Chemicals of Life 2024

A-LEVEL BIOLOGY: CHEMICALS OF LIFE BY KUGONZA H ARTHUR – FEB, 2024
CHEMICALS OF LIFE
These are compounds needed to maintain life of living organisms. They are divided into two groups,
i.e.
i) Inorganic compounds e.g. water, vitamins, salts, acids and roughages.
ii) Organic compounds e.g. carbohydrates, lipids, proteins and nucleic acids.
WATER
It is the most important inorganic compound in life and most abundant within living organism.
A human cell contains about 80% water and the whole body has over 60% water.
Water is formed when two hydrogen atoms combine with an oxygen atom by sharing electrons. The
shape of a water molecule is triangular and the angle between the nuclei of atoms is approximately
1050
Water molecules form weak hydrogen bonds with other water molecules nearby and its bonds give
it the unique properties.
Properties of water
i) It is liquid at room temperature.
ii) It has a high heat capacity therefore much energy is used to raise its temperature because it is
used to break the hydrogen bonds which restrict the mobility of the molecules. As a result water
is relatively slow to heat up or to cool down thus a high heat capacity.
iii) Water expands as it freezes unlike other liquids which contract on cooling.
iv) Water reaches its maximum density above its freezing point at 4oC hence when water freezes,
the ice formed is less dense than the water and hence floats on top of the surface. In this way,
ice insulates water below making it less dense and able to float hence the water will be warmer
than the air above.
v) Water has a high surface tension. Surface tension is the force that causes the surface of a liquid
to contract so that it occupies the least area. It is high due to the fact that molecules are oriented
so that most hydrogen bonds point inwards towards other water molecules.
vi) It has a high latent heat of fusion i.e. much heat must be removed before freezing occurs.
vii) It has high adhesive and cohesive properties preventing it from breaking under tension.
viii)It is colourless and transparent.
ix) It has a low viscosity i.e. water molecules slide over each other very easily.
x) It dissolves more substances than any other liquid i.e. it is a universal solvent.
Functions of water
➢ It is a component of cells
➢ It is a solvent and a medium of transport
➢ It is a reagent in hydrolysis
➢ It enables fertilization by swimming gametes
➢ It enables dispersal of seeds, fruits, gametes and larvae stages in aquatic organisms.
Kugonza H. Arthur @ 0701 366 474 - Page 1 of 45

➢ It is important in transpiration in plants.

➢ It is important in translocation in plants.
➢ It enables germination to proceed by activating enzymes, transporting hydrolyzed stored food,
swelling and breaking open the testa.
➢ It is involved in Osmo-regulation in animals
➢ It enables cooling by evaporation as a result of sweating and panting.
➢ It is a component of lubricants at joints e.g. the synovial fluid.
➢ It offers support in hydrostatic skeleton.
➢ It offers protection as a component of mucus and tears.
➢ It enables migration to occur as a result of river flow or ocean currents.
QUESTION: HOW DO THE PROPERTIES OF WATER RELATE TO ITS BIOLOGICAL ROLE?

1) Water is transparent and this allows light penetration in aquatic habitats to enable photosynthesis
of aquatic autotrophs and visibility of aquatic animals.
2) Water has a low viscosity and this allows for smooth flow of water and other dissolved substances
in an aquatic medium for easy transport.
3) It has a high surface tension providing support to aquatic organisms and allowing movement of
living organisms on water surface.
4) Has a high latent heat of vaporization hence a cooling effect on the body surface since
evaporation of water from the body of an organism draws out excess heat.
5) It has a high boiling point thus provides a stable habitat and medium since a lot of heat which is
not normally provided in the natural environment is needed to boil the water.
6) It has a high latent heat of fusion and hence a low freezing point thus providing a wide range of
temperature for survival of aquatic organisms since it prevents freezing of cells and cellular
components.
7) It has a high specific heat capacity which minimizes drastic temperature changes in biological
systems and provides a constant external environment for many plant cells and aquatic
organisms.
8) It has a maximum density at 4o C hence ice floats on top of water insulating the water below
hence increasing the chances of survival of aquatic organisms below the ice.
9) Water is liquid at room temperature providing a liquid medium for living organisms and metabolic
reactions and a medium of transport.
10) It has high adhesive and cohesive forces creating enough capillarity forces for transport in narrow
tubes of biological systems.
11) It is a universal solvent hence providing a medium for biochemical reactions.
12) Water is a polar molecule allowing solubility of polar substances, ionization or dissociation of
biochemical substances.
13) Water is incompressible thus providing support in hydrostatic skeleton and herbaceous stems.
14) Water is neutral hence does not alter the pH of cellular components on their environment.
15) A water molecule is relatively small for easy and fast transport across a membrane.

QUESTION: OUTLINE THE ROLE OF MINERALS AND IONS IN BIOLOGICAL SYSTEMS.

1) They are components of smaller molecules e.g. phosphorus is contained in ATP and iodine is
contained in thyroxin, etc.
2) They are constituents of large molecules e.g. proteins contain nitrogen and sulphur,
phospholipids contain phosphorus, nucleic acids contain nitrogen and phosphorus, etc.
3) They are components of pigments e.g. haemoglobin and cytochromes which contain ion,
chlorophyll contain magnesium, etc.
4) They are metabolic activators e.g. activates glucose before it is broken down in cell respiration,
calcium ions activate ATPase enzyme during muscle contraction.
5) They determine the anion, cation balance e.g. Na+, K+ and Ca+ are important in transmission of
impulses and muscle contraction.
6) They determine the osmotic pressure and water potential so that it does not fluctuate beyond
narrow limits e.g. Na+, K+ and Cl- are involved in water balance in the kidneys.
7) They are constituents of structures in cell membranes, cell walls, bones, enamel and shells.
CARBOHYDRATES
These comprise of a large group of organic compounds which contain C, H and O. They have a
general formula CX(H2O)Y though some do not conform to it e.g. deoxyribose C5H10O4.
Main functions of carbohydrates
➢ They are a primary source of energy being oxidized in the body to release energy.
➢ They are structured components of cells e.g. cellulose making up the cell wall.
➢ They are determinants of osmotic potential of body fluids therefore maintain blood pressure.
➢ They are recognized units on the surface of body cells, i.e. they are component structures of the
surface cell membranes recognized by antibodies.
Types of carbohydrates
1. Monosaccharides (single unit sugars)
2. Disaccharides (double unit sugars)
3. Polysaccharides (several unit sugars)
MONOSACCHARIDES
Monosaccharides (mono=one, saccharide= sugar) are substances consisting of one molecule of
sugar. They are also known as simple sugars.
Properties of monosaccharides
• They have a sweet taste
• They dissolve in water
• They form crystals
• They have a low molecular mass
• Can pass through a selectively permeable membrane.
• They change the colour of benedict’s solution from blue to orange when boiled with the solution
thus they are known as reducing sugars.

Monosaccharides are named using a suffix ‘ose’. They contain either an aldehyde group (CHO) and
are called aldoses or they contain a ketone group (C=O) and are called ketones. Monosaccharides
have a general formula (CH2O) n where:
➢ n=3 (triose sugar)
➢ n=5 (pentose sugar)
➢ n=6 (hexose sugar)
➢ n=7 (heptose), etc.
The most frequent monosaccharides are the hexose sugars; glucose, fructose and galactose.
Hexose sugars
These are sugars with molecular formula C6H12O6 and structural formulae as shown below:
Glucose (aldose)
Glucose Fructose Galactose
Glucose can exist in a number of isomers where it has different structural formulae remaining with
the same molecular formulae.
The hexose sugars can exist in straight or chain form as shown above or in ring form as shown
below:
Fructose exists in rings which are either 5 sided or 6 sided. The six sided are also known as
pyranoses while the 5 sided are also known as furanoses.
Fructose (pyranose) Fructose (furanose) Galactose

Pentose sugars
They have 5 carbon atoms. They are found in nature as ribose and deoxyribose. They exist in
straight and ring forms.
Straight forms Ring forms
Ribose Deoxyribose Ribose Deoxyribose
Ribose occurs in co-enzymes, adenosine triphosphate (ATP) and ribonucleic acid (RNA).
Deoxyribose occurs in DNA (Deoxyribo Nucleic Acid).
TRIOSE SUGARS
They contain 3 carbon atoms. The two occurring trioses are glyceraldehyde and dihydroxyacetone.
Both of them are found in plant and animal cells playing a role in carbohydrate metabolism.

DISACCHARIDES
Monosaccharides combine together in pairs to form disaccharides. This union involves loss of a
water molecule and therefore the reaction is a condensation reaction. The bond formed is a
glycosidic bond. The most common disaccharides are:
1. Maltose formed from linkage of two glucose molecules. It is common in most germinating
seeds and cereals.
2. Sucrose from union of glucose and fructose. It is the main form in stems of sugar canes and
roots of sugar beets which are sources of commercial sugars.
3. Lactose resulting from the union of glucose and galactose and found in milk.
The disaccharides have the following properties:
i) They are sweeter than monosaccharides
ii) They can be crystallized
iii) They are soluble in water
iv) Do not change the colour of Benedict’s solution when heated with it (apart from maltose)- they
are known as non-reducing sugars
v) Can be broken down into simple sugars by dilute mineral acids and enzymes
Note: Maltose can also be formed as a product of starch hydrolysis.
Formation of maltose
C6H12O + C6H12O C12H22O + H2O
Formation of sucrose
POLYSACCHARIDES
Many monosaccharides may combine by condensation reactions to form polysaccharides. A number
of monosaccharides which combine may be variable and the chain can be branched or unbranched.
Properties of polysaccharides include:

✓ Are not sweet

✓ Do not dissolve in water
✓ Cannot be crystallized
✓ They have a high molecular mass.
✓ They are non-reducing sugars
The chains may be folded to make them compact which are ideal for storage. Such a large size of
the molecules makes them insoluble in water and suitable for storage as they exert no osmotic
influence and do not easily diffuse out of the cell.
Starch is the main storage material in green plants while glycogen is for animals.
Upon hydrolysis, polysaccharides are broken down into their constituent monosaccharides.
Not all polysaccharides are used for storage e.g. cellulose is a structural polysaccharide giving
support and strength to the cell walls.
STARCH
It is found in plant parts in form of granules. It is a reserve food formed from any excess glucose
during photosynthesis. It is common in seeds e.g. maize where it is the main food supply during
germination.
Structure: It is a polymer of α-glucose molecules which are held by glycosidic bonds forming chains
of α-glucose units which get folded or coiled into a helix.
Starch has two components i.e. amylose and
amylopectin, that is, 20% amylose, 79% amylopectin
and 1% other substances e.g. phosphates and fatty
acids.
Starch 1-4 linkages of α-glucose monomers. All Amylose stains deep blue with iodine while amylopectin
monomers are in the same orientation. (Compare stains red to purple with iodine.
the positions of the -OH groups highlighted with
those in cellulose)
Amylose is structurally unbranched while amylopectin is branched.

Differences between amylose and amylopectin
Amylose Amylopectin
Consists of unbranched chains. Consists of branched chains
Comprises of only 1,4 glycosidic bonds Comprises of both 1,4 and 1,6 glycosidic bonds.
Gives a blue-black colour with iodine solution Gives a red-violet colour on addition of iodine
solution.
Has a lower RFM Larger RFM
Has less glucose units. Has more glucose units.
QUESTION: How does the structure of starch relate to its roles?

• It is a polymer of α-glucose molecules hence a large molecule making it relatively insoluble in water
hence an ideal storage molecule.
• The α-glucose molecules are held by glycosidic bonds which can be broken down to free glucose
molecules from the stored starch for ATP synthesis during respiration.
• The starch molecule is coiled into a helix with a hydroxide group projecting interiorly making it
insoluble in water hence exerts no osmotic effects in cells and is ideal for storage.
• It is insoluble in water implying that it cannot be lost from the storage cells and tissues in solution
form.
• It is insoluble in water hence it does not affect the osmotic properties of the cells.
• It is highly coiled into a helix making it compact implying that a lot of it can be stored in a limited
space.
Glycogen
It is a major polysaccharide storage material in animals. It stored mainly in the liver and muscles. It
is also made up of α-glucose molecules and exists as granules. However, its chains are shorter (10-
20 glucose units) and is more branched. Glycogen is more soluble than starch.
Cellulose
It comprises up to 50% of a plant cell wall and in cotton it makes up to 90%.
It is a polymer of about 10000 β-glucose molecules forming long unbranched chains which are
parallel to each other with cross linkages between them which give it its stability and a good structural
material.
Structure:
It is a polymer with straight chains of β-glucose units held by glycosidic bonds with the -OH group
projecting out wards from each chain forming cross linkages of hydrogen bonds with adjacent
chains. The cross linking binds the chains together which associate to form micro fibrils that are
arranged in larger bundles to form macro fibrils. In cellulose, every other β-glucose monomer is
upside down with respect to its neighbors

Note: starch lacks the structural properties possessed by cellulose because it lacks cross linkages.
The stability of cellulose makes it difficult to digest and therefore not a good source of food to animals
except those which have cellulase producing microorganisms which live in them in a symbiotic way
e.g., in the rumen of cattle, goats, sheep, etc.
Arrangement of cellulose fibres and microfibers in a leaf tissue
Uses of cellulose
• Rayon produced form cellulose extracted from wood is used in the manufacture of tyre cords.
• Cotton is used in the manufacture of fibres and closes.
• Cellophane used in packaging is produced from cellulose.
• Paper is a product of cellulose.
• Celluloid used in photographic films is also a derivative of cellulose.

QUESTION: how does the structure of cellulose

relate to its roles?
• The cross linking binds the chains together offering
much tensile strength.
• The micro fibrils in cell walls are arranged in
several layers offering protection to the plant cell
preventing it from bursting when water enters by
osmosis.
• The arrangement of micro fibrils in cell walls
contributes to turgidity hence offering support.
• The parallel layers of cellulose are fully permeable
to water and solutes.
• The arrangement of micro fibrils determines the
shape of the cells and hence plant organs since it
determines the direction in which cells expand as
they grow.
• The glycosidic bonds holding the β-glucose units in cellulose can be broken down in presence of
enzyme cellulase so that a free glucose molecule can be respired.
Differences between cellulose and starch

Cellulose Starch
• Consists of a straight chain of beta glucose. • Consists of long chains of 1-4 linked alpha
glucose.
• It’s a structural polysaccharide in plant cell • It’s a storage polysaccharide.
walls.
• Hydroxyl groups project in all directions of the • Hydroxyl groups in the polysaccharide chain
chain. project into the interior.
• Consists of unbranched chains. • Consists of branched chains in amylopectin.
• Neighboring chains form cross linkages. • Does not form linkages between neighboring
chains.
• It is not easily hydrolyzed into constituent • It is easily hydrolyzed into constituent
monosaccharides and disaccharides. monosaccharides and disaccharides.
• The polysaccharide chains are straight and • The polysaccharide forms are coiled to form
parallel. helices.
OTHER POLYSACCHARIDES
1. Chitin: Chemically and structurally, chitin resembles cellulose but differs in possessing an acetyl
group (NH-OCH3) instead of one of the OH groups. Like cellulose, it has a structural function and
is a major component of exoskeleton of insects and crustacea. It is also found in fungal cell walls.
2. Inulin: It is a polymer of fructose and found as a storage carbohydrate in some plants.

3. Mucopolysaccharides: These are carbohydrate derivatives derived from a combination of

sugar molecules and amino acids in a condensation reaction. This group includes hyaruronic
acid which forms part of the matrix of vertebrae connecting tissue.
Heparin, an anti-coagulant also contains mucopolysaccharides. They contain amino sugars and
are found in;
(i) The basement membrane of epithelium
(ii) The matrix of connective tissues
(iii) Synovial fluid in joints of vertebrates
(iv) Matrix of bone and cartilage.
(v) vitreous humor of the eye
Reasons why carbohydrates form a variety of polysaccharides
• They form both 1, 4 and 1, 6 glycosidic bonds. This increases the variety of polysaccharides since
branching can occur e.g. cellulose has only 1, 4 while glycogen and starch have both 1, 4 and 1,
6 glycosidic bonds.
• They use both pentoses and hexoses to form polysaccharides. In some cases, one
monosaccharide is used while in other cases, two or more different monosaccharides are used
in alternating sequences.
• The difference in the level of branching shown by carbohydrate polymers, leads to the formation
of different polysaccharides e.g glycogen is more branched than starch.
• The existence of both alpha and beta forms of certain monomers increases the variety of
polysaccharides. This causes the difference between starch and cellulose.
• The high chemical reactivity of monomers makes them combine with other groups to form related
monomer units. These combine to form different polysaccharides e.g cellulose differs from chitin.
• The existence of both ketoses and aldoses which form both five numbered and 6 numbered rings.
This causes the difference in certain polysaccharides e.g insulin is different from starch.
FOOD TESTS ON CARBOHYDRATES

1. Test for reducing sugars
The reagent used is Benedict’s solution (blue) or Fehling’s solution (blue). Boiling is required.
Procedure Observation Conclusion
To 1 cm3 of food Colourless or turbid solution turned to a blue Too much; reducing
solution, add 1 solution, then to a green solution, to a yellow sugars present.
cm3 of Benedict’s precipitate, to orange precipitate and to a brown
solution and boil. precipitate on boiling.
Colourless or turbid solution turned to a blue Reducing sugars absent.

solution which persists on boiling.
If Fehling’s solution is used, the change is from blue solution to orange precipitate if reducing sugars
are present. It remains a blue solution if they are absent.
Examples of reducing sugars include:
1) Glucose (present in grapes)
2) Fructose (present in many edible fruits)

3) Galactose and lactose (present in milk)

4) Maltose (present in germinating seeds)
2. Test for non-reducing sugars

procedure Observation conclusion
3
To 1 cm of food solution add 1 Colourless or turbid solution Little or
cm3 of dilute hydrochloric acid turned to a blue solution, then Moderate or
and boil, cool under water then to a green solution, to a yellow Much or
add 1 cm3 of sodium hydroxide precipitate and to a brown Too much; non-reducing
solution, followed by 1 cm3 of precipitate on boiling. sugars present.
Benedict’s solution and boil.
Colourless or turbid solution Non-reducing sugars absent.
turned to a blue solution which
persists on boiling.
Note:
i) When boiled with dilute HCl, the non- reducing sugars breaks down into the reducing sugars.
ii) Sodium hydroxide solution or sodium hydrogen carbonate powder is added to neutralize the acid
so that Benedict’s solution can work.
An example of non-reducing sugars is Sucrose (present in sugar cane)
3. Test for starch:

The reagent used is iodine which is a brown or yellow solution).
3
To 1 cm of food solution, add Colourless or turbid solution Much or moderate or little
3 drops of iodine solution. turned to a black or blue-black starch present.
or blue solution or brown
solution with black specks.
Colourless or turbid solution Starch absent.

turned to a yellow or brown
solution.
LIPIDS
These are large group of organic compounds. Like carbohydrates, they contain carbon, hydrogen
and oxygen but the proportion of oxygen is smaller than in carbohydrates hence they are more
reduced than the carbohydrates.
Lipids are insoluble in water. They are of two types i.e. fats and oils. Fats are solid at room
temperature while oils are liquids at room temperature.

Properties of lipids
• They are insoluble in water but soluble in non-polar solvents like benzene, chloroform, diethyl
ether, etc. The low solubility is due to the low oxygen content which results into a small number
of polar hydroxyl groups in lipids hence very few hydrogen bonds.
• They have a high proportion of hydrogen in their molecules.
• They are non-polar compounds.
• They are less dense than water.
• They can be solids or liquids at room temperature.
• Their melting point increases with increase in saturation.
• They undergo high oxidation in respiration to yield large amounts of energy.
• They are poor conductors of heat.
Formation of triglycerides
Lipids are made of fatty acids and glycerol. Glycerol has 3 OH groups and each combines with a
separate fatty acid to form a lipid chemically known as a triglyceride. This is a condensation reaction
that leads to liberation of 3 water molecules.
Metabolic water is formed and an ester bond is formed between the glycerol and fatty acid. Since
the glycerol possesses 3 hydroxyl groups to which 3 fatty acids attach themselves, 3 water
molecules are formed. In this reaction, the fatty acids may all be the same or different, saturated or
unsaturated.
For example

Question: using the structural formula:
For glycerol, and molecular formula

CH3(CH2)nCOOH for a fatty acid, show
the formation of a triglyceride from
fatty acids and glycerol.
FATTY ACIDS
All occurring lipids have glycerol and therefore it is the nature of the fatty acids which determines
the characteristics of any particular lipid. All fatty acids have a carboxyl group (COOH), the reminder
of the molecule being a hydro carbon chain of varying length.
These chains may possess one or more double bond in which case it is said to be unsaturated. If it
possesses no double bonds, it is said to be saturated.
Nature of fatty acid General formula Saturated/unsaturated Occurrence
1. Butyric acid C3H7COOH Saturated Butter fat
2. Linoleic acid C17H31COOH Unsaturated Seed oil
3. Oleic acid C17H33COOH Unsaturated All fats
4. Palmitic acid C15H31COOH Saturated Animal & veg fat
5. Selotic acid C25H51COOH Saturated Wood oil
6. Arachidic C19H39COOH Saturated P.nut oil
acid
From the table, it is seen that the hydrocarbon chains may be very long forming long tails which
extend from the glycerol molecules. These trails are hydrophobic (water repelling) which makes the
lipids insoluble in water.
Saturated and unsaturated fatty acids
In saturated fatty acids all the available bonds in carbon atoms are used and there are a maximum
possible number of hydrogen atoms. Saturated fatty acids lack double bonds in the hydrocarbon tail.
Unsaturated fatty acids do not contain the maximum number of hydrogen atoms, they have one or
more double bonds between some of the carbon atoms in the hydrocarbon chain.
Saturated fatty acids have high melting points and are therefore found in fats while in unsaturated
fatty acids, the presence of the double bonds lowers the melting point and are therefore found in
oils. Since there are many types of fatty acids but one type of glycerol, lipids (fats and oils) vary due
to the fatty acids.

Essential fatty acids

These are fatty acids which cannot be synthesized by the body and must be supplied in the diet.
Common sources of essential fatty acids are; vegetables and seed oils. A deficiency of these fatty
acids results in retarded growth, reproductive disorders and kidney failure.
Non-essential fatty acids
These are fatty acids that can be synthesized by the body from metabolism of other compounds like
proteins and carbohydrates.
How cholesterol causes arthesclerosis
Cholesterol is produced by the liver and is used as the starting point for the synthesis of other steroid
molecules. The major source of cholesterol is diet and many dairy products are rich in cholesterol
or fatty acids from which cholesterol can be synthesized. Thyroxin stimulates cholesterol production
in the liver and also increases the rate of excretion of bile. Excessive amounts of cholesterol in blood
can be harmful. It can be deposited in walls of arteries leading to arthesclerosis and increased risk
of formation of a blood clot which may block blood vessels, a condition known as thrombosis. This
is often fatal if it occurs in the coronary artery in the wall of the heart (coronary thrombosis or heart
attack) or brain (cerebral thrombosis). Although cholesterol is harmful in excess, it is essential to
have some in the diet for reasons stated.
Question: explain why lipids are insoluble in water?
LIPID DERIVATIVES
1. Waxes; these are composed of one fatty acid and a long-chained alcohol other than glycerol.
They are used as water proof substances by plants and animals. In plants they occur in the
cuticle of the leaves, meristems, fruits and seeds of some plants. In animals they are a constituent
of the exoskeleton of insects, arthropods. They also form the combs of bees.
2. Glycolipids; these are a combination of a carbohydrate and a liquid. They are found in the cell
membrane where they have a structural function and they are important in transportation of
materials across the cell membrane.
3. Phospholipids; these are lipids containing a phosphate group. In the formation of a
phospholipid, a phosphate group is added to the third carbon atom in the position of the hydroxyl
group. The other two hydroxyl groups of the glycerol react with fatty acids.
A phospholipid therefore has a phosphate group and two fatty acid chains. The phosphate group
carries an electric charge and hence contributes to the polarity of the phospholipid molecule. The
phosphate group forms the polar end i.e water soluble hydrophilic head while the fatty acid
hydrocarbon chains form the nonpolar water-insoluble hydrophobic end of the phospholipid
molecule.
Phospholipids are able to dissolve in both water and non-polar solvents. This property is
important in determining the structure and function of the plasma membrane.

Structure of the phospholipid
A phospholipid can be simply represented as
4. Steroids; these are biologically important substances in both plants and animals.
The skeleton of a steroid molecule consists of four complex rings of
carbon atoms. Three of these are six sided while one is 5 sided. The
various steroids differ in the side groups attached to the carbon atoms
of the skeleton. Like lipids, they contain hydrogen atoms and oxygen
atoms but do not contain any fatty acid. They have a general skeleton
shown below.
Examples of steroids include;
Cholesterol which is a component of the plasma membrane and a raw material for many other
steroids like bile acids.
Bile acids e.g glycolic acid and taurochloric acid used in the emulsification of fats during digestion.
Vitamin D (calciferol) which promotes phosphorous and calcium absorption and metabolism.
Sex hormones e.g testosterone and oestrogen. Hormones from adrenal cortex are referred to as
corticosteroids.
FUNCTIONS OF LIPIDS
Structural:
i) They are components of the plasma/cell membrane.
ii) They form subcutaneous fat in the dermis of the skin hence insulating the body since they are
poor conductors of heat.
iii) They are components of the waxy cuticle in plants and insects there by preventing water loss
(desiccation).
iv) They form a component of the myelin sheath of nerves hence playing a role in the transmission
of impulses.
v) They protect delicate organs e.g. the heart and kidney from injury.
vi) They coat on fur of animals enabling it to repel water which would otherwise wet the organism.
vii) They are component of adipose tissue.
Physiological:
i) They provide energy through oxidation.
ii) They are solvents for fat soluble vitamins (ADEK).

iii) They are a good source of metabolic water to desert animals, young birds and reptiles while still
in their shells.
iv) They are a constituent of the brown adipose tissue which provides heat for temperature
regulation (thermogenesis).
Other functions:
i) Some lipids provide a scent in plants which attracts insects for pollination.
ii) Wax is used by bees to construct honey combs.
iii) Wax from bees is used in the manufacture of candles.
QUESTION: What properties do lipids possess as storage compounds?

i) They are compact taking up little space.
ii) They are insoluble in water hence cannot be lost in solution.
iii) They are light to keep the weight to a minimum and allow buoyancy.
iv) They have a high calorific energy value.
v) They have a high hydrogen-oxygen content hence can yield a lot of water on oxidation.
TESTS FOR LIPIDS

They are tested for using the emulsion test or the grease spot (translucent spot) test.
a) Sudan III test:
Procedure Observation Deduction
To 1 cc of food solution, A turbid solution turns a red emulsion. Lipids present.
add 1 cc of Sudan III
and shake. Turbid or colourless solution remains a Lipids absent.
turbid or colourless solution.
b) The emulsion test:

The reagents used are ethanol and water.
Procedure Observation Deduction
To 1 cc of food solution, add A turbid solution turns to a cream Lipids present.
1 cc of ethanol and shake. emulsion
Then add 5 drops of water Turbid or colourless solution remains a Lipids absent.
and shake. turbid or colourless solution.
c) Translucent spot test:

Add 2 drops of test solution A translucent spot or patch is left on the Lipids present
on a piece of filter paper. paper.
Allow to dry and observe No translucent spot is formed on the paper. Lipids absent.
under light.

PROTEINS
These are organic compounds of large molecular mass and insoluble in water. In addition to C, H
and O, they always contain N, usually S and sometimes P.
Whereas there are few carbohydrates and fats, the number of proteins is limitless e.g. a single
bacterium may have around 800 types of proteins while man has 10,000 types. This is because
there are several amino acids which may join in different patterns hence forming the various types
of proteins.
Proteins are specific to each species hence determine the character of the species.
Proteins are not stored in the organism except in eggs and seeds where they are used to form new
tissues.
Proteins form the structural basis of all living cells.
Their building blocks are the amino acids.
Amino acids
These are groups of many chemicals of which around 20 occur in proteins. They contain an amino
group (NH2) and a carboxyl group (COOH). Most amino acids have one of each and are therefore
neutral but a few have more amino groups than carboxyl making them alkaline or may have more
carboxyl than amino groups making them acidic.
Chemical structure of an amino acid
Amino acids are soluble in water and ionize to form ions.

The carboxyl end of the amino acid is acidic in nature. It will ionize in water to give H+. This will make
the COOH group negatively charged.
The amino end (NH2) is basic in nature. It attracts the H+ in solution making it positively charged.
The ion is now dipolar i.e. having a negative and a positive pole. Such ions are called zwitter ions
i.e. the negative and positive charges exactly balance and the amino acid ion has no overall charge
i.e.
Zwitter ion (no overall charge)

Therefore, in acidic solutions, an amino acid acts like a base and in alkaline solutions, it acts as an
acid. In neutral conditions found in the cytoplasm of most living organisms, the amino acid acts as
both.
Amino acids therefore show both acidic and basic properties i.e. they are amphoteric.
The overall charge of the amino acid depends on the pH of the solution.
At some characteristic pH, the amino acid has no overall electric charge i.e. it exists as a zwitter ion.
This pH is called the isoelectric point of an amino acid.

If the pH falls below the iso-electric point i.e. the solution becomes more acidic, H+ are taken up by
the carboxyl ion. This reduces the concentration of the H+ in solution making the solution less acidic
and the amino acid gains an overall positive charge.
If the pH rises above the iso-electric point i.e. it becomes less acidic or more alkaline, hydrogen ions
are lost by the amino group. This increases the concentration of free H + in the solution making it
more acidic and the amino acid gains an overall negative charge. Therefore, being amphoteric,
amino acids are buffers.
NOTE: a buffer solution is one which resists the tendency to alter its pH even when small amounts
of acid or base are added to it.
Questions: How do amino acids act as buffer solutions?

Amino acids make the proteins serve as buffers. The amphoteric nature of amino acids is useful
biologically as it means that they serve as buffers in solution resisting changes in pH. The buffer
action depends on concentration of hydrogen ions. When a medium/solution becomes acidic (more
H+), the hydrogen ions are accepted by the amino groups on the amino acids making them positively
charged hence reducing the H+ concentration in the solution. When a medium/solution becomes
alkaline (decrease in H+ concentration of the solution) the carboxyl group of the amino acid releases
H+ to the solution making them negatively charged hence adding H+ to the solution.
Types of amino acids

1. Essential Amino acids 2. Non-Essential amino acids
These are amino acids that cannot be These are amino acids that are synthesized by
synthesized by the body and therefore got from the body through a process called
the diet that the organism feeds on (essential in transamination. They are not a dietary
the diet). There are nine amino acids—histidine, requirement. There are 11 non-essential amino
isoleucine, leucine, lysine, methionine, acids which include Alanine, Arginine,
phenylalanine, threonine, tryptophan, and Asparagine, Aspartic acid, Cysteine, Glutamic
valine. acid, Glutamine, Glycine, Tyrosine, Proline, and
A simple mnemonic to remember the essential amino Serine.
acids is Try THis VIP MaLL A simple mnemonic to remember the non-essential amino
Tryptophan acids is “Ah, Almost All Girls Go Crazy After Guys Take
Threonine Proposal Seriously”.
Histidine Alanine
Valine Arginine
Isoleucine Asparagine
Phenylalanine Glutamic acid
Methionine Glutamine
Lysine Cysteine
Leucine Aspartic acid
Glycine
Tyrosine
Proline
Serine
Proteins can be classified as first-class proteins which contain all the essential amino acids e.g.
beans and second-class proteins which are deficient in one or more of the essential amino acid.

Formation of polypeptides
They are formed as a result of condensation reaction between the amino group of one amino acid
and the carboxyl group of another amino acid to form a dipeptide.
Further combinations of this type extend the length of the chain to form a polypeptide which usually
contains many amino acids.
The shape of the polypeptide molecule is due to four types of bonding which occur between the
various amino acids in the chain.
Formation of cross linkages in polypeptide chain(s)
The polypeptide chains in a protein are joined together by bonds of different types. The bonds are
formed between the amino acids in the chains due to their different properties i.e acidic, basic,
hydrophobic, etc. these bonds include;
i) Ionic bonds:
These are formed between basic and acidic groups of some amino acids forming a strong
interaction. These bonds are formed between acidic amino acids and basic amino acids e.g between
aspartic acid and lysine.
ii) Disulphide bonds:
These occur between amino acids that have sulphur. These amino acids contain the sulphurdyl
group (-SH) in their R groups. If two molecules of cysteine line up alongside each other, the
neighboring sulphurdyl groups are oxidized to form a disulphide bond.
Disulphide bonds may be formed between different chains of amino acids or between different parts
of the same polypeptide chain. These are the strongest bonds and are not easily broken.
iii) Hydrogen bonds:
These are weak bonds formed between hydrogen
atom in one amino acid and a highly electronegative The polypeptide chain
element in another amino acid.
Though they are weak, their occurrence is frequent
and their total effect makes a considerable
contribution to the stability of the protein molecule.
iv) Hydrophobic bonds/interactions:
These are as a result of non-polar R groups of amino
acids in polypeptide chains. They are weak forces of
attraction and point inward to the protein. If a
polypeptide chain has hydrophobic groups and is in
an aqueous environment, the chain folds because of
the attraction between the hydrophobic groups. The
hydrophobic groups come into close contact and
exude water, hence pointing inwards as the
hydrophilic groups point outwards.
Protein structures
There are four protein structures i.e., primary, secondary, tertiary and quaternary structures.

1. Primary structure:
It is a sequence of amino acids in a polypeptide chain. It is made up of 2 polypeptide chains held
together by di-sulphide bridges. The sequences of amino acids of a protein dictate its biological
functions. Examples of primary structures are insulin and lysosomes.
2. Secondary structure:
This involves folding or twisting of the polypeptide chains into a spiral shape or beta-pleated shape.
It is maintained by many ionic bonds which are formed between neighboring COO- and NH3+ groups.
(i) Spiral shape;
Proteins take the shape of an alpha helix. They are hard but stretchable. The
helical structure is maintained by hydrogen bonds. Examples of such
proteins include; keratin, collagen, etc. keratin is found in hair, beaks, nails,
feathers, claws, horns, etc.
(i) Beta pleated sheets:

Beta pleated sheets have a flat zig zag structure which result
from the folding of two or more adjacently joined parallel
polypeptide chains which are stabilized by hydrogen bonds.
They then get arranged into sheets. Proteins with this
structure are very stable and rigid (unstretchable) e.g fibroin
protein found in silk. They commonly occur in insoluble
structural proteins but also in parts of some soluble proteins.
Tertiary structures
The polypeptide chain coils extensively forming a compact globular shape. This structure is
maintained by interaction of the four types of bonds i.e., ionic, hydrogen, di sulphide bonds and
hydrophobic interactions.
The hydrophobic interactions are quantitatively the most important and occur when a protein folds
to shield the hydrophobic side groups from the aqueous surrounding and at the same time exposing
hydrophobic side chains.
Quaternary structure
It is a combination of several polypeptide chains clumped together and associate with non-protein
parts to form complex proteins e.g., in haemoglobin.

Types of proteins
1. Fibrous proteins (plays structural roles)
These form long chains which may run parallel to one another being linked by cross bridges. They
are very stable molecules and have structural roles within the organism e.g. collagen in made of
such proteins.
It has a primary structure which is a repeat of tri peptide sequence (glycine, proline and alanine) and
forms a long unbranched chain.
2. Globular proteins (plays metabolic roles)
They have a highly irregular sequence of amino acids in their polypeptide chains. Their shape is
compact and globular. All enzymes are globular proteins. Others include hormones and
haemoglobin.
3. Conjugated proteins
These are proteins which incorporate other chemicals within their structure. The non-protein part is
the prosthetic group and plays a virtual role in the functioning of the proteins e.g.
Name of protein Where it is found Prosthetic group
Haemoglobin Blood Haem (iron)
Mucin Saliva Carbohydrate
Casein Milk Phosphoric acid
Cytochrome oxidase Electron carrier path way Copper
Nucleoplasm Ribosomes Nucleic acid
QUESTION: How does the molecular structure of proteins relate to their roles?
• Some proteins have a structural function, these are fibrous proteins with a secondary structure
insoluble in water and physically tough e.g., collagen in connective tissues, bone, tendons and
cartilage. Other structural proteins include keratin in feathers, nails, hair, horns, beaks and skin.
• Some proteins function as enzymes. These have a globular structure and are soluble in water
e.g., digestive enzymes like pepsin, respiratory and photosynthetic enzymes.
• Some proteins function as hormones regulating metabolic processes. These are globular and
soluble in water e.g., insulin which regulates metabolic activity.
• Some proteins functions as respiratory pigment. These are globular proteins with a quaternary
structure that increases their surface area for transport or storage of respiratory gases e.g.,
haemoglobin which transports oxygen in blood and myoglobin that stores oxygen in muscles.
• Some proteins are involved in transport and are globular with primary or tertiary structures e.g.,
serum albumen that transports fatty acids and lipids in blood.
• Some proteins are involved in immunological responses hence protecting the body. These are
globular e.g., antibodies, fibrinogen and thrombin.
• Some proteins are contractile e.g., they are fibrous with a secondary structure e.g., myosin and
actin filaments in muscles.
• Storage proteins are toxins and soluble and water with a globular structure e.g., snake venom,
bacteria toxins, etc.
• Globular proteins in blood are buffers since they are soluble in water.

• Some proteins are insoluble in water e.g., ovalbumin that occurs in egg white, casein in milk,
which act as water reservoir.
• Globular proteins form colloidal suspensions that hold molecules in position within cells e.g.
proteins in the cytoplasm of most cells where they are soluble in water and have a large surface
area.
Differences between globular and fibrous proteins
Globular Fibrous
Soluble in water Insoluble in water
Easily denatured by very high temperature Not easily denatured by high temperature
Functional in nature Structural in nature
Tertiary proteins Secondary proteins
Non identical polypeptide chain length Identical polypeptide chain length
Consist of compact and spherical molecules. Consist of long fibrous molecules.
Denaturation of proteins
The dimensional structure of the protein is due to weak ionic and hydrogen bonds. Any agent which
breaks these bonds causes the three-dimensional shape to be changed to a more fibrous form. This
process is known as denaturation.
In case the actual sequence of the amino acid is not altered but only the overall shape of the
molecule is changed.
Factors causing protein denaturation
Factor Explanation Example
1. Heat Causes the atoms of the protein to vibrate more Coagulation of albumen
thus breaking the hydrogen and ionic bond hence (egg white becomes more
distorting the protein structure. fibrous).
2. pH Alkalinity or acidity causes the charged ions of a Pepsin structure is changed
protein to reassociate causing a change in the in alkaline medium.
protein structure.
A change in pH also weakens the forces holding
the protein molecule together hence changing the
shape and denaturing the protein.
3. Acids Addition of hydrogen ions in acids combine with Souring of milk by acid and
COO- of amino acids and form COOH ionic bonds lowering pH of casein
are hence broken. making it insoluble.
4. Alkalis + + +
Reduced number of H cause NH group to lose H Souring of milk by alkalis.
to form NH2 therefore ionic bonds broken.
5. Inorganic Ions of heavy metals e.g., mercury and silver Enzymes are inhibited by
chemicals combine with COO- groups destructing the ionic being destructed in
bonds. presence of ions e.g.
cytochrome oxidase.
6. Organic Organic solvents alter hydrogen bonding with a Alcohol denatures certain
chemicals protein. bacterial proteins.

7. Mechanical Physical movement can break hydrogen bonds. On stretching a hair, the
force hydrogen bonds in the
keratin helix are extended
and hair stretches.
Functions of proteins
Vital activity Protein example Function
1. Nutrition Digestive enzymes e.g., Enzymes catalyze hydrolysis of complex
trypsin, amylase substrates to small soluble products.
Fibrous proteins in grana Helps to arrange chlorophyll molecules to receive
lamellae light.
Casein Provides the body with all of the amino acids
necessary to help build muscle. Casein protein is
digested more slowly than other proteins, so it
might be better at reducing appetite and
increasing feelings of fullness.
2. Respiration Haemoglobin. Transport of oxygen.
and transport. Myoglobin Stores oxygen in muscles.
Prothrombin/fibrinogen Required for blood clotting.
Antibodies. Essential for body immunity.
3. Growth Hormones e.g. thyroxine Controls growth and metabolism.
4. Excretion Enzymes e.g. urease Catalyzes reaction in ornithine cycle and helps in
protein break down and urea formation.
5. Support and Actin/myosin Makes it easy for muscle contraction.
movement Collagen Gives strength with flexibility in tendons and
cartilage.
Keratin Tough for protection e.g., in scales, claws, nails,
hooves, etc.
Resilin Provide strength in arthropod exo-skeleton
6. Sensitivity and Hormones e.g. insulin Control of blood sugars
co-ordination. Vasopressin Control of blood pressure
Rhodopsin Visual pigments in retina.
8. Reproduction Hormones e.g. prolactin Induces milk production in mammals.
Chromatin Gives structural support to chromosomes.
Globulins Storage of proteins in seeds which nourishes the
embryo.
Keratin Forms horns and antlers which are used for sexual
display.
ENZYMES
Enzymes are biochemical catalysts made up of globular proteins. An enzyme is always associated
with a non-protein component known as co-factor which is tightly bonded to the enzyme.

Enzymes are organic compounds protein in nature that speed up the rate of biochemical reactions
in the body of an organism and remains unchanged at the end of the reaction.
Importance of enzymes in biosystems

• Enzymes are highly specific biocatalysts that alter rates of metabolic reactions. They speed up
otherwise slow reactions in biological systems.
• Enzymes work reversibly allowing homeostatic control/regulations of biochemical reactions. They
stabilize otherwise violent reactions.
• The control/regulation of enzymes activity allows control of rates of specific metabolic reactions.
The available quantity of an enzyme determines the rate of a corresponding reaction.
Mechanism of enzyme action
Each enzyme has a unique surface structure which provides a precise position known as active site,
at which the substrate can join the enzyme molecules to form an enzyme substrate complex.
This infinite contact is maintained until the reaction is complete. The precise and specific fit between
enzyme and substrate is sometimes compared with the lock and key mechanisms. There are two
theories put forward to describe the mechanism of enzyme action i.e.
(i) Lock and key hypothesis
(ii) Induced fit hypothesis
The lock and key mechanism
The widely accepted mechanism by which enzymes are known to work is the “key and lock” theory.
The theory suggests that the enzyme has a specific region known as the active site where the
substrate fits like a key fit in a lock. The substrate must have a complementary shape to the active
site of the enzyme. In this theory the key is analogous to the substrate and the lock to the enzyme.
When the substrate combines with the enzyme, an enzyme- substrate complex is formed. This
breaks down to release the products and the enzyme, which can pick other substrates.
Illustration
Advantages of the lock and key hypothesis

1. It explains why enzymes are specific in action i.e., only substrates with complementary shapes
to the active site fit into the active sites and are converted to products.

2. It explains why the rate of enzyme-controlled reaction is affected by substrate concentration. If

all the active sites are in use, no more substrates a can fit or occupy the active site hence the
rate is constant.
3. It explains why and how enzymes can be inhibited.
4. It explains why enzymes are able to lower the activation energy in a chemical reaction.
The induced fit theory

The bonds between the amino acids of the active site of the enzyme are relatively flexible. When
the substrate combines with an enzyme, the active site may mould into the shape of the substrate.
The theory says that when the substrate molecule enters the active site, it causes the enzyme to
change its shape so that the two molecules fit together more tightly. The induced fit hypothesis is
believed to make the substrate molecules more active because as the active site changes shape, it
presses on the substrate molecule exposing the weak bonds.
Enzyme inhibitors
Inhibition occurs when the action of an enzyme is slowed down by another substance. There are
two types of inhibitors.
1. Competitive inhibitors.
These substances are chemically and structurally similar to the usual substrate. When both
substrate and inhibitor molecules are present, they ‘compete’ for the active site so that the
catalytic action of the enzyme is slowed down. The reaction can be reversed if the substrate
concentration is increased or by reducing the concentration of the inhibitor.
2. Non-competitive inhibitors.
These substances do not combine with the active site of the enzyme and are not affected by
substrate concentration. They combine with the enzyme molecule, producing a change which
indirectly affects the shape of the active site. This is known as non-competitive enzyme
inhibition. The inhibitor attach itself not to the active site of the enzyme but elsewhere on the
enzyme molecule. This cause breakage of some bonds in the enzyme molecule leading to
alteration of the 3-dimensional structure and hence the shape of the enzyme molecule. Change
in the shape of the enzyme molecule leads to change of the shape of the active site thus the
substrate can no longer fit in the active site.

An increase in the substrate concentration does not change the rate of reaction. This is because
the inhibitor alters/changes the shape of the enzyme and that of the active site permanently
whenever it comes into contact with the enzyme hence it leaves the active site non
complementary. Non-competitive inhibitors are mostly non reversible inhibitors. The commonest
types include heavy metal ions such as mercury and silver. Others are cyanide, nerve gas,
insecticides, herbicides, etc.
End product inhibition

This takes place in some metabolic pathways when the end product combines with the first enzyme
controlling the first step of the pathway for its production so that further formation of the end products
is slowed or stopped. This is an example of negative feedback which is important in regulation of
body processes. The end product acts as an allosteric inhibitor.
Enzyme 1 inhibited by end
product D
enzyme 1 enzyme 2 enzyme 3

A B C D
Allosteric enzymes
These are enzymes that occur in two forms, i.e., active and inactive. The inactive form is shaped in
such a way that the substrate will not fit into its active sites. Therefore, for such enzymes to work, it
must be transformed into the active form. Allosteric enzymes can be inhibited by molecules which
do not combine with the active site but with the other parts of the enzyme. In this case, the inhibitor
prevents the enzymes from changing into the active form, and substrates which bring about this are
known as allosteric inhibitors.
Importance of inhibitors
• They can be used in medicine and agriculture
• They control metabolic pathways by regulating the different stages in them
• They provide important information about the shapes and properties of enzymes.
• They are used to combat bacterial infections in the body. Some inhibitors work by
inhibiting/interfering with bacterial enzymes responsible for bacterial metabolism (e.g. formation

cross-links in bacteria cell walls, formation of proteins, etc) which halts bacterial reproduction in the
body of the host.
Enzyme cofactors
Co-factors are non-protein components required by enzymes within their active sites for them to
function efficiently. Cofactors usually acts as a ‘bridge’ between the enzyme and its substrate; often
it contributes directly to the chemical reactions which bring about catalysis. Sometimes the cofactor
provides a source of chemical energy, helping to drive reactions which would otherwise be difficult
or impossible.
Examples of such cofactors that must be associated with active sites in order for the enzymes to
function properly are:
• Metal ions like Mg2+, Fe2+ and the ions of trace elements such as Zn2+ or Cu2+. The metal ion may
help to bind the enzyme and substrate together, or it may serve as the catalytic centre of the
enzyme itself. For example, iron is the catalytic centre of catalase. Indeed, iron alone will catalyze
the decomposition of hydrogen peroxide, though not as effective as when it is associated with the
enzyme. Salivary amylase activity is increased by the presence of chloride ions.
• Prosthetic groups; these are non-protein organic molecules covalently and tightly bonded to the
enzyme in a more or less permanent way. They transfer atoms or chemical groups from the active
site of the enzyme to some other substance. For example, in respiration the enzyme cytochrome
oxidase has a prosthetic group which transfers hydrogen atoms to oxygen with the formation of
water. Haem in haemoglobin carries oxygen.
• Coenzymes. These are small non-protein organic molecules closely related to vitamins, which
represent the essential raw materials from which coenzymes are made. Often the coenzyme
functions as a carrier, transferring chemical groups or atoms from the active site of one enzyme to
the active site of another. An example is nicotinamide adenine dinucleotide (NAD) which carries
hydrogen atoms in respiration. Coenzymes are loosely bound to the enzyme.
Most enzymes are pure proteins consisting of polypeptide chains; any coenzymes required are
bound loosely and possibly only briefly while the enzyme carries out its catalytic function.
Regulation of enzyme activity

1. Some enzymes are potentially damaging if they become active in the wrong place, giving rise to
a need for containment. For example:
• Secreting enzymes which would be of a potential damage in an inactive form. The protein-
digesting enzyme pepsin is secreted as pepsinogen which is activated by hydrochloric acid in
the stomach. This prevents it from destroying stomach wall which is protected by mucus.
• Retaining enzymes within the cell. Cell damage is thus prevented by enclosing the enzymes
inside small membrane-bound structures called lysosomes.
2. Precursor activation where accumulation of a potential substrate causes a particular reaction
pathway to be opened up. It involves an allosteric site; however, the binding molecule activates
rather than inhibiting the enzyme involved. This is important because they help the cell make use
of whatever substances are available.

3. Genetic control where genes contained in the nucleus determine which enzymes are to be
synthesized during protein synthesis and therefore determine the limits of certain chemical
processes.
4. Accumulation of end products of a metabolic pathway/sequence of enzyme reactions exerts an
inhibitory effect on the enzyme catalyzing the first step in the pathway. This is done by the end
products binding on allosteric site of the enzyme resulting into distortion of active sites. Therefore,
the end product switches off the series of reactions producing it as it accumulates.
5. Spatial arrangement where successive enzymes controlling reactions that take place in a
particular order to complete a metabolic pathway are normally present in a precise spatial
arrangement such that substrate molecules can be ‘handed on’ from one enzyme to another. The
products from one step in the pathway are transferred to the enzyme catalysing the next step.
e.g., the attachment of enzymes to the membrane systems inside the cell is in specific and orderly
arrangements like in mitochondria and chloroplasts.
Nomenclature of enzymes
Enzymes are named by adding a suffix “ase” to their substrates. A substrate is a substance, which
the enzyme acts upon, or simply it is the raw material for the enzyme.
Examples of enzymes and their substrates
Enzyme Peptidase Lipase Maltase Sucrase Lactase Cellulase
Substrate Peptides Lipids Maltose Sucrose Lactose Cellulose
Some enzymes however retained their names they had before this convention. Such enzymes
include pepsin and trypsin.
Sometimes the enzymes digesting carbohydrates are generally called carbohydrases and those
digesting proteins as proteases.
Classification of enzymes
Each enzyme is given two names; a synthetic name based on the six classification groups. The
trivial names are derived by the following;
• Start with the name of the substrate on which the enzyme acts e.g. Succinate.
• Add the name of the type of reaction which is catalysed e.g. dehydrogenation.
• Convert the end of the last word to an ”ase” suffix e.g. Succinate Dehydrogenase.
Enzyme group Type of reaction catalysed Examples of enzymes

1. Oxidoreductases Oxidation and reduction reaction Dehydrogenase and
oxidase
2. Transferases Transfer of chemical groups Transaminase and
phosphorylase
3. Hydrolases Hydrolysis reactions Maltase, amylases, lipase,
peptidase
4. Lyases Addition or removal of a chemical group by decarboxylase
hydrolysis
5. Isomerases Arrangement of groups within the molecule Isomerases, mutases

6. Ligases Formation of bonds between two molecules synthetases

using energy derived from the breakdown of
ATP
Enzymes are classified depending on the type of reaction they catalyze. The following are some of
the classes of enzymes.
1) Isomerase; these catalyze reactions involving isomerism
2) Phosphorylases; these catalyze reactions involving addition of a phosphate
3) Hydrogenases; these catalyze reactions involving addition of hydrogen.
4) Dehydrogenase; these catalyze reactions involving removal of hydrogen.
5) Kinases; these catalyze reactions involving movement of molecules from one area to another.
6) Carboxylases; these catalyze reactions involving addition of Carbon dioxide.
Properties of enzymes
1) They are all protein in nature.
2) They are specific in their action i.e. they catalyze specific food i.e. Maltase on Maltose.
3) They speed up the rate of chemical reactions (they are catalysts).
4) They are effective even in small amounts.
5) They remain unchanged at the end of the reaction.
6) They are denatured by high temperatures since they are protein in nature and are inactivated by
low temperatures.
7) They are inactivated by inhibitor chemicals (poisons e.g. cyanide).
8) They work at a specific PH. (either acidic or alkaline).
9) Their reactions are reversible.
10) Their activity can be enhanced by enzyme activators e.g. chloride ions activate amylase.
FACTORS AFFECTING THE RATE OF ENZYME CONTROLLED REACTIONS

1. Substrate concentration;
The rate of enzyme-controlled reaction increases with increase in substrate concentration until all
the active sites of the enzyme are occupied by the substrate molecule. At this point the rate of
reaction can only be increased by increasing the enzyme concentration.
A: The rate of reaction increases with enzyme concentration because there are free active sites into
which more substrates fit increasing the rate of product formation

B: The rate of reaction is constant because all the enzyme active sites are occupied by substrates.
Any more substrate molecules added will have no active sites to be occupied hence constant rate
of reaction. The limiting factor at this point is the low enzyme concentration.
2. Temperature;
Within the physiological range (40C-400C) the rate of the enzyme-controlled reaction increases with
increase in temperature. This is because temperature increases the kinetic energy of reacting
molecules leading to more collisions between the enzyme and substrate molecules.
Beyond 400c, the rate of the reaction
decreases with increase in temperature due to
Denaturation of the enzyme molecules.
Very high temperatures lead to breakage of
some bonds that maintain the enzyme
structure. As a result, the 3-dimensional
structure of the enzyme is altered leading to a
change in the shape of the active site. The
shape of the active site at this point can no
longer fit in it hence no enzyme reaction.
3. Enzyme concentration;
Provided there is an excess of substrate molecules, the rate of an enzyme-controlled reaction
increases with increase in enzyme concentration. This is because the number of active sites
increases which leads to increase in number of substrate molecules that fit into and occupy the
active sites hence increase in the rate of product formation.
4. PH of the medium;
All enzymes work efficiently within a particular PH range. However, there is an optimum PH for each
enzyme. Any deviation from the optimum PH results in denaturation of the enzyme hence decrease
in the rate of reaction. A change in pH weakens the forces holding the enzyme molecule together
hence changing the shape and denaturing the enzyme shape. Alkalinity or acidity causes the
charged ions of the active sites in some enzymes to reassociate causing the uncharged groups to
fail to interact with the substrate hence losing the catalytic activity.
Enzyme Optimum
PH
Pepsin 2.00
Sucrase 4.50
Enterokinase 5.59
Salivary amylase 4.80
Catalase 7.60
Chymotrypsin 7.00-8.00
Pancreatic lipase 9.00

5. Enzyme inhibitors; These lower the rate of enzyme-controlled reactions or they may stop
enzyme action altogether.
6. Presence of cofactors; For some enzymes, the rate of enzyme-controlled reaction depends on
cofactors.
How enzymes work
Enzymes work by lowering the activation energy to allow the reaction to take place. Activation energy
is the energy barrier that has to be overcome before a reaction takes place. Since heat is usually
the source of energy, enzymes make it possible for reactions to take place at low temperature.
For enzymes to work, they lower the activation energy so that there is easy conversion of reactants
to products.
Advantages of using enzymes in industrial processes

• They are specific in their action and are therefore less likely to produce unwanted by-products.
• They are biodegradable and therefore cause less environmental pollution.
• They work in mild conditions, i.e., at low temperatures, neutral pH and normal atmospheric
pressure, and are therefore energy saving.
The main disadvantage of enzymes is that they are denatured by an increase in temperature and
are susceptible to poisons and changes in pH.
NUCLEIC ACIDS
Examples of nucleic acids are Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA)
General structure of nucleic acids

Nucleic acids are polymers made of subunits called nucleotides.
A nucleotide is made up of three molecules:

• Phosphate group
• Pentose sugar – either Deoxyribose (in DNA) or Ribose (in RNA)
• Nitrogen base – any purine (Adenine, Guanine) or pyrimidine (Cytosine and either Thymine in
DNA or Uracil in RNA)
Nucleoside forms when a pentose sugar joins an organic base by condensation reaction (a water
molecule is lost).
Nucleotide forms when a nucleoside (pentose sugar + organic base) joins a phosphate by loss of
second water molecule.
The sugar-phosphate-sugar backbone is formed when the 3’ carbon on one sugar joins to the 5’
carbon on the next sugar by phosphodiester bonds repeatedly to form a polynucleotide (long
chain of nucleotides) with organic bases protruding sideways from sugars.
DNA structure according to Watson and Crick

DNA is a polymer of nucleotide monomers arranged into two
polynucleotide chains running parallel to each connected together
by hydrogen bonds through nitrogen bases.
A DNA nucleotide is made up of three molecules:
• Phosphate group
• Deoxyribose sugar
• Nitrogen base - either adenine (A), guanine (G), thymine (T) or
cytosine (C).
The polynucleotide chains/strands are antiparallel (face in opposite
directions) i.e., one runs from 3’ to 5’ direction while other runs from
5’ to 3’ direction.
The chains run twisted to form a double helix.
The sugar-phosphate-sugar backbone is held by covalent
phosphodiester bonds, while the nitrogen bases from the two
strands form weak hydrogen bonds by complimentary base
pairing of adenine with thymine, and Cytosine with Guanine.

Adaptations of DNA
• Sugar-phosphate backbone is held together by strong covalent phosphodiester bonds to provide
stability.
• The two sugar-phosphate backbones are antiparallel which enables purine and pyrimidine
nitrogen bases to project towards each other for complimentary pairing.
• Sugar-phosphate backbones are two (double stranded) to provide stability.
• The two sugar-phosphate backbones form a double helix to protect bases/hydrogen bonds.
• Long/large molecule for storage of much information.
• Double helical structure makes the molecule compact to fit in the nucleus.
• Base sequence allows information to be stored.
• Double stranded for replication to occur semi-conservatively/ strands can act as templates.
• There is complementary base pairing; A-T and G-C for accurate replication/identical copies can
be made.
• Weak hydrogen bonds enable unzipping/separation of strands to occur readily.
• There are many hydrogen bonds which increase stability of DNA molecule.
Theories of DNA replication
DNA replication is the process by which the parent DNA molecule makes another copy of itself.
1. Fragmentation hypothesis (Dispersive hypothesis)
The parent DNA molecule breaks into segments and new nucleotides fill in the gaps precisely.

2. Conservative hypothesis
The complete parent DNA molecule acts as a template for the new daughter molecule, which is
assembled from new nucleotides. The parent molecule is unchanged.
3. Semi-conservative hypothesis
The parent DNA molecule separates into its two component strands, each of which acts as a
template for the formation of a new complementary strand. The two daughter molecules therefore
contain half the parent DNA and half new DNA.
The semi conservative hypothesis was shown to be the true mechanism by the work of Meselsohn
and Stahl (1958) in their experiment on bacterium E.coli using radioactive 15N.
Illustration of three possible theories of DNA replication
Dispersive conservative Sem-conservative
Description of DNA replication

DNA replication is the process by which parent DNA molecule makes another copy of itself, semi
conservatively. It occurs during interphase.
DNA Helicase enzyme untwists and unzips DNA by breaking the hydrogen bonds to expose the
bases, creating the Y-shaped replication fork, the two opened strands of DNA behind it (DNA is
replicated a bit at a time and the whole molecule is never completely uncoiled).
RNA primase enzyme lays down an RNA primer at the 3’ end of the old DNA strand to guide the
action of DNA polymerase.
DNA polymerase enzyme removes the RNA primer from the new strand then moves along the
exposed base sequences, attaching free DNA nucleotides of complementary bases to create a new
DNA strand as it goes.
DNA ligase joins adjacent Okazaki fragments on the lagging strand (new strand laid down in the
opposite direction of the replication fork) and any sections of new DNA on the leading strand (new
strand laid down in the direction of the replication fork) that need to be joined.

DNA polymerase reads the exposed code from 3’ to 5’ end and therefore assembles the new strand
from 5’ to 3’end
Several molecules of DNA polymerase act simultaneously at multiple sites, each assembling a
separate section of the new strand of DNA.
These new DNA segments are then joined together by the enzyme DNA ligase.
The two new daughter molecules then coil up again to reform the double helix structure.
General structure of RNA

RNA molecules are small/short, single stranded (rRNA and mRNA) or double stranded (tRNA)
polymer of nucleotides.
RNA nucleotide is made up of three molecules: (i) Phosphate group (ii) Ribose sugar (iii) Nitrogen
base - either adenine (A), guanine (G), cytosine (C) or uracil (U)
The sugar-phosphate-sugar backbone is held by covalent phosphodiester bonds.
RNA occurs in three types whose sizes, shapes, amount/abundance and roles vary:
1. Ribosomal RNA (rRNA) 2. Messenger RNA (mRNA)
Forms 80% of the total RNA in a cell. Forms 3-5% of the total RNA in a cell.
rRNA in different species vary in size e.g. in Single stranded polynucleotide chains with 5’
humans 18S rRNA has 1868 nucleotides while to 3’ polarity
28S rRNA has 5025. Average size of eukaryotic mRNAs is 1500 to
Permanently combined with protein to form 2000 nucleotides
catalytic component of ribosomes. Manufactured in the nucleus
Manufactured in nucleolus. mRNA carries coded information from DNA to
rRNA is a site of protein synthesis in cells. ribosomes in the cytoplasm

3. Transfer RNA (tRNA)

Forms about 15% of the total cell RNA.
Primary structure in all tRNAs has sequences of 73 to
93 nucleotides.
3’ end always terminates with the sequence CCA,
where amino acid attaches while the 5’ end
terminates in base G.
Secondary structure forms a clover leaf shape with 4
hydrogen bonded base-paired stems
Cloverleaf contains three non-base-paired loops:
(i) Amino acyl synthetase binding loop
(ii) Anticodon
(iii) Ribosomal binding loop.
Tertiary structure is a compact “L” shape whereby the anticodon stem and acceptor stem form a
double helix.
Anticodon is a single stranded loop at the bottom.
tRNA carries amino acids in the cytoplasm to ribosomes.
Adaptations of tRNA
• Active sites (anticodon and amino acid) are maximally separated to avoid interference.
• Small size for easy mobility.
Comparison of DNA and RNA
Similarities
Both: (1) are polymers of nucleotides (2) carry genetic information (3) have same purine bases
adenine and guanine plus pyrimidine bases cytosine (4) originate from the nucleus (5) occur in the
cytoplasm
Differences
Aspect Deoxyribonucleic Acid (DNA) Ribonucleic Acid (RNA)
• Stores genetic information for a long • Transfers genetic code needed for
Function time and transmits it. the creation of proteins from the
nucleus to the ribosome.
• Double-stranded. • Single-stranded.
• Hydrogen bonds occur between • Base pairing through hydrogen
complementary nitrogen bases of bonds occurs in the coiled parts.
opposite strands (A-T, C-G)
Structure
• Spirally twisted to produce a regular • The strand may fold at places to form
helix. a secondary helix.
• Occurs in form of chromatin or • Occurs in ribosomes or forms
chromosomes association with ribosomes

• Adenine links to thymine (A-T). • Adenine links to uracil (A-U).

Base • Purine and pyrimidine bases are in • No proportionality between
Pairing equal number numbers of purine and pyrimidine
bases.
• Much of DNA is in the nucleus of a cell, • Much of RNA is in the cytoplasm,
Location
little in mitochondria and chloroplasts. little in the nucleus.
• Stable in alkaline conditions. • Not stable in alkaline conditions.
• Long lived • Some RNA are very short lived
Stability
while others have somewhat longer
life.
• DNA is self-replicating. • RNA is synthesized from DNA
Propagation
when needed.
Unique • DNA is protected in the nucleus, as it is • RNA strands are continually made,
Features tightly packed. broken down and reused.
• Very large/long (has over a million • Much shorter (Depending on the
nucleotides) type, RNA contains 70 – 12,000
Size
nucleotides).
• Quantity is fixed in a cell • Quantity is variable
• Only two types: intra nuclear and extra • Three different types: mRNA, tRNA
Types
nuclear DNA and rRNA
PROTEIN SYNTHESIS
Protein synthesis is the process by which individual cells construct proteins. Protein synthesis
requires the supply of amino acids, energy and information. When these are grouped or brought
together, proteins are synthesized in 3 steps, i.e. Transcription, Activation and Translation.
1) Transcription:
This is the process of transferring part of the coded information of DNA in the nucleus to the ribosome
in the cytoplasm. It involves a nucleic acid molecule made of RNA, known as mRNA, which is a
single stranded molecule manufactured in the nucleus from one strand of DNA double helix referred
to as coding strand.
The enzyme catalyzing the reaction of transcription is known as RNA polymerase. The beginning of
protein synthesis starts by RNA polymerase attaching itself to the DNA double helix and the
hydrogen bonds are broken down in the region of DNA to be coded (copied) and the DNA strand
unwinds.
One DNA strand is then coded by base pairing of ribo-nucleotides, which are condensed together
to form a strand of mRNA. The base sequence of mRNA is complementary to the coding strand of
DNA. Once formed, the mRNA passes out into the cytoplasm and becomes attached to the
ribosome.

2) Amino acid activation:

Amino acids are activated for protein synthesis by combining with a short length of RNA known as
transfer RNA (tRNA). The activation process involves ATP for provision of energy.
There are more than 20 amino acids coded for in all proteins. All tRNA have a globally leaf shape
but differ in sequence of bases known as anticodon which is exposed on one of the leaves. This
anticodon is complementary to the codon of mRNA.
Each type of tRNA binds with a specific amino acid. The amino acid molecules join to the free ends
of tRNA molecules. The tRNA amino acid complexes now move to the ribosomes.
3) Translation:
This process occurs in the ribosomes. It is mainly placing of the activated tRNA anticodon to the
right mRNA codon by the ribosome in order to make a polypeptide chain.
Ribosomes move along the length of the mRNA strand reading the codon from the start codon
starting at one end of the mRNA molecule. A ribosome works its way along the mRNA positioning
the anticodons of the tRNA on the complementary codon of the mRNA strand.
In the ribosome, complementary anticodons of amino acids, tRNA complexes are held in place by
hydrogen bonds.
The amino acids are then joined by peptide bonds therefore meaning that the ribosome is acting as
a supporting frame work, holding the mRNA and two amino acids.
tRNA complexes together and enables and enzyme to catalyze the formation of a polypeptide bond
between the adjacent amino acids.

The ribosomes move along the mRNA and as it does it positions two activated tRNA having one
amino acid at the same time.
The ribosome has two sides, A and P sides. At the starting codon, the side A is attached to the first
tRNA which the P side is empty.
When it continues to move, a second tRNA attracts itself to the empty side corresponding to the
second codon of mRNA.
The presence of the second amino acids on the second tRNA stimulates the formation of a
polypeptide bond between the amino acids.
This makes the earlier tRNA to lose contact from the mRNA and its amino acids making it free going
back to the cytoplasm.
For further activation, the ribosome continues to move along the codons of the mRNA, placing the
activated tRNA in their right positions, together with their amino acids in the process forming a
polypeptide chain which is released into the cytoplasm when the ribosome reaches the stop codon.
Termination occurs when all the codons on mRNA are read. The ribosome reaches one or more
stop codons on mRNA (UAA, UAG, UGA). The ribosome detaches from the mRNA and splits into
its small and large sub-units, while the new protein floats away
Note:
1. Several ribosomes can attach to a molecule of mRNA (to form polysomes/polyribosomes) one
after another so that several proteins of the same type can be made from one mRNA at the same
time.
2. Newly synthesised proteins are packaged and sent to Golgi complex for modification/processing.
This is called post-translation processing of the protein

Diagram illustrating synthesis of proteins by polysomes
Questions:
1. How does DNA regulate the synthesis of proteins? (Protein synthesis but focus on DNA)
2. Outline the role played by the different types of RNA in protein synthesis.

Comparison of the processes of DNA replication and transcription

Similarities
Both: (1) involve unwinding the helix (2) involve separating the two strands (3) involve breaking
hydrogen bonds between bases (4) involve complementary base pairing (5) involve C pairing with
G (6) work in a 5` to 3` direction (7) involve linking/ polymerization of nucleotides (8) DNA or RNA
polymerase require a start signal
Differences
DNA replication Transcription
Involves DNA nucleotides, where the pentose Involves RNA nucleotides where the pentose
sugar is deoxyribose, and the base adenine pairs sugar is ribose, and the base adenine pairs with
with thymine uracil
Both strands are copied Only one strand copied not both
Ligase enzyme / no Okazaki fragments are No ligase enzyme / no Okazaki fragments
involved
Has multiple starting points Has only one starting point
Replication gives two DNA molecules Transcription gives mRNA
Comparison of DNA transcription with translation

Both: (1) Occur in 5’ to 3’ direction (2) Require ATP
Differences
• DNA is transcribed while mRNA is translated
• Transcription produces RNA while translation produces polypeptides/ protein
• RNA polymerase for transcription while ribosomes for translation/ ribosomes in translation only
• Transcription occurs in the nucleus (of eukaryotes) while translation occurs in the cytoplasm/ at
ER
• tRNA is needed for translation but not transcription
THE GENETIC CODE

The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA
sequences) is translated into proteins (amino acid sequences) by living cells. There are four bases
on the DNA strand that are used for coding of amino acids. Their combination ought to give a coding
total of 20 amino acids found in the body. If each base was on its own codes for an amino acid, only
four amino acids would be coded. If the bases acted in pairs only 16 amino acids would be coded.
In both cases, 20 amino acids are not arrived at it. It therefore appears reasonable to theorize that
3 base pairs are required for coding an amino acid.

The genetic code chart / table
Having established that each amino acid is determined by a triplet base pair, it has been used to
establish and read the code dictionary. The three base pair hypothesis means that to code for the
20 amino acids occurring in the body, 64 possible combinations exist. The 44 combinations are not
used in amino acid coding and are referred to as degenerate or nonsense codons/stop codons.
Because of this, more than one but nearly similar triplet can code for an amino acid.
The three bases of an mRNA codon are designated here as the first, second, and third bases,
reading in the 5` to 3` directions along the mRNA. The codon AUG not only stands for the amino
acid methionine (met) but also functions as a “start” signal for ribosomes to begin translating the
mRNA at that point. Three of the 64 codons function as “stop” signals, marking the end of a genetic
message.

General characteristics/properties of the genetic code

Property Explanation
The nucleotides of mRNA are arranged as a linear sequence of

codons, each codon consisting of three successive nitrogenous
1. The code is a triplet bases, i.e., the code is a triplet codon, which provides a total of 64
codon codons which are more than enough to code for the 20 different
amino acids required to form a protein. If it were to be a 2-base codon,
only 16 amino acids would be coded for, not enough to form a protein.
In translating mRNA molecules, the codons do not overlap but are

“read” sequentially.
2. The code is non-

overlapping
This means that no codon is reserved for punctuations. After one

3. The code is amino acid is coded, the second amino acid will be automatically
commaless coded by the next three letters and that no letters are wasted as
punctuation marks.
4. The code is non- A particular codon will always code for the same amino acid. The
ambiguous same codon shall never code for two different amino acids.
The code is always read in a fixed direction, i.e., in the 5’→3′
5. The code has polarity
direction.
More than one codon may specify the same amino acid; For example,
except for tryptophan and methionine, which have a single codon
each, all other 18 amino acids have more than one codon.
Biological advantages of degeneracy
6. The code is • It permits essentially the same complement of enzymes and other
degenerate proteins to be specified by microorganisms varying widely in their
DNA base composition.
• It provides a mechanism of minimizing mutational lethality. E.g.
Substitution of the third base-U in GUU (for valine) with C/A/G does
not change the amino acid coded for.
7. Some codes are start In most organisms, AUG codon is the start or initiation codon, i.e.,
codons the polypeptide chain starts with methionine.
Three codons UAG, UAA and UGA are the chain stop or termination
8. Some codes are stop codons. They do not code for any of the amino acids. These codons
codons are also called nonsense codons, since they do not specify any
amino acid.

Same genetic code is found valid for all organisms ranging from
bacteria to man.
Advantages of universality:
• Genetic material can be transferred between species/ between
humans
• One species could use a useful gene from another species
9. The code is universal • Bacteria/ yeasts can be genetically engineered to make a useful
product
Disadvantages of universality:
• Viruses are able to cause diseases to other organisms by using the
host genetic machine
• Viruses can invade cells and take over their genetic apparatus e.g.
HIV
“Whatever the mind of man can conceive and believe, it can achieve” (Napoleon Hill, 1983).

Chemicals of Life 2024

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A-LEVEL BIOLOGY: CHEMICALS OF LIFE BY KUGONZA H ARTHUR – FEB, 2024

Kugonza H. Arthur @ 0701 366 474 - Page 1 of 45

➢ It is important in transpiration in plants.

QUESTION: HOW DO THE PROPERTIES OF WATER RELATE TO ITS BIOLOGICAL ROLE?

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QUESTION: OUTLINE THE ROLE OF MINERALS AND IONS IN BIOLOGICAL SYSTEMS.

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Glucose Fructose Galactose

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Properties of polysaccharides include:

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✓ Are not sweet

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Differences between amylose and amylopectin

QUESTION: How does the structure of starch relate to its roles?

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QUESTION: how does the structure of cellulose

Differences between cellulose and starch

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3. Mucopolysaccharides: These are carbohydrate derivatives derived from a combination of

FOOD TESTS ON CARBOHYDRATES

Colourless or turbid solution turned to a blue Reducing sugars absent.

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3) Galactose and lactose (present in milk)

2. Test for non-reducing sugars

3. Test for starch:

Colourless or turbid solution Starch absent.

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Question: using the structural formula:

For glycerol, and molecular formula

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Essential fatty acids

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Structure of the phospholipid

A phospholipid can be simply represented as

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QUESTION: What properties do lipids possess as storage compounds?

TESTS FOR LIPIDS

b) The emulsion test:

c) Translucent spot test:

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Chemical structure of an amino acid

Amino acids are soluble in water and ionize to form ions.

Zwitter ion (no overall charge)

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Questions: How do amino acids act as buffer solutions?

Types of amino acids

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(i) Beta pleated sheets:

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Importance of enzymes in biosystems

Advantages of the lock and key hypothesis