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CHEMICALS OF LIFE

All living organisms are made up chemicals which make up the protoplasm of
their cells. These are known as chemicals of life. They can be grouped into
organic and inorganic chemicals of life.
1. Inorganic chemicals of life

These include water, mineral salts, acids and bases.

Water:
This is the most abundant and most important chemical of life.
The importance of water as a chemical of life originates from its properties.

The physical properties of water

 Water is a liquid at room temperature; because of the strong hydrogen
bonds between the water molecules that keep the molecules close
together;
 Water has a high specific heat capacity; meaning that a relatively large
amount of energy is needed to raise the temperature of water, as much of
the energy is used to break the strong hydrogen bonds;
 Water has a high latent heat of fusion; meaning that ice requires
relatively high amounts of anergy to melt it; and liquid water must lose a
relatively large amount of energy to freeze;
 Water has a high latent heat of vapourisation; meaning that a relatively
large amount of energy is required to vapourise water because of the
strong hydrogen bonds between its molecules;
 Water has a high surface tension; therefore, a very strong film is formed
on its surface as a result of the strong cohesion forces between its
molecules;
 Water has a low viscosity; that is, water molecules can easily slide past
each other;
 Water is a universal solvent; dissolves more substances than any other
solvent;
 Ice is less dense than water; that is, it floats on water insulating the
water below it;

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The significance of the physical properties of water.

 Water is a liquid at room temperature; providing a medium for chemical
reactions in the cells; and an environment to live in by aquatic organisms;
 Water has a high specific heat capacity; temperature changes within water
are minimized, thus enabling aquatic organisms to have a relatively stable
temperature; and their biochemical processes to proceed at more constant
rates;
 Water has a high latent heat of fusion; making cells contents and the
aquatic environments slow to freeze in cold weather;
 Water has a high latent heat of vaporization; therefore, much heat is lost
with minimal loss of water from the body; and evaporation of water during
sweating or transpiration causes marked cooling;
 Water has a high surface tension; enabling some organisms like pond
skaters to land and move on the water surface without sinking; it also
enables water to form droplets on surfaces and run off for example on
feathers of birds;
 Water has a low viscosity; therefore, water can readily flow through
narrow capillaries; and can serve as a lubricant e.g. synovial fluid in
joints;
 Water is a universal solvent; making it a transport medium as in blood,
lymphatic and excretory systems, the alimentary canal, xylem and
phloem;
 Ice is less dense than water; ice floats on the water insulating the water
below it and thus increasing the chances of survival of aquatic organisms
below the ice;
 Water is colourless and transparent; enabling light to penetrate through
allowing aquatic plants to photosynthesis; and enabling aquatic animals
to see through;
 Water is incompressible; providing support in non-woody plants and
maintaining the hydrostatic skeleton in some animals e.g. earthworms;
 Water has a high tensile strength; this allows transportation of a
continuous water column up the xylem of tall trees without splitting;

The importance of water in organisms

 Provides support: e.g results in turgidity of plant cells and it is a
component of the hydrostatic skeleton of some animals like annelids.
 Cooling by evaporation: e.g sweating, panting and evaporation.
 Lubrication in joints.
 Transport medium in plant and animal systems.

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 Habitat for aquatic animals.

 Required for germination of seeds.
 Reagent in hydrolytic reactions in cells.
 Agent of dispersal of seeds and fruits.
 Raw material for photosynthesis.
 Medium of fertilization for swimming gametes like in ferns and mosses.
 Component of cell structure.

2. Organic chemicals of life

Organic chemicals of life are composed of mainly carbon, with other
elements such as hydrogen, oxygen and nitrogen.
They include; carbohydrates, lipids, proteins, nucleic acids and vitamins.

(a) Carbohydrates
 Contain elements carbon, hydrogen and oxygen.
 Have general formula Cx(H2O)y where x and y are whole
numbers.
 The ration of hydrogen to oxygen in the molecule is usually 2:1.
 They can be grouped into: Monosaccharides, disaccharides and
polysaccharides.

(i) Monosaccharides

These consist of a single sugar unit and have general molecular

formula (CH2O)n where n is a whole number.
They are either aldehydes (aldoses) or ketones (ketoses).
They can be categorized depending on the number of carbon atoms
they contain ie:

 Trioses (3C); contain 3 carbon atoms e.g glyceraldehyde and

dihydroxyacetone.
 Tetroses (4C); contain 4 carbon atoms e.g erythrose.
 Pentoses (5C); contain 5 carbon atoms e.g ribulose, ribose and
deoxyribose.
 Hexoses (6C); contain 6 carbon atoms e.g glucose, fructose and
galactose.

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Aldoses and ketoses

In monosaccharides, all the carbon atoms except one have a hydroxyl
group(-OH) attached. The remaining carbon atom is either part of an
aldehyde group in which case the monosaccharide is called an aldose or
aldo sugar, or is part of a keto group in which case the monosaccharide
is called a ketose or keto sugar. Thus all monosaccharides are aldoses
or ketoses. In general aldoses such as glyceraldehyde, ribose, and
glucose are more common than ketoses such as dihydroxyacetone,
ribulose and fructose.

Structures of glyceraldehyde and dihydroxyacetone

Glyceraldehyde Dihydroxyacetone
(aldo sugar) (keto sugar)

Structure of the open chain and ring forms of glucose

Glucose exits in two forms; the open chain form and the ring forms.
There are two ring forms of glucose; alpha (𝛼) glucose and beta (𝛽)
glucose. The three forms exist in equilibrium in aqueous solution, with
0.02% open chain, 36% 𝛼 glucose and 64% 𝛽 glucose.

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Open chain

𝜶 glucose 𝜷 glucose

Functions of monosaccharides in living organisms

 Glyceraldehyde and dihydroxyacetone are intermediates in respiration,
photosynthesis and other carbohydrate metabolic pathways.
 Ribose is used in the synthesis of RNA, ATP and some coenzymes like
NAD and NADP.
 Deoxyribose is used in the synthesis of DNA.
 Ribulose is used in the synthesis of ribulose bisphosphate which is a
carbon dioxide acceptor in photosynthesis.
 Hexoses mainly glucose are a source of energy when oxidized in
respiration.
 Hexoses are used in the synthesis of disaccharides; two
monosaccharide units can be joined forming a disaccharide.
 Glucose is used in the synthesis of polysaccharides which include
starch, glycogen and cellulose.
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General properties of monosaccharides

 Are soluble in water.
 Are sweet.
 Are crystalline.
 Are reducing sugars.

(b) Disaccharides

These are formed when to monosaccharide molecules usually hexoses

combine in a condensation reaction.
The bond formed between two monosaccharides as a result of
condensation is called a glycosidic bond.
Examples of the most common disaccharides include: maltose, lactose
and sucrose.
𝑀𝑎𝑙𝑡𝑜𝑠𝑒 = 𝑔𝑙𝑢𝑐𝑜𝑠𝑒 + 𝑔𝑙𝑢𝑐𝑜𝑠𝑒
𝐿𝑎𝑐𝑡𝑜𝑠𝑒 = 𝑔𝑙𝑢𝑐𝑜𝑠𝑒 + 𝑔𝑎𝑙𝑎𝑐𝑡𝑜𝑠𝑒
𝑆𝑢𝑐𝑟𝑜𝑠𝑒 = 𝑔𝑙𝑢𝑐𝑜𝑠𝑒 + 𝑓𝑟𝑢𝑐𝑡𝑜𝑠𝑒
 Maltose ccurs mainly as a breakdown product during digestion
of starch by enzyme amylase.
 Lactose is also known as milk sugar. It is exclusively found in
milk. It is an important energy source for young mammals.
 Sucrose is also known as cane sugar. It is the most abundant
disaccharide in nature. It is most commonly found in plants
where it is transported in large quantities in the phloem.

Qn. Explain why sucrose I suitable for transportation in the phloem.

 Sucrose is highly soluble in water and therefore can be moved
efficiently in high concentrations.
 Sucrose is relatively unreactive and therefore cannot be used in
metabolism during its transportation.

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Formation of a disaccharide e.g maltose

Maltose is formed when two alpha glucose molecules are combined in a
condensation reaction as shown below.

General properties of disaccharide

 Are sweet.
 Are soluble in water.
 Are crystalline.
 Maltose and lactose are reducing sugars while sucrose is a non-reducing
sugar.

(c) Polysaccharides

These are formed as a result of condensation of many monosaccharide

molecules. i.e they are polymers of monosaccharides.
They include starch and glycogen which are storage polysaccharide and
cellulose which is a structural polysaccharide.

Starch
Starch is a polymer of alpha (𝛼) glucose.
It is a storage carbohydrate in plants but absent in animals.
Starch has two components; amylose and amylopectin.

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Amylose has a straight chain structure consisting of thousands of glucose

molecules linked by 1,4-glycosidic bonds which cause the chain to coil helically
into a more compact shape.
Amylopectin has many branches caused by 1,6-glycosidic bonds and in each
chain, glucose residues are joined by 1,4-glycosidic bonds which cause the
chains to coil helically into a more compact shape;
Amylopectin has twice as many glucose residues as amylose.

Structure of amylose

Structure of amylopectin

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Glycogen
It is also a polymer of alpha (𝛼) glucose but with a more compact and highly
branched structure than starch.
It is a storage polysaccharide in animals and fungi. In animals, it is stored
mainly in the liver and muscles which are both centres of high metabolic
activity.
Glycogen can easily be converted to glucose which is oxidized to release energy
quickly.

Cellulose
It is a polymer of beta (𝛽) glucose. It consists of unbranched straight chains in
which the glucose molecules are linked by 1,4-glycosidic bonds. Hydroxyl
groups project from each chain in all directions and form hydrogen bonds with
the neighbouring chains. The chains associate in groups to form microfibrils
which are arranged in larger groups to form macrofibrils.
When two molecules of 𝛽 glucose line up, the –OH group on carbon atom 1 of
one molecule can only line up alongside the –OH group on carbon atom 4 of the
other molecule if one of the molecules is rotated at 1800 to the other. This is
because the –OH group on carbon atom 1 projects below the ring and the –OH
group on carbon atom 4 projects above the ring. This rotation of successive
glucose residues is the underlying reason why cellulose has a different
structure to that of starch.

Formation of cellulose

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Apart from being a structural carbohydrate, cellulose is an important food

source for some animals, bacteria and fungi.
The enzyme which digests cellulose however is relatively rare in nature and
most animals including humans cannot utilize cellulose.
Ruminant mammals like cows have bacteria living symbiotically in their gut
which produce cellulose enzyme to digest cellulose.
The abundance of cellulose and its relatively slow rate of breakdown means
that substantial quantities of carbon are locked up in this substance.

Lignification
In this process, lignin, a polymer of various sugars and amino acids is
deposited in the spaces between the cellulose molecules making the cell wall
much more rigid and rendering it impermeable.
Once lignification is complete, the protoplasm can no longer absorb materials
from outside the cell, and hence the cell dies. Hence lignified tissue is always
dead.
Plant cells usually concerned with support and conducting water are lignified.

Other sugar related compounds

Some sugars contain nitrogen and hence are called amino sugars.
e.g glucosamine and 𝛽-acetylglucosamine.

Structure of glucosamine Structure of 𝜷-acetylglucosamine

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A polysaccharide that contains amino sugars is called a mucoplysaccharide.

They are found in;
 Basement membranes of epithelial tissues.
 Matrix of connective tissue.
 Synovial fluid of vertebrates.

Compounds closely related to polysaccharides

 Chitin
It closely resembles cellulose in structure and function. It occurs in the cell
wall of fungi and exoskeleton of arthropods.
Structurally it is identical to cellulose except that the –OH group at carbon
atom 2 is replaced by –NHCOCH3.

 Murein
Murein is a polysaccharide which acts as the strengthening material of
bacterial cell walls. It is similar to chitin in structure, containing nitrogen like
chitin.

Qn. Compare the structure of starch and cellulose.

Qn. Explain the adaptations of starch and cellulose for their functions.

(b) Lipids
These include natural fats and oils.
Fats differ from oils in being solids at room temperature while oils are liquids at
room temperature.
Like carbohydrates, lipids contain elements carbon, hydrogen and oxygen but a
fat molecule contains a much smaller proportion of oxygen than a molecule of
carbohydrate.
Lipids are insoluble in water and are said to be hydrophobic. They are non-
polar and cannot hydrogen bonds with water.
Lipids are esters formed by a condensation reaction between an alcohol,
glycerol and organic acids called fatty acids.
Some fatty acids contain one or more double bonds in their hydrocarbon tail
and in this case they are said to be unsaturated. Such fatty acids form fats of
very low melting point or oils which are liquids at room temperature. Such oils
or soft fats can be hardened by hydrogenation as seen in the manufacture of
magarine.
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Fatty acids without a double bond in their hydrocarbon tail are described as
saturated fatty acids and the lipids containing them also said to be saturated.
Lipids formed from such fatty acids are solids at room temperature.

Formation of a lipid
The most common lipids are triglycerides.
A triglyceride is formed from a glycerol molecule and three fatty acid molecules
where each of the three hydroxyl groups of glycerol undergoes a condensation
reaction with a carboxyl group of a fatty acid molecule with formation of an
ester bond.

Functions of lipids
 Act as energy storage compounds; Lipids when oxidized in respiration
release energy which is made available to the cells in form of ATP.
Lipids are good energy storage compounds because:
 They are insoluble in water and therefore can be stored in high
concentrations without affecting the osmotic properties of the cell in
which they are stored and cannot be lost from the cell in solution
 They are compact and hence a lot of energy can be stored within a
small volume of the cell. This is useful in animals where locomotion
requires mass of the body to be kept to a minimum and in plants where
seed dispersal is by wind or insects and a small mass is necessary.
 They have a higher calorific value than carbohydrates i.e a given mass
of a lipid yields more energy on oxidation than an equal mass of a
carbohydrate. This is because lipids have a higher proportion of
hydrogen and an almost insignificant proportion of oxygen compared
with carbohydrates.

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 Insulate the body against heat because fats conduct heat only slowly. For
example in mammals fat is stored beneath the skin (subcutaneous fat)
which increases the body’s ability to retain its heat.
 Source of metabolic water for inhabiting water scarce areas for example in
the case of a kangaroo rat.
 For protection; Fat is usually deposited around delicate body organs such
as kidney and the heart protecting them from physical damage.
 Buoyance; Lipids are less dense than water and hence provide buoyance
in aquatic vertebrates such as sharks and whales.
 Water proofing; Animal skins produce oil secretions which water proofs
the body. Insects have a waxy cuticle to prevent evaporation of water as
do the plants to reduce transpiration.
 Structural components of the cell membrane in form of phospholipids
contributing to its properties.
 Constituent of a myelin sheath which ensures faster transmission of
impulses in myelinated neurons of vertebrates.
 Are solvents of fat soluble vitamins, A, D, E and K.

Phospholipids
These are lipids which contain a phosphate group. The commonest type is
formed when one of the three hydroxyl groups of glycerol combines with
phosphoric acid in a condensation reaction instead of a fatty acid as in
formation of a triglyceride.
The molecule consists of a phosphate head with two hydrocarbon tails from the
two fatty acids. The phosphate head carries an electrical charge and is
therefore soluble in water, i.e it is hydrophilic. The tails are insoluble in water.
Thus one end of the molecule is soluble in water and the other is not, a
property which is important in the formation of membranes.

Waxes
These are esters formed from fatty acids and complex alcohols other than
glycerol. They are used as waterproofing materials by both plants and animals.
Waxes in plants occur in the cuticle of the epidermis on leaves, stems, fruits
and seeds while in animals they occur on the skin and on feathers.

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Steroids
Structurally, steroids are quite different from lipids. They occur in both plants
and animals. Cholesterol is a steroid only found in animals and not in plants.
From cholesterol are made the bile salts, the sex hormones; progesterone,
oestrogen and testosterone, vitamin D and hormones of the adrenal cortex.

Glycolipids
A glycolipid is formed when a carbohydrate is attached to a lipid. The
carbohydrate forms a polar head to the molecule and are also a component of
membranes.

(c) Proteins
These organic chemicals of life differ from carbohydrates and lipids as they
always contain nitrogen in addition to carbon, hydrogen and oxygen and
sometimes sulphur and phosphorous may be present.
Proteins are polymers of amino acids linked together by peptide bonds.

Amino acids
These are the building blocks for proteins. Many amino acids are known to
occur in cells but only 20 are present in proteins.
Plants are able to synthesize all the amino acids they require from simpler
substances but animals cannot synthesize all they need and therefore have to
obtain some amino acids from the diet. Such amino acids that cannot be
synthesized by the animal’s body and are instead obtained directly from the
diet are described as essential amino acids. Those synthesized by the animal’s
body are described as non-essential amino acids and they are made from the
essential ones.

Structure of an amino acid

An amino acid consists of a central alpha (𝛼) carbon atom to which a carboxyl
(-COOH) group, amino(-NH2) group, hydrogen atom and a varying R group are
attached.

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Amino acids are amphoteric

Amino acids have both acidic and basic groups. This means that in solution,
amino acids act as buffers because they prevent changes in pH when a small
amount of an acid or base is added.

Qn. Describe how amino acids act as buffers.

Amino acids are polar molecules

In neutral solution, amino acids exist as ions, with both positive and negative
charges on the basic and acidic parts respectively. Such molecules are
described as dipolar and are called zwitterions.
The pH at which a given amino acid forms a zwitterion is called isoelectric
point.
Below is the structure of a dipolar amino acid molecule (zwitterion).

Formation of a polypeptide
A polypeptide is formed by joining many amino acids.
The carboxyl group of one amino acid undergoes a condensation reaction with
the amino group of another amino acid forming a dipeptide with formation of a
peptide bond between the two amino acids. The dipeptide formed has a free
amino group at one end and a free carboxyl group at the other end and therefore
further condensation between the dipeptide and several other amino acids can
take place forming a polypeptide.

Biological functions of amino acids

 Amino acids are monomers/building blocks during protein synthesis.
 Act as buffers, neutralising hydrogen ions in acidic solution and
hydroxide ions in alkaline solution.
 Act as intermediate metabolites in metabolic pathways; for example in the
Krebs cycle where they are oxidized to release energy during starvation.
 Some act as neurotransmitters e.g glycine and GABA.

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Types of bonds found in protein structure

 Peptide bond; formed by condensation between the carboxyl group of
one amino acid and the amino group of another amino acid.
 Hydrogen bond; formed by the attraction between the hydrogen of the
–OH or –NH group and the oxygen of the –C=O or the nitrogen of the –
NH group.

 Ionic bond; formed by the attraction between the positively charged

basic R groups and the negatively charged acidic R groups.

 Disulphide bond; formed by the oxidation of the neighbouring

sulphydryl groups of two cysteine molecules lining up alongside each
other.

 Hydrophobic interractions; formed by the interaction between the non-

polar R groups of the polypeptide chain.

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Protein conformation
Protein conformation refers to the characteristic three-dimensional shape of a
protein molecule.

The different levels of protein structure

There are four different levels of organization of protein structure which
include; primary structure, secondary structure, tertiary structure and
quaternary structure.

 Primary structure; This refers to the linear sequence of amino acids in a

polypeptide. Each protein possesses a primary structure.

 Secondary structure; The polypeptide chain is folded or twisted in

various way for example into an alpha helix, a beta pleated sheet or a
triple helix. Keratin forms an alpha helix, fibroin forms a beta pleated
sheet, and collagen forms a triple helix.
Keratin is entirely alpha helical and hence fibrous. It is a structural
protein of hair, wool, nails, beaks, feathers, claws, horns and as well as
the vertebrate skin. Its helix is stabilized by hydrogen bonds.
Collagen has three polypeptide chains which are wound around each
other like the strands of a rope to form a triple helix. The three strands
are held together by hydrogen bonds.
Keratin and collagen are structural proteins and this is promoted by the
fact that they are fibrous and insoluble in water.
The presence of disulphide cross-linkages between neighbouring chains
makes keratin tough and within the molecule makes it fold and stretch
like in hair.
In collagen however, stretching does not occur. Its strength is increased
by many triple helices lying parallel to each other to form fibrils, with
covalent bonds between the neighbouring chains. The fibrils can then
unite to form fibres.
Collagen is common in tendons, skin, bone and connective tissue.
Fibroin is a protein found in silk with a beta pleated sheet structure. Its
composed of polypeptide chains adjacent to each other joined together by
hydrogen bonds which are numerous, hence making the structure very
stable and rigid. This structure has a high tensile strength.

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 Tertiary structure; The polypeptide chain bends and folds more

extensively into a compact globular shape; for example myoglobin in
muscles. The tertiary structure of a protein is maintained by all the four
types of bonds and hydrophobic interactions.
Hydrophobic interactions are important in this structure because they
fold the molecule so that the hydrophobic side chains are shielded from
the aqueous surroundings at the same tie exposing the hydrophilic side
chains. This explains why globular proteins are soluble in water despite
having hydrophobic side chains.
 Quaternary structure; More than one polypeptide chain are linked
together by ionic bonds, hydrogen bonds and hydrophobic interactions
forming a large complex protein molecule; for example haemoglobin which
has four polypeptide chains;

Globular and fibrous proteins

(a) Fibrous proteins

These are composed of long parallel polypeptide chains, are insoluble in

water and are very tough. They are mainly structural proreins like keratin
and collagen.
(b) Globular proteins

These consist of highly folded polypeptide chains, are soluble in water and
have metabolic/physiological roles within an organism e.g enzymes and
some hormones.
NB: Fibrinogen is a fibrous protein soluble in water. It forms insoluble fibrin
during blood clotting.

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Differences between globular and fibrous proteins

Globular proteins Fibrous proteins

Are Soluble in water forming Are insoluble in water

colloidal suspensions
Have metabolic functions Has support and structural
functions

Polypeptide chains are folded into a Polypeptide chains form long

spherical shape parallel strands

Have irregular amino acid Have repetitive regular sequences

sequences of amino acids

Amino acid sequence is highly Actual sequence may vary between

specific and never varies between two examples of the same protein
two examples of the same protein
Have relatively unstable structure Have stable structure

Examples include all enzymes and Examples include keratin and

some hormones collagen

Protein denaturation
This refers to the loss of the three dimensional structure of a protein making it
to lose its normal biological function.

Factors which cause protein denaturation

 Heat or radiation(e.g infra-red or ultra-violet light); These supply kinetic
energy to the protein causing its atoms to vibrate violently and so disrupting
the weak hydrogen and ionic bonds.
 Strong acids, strong alkalis and high concentrations of salts; These
interact with negatively charged carboxyl groups or positively charged amino
groups thereby disrupting ionic bonds and long term exposure breaks the
peptide bonds.
 Heavy metals; Cations of heavy metals form strong bonds with negatively
charged carboxyl groups on the R groups of proteins thereby disrupting ionic
bonds.

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 Organic solvents and detergents; These form bonds with hydrophobic

groups and disrupt hydrophobic interactions and this in turn disrupts
hydrogen bonding.
 Mechanical force; Physical movement may break hydrogen bonds.

Functions of proteins in living organisms

 Homeostasis; Act as buffers; for example plasma proteins;
 Transport materials into and out of the cell; for example carrier and
channel proteins;
 Transport oxygen; e.g Haemoglobin;
 Storage of oxygen; e.g myoglobin;
 Aid in blood clotting; e.g fibrinogen;
 Act as receptor sites; e.g proteins in cell membrane;
 Defend the body against disease; for example antibodies;
 Coordination of body activities; e.g hormones like insulin;
 Protection against U.V rays; e.g melanin;
 Act as a source of energy during starvation; e.g storage proteins;
 Support and movement; e.g myosin and actin for muscle contraction;
chondrin for structural support in bone and cartilage; collagen gives
strength in bone, tendons and connective tissue;
 Act as enzymes; e.g digestive enzymes like lipase;
 For sensitivity; e.g Rhodopsin is a photosensitive pigment in the retina;
 Storage of food; for example casein in milk;

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Enzymes
Enzymes are organic catalysts, protein in nature that speed up biochemical
reactions in the body of living organisms.

The importance of enzymes in cells

Enzymes speed up chemical reactions in the body at temperatures suitable for
living organisms. Without enzymes, these reactions would be too slow to sustain
life.
Enzymes control metabolism. Many different metabolic reactions occur in a
single cell at the same time and therefore there is need for function organization
and this is achieved by each reaction being catalyzed by a specific enzyme and
thus metabolism proceeds in gentle steps in an orderly fashion.

Classification of organisms
Enzymes can be grouped into six groups depending on the type of reaction they
catalyse.
(i) Oxidoreductases; catalyse oxidation and reduction reactions e.g
hydrogenases and oxidases.
(ii) Transferases; catalyse the transfer of a chemical group from one molecule
to another e.g transaminases.
(iii)Hydrolases; catalyse hydrolytic reactions in which a large molecule is
broken into two products e.g lipases, peptidases.
(iv) Isomerases; catalyse the rearrangement of groups of atoms within a
molecule e.g mutases.
(v) Lyases; catalyse non-hydrolytic removal of parts of a molecule e.g
decarboxylases.
(vi) Ligases; catalyse the formation of bonds between two molecules using
energy from ATP e.g synthatases.

Different properties of enzymes

 Are protein in nature.
 Are specific in action, that is, each reaction is catalyzed by a specific
enzyme.
 They work efficiently and rapidly. A very small amount of the enzyme
turns a large amount of the substrate into products per minute.
 Enzymes are sensitive to pH changes. Each enzyme has its own pH
range within which it functions efficiently.

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 Enzymes are denatured by excessive heat.

 All enzyme controlled reactions are reversible.
 Enzyme activity is affected by substrate concentration; and enzyme
concentration.
 Rate of enzyme activity is reduced by inhibitors.
 Enzymes lower the activation energy of the reactions they catalyse.

Mechanisms of enzyme action

(a) Lock and key hypothesis

Acccording to the lock and key hypothesis, the shape of the active site of the
enzyme is complementary to that of the substrate. Therefore, the substrate with
the complementary shape binds and fits into the active site exactly, like the way
a key fits into a lock, thereby forming an enzyme-substrate complex which is
maintained by bonds formed between the enzyme and the substrate. At this
point, activation energy is lowered and the reaction occurs forming an enzyme-
product complex. Once the product is formed, it no longer fits into the active site
and escapes into the surrounding medium leaving the active site free to bind
with other substrate molecules;

(b) Induced fit hypothesis

According to this hypothesis, the shape of the active site is not complementary
to that of the substrate but the enzyme and its active site are instead physically
flexible. As the enzyme interacts with the substrate, the shape of the active site
is moulded into a precise shape into which the substrate fits exactly thereby
forming an enzyme-substrate complex which is maintained by bonds formed
between the enzyme and the substrate. At this point, activation energy is lowered
and the reaction occurs forming an enzyme-product complex. Once the product
is formed, it no longer fits into the active site and escapes into the surrounding
medium leaving the active site free to bind with other substrate molecules.

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Factors affecting the rate of enzyme-controlled reactions

(a) Substrate concentration.

At low substrate concentration, the rate of enzyme activity is low because most
of the active sites of the enzymes are unoccupied. Increasing the substrate
concentration increases the rate of enzyme activity because the enzyme-
substrate interactions increase. The rate of enzyme activity increases with
increasing substrate concentration up to a certain point beyond which any
further increase in substrate concentration produces no significant change in
enzyme activity because at this point all the active sites of the enzymes are
saturated and so any extra substrate has to wait until the products are released
from the enzyme’s active site.

(b) Temperature.

Increase in temperature to the optimum increases enzyme activity because

increase in temperature increases the kinetic energy of the enzyme and substrate
molecules thereby increasing their chances of collision leading to formation of
more enzyme-substrate complexes and hence more products are formed.
Above the optimum temperature, increase in temperature decreases enzyme
activity because the bonds that maintain the 3-dimensional shape of the enzyme
are broken causing the shape of the active site to change so that substrates no
longer fit into and hence no enzyme-substrate complex can be formed.

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(c) pH.

Provided the substrate concentration is maintained at a high level and the

temperature is kept constant, an enzyme works efficiently over a particular
narrow pH range. When the pH is altered above or below the optimum pH for
maximum activity of the enzyme, the rate of enzyme activity decreases. This is
because changes in pH alter the ionic charge of the acidic and basic groups of
the enzyme, thereby disrupting the ionic bonding within the enzyme molecule
which in turn leads to distortion of the 3D-shape of the enzyme. The shape of
the active site is altered such that the substrate no longer fits into it preventing
formation of the enzyme-substrate complex and thus enzyme activity reduces.

(d) Enzyme concentration

Provided temperature and other factors are kept at optimum levels, the
rate of enzyme reaction increases with increase in enzyme concentration.

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Enzyme inhibition
A variety of small molecules can reduce or stop the rate of an enzyme-
controlled reaction. These are called inhibitors.
Enzyme activity is a normal part of the regulation of enzyme activity within
cells.
Enzyme inhibition may be competitive or non-competitive.

Competitive inhibition
In competitive inhibition, the inhibitor molecule has a structure which is
sufficiently similar to that of the normal substrate. The inhibitor binds into the
active site of the enzyme preventing the normal substrate from doing so and as
a result, an enzyme-substrate complex is not formed and the rate of enzyme
reaction decreases.
The degree of inhibition depends on the relative concentration of the substrate
and inhibitor present. Therefore, increasing the substrate concentration
increases the rate of the reaction.
For example the enzyme RuBP carboxylase which catalyses the combination of
RuBP with carbon dioxide during photosynthesis is competitively inhibited by
oxygen.

Non-competitive inhibition
In non-competitive inhibition, the structure of the inhibitor molecule is not
similar to that of the substrate and binds to the enzyme at a site other than the
active site thereby distorting the structure of the enzyme and the shape of the
active site and as a result, the enzyme-substrate complex is not formed and the
rate of enzyme reaction reduces; Non-competitive inhibition can be reversible if
the inhibitor binds loosely to the enzyme or irreversible if the inhibitor binds
permanently to the enzyme.
Increasing the substrate concentration does not reduce the effect of the inhibitor
since there is no competition between the substrate and the inhibitor for the
active site.
For example cyanide is a non-competitive inhibitor of enzyme cytochrome
oxidase in the respiratory chain by attaching itself to the copper prosthetic group
of the enzyme.

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Allosteric inhibitors
These are substances present in cells that reversibly bind with an enzyme away
from the active site and cause a change in the structure of the active site so that
the substrate can no longer fit in the active site. These are called allosteric
inhibitors and they provide a way of controlling enzyme activity.

Enzymes and the control of metabolism

In addition to catalyzing the individual reactions in metabolism enzymes play a
part in the control of metabolism and this is achieved in a number of ways
which include:

 End-product inhibition
In a metabolic process that occurs in a series of steps, the end-product acts
as an allosteric inhibitor for the enzyme controlling the first step.
i.e

In the excess of the end-product, D it inhibits the enzyme E1 controlling the

first step so that further formation of B can be temporarily slowed. This
prevents the accumulation of unnecessary intermediates.
End-product inhibition is an example of negative feedback.

 Position of enzymes in the cell

Some enzymes are isolated in particular organelles and in specialized
membranes in that organelle. Substrates are the selectively transported across
the membranes to the particular enzyme system for catalysis to take place.

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 The specificity of enzymes

Enzymes are highly specific in the reactions they catalyse and enzymes are also
very efficient in that a small quantity of enzyme catalyses a large amount of
substrate and so the formation of few enzyme molecules will enhance a given
reaction in metabolism.

Enzyme cofactors
These are non-protein substances which are essential for efficient functioning
of some enzymes.
There are three types of cofactors: Activators, coenzymes and prosthetic
groups.

Enzyme activators
These are inorganic ions that enhance the activity of an enzyme.They mould
the shape of the enzyme or active site such that an enzyme-substrate complex
can be formed. For example enzyme salivary amylase works efficiently in
presence of chloride ions.

Coenzymes
These are non-protein molecules which bind loosely to the enzyme aiding its
catalytic activity; for example NAD, NADP, coenzyme A and ATP. Coenzymes do
not remain attached to the enzyme between reactions. All coenzymes are
derived from vitamins.

Prosthetic groups
These are non-protein organic molecule that bind permanently to the enzyme
aiding it’s catalytic activity; for example haem and FAD;
Haem is an iron containing prosthetic group found in cytochrome and catalase
enzyme.

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NUCLEIC ACIDS
These form the genetic material of all living organisms including the simplest
viruses. The term nucleic acids comes from the fact that they are found mainly
in the nucleus. Nucleic acids are large molecules made of small subunits called
nucleotides. Hence nucleic acids are also called polynucleotides.
There are two types of nucleic acids found in cells;

 Deoxyribonucleic acid (DNA)

 Ribonucleic acid (RNA)

Structure of a nucleotide
A nucleotide has three components:
 A pentose (5-carbon) sugar.
 A nitrogenous(organic) base.
 A phosphate group.
The nitrogenous base is linked to carbon atom 1 while the phosphate group is
linked to carbon atom 5 of the pentose sugar.

The pentose sugar

The pentose sugar in a nucleic acid is either ribose or deoxyribose.
If the nucleic acid contains ribose, it it is called ribonucleic acid (RNA) and if it
contains deoxyribose, it is called deoxyribonucleic acid (DNA).
The only difference in the structure of ribose and deoxyribose is at carbon atom
2 whereby ribose has an oxygen atom attached to carbon atom 2 while
deoxyribose lacks an oxygen atom attached to carbon atom 2.

Ribose Deoxyribose

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Nitrogenous (organic) bases

Each type of nucleic acid, RNA or DNA contains four of the five nitrogenous
bases found in nucleic acids.
These nitrogenous bases include: adenine(A), guanine(G), cytosine(C),
thymine(T) and uracil(U).
RNA contains, A, G, C and U while DNA contains A, G, C and T.
Adenine and guanine are purines while cytosine, thymine and uracil are
pyrimidines.
A purine consists of two rings, one pentagonal and the other hexagonal while a
pyrimidine consists of one ring which is hexagonal.
During the formation of a nucleotide, a condensation reaction occurs between
phosphoric acid and the pentose sugar and between the nitrogenous base and
the pentose sugar resulting in elimination of two water molecules.

Formation of a nucleotide

Diagram for the structure of a nucleotide

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Formation of a dinucleotide and polynucleotide

A condensation reaction occurs between the phosphate group of one nucleotide
and the pentose sugar of the other forming a dinucleotide with formation of a
phosphodiester bond.
The dinucleotide formed has a phosphate group at one end and a pentose
sugar at the other end and therefore further condensation with very many
other nucleotides can take place leading to formation of a polynucleotide.

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Diagram for the structure of a polynucleotide

Ribonucleic acid (RNA)

RNA is a single-stranded polynucleotide where the pentose sugar is always
ribose and the organic bases are adenine, guanine, cytosine and uracil.
There are three types of RNA and these are messenger RNA (mRNA), transfer
RNA (tRNA) and ribosomal RNA (rRNA). All the types of RNA are synthesized on
DNA and are all involved in protein synthesis.

 Ribosomal RNA (rRNA)

It makes up about 80% of the total RNA in cells. It is found in the cytoplasm
where it is associated with protein molecules which together form the cell
organelles called ribosomes.

 Transfer RNA (tRNA)

It makes up about 15% of the total RNA in cells. It is the smallest of all the
three types of RNA. tRNA transfers amino acids found in the cytoplasm to
the ribosome for translation.
There are many different tRNA molecules(more than 20) in a given cell
carrying specific amino acids.

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All tRNA molecules have the same basic structure. The 5’-end of the tRNA
always ends in the base guanine while the 3’-end ends in the base sequence
CCA. The base sequence of the rest of the molecule is variable. The triplet
base sequence at the anticodon is directly related to the amino acid carried
by that tRNA molecule.

Structure of tRNA

 Messenger RNA (mRNA)

It makes up about 3-5% of the total RNA in cells.
This is a single-stranded molecule formed on a single strand of DNA by a
process called transcription.
In the formation of RNA, only one strand of DNA is copied. The base
sequence of mRNA is a complementary copy of the DNA strand copied and
varies in length depending on the length of the polypeptide chain it codes
for. Most mRNA exists within the cell for a short time.

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Deoxyribonucleic acid (DNA)

DNA is a double-stranded polynucleotide where the pentose sugar is always
deoxyribose and the organic bases are adenine, guanine, cytosine and thymine.

Structure of DNA
DNA consists of two polynucleotide chains and therefore it is described as
double-stranded. Each chain forms a right-handed helical spiral and the two
chains coil around each other to form a double helix. The two chains run in
opposite directions, that is they are anti-parallel. Each chain has a sugar-
phosphate backbone with nitrogenous bases which project from it at right angles
and form hydrogen bonds with complementary bases of the opposite chain. This
is called complementary base pairing. Adenine hydrogen bonds with thymine
while cytosine hydrogen bonds with guanine. The distance between the two
sugar-phosphate backbones is constant and equal to the width of a base pair.
A purine pairs with a pyrimidine because two purines would be too large and
two pyrimidines would be too small to span the gap between the two
polynucleotide chains.

Diagram for the structure of DNA

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DNA replication
This is the process by which the cell makes and identical copy of its DNA.
DNA replication starts with the unwinding of the DNA double helix, catalyzed by
enzyme helicase forming single strands of DNA which then act as templates for
the synthesis of new DNA double helices. Enzyme DNA polymerase binds to
each strand and starts to move along it. Every time it meets the next base on the
DNA strand, free nucleotides approach and the one with the correct
complementary base hydrogen bonds with the base in the DNA strand. The free
nucleotide is held in position by this enzyme until it bonds with the preceding
nucleotide. The enzyme continues to move along the strand one base at a time
with the new DNA strand growing as it does so. Since the enzyme moves in only
the 5′ → 3′ direction, the leading strand is copied/replicated continuously while
the lagging strand is copied/replicated discontinuously leaving small gaps in the
newly synthesized strand which are closed by enzyme DNA ligase.
DNA replication is a semi-conservative process because each newly synthesized
DNA molecule retains on the two strands of the parent DNA molecule.

Illustration

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The role of DNA

DNA is a molecule of inheritance. It contains information which controls the
activities of the cell and hence of the whole organism.
Cell activities are directly controlled by enzymes which determine what the cell
breaks down, what it makes and what it developes into. However the
information required for a cell to make a particular enzyme is found in DNA.
Hence DNA controls the activities of the cell through enzymes which are
essentially enzymes.
DNA is a very long molecule compared to an enzyme and given that so many
different enzymes and other proteins are synthesized by cells, the information
necessary for synthesis of a particular enzyme must be only a small
portion/section/piece of DNA. This section is known as a gene.

The gene
The gene can be defined as:
 The basic unit of inheritance.
 The section of DNA that codes for the synthesis of a polypeptide.
A protein/polypeptide is composed of many amino acids. Each amino acid to be
assembled in the protein is determined by a sequence of bases on the DNA.
This relationship between the bases and amino acids is known as the genetic
code. The genetic code is a set of instructions encoded in DNA or RNA that
determines the sequence of amino acids in a protein.

Features of the genetic code

 It is a triplet code: a sequence of three bases codes for one amino acid in
a polypeptide.
 It is degenerate: a single amino acid can be coded for by more than one
codon. E.g the codons GUU, GUC, GUA and GUG all code for the amino
acid valine.
 It is universal: the same codons code for the same amino acids in all
organisms.
 It is non-overlapping: no base of a given codon contributes to the adjacent
codon.
 It is punctuated: has stop codons e.g UGA, UAG and UAA which do not
code for any amino acids and thus mark the end point of a gene and has
start codons e.g AUG which code for amino acids that initiate a polypeptide
chain.

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Protein synthesis
The instructions for the manufacture of enzymes and all other proteins are
located in the DNA which is found in the nucleus while the actual protein
synthesis occurs in the cytoplasm.
Instructions from DNA are carried to the cytoplasm by a molecule called
messenger RNA (mRNA). The process of copying the base sequence of DNA into
a complementary base sequence in the mRNA is called transcription.

Transcription
This is the process by a sequence of bases in a given section of DNA representing
a gene is copied into a complementary base sequence in mRNA. It occurs within
the nucleus of the cell.
A section of DNA unzips/unwinds by breakage of hydrogen bonds between
complementary base pairs by enzyme helicase, thereby exposing single strands
of DNA in that region. One of the strands is selected as a template on which
mRNA is synthesized and this is called the transcribing strand. Enzyme RNA
polymerase attaches to the transcribing strand at a particular base
sequence/promoter site to initiate transcription. Free nucleotides are attracted
and line up opposite the complementary bases on the template DNA strand. As
RNA polymerase moves along the DNA strand, it links these free nucleotides
forming forming mRNA. Once formed, the mRNA molecule peels off its DNA
template and moves out of the nucleus through the nuclear pore to the
cytoplasm. RNA polymerase leaves DNA and the unzipped section of DNA zips
up again.

Amino acid activation

Amino acids are activated by combining with transfer RNA (tRNA) using energy
from hydrolysis of ATP to form an activated aminoacyl-tRNA complex.
The transfer RNA molecule has a sequence of three bases which is
complementary to the base sequence in the mRNA codon and this is called the
anticodon.
The anticodon in tRNA binds to the codon in mRNA during translation.

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Translation
This is the process by which a sequence of bases in mRNA is converted into a
sequence of amino acids in a polypeptide. It occurs within the cytoplasm of the
cell on the ribosome.
The first two codons in mRNA enter the ribosome. The first codon binds with the
aminoacyl-tRNA molecule having the complementary anticodon and carrying the
first amino acid. The second codon then also binds with another aminoacyl-tRNA
molecule having the complementary anticodon. The ribosome holds the mRNA,
tRNA and the associated enzymes in position until a peptide bond is formed
between the adjacent amino acids. Once a new amino acid has been added to
the growing polypeptide chain, the ribosome moves one codon along mRNA. The
first tRNA molecule attached to the polypeptide now leaves the ribosome and
passes back into the cytoplasm to bind with its specific amino acid again. The
ribosome continues to read and translate the mRNA code until it meets the stop
codon. At this point, the polypeptide chain is terminated and it leaves the
ribosome. The polypeptide can then assume secondary, tertiary or quaternary
structure.
NB: Several ribosomes may be attached on a single mRNA molecule forming a
polysome/polyribosome. This allows many polypeptides to be assembled from
a single mRNA strand in a short period of time.
In summary, the process of protein synthesis involves three major stages:
 Transcription.
 Amino acid activation.
 Translation.

Evidences showing that DNA is the hereditary material

 Metabolic stability of DNA: DNA undergoes little or no alteration in
structure.
 Constancy of DNA within a cell: the amount of DNA remains constant for
all body cells since the amount of DNA doubles before mitosis.
 Correlation between mutagens and their effects on DNA: mutagens
alter the structure of DNA and the characteristics of an organism that can
be inherited are also altered.
 Evidence from bacterial transformation: The characteristics of a given
bacterial strain can change if it takes up a free DNA molecule from the
environment and incorporates it into its DNA. This shows that the new
characteristics that the bacterium has acquired are determined by the DNA
it took up from the environment.
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 Evidence from transduction experiments: If a vector virus transfers a

piece of DNA from one bacterium to another, the infected bacterium can
acquire characteristics of the donor.


Adaptations of DNA for its functions

 Sugar-phosphate backbone is held by strong phosphodiester bonds, giving
the molecule stability.
 DNA coils up into a double helix making it more compact to fit in a small
volume of the nucleus.
 The hydrogen bonds between the complementary base pairs are weak,
therefore can be broken to separate the two strands during transcription
and DNA replication.
 Complementary base-pairing enables accurate replication and hence
ensures that DNA remains in the same form from one generation to
another.
 DNA is metabolically stable, therefore it cannot be degraded in the cells
allowing it to remain the same throughout the lifetime of an individual until
it is inherited.
 DNA is a very long molecule and thus stores a lot of information.
 The two strands of DNA are antiparallel which enables the nitrogenous
bases to project towards each other for complementary base pairing.
 The sugar-phosphate backbones form a double helix which protects the
bases against any form of damage.

Differences between DNA and RNA

DNA RNA
Double stranded polynucleotide; Single stranded polynucleotide;
Contains deoxyribose; Contains ribose;
Contains pyrimidine base Contains pyrimidine base uracil;
thymine;
Chemically very stable; Chemically less stable;
Found in the nucleus; Found mainly in the cytoplasm;
Has larger molecular mass; Has smaller molecular;
Exists in one form; Exists in three forms: tRNA,
mRNA, and rRNA;
Ratio of purines to pyrimidines is Ratio of purines to pyrimidines
constant; varies;

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