substances needed by
the cell are manufactured.
Cell Membrane
Studies with the electron microscope reveal that the cell membrane, plasma membrane or
plasmalemma consists essentially of two back-to-back layers of phospholipids with randomly
dispersed protein molecules. The hydrophilic heads of the phospholipid molecules point outwards,
forming hydrogen bonds with the surrounding water molecules while the mutually attracting
hydrophobic tails point inwards. The lipoprotein complex is not a rigid assemblage but a “sea” of
lipid molecules that can move about from side to side quite freely within their own layers. Among the
lipid molecules are interspersed protein molecules that may “float” only on one or both sides of the
membrane or traverse the whole width of the lipid bilayers. This has become known as the “fluid
mosaic” model (Figure 8) which is currently the more widely accepted explanation of the structure of
plasma membrane.

The cell membrane is thin but sturdy and it is selectively or differentially permeable. Some
materials can pass through it with ease, like gases (CO 2 and O2), water, hydrocarbons, alcohol, urea
and lipid-soluble substances while others enter slowly and with difficulty, including amino acids and
glucose. Whereas, carbohydrates, fats and proteins cannot enter at all; they have to be digested or
broken down into simpler and smaller molecules first before the cell membrane permits them to pass
through.

Membrane Functions
1. It encloses every cell and maintains cellular integrity; it keeps all contents from spilling
out.
2. It is a selective barrier that separates the external from the internal environment of the
cell.
3. It regulates the vital flow of molecular traffic into and out of the cell.
4. It acts as a selective gatekeeper for the entrance and exit of the many substances involved
in cell metabolism.
5. It provides many of the unique functional properties of specialized cells.

Transport Processes Across Biological Membranes

1. Diffusion. This is the movement of particles from an area of higher concentration to an area
of lower concentration of the diffusing particles, thus leading to equalization of the
concentration throughout the area of diffusion. It is also defined as the spreading of the
particles of one substance among the particles of another substance following concentration
gradient (or “downhill” movement of the substance). This include:
a) diffusion of liquid in liquid
b) diffusion of solid in solid
c) diffusion of gas in gas
d) diffusion of liquid in gas
e) diffusion of solid in liquid

2. Osmosis. This is the movement of water across a semi-permeable membrane down a

concentration gradient from an area where the water molecules are more concentrated to an
18
 area on the other side of the membrane where they are less concentrated.The two important
requirements for osmosis to take place are: 1) presence of a semi-permeable membrane and 2)
presence of a concentration gradient.

The concept of osmosis is very important in understanding how animals control their
internal fluid and solute environment. A marine bony fish is hypoosmotic to sea water. As fish
swims into a river mouth, the fish is isoosmotic (the blood solutes are equal in concentration)
to the environment. When it enters freshwater, its blood solutes are hyperosmotic to those in
the environment. The fish must have physiological mechanisms to avoid net loss of water in
the sea and gain of water in the river.

3. Mediated Transport. Nutrients, such as sugars and materials for growth, such as amino acids
must enter the cell and the wastes of metabolism must leave. Such molecules are moved
across the membrane by special proteins called transporters or permeases. .

Permeases form a small passageway through the membrane, enabling solute

molecules to cross the phospholipids bilayer. They are quite specific, recognizing and
transporting only a limited group of chemical substances or even a single substance only.
However, at high concentration of solutes, mediated transport systems show a saturation
effect, meaning the rate of influx reaches a plateau beyond which increasing a solute
concentration does not anymore increase the influx rate. This is because the number of
transporters available on the membrane is limited. When all transporters become occupied by
solutes, the rate of transport is already at a maximum. There are two kinds of mediated
transport mechanisms:

a. facilitated diffusion – the permease assists a molecule to diffuse through the

membrane that it cannot otherwise penetrate. Movement is in a “downhill” direction
only and requires no metabolic energy to drive the transport system. Example:
transport of glucose to body cells

b. active transport – here, energy is supplied to the transport system to move the
molecules against concentration gradient (“uphill” movement). Energy is always
needed to achieve the transport. Example: transport system that maintains the Na and
K ion gradients between cells and the surrounding extracellular fluid.

Most animal cells require a high internal concentration of K +, about 20-50 times
greater inside than outside, for protein synthesis and other enzymatic functions. Na +
may be 10 times more concentrated outside the cell than inside. Both ionic gradients
are maintained by the active transport of K+ into and Na+ out of the cell. In many cells,
the outward pumping of Na+ is linked to the inward pumping of K+ and the same
transport molecule does both. As much as 10% to 40% of the energy produced by the
cell is consumed by the Na-K exchange pump.
4. Endocytosis. This literally means ingestion of material by a cell. It is a collective term that
describes three similar processes: phagocytosis, potocytosis and receptor- mediated
endocytosis.

a. Phagocytosis (“cell eating”) – the pathway for specifically internalizing solid particles.
It is a common method of feeding among protozoans and lower metazoans and it is the
way by which white blood cells engulf cellular debris and uninvited microbes in the
blood. By phagocytosis, an area of the cell membrane, coated internally with actin-
19
 myosin, forms a pocket that engulfs the solid material. The membrane-enclosed
vesicle then detaches from the cell surface and moves into the cytoplasm where its
contents are digested by intracellular enzymes.

b. By photocytosis, small areas of the surface membrane are invaginated into cells to
form tiny vesicles called caveolae. The surface of the caveolae contains specific
binding receptors for the molecule or ion to be internalized. Functions: 1) for intake of
some vitamins 2) translocating substances from one side of the cell to the other and 3)
internalizing signal molecules, such as hormones or growth factors. Potocytosis is
equated with pinocytosis or “cell drinking”.

c. Receptor-mediated endocytosis is a specific mechanism for bringing large molecules

within the cell. Proteins of the plasma membrane specifically bind particular
molecules called ligands, which maybe present in the extracellular fluid in very low
concentrations. The invaginations of the cell surface that bear the receptors are coated
within the cell with a protein called clathrin, hence they are described as clathrin-
coated pits.

As a clathrin-coated pit with its receptor-bound ligand invaginates and is

brought within the cell, it is uncoated, the receptor and the ligand are dissociated and
the receptor and membrane material are recycled back to the surface membrane.
Function: to bring into cells some important proteins and peptide hormones.

5. Exocytosis. The process by which the membrane of a vesicle formed by endocytosis fuses
with the plasma membrane and extrudes its contents to the outside or surrounding medium.
Functions: 1) to remove undigestible residues of substances brought in by endocytosis, 2) to
secrete substances from the cell, such as hormones, and 3) to transport a substance completely
across a cellular barrier. For example: a substance maybe picked up on one side of the wall of
a blood vessel by potocytosis, moved across the cell and then released by exocytosis.

Figure 8. Fluid mosaic model of cell membrane structure

20
Nucleus
Known as the ‘control center’, the nucleus is the most conspicuous part of the cell. It is
generally oval or spherical-shaped, centrally located and filled with a semi-fluid medium called
karyoplasm, nucleoplasm or nuclear sap which is separated from the cytoplasm by a nuclear
membrane. The double-layered nuclear membrane contains nuclear pores for the passage of large
molecules and for exchange of materials between the nucleus and cytoplasm.

Suspended in the nucleoplasm is the nucleolus which is composed of ribonucleic acid (RNA)
and protein. The nucleolus is the site where subunits of ribosomes are formed. Also found inside the
nucleus is the chromatin material which is chemically made up of deoxyribonucleic acid (DNA) and
protein.

Cytoplasm
This cellular part is largely composed of water. The cytoplasm contains two groups of
structures that are essential for maintaining and sustaining the life of the cell. The first group includes
the membrane systems, namely the nuclear envelope, endoplasmic reticulum, Golgi body and
lysosome. The membranes of these structures are also selectively permeable being chemically
composed of phospholipids and protein molecules. The other group of structures is non-membranous
and they are embedded in the aqueous hyaloplasm of the cytoplasmic matrix.

1 Endoplasmic reticulum (E.R.). This consists of an intricate system of flattened cavities lined
with membranes, called cisternae, and is often interconnected with one another. The ER is
most highly developed in secretory cells. There are two kinds: (1) rough ER which is
encrusted on its outer surfaces with small granular particles, the ribosomes. which are
responsible for making proteins for “export” (2) smooth ER, without attached ribosomes and
functions for the synthesis of lipids.

2 Golgi body (Golgi complex, Golgi apparatus) comprises a stack of flattened disc-shaped
cisternae lined with smooth ER. Its main function is to add a carbohydrate group to the
protein manufactured by the rough ER, forming molecules called glycoproteins. Almost all
proteins present in cell secretions are glycoproteins.

Figure 9. Golgi Body

3 Lysosomes are small membrane-bound structures derived from the Golgi body. They contain a
variety of powerful hydrolytic enzymes for intracellular digestion, breakdown of food
materials or foreign bodies that are taken in by phagocytosis and attack worn-out cell
organelles. They are also involved in the rapid breakdown of cellular debris after cell death
through a process called autolysis. Autolysis also occurs during insect metamorphosis or
21
 when a tadpole resorbs its tail. Lysosome malfunction is suspected to be a contributing factor
in certain types of cancer, such as leukemia. Lysosomes are dramatically referred to as
‘suicide bags’.

4 Nuclear envelope provides a barrier which separates the cytoplasmic matrix from the fluid
interior of the nucleus. The nuclear pores are plugged with proteins that actively regulate the
constant traffic of substances between the nucleus and the cytoplasm.

5 Peroxisomes are membrane-bound vesicles that contain enzymes for oxidizing certain organic
molecules resulting in the formation of toxic hydrogen peroxide. The latter is then broken
down by another peroxisomal enzyme into water and oxygen. Peroxisomes are found
abundant in liver cells that metabolize fats and lipids. In germinating seeds, they convert fatty
acids into sugars that are needed by the growing seedlings.

6 Vacuoles are membranous sacs in cells. In animal cells, some of them store food or water
while others excrete waste materials. In most protozoans, contractile vacuoles rid the cell of
excess water.

Organelles
The term organelle describes any self-contained structure found inside living cells. Most
organelles are enclosed by their own membranes (nucleus, mitochondria and lysosomes) while others
are not (ribosomes, nucleolus, microfilaments, microtubules, centriole, cilia and flagella). Organelles
play definite roles in the metabolic activities of the cell.

1. The mitochondria (Figure 7) are the ‘powerhouses’ of the cell that provide energy to power
its activities. They are small round or sausage-shaped organelles found in all eukaryotic cells. Each
has a smooth outer membrane and an inner membrane with folds or cristae that project like shelves
toward the mitochondrial interior. The cristae serve to increase the surface area for the alignment of
enzymes involved in respiration.

22
 Figure 10. Structure of a mitochondrion

The number of mitochondria per cell varies with type and function of the cell. Active cells,
like those of the liver and muscle, have the largest numbers of mitochondria with their interior
containing more cristae than in less active tissues. The organelles are usually located near the sites of
maximum energy utilization. In liver cells, they are interspersed with the rough ER where they
supply the energy needed for protein synthesis.

2. The nucleolus is a dense spherical body located inside the nucleus; it does not have its own
membrane. It is composed of ribonucleic acid (RNA), along with some DNA and proteins. A nucleus
may have more than one nucleolus to manufacture ribosomes. The nucleolus breaks down and
disappears when the cell divides and reforms only when the daughter cells have separated during
telophase.

3. The rigid microtubules form intracellular skeleton or cytoskeleton and act as supporting
structures within the cell. They are also involved in transporting substances from place to place inside
the cell. On the other hand, the microfilaments are associated with cell movements, endocytosis and
migration of whole cells, such as the white blood cells. Microfilaments are long thin threads
composed of a protein called actin while microtubules are bigger, composed of tubulin protein.

4. Animal cells contain a pair of centrioles which usually lie at right angles to each other
adjacent to the nuclear envelope. They do not occur in most plant cells. During cell division, the
centrioles divide and migrate to opposite poles of the cell where they act as a focus for the formation
of the spindle which pulls the chromatids apart to form the future nuclei of the daughter cells.

6. Cilia and flagella are hair-like extensions of the cell involved in cell locomotion and
transport. Cilia are shorter than flagella and act or function in unison while each flagellum is
larger and usually acts individually. Cilia are found lining tubes and ducts in the bodies of
many animals where their beating action helps to maintain a flow of fluid. Whereas, the
whipping action of flagella is responsible for the movement of many protozoans and the
swimming movement of most sperms. Cilia, flagella and centriole are all composed of
microtubules.

Types of cells
There are two basic types of cells that compose all living organisms --- prokaryotic (Figure
11) and eukaryotic (Figure 12) cells. Prokaryotic cells are cells without a distinct or true nucleus
while eukaryotic cells (eu = true) possess a true nucleus. A true nucleus is one that is surrounded by a
nuclear envelope, making it distinct from the rest of the cytoplasm.

23
Table 2. Comparison between prokaryotic and eukaryotic cell.
Characteristics Prokaryotic Cell Eukaryotic Cell
Nucleus Indistinct Distinct
Nuclear membrane absent present
DNA DNA loop in the DNA organized into
cytoplasm chromosomes found
inside the nucleus
Cytoplasm has no cytoskeleton with cytoskeleton and many
very few organelles organelles present
RNA and protein both synthesized in the RNA synthesized in the
same compartment nucleus; protein in the
cytoplasm
Cellular organization mainly unicellular mostly multicellular with
differentiated cells
Cell size generally 1 to 10 um in generally 10 to 100 um
linear dimension in linear dimension
Examples bacteria and protists, fungi, multi-
cyanobacteria cellular plants and
animals

Figure 11. Anatomy of a prokaryotic cell

24
 Figure 12. Anatomy of a eukaryotic cell

Plant vs. Animal cells

Figure 13. Structure of a plant cell

25
 Figure 14. Structure of an animal cell

Table 3. General characteristics of plant and animal cell

Plant Cells
1. Possess cell membrane,
nucleus and cytoplasm
2. Autotrophic nutrition
3. Larger diameter (50 um) 3. Smaller diameter (20 um)
4. Regular shape
5. Rarely motile
6.Chloroplasts usually
present
7. Large sap vacuole at
center of cell
8. Food storage in starch
grains
9. Cellulose cell wall
present
10. Centrioles absent
Animal Cells
1. Possess cell membrane,
nucleus and cytoplasm
2. Heterotrophic nutrition
4. Irregular shape
5. Often able to move about
6. Chloroplasts absent
7. Large sap vacuole absent
8. Food storage in glycogen
granules
9. Cellulose cell wall absent
10. Centrioles present

Levels of Cellular Organization

An organism is unicellular if it consists of only one cell. All the functions of life are
performed within the confines of one microscopic package. Unicellular organisms are so tiny that
they cannot be seen without the use of a compound microscope. These include the bacteria, most
protists and some fungi.

Some unicellular organisms live in colonies, like Volvox. The cells in a colony of Volvox are
of two types; one type functions for reproduction and the other type functions for growth, movement
and maintenance.

Many organisms, including plants and animals, are multicellular, being composed of millions
of cells. A multicellular organism is made up of a hierarchy of cellular organization: cells are
organized into tissues and tissues into organs.

26
 CELLULAR PROCESSES

1. Protein Synthesis
A protein molecule is a macromolecule just like the nucleic acids. It consists of a long chain
of amino acids linked end to end. Some twenty (20) different kinds of amino acids are known to
serve as building blocks of all proteins found in plants and animals. Each of these amino acids is
coded for by a specific genetic code/codon carried by the mRNA molecule. According to the Central
Dogma, protein synthesis is controlled by DNA. The process is summarized as follows: DNA →
messenger RNA → Protein

There can be no protein to perform various functions in the cell without DNA. However,
DNA does not participate directly in the process; instead, an intermediary in the form of messenger
RNA is required. The other two types of RNA, ribosomal and transfer RNAs, are also involved in the
process.

The central dogma implies that protein synthesis involves two important stages or phases ─
transcription and translation. At the beginning of protein synthesis, the parent DNA molecule
replicates or unwinds, resulting in the formation of two unpaired daughter strands. This process is
catalyzed by the enzyme called DNA polymerase.

Transcription
Next, using the enzyme, RNA polymerase, one of the two daughter strands is used as template
or ‘coding strand’ for synthesis of messenger RNA. Only one of the two strands is used because only
one bears the AUG codon (Table 5) that initiates a message. The formation of the messenger RNA
out of the template DNA in the nucleus is called transcription. The coded message in the DNA is
being ‘transcribed’ (copied across) into the new messenger RNA as illustrated below:

Figure 15. Transcription

Transcription sets in when the enzyme RNA polymerase recognizes the “start" sequence in
the DNA coding strand at the beginning of the gene and becomes attached to the DNA at this point.
The DNA-dependent RNA polymerase molecule now travels along the gene and new nucleotides
(from a ‘metabolic pool’) complementary to those in the DNA coding strand are inserted into the
growing mRNA. When the enzyme encounters the base thymine (T), adenine (A) is inserted and
27
similarly, when cytosine (C) or guanine (G) occur in the DNA, G and C, respectively, are inserted
into the mRNA molecule. Since thymine does not occur in RNA, positions in the mRNA strand
opposite adenine in the DNA template are occupied, instead, by uracil (U). Thus, the final mRNA
molecule formed is precisely matched to the DNA template and contains an exactly equivalent set of
instructions, except that the T’s are replaced by U’s.

At the end of transcription, the polymerase enzyme recognizes the “stop” sequence and
becomes detached from the gene region, allowing the DNA molecule to rewind into its normal
double-helix configuration. The completed mRNA molecule is released and travels outside through
one of the pores in the membranes of the nuclear envelope. In this way, the instructions needed for
protein synthesis are transferred to the cytoplasm. These instructions or codes of the mRNA are
technically called codons.

Translation: Final Stage in Information Transfer

Just recently, it was discovered that pieces of the nuclear mRNA were removed in the nucleus
before the finished mRNA was transported to the cytoplasm. Many genes that do not code for the
final protein product are split from the mRNA. Thus, the transcribed mRNA was first ‘edited’ or
‘matured’ before translation in the cytoplasm. The gene segments that were split because they do not
code for the desired protein are now known as introns while those that code for part of the mature
RNA and are actually translated into protein are exons. Moreover, before the mRNA leaves the
nucleus, a methylated guanine “cap” is added at the 5’ end and a tail of adenine nucleotides (poly-A)
is often added at the 3’end. The cap and the poly-A tail are characteristic of mRNA molecule.

The translation process takes place in the ribosomes, each containing about 50% ribosomal
RNA (rRNA) and about 50% protein. The ribosome consists of a large subunit (60S) and a smaller
subunit (40S), both of which are synthesized in the nucleolus and later pass out and assembled in the
cytoplasm. The two subunits of the ribosome remain separate until a molecule of mRNA is available.
Then they lock onto a special sequence of nucleotides at one end of the mRNA called a ribosome
binding site.

Translation process can only take place when the mRNA molecule is attached to a ribosome.
The assembly of proteins on the mRNA-ribosome complex requires the action of another kind of
RNA called transfer RNA (tRNA). Transfer RNAs are large molecules that are folded in a
complicated way in the form of a cloverleaf. The tRNAs pick up free amino acids from the
cytoplasm and deliver them to the ribosome. Each tRNA is accompanied by a specific tRNA
synthetase that sorts and attaches the amino acid to a site at its end by a process called charging.
There are two tRNA sites within the ribosome where a codon or triplet from mRNA can become
attached by base-pairing to a molecule of tRNA (Figure 15 –B).

Each tRNA has a triplet of nucleotides called anticodon at one end and a specific amino acid
linked to its opposite end which is brought into position at the beginning of the protein chain. When
two amino acids are brought together in this way, they become linked with a peptide bond using
energy from a molecule of guanosine triphosphate (Figure 15 C). At the same time, the first tRNA
is disconnected from its amino acid and leaves the ribosome which moves one notch along the
mRNA strand to bring the next codon into position. As this process continues, the ribosome travels
along the mRNA strand adding more amino acids to the growing protein chain (Figure 15 D).

Accurate interpretation of the mRNA message is only possible because each tRNA molecule
has a particular anticodon specific for only one amino acid. However, for reasons which are not fully
28
understood, the first codon to be translated from an mRNA molecule is always the sequence of AUG
corresponding to the amino acid methionine and is called the initiation codon. Therefore,
methionine occurs at the beginning of every protein chain. Translation is terminated when the
ribosome encounters the sequence of the stop codon.

Figure 16. Translation

Amino Acid Activation

Protein synthesis directed by mRNA can continue provided that supplies of tRNA molecules
carrying the appropriate amino acids remain available. The tRNA molecules needed are first
synthesized in the nucleus and become linked to amino acids in the cytoplasm through the process of
amino acid activation. It uses up ATP and requires a specific enzyme for each of the possible tRNA-
amino acid pairs. Energy obtained from ATP is transferred into the formation of a high energy bond
between each tRNA and its corresponding amino acid. This bond energy is greater than that required
for making a peptide bond, so that the formation of peptide bonds within the ribosome becomes a
‘downhill’ process. tRNA molecules released from the ribosomes are reused, thus the cell’s supplies
of tRNA are economically recycled.

29
2. Cellular Respiration
Also known as aerobic respiration, cellular respiration is the oxidation of fuel molecules to
form CO2 and H2O with molecular oxygen as the final acceptor. Oxidation of fuel molecules involves
the removal of electrons and the reduction of the molecule that gains the electrons (redox reaction).

There are three stages of aerobic respiration:

1. Glycolysis – the conversion of one molecule of glucose (6 – C) to two molecules of
pyruvic acid (3- C) through a series of enzyme-catalyzed reactions. During glycolysis, a single
oxidation occurs and each molecule of glucose yields two molecules of ATP. In this pathway, the
glucose molecule is phosphorylated twice: first to glucose - 6 phosphate and then to fructose 1- 6 –
diphosphate using two molecules of ATP. Thus, the fuel has now been “primed” with phosphate
groups and is sufficiently reactive to enable subsequent reactions to proceed.

Phosphorylation is the addition of a phosphate group to a molecule or compound as in:

glucose + P → glucose – 6 - phosphate (here, the phosphate group is attached to C atom
number 6 of glucose). P is derived from ATP through the following reaction: ATP + H 2O →
ADP + P + energy

Fructose – 1 – 6 diphosphate is cleaved into two 3 – C sugars called PGAL or

phosphoglycerate which undergo an oxidation reaction (electrons are removed) with the electrons and
one of the hydrogen ions being accepted by NAD (nicotinamide adenine dinucleotide). NAD then
becomes reduced as NADH. NADH serves as a carrier molecule to convey high-energy electrons.

Figure 17. Glycolysis

The 3 – C sugars next undergo a series of catalyzed reactions ending with the formation of
two molecules of pyruvic acid. Each 3 – C sugar yields two ATP molecules and since there are two 3
– C sugars, four ATP molecules are generated. However, two ATP molecules were used to prime the
glucose initially, thus the net yield ATP molecules are only two. To summarize the 10 enzymatically-
catalyzed reactions in glycolysis: Glucose + 2 ADP + 2 Pi + 2 NAD → 2 pyruvic acids + 2 NADH
+ 2 ATP
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Pyruvic acid is the undissociated form of the acid but under physiological conditions, pyruvic acid
typically dissociates into pyruvate, thus it is correct to use either term.

Glycolysis occurs in the cytoplasm. The two molecules of pyruvic acid formed enter a
mitochondrion. There, each molecule is oxidized and one of the carbons is released as CO 2. The 2 –
carbon residue condenses with coenzyme A to form acetyl coenzyme A or acetyl Co-A. (The removal
of C from a molecule is called decarboxylation.)

Acetyl Co-A is a critically important molecule for it serves as the starter molecule for the
Krebs cycle. Its oxidation in the Krebs cycle provides energized electrons to generate ATP. It is also a
crucial intermediate in lipid metabolism.

2. Krebs Cycle or Citric Acid Cycle or Tricarboxylic Acid Cycle – the degradation
(oxidation) of the 2 – carbon acetyl Co-A in a cyclic sequence. The events that occur during the
Krebs cycle are detailed in Figure 18.

Figure 18. The Krebs cycle in outline form

Hydrogen ions and electrons in the oxidations transfer to NAD (forming NADH) and to
FAD (forming FADH) and a pyrophosphate bond is generated in the form of GTP (guanosine
triphosphate). This high-energy phosphate readily transfers to ADP to form ATP. The overall products
of the Krebs cycle are CO2, ATP, NADH and FADH2.

3. Electron Transport Chain – the transport of H + and electrons from reduced NAD (NADH)
and reduced FAD (FADH2) to the final electron acceptor which is molecular oxygen (O 2); The
elaborate electron transport chain is embedded in the inner membrane or cristae of the mitochondria.
Each carrier molecule in the chain, labeled I to IV, is a large protein-based complex that accepts and
releases electrons at lower energy levels, than the carrier preceding it in the chain. As electrons pass
from one carrier to the next, free energy is released, some of which drives the synthesis of ATP by

31
setting up a H + gradient across the mitochondrial membrane. At three points along the electron
transport system, ADP is phosphorylated to form ATP.

FADH enters the electron transport chain at a lower level than NADH and so yields two
ATP molecules only, unlike NADH that yields three ATP molecules. This method of energy capture is
called oxidative phosphorylation because the formation of high-energy phosphate is coupled to
oxygen consumption.

Figure 19. Oxidative phosphorylations during the electron transport chain

So far, the most widely accepted explanation for the actual generation of ATP during
oxidative phosphorylation is a process called chemiosmotic coupling or chemiosmosis. According to
this model, as electrons from NADH and FADH 2 are carried down the electron transport chain, they
activate proton pumping channels which pump protons (H +) outward and into the space between the
two mitochondrial membranes. As a result, the proton concentration outside rises, producing a
diffusion pressure that drives protons back into the mitochondrion through special proton channels.
These channels are composed of protein complexes that can form ATP by using the inward passage of
protons as inducers. However, until recently, it is not yet understood how the movement of protons is
coupled to ATP synthesis.

The total ATP molecules generated in aerobic respiration using one molecule of glucose is
calculated as follows:

ATP Generated Source

4 Directly in glycolysis
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 2 As GTP ( → ATP) in Krebs cycle

4 From NADH in glycolysis

6 From NADH produced in pyruvic acid to
Acetyl Co - A

4 From FADH2 in Krebs cycle

18 From NADH produced in Krebs cycle

__________

Total 38

- 2 Used in priming reactions in glycolysis

____________
Net 36

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 Figure 20. Summary of aerobic respiration
3. Cell Division

The Role of Chromosomes in Cell Division

34
 Chromosomes are the repositories of the genes that determine the traits of an individual. They
carry the genetic information during asexual (mitosis) and sexual (meiosis) reproduction.
Chromosomes are one of the cellular parts that undergo significant changes during cell division.

Many cells in an organism pass through a well-defined sequence of stages, called cell cycle,
which culminates in division and formation of new cells. Cell division is an essential factor for the
survival of organisms. It is also embodied in the second part of the cell theory previously discussed,
“that cells come from pre-existing cells by cell division”.

Chromosome Structure
DNA in eukaryotic cells occur as chromatin, a complex of DNA with histone and non-histone
proteins, inside the nucleus. In non-dividing cells, chromatin is loosely organized and dispersed in the
nucleoplasm but just before cell division, the chromatin condenses and becomes organized into a
number of discrete bodies called chromosomes (‘color bodies’), so named because they stain deeply
with certain biological dyes. Chromosomes are most distinctly seen under the microscope during the
metaphase stage of mitosis.

Figure 21. Structure of a metaphasic chromosome.

Chromosomes are varied in shapes and lengths. Some are bent and some are rod-like. Their
number is constant for the species. Every somatic or body cell is 2N (contains two sets of
chromosomes) or diploid while sex cell is N (contains one set of chromosomes) or haploid. For
example, each human somatic cell has 46 chromosomes and only 23 chromosomes in each of his sex
cells.

The Cell Cycle

With the exception of nerve and muscle cells, most cells in the body go through a well-
defined sequence of stages, more commonly known as the cell cycle. The cell cycle culminates in cell
division and formation of new cells. It is composed of two periods:
1. Period of non-apparent division known as interphase. This consists of S phase or
synthetic phase preceded by G1 phase and followed by G2 phase (G stands for ‘gap’).

35
 2. Period of division, M phase, which is subdivided into prophase, metaphase, anaphase and
telophase.

Figure 22. The cell cycle

Interphase
During interphase, the cell is metabolically active, synthesizing new proteins and DNA. Thus,
to refer to interphase as “resting stage”.

At the start of interphase, the nucleus of the cell contains a fixed number of chromosomes.
The chromosomes are uncoiled and uncondensed, forming fine threads called chromatin. Also, inside
the nucleus are spherical structures, the nucleoli, which are responsible for synthesizing ribosomal
RNA, transfer RNA and some ribosomal proteins.

Interphase is divided into three shorter stages, G1, S and G2. The most prolonged phase in the
cell cycle is G1 (Figure 22). Its duration usually determines the time for cell multiplication to take
place in different tissues. RNA and functional proteins, including several enzymes are synthesized
during this ‘gap’ resulting in the increase in cell volume. The cell also imbibes water and nutrients,
builds new protoplasm and cytoplasmic organelles like ribosomes, mitochondria, endoplasmic
reticulum, chloroplasts and microtubules.

For most cells, G1 is an important preparatory stage for the replication of DNA that follows.
However, in many organisms, differentiated tissue cells lose the ability to divide and remain locked
in G1. Whereas, nerve cells and muscle cells which also lost proliferative ability, leave the cycle in G 1
and enter G0.

The S phase is considered as the most critical period in the cell cycle which lasts for about 6
hours. Both strands of DNA replicate, that is, new complementary partners are synthesized for both
strands so that two identical DNA molecules (replica) are produced out of the original/parent DNA.
The following example using a short segment of DNA illustrates the process of DNA replication:
A–T A T A−T A−T
G−C G C G−C G−C
C – G unwinding C G replication C − G C−G
T–A T A T−A T−A
T–A T A T−A T−A

36
 G–C G C G−C G−C
Parent DNA 2 unpaired strands 2 daughter DNA molecules

After replication, the two identical DNA molecules lie side by side and provide the two
complete sets of genetic instruction which will eventually pass into the two daughter cells in mitosis.
It is also during the S phase that the centrioles undergo maturation and duplication. These structures
later migrate towards opposite poles of the cell and help in the formation of the mitotic spindle.

The final stage of interphase and preparatory for division is the G2 phase. This represents the
interval during which the RNA and structural proteins needed for the synthesis of chromosomes and
spindle fibers are produced.

The cell cycle is generally completed in 18-24 hours with interphase normally accounting for
at least, 90% of the total cycle. The remaining events are concentrated into a comparatively short
division or M phase (Figure 17). The M phase or period of cell division which typically lasts for 1-2
hours marks the culmination of the cell cycle.

Mitosis
Based on the number of chromosomes, there are two kinds of cells in multicellular organisms:
1) somatic or body cells with characteristically two sets of chromosomes or diploid (2N), and 2) sex
cells or gametes with only one set of chromosomes or haploid (N). Correspondingly, there are also
two methods of cell division. Somatic cells divide and multiply in number by mitosis while sex cells
multiply by meiosis.

Mitosis is a form of cell division in which the daughter cells produced are genetically
identical to the parent cell. In mitosis, one cell gives rise to two daughter cells with chromosome
number that is the same as that of the parent cell. Mitosis functions primarily for growth, repair of
damaged tissues, maintenance of the chromosome number of the species and it is the process that is
involved in asexual reproduction

Mitosis is divided into five stages, namely prophase, prometaphase metaphase, anaphase and
telophase. Some authors distinguish cytokinesis, the cytoplasmic division and separation of the
daughter cells, as the sixth stage. This distinction is important since there are many organisms in
which mitotic division of the nucleus is not directly followed by cytoplasmic division, as in many
fungi.

Prophase
From G 2 phase of interphase, the chromosomes slowly condense; they shorten and
thicken. Under the light microscope, each chromosome visibly consists of sister chromatids linked
together by a structure called centromere. The two chromatids correspond to two identical molecules
of DNA produced during the S phase. Each chromatid contains one molecule of DNA and each is an
exact copy of the other.

As condensation continues, the nucleoli shrink and finally disappear. Prophase is also
marked by the development of an arrangement of microtubules known as the mitotic spindle. The
cytoplasmic microtubules that form the cytoskeleton are broken down, allowing the cell to round up
into a spherical shape and providing a large ‘pool’ of tubulin molecules which are gradually
incorporated into new microtubules. The first of these to appear are the polar fibers which radiate
from a pair of mitotic centers where a pair of centrioles is located in each. The mitotic centers then
move slowly towards opposite poles of the cell.
37
 In animal cells, an aster is formed at each end of the spindle, with fibers radiating in all
directions. In plant cells, the mitotic centers are less well-defined, there is no aster and centrioles are
completely absent. This indicates therefore that centrioles are not directly essential for spindle
formation.

Prometaphase
This stage is marked by the sudden disintegration of the nuclear envelope. The spindle
moves to occupy the central region of the cell and the centromere of each chromosome forms
kinetochores (Figure 16) that come to lie on either of its side. Kinetochore microtubules or
kinetochore fibers project in opposite directions and interact with the spindle, resulting in agitated
movement of the chromosomes.

Metaphase
All the chromosomes are arranged and aligned in the metaphase plate with their
centromeres near the equator of the cell. The kinetochore microtubules lie parallel to the spindle and
pull towards opposite poles, holding the chromosomes in place under tension. Metaphase may last for
a long time, unlike the other stages.

Figure 23. Mitosis

Anaphase
The kinetochores at each centromere suddenly split. The kinetochore fibers then slide
towards opposite poles of the spindle actively pulling the chromatids apart; at the same time, the
spindle lengthens. The net effect of these movements is to form two daughter nuclei, each genetically

38
identical to the other. The two nuclei are identical because the chromatids themselves are identical
molecules of DNA produced by replication.

Telophase
The nuclear membrane reforms, the chromosomes start to uncoil or decondense and the
nucleoli reappear.

Cytokinesis
This is the process of cytoplasmic division, sometimes called cleavage, which usually begins
during the later stages of anaphase or in telophase. A cleavage furrow appears at the equator of the
cell and deepens progressively until the daughter cells separate (Figure 23).

Meiosis

Meiosis is valuable to organisms that undergo sexual reproduction. It is through meiosis that
sex cells or gametes, which are important prerequisites for sexual reproduction, are formed.

Cells that undergo meiosis are diploid, containing two sets of chromosomes, one set coming
from the father and the other set, from the mother, like human spermatogonia and oogonia and
normal human body cells. In these cells, 22 pairs of chromosomes (or 44) match one another exactly
in appearance; they are the autosomes. The 23rd pair consists of the sex chromosomes, X and Y,
which do not look alike. In the spermatogonia of the male, the chromosome complement consists of
44 autosomes + XY while in the oogonia of the female, 44 autosomes + XX. However, even if the
sex chromosome pair (XX) look alike, they need not be genetically identical.

The gametes that are produced in meiosis contain haploid number of chromosomes which is
exactly one half the diploid number. Human gametes have 23 chromosomes, made up of one of each
of the 22 autosomal pairs together with one sex chromosome, either X or Y. The male and female
gametes fuse at fertilization, restoring the diploid number, so that all the cells in the body of the
offspring contain 46 chromosomes again.

Figure 24 shows that meiosis involves two separate cell divisions, referred to as meiosis I and
meiosis II. Mitosis and meiosis have many features in common, except for the occurrence of two
additional processes − synapsis and crossing-over. Both processes occur during prophase I of meiosis
I and they are primarily responsible for the reduction of the chromosome number from 2N to N as
well as variations in the products of sexual reproduction.

Synapsis. This is the pairing of homologous chromosomes to form bivalents. Homologous

chromosomes are two chromosomes that are identical in shape, size and traits that are influenced by
them. One of the chromosomes is contributed by the father and the other chromosome is contributed
by the mother.

Crossing-over. Following synapsis, the sister chromatids of each chromosome break and
rejoin at precisely corresponding points to allow for the exchange of genetic material between them.
Crossing-over is a random event leading to genetic recombination, generating new combinations of
genes. The cross-overs, also called chiasmata, can occur anywhere along the length the
chromosome. Two or 3 chiasmata are typically formed on each pair of chromosomes in the
39
production of human gametes. Gametes which contain new arrangements of genes are called
recombinant types.

Figure 24. Meiosis

Prophase I normally lasts for several days, the chromosomes becoming fully condensed and
undergo desynapsis, remaining linked only where chiasmata have been formed. Subsequently, the
members of each homologous pair, the entire chromosomes with two daughter chromatids each,
separate and later become segregated into the daughter cells of meiosis I.

40
 Meiosis II that follows is simply mitosis and merely serves to separate the chromatids,
resulting in the production of four haploid (N) gametes.

Gametogenesis
This refers to the production of gametes in the testes of the male and the production of eggs in
the ovaries of the female, by spermatogenesis and oogenesis, respectively. Gametogenesis is equated
with meiosis. You will now examine spermatogenesis and oogenesis in Figure 25 and compare the
two processes with meiosis in Figure 24.

Spermatogenesis Oogenesis

Figure 25. Gametogenesis

There are five stages of spermatogenesis, namely spermatogonium, primary spermatocyte,

secondary spermatocyte, spermatid and spermatozoon or sperm. The spermatogonium and primary
spermatocyte are diploid, whereas, the two secondary spermatocytes that are formed after meiosis I,
are haploid. Each secondary spermatocyte enters meiosis II, in turn, producing two haploid
spermatids, or a total of four spermatids from the two secondary spermatocytes. Then the spermatids
transform into tailed spermatozoa by spermiogenesis without undergoing further division but only a
change in shape. There are two genotypes of human sperms produced; these are two X or female
sperms and two Y or male sperms.

41
 Correspondingly, oogenesis is also composed of five stages: oogonium (2N), primary oocyte
(2N), secondary oocyte (N), ootid (N) and ovum (N). The events that occur during each stage of
oogenesis are similar to those of spermatogenesis, except that only one functional ovum is formed at
the end of the process, instead of four. Moreover, remarkably small cells called polar bodies are
formed in oogenesis, none in spermatogenesis. Polar bodies are non-functional cells, meaning that
they are unfertilizable by sperms. They are formed as a result of the unequal distribution of the yolk
substance that is normally found in egg cells, after the first and second meiotic division. Polar bodies
simply serve to receive one-half of the chromosomes in order to produce haploid egg cells.

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