Cytology and Biochemistry notes for A-Level students

1. Cytology and Biochemistry

1.1. Cytology
This is the branch of biology which deals with the study of structure, function and behavior
of the cell. The cells are the smallest structures that show all the features of living things.
Each cell is a complex system consisting of many different building blocks enclosed in
membrane bag. There are unicellular and multi-cellular organisms.

In 1865 a British scientist Robert Hooke coined the term "cell" while looking at the
nonliving tissue known as cork under the light microscope.

Since there were several definitions put forward by different scientists to explain the cell
such as;-

i. Cell is the smallest living organism like amoeba

ii. Cell is smallest unit in the body of living organism
iii. A cell is the basic unit of life.

The basic meaning of the cell which combines all the three statement above is;

A cell smallest functional and structural unit of living organism. Therefore cells are the
building blocks of organisms.

1.1.2 The Cell Theory.

After the discovery of a cell by Robert Hooke two other scientist Theodor Schwann (a
zoologist) and Mathias schriden (a botanist) using the idea of Hooke put forward the cell
theory which consists of the following tenets;

i. All living organisms are composed of one or more cells.

ii. Cell is the basic unit of life
iii. All new cells come from pre-existing cells by cell division.
iv. All metabolic activities of an organism take place within the cell.
v. Cells contain hereditary material which are passed from generation to another or
parent to offspring

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 Cytology and Biochemistry notes for A-Level students

1.1.3 Type of Cell

According to the structure and organization there are two fundamentally different types of
cells. These are:-

i. Prokaryotic cell and

ii. Eukaryotic cell

Prokaryotic Cell
The term prokaryotic come from two Greek words which are “Pro”- means before and
“karyo” means nucleus.

Therefore Prokaryotic cell is the cell whose nuclear materials are not enclosed by nuclear
membrane. In other word Prokaryotic cell can be defined as the cell which has no true
nucleus.

Prokaryotic cells are smaller than eukaryotic cells of about 1 micron in diameter and have
simpler structure .The organisms possessing prokaryotic cells are called prokaryotes,
including all bacteria. Prokaryotes are single cellular organisms, but note that being a single
cell does not mean that an organism is a prokaryote.

Structure of the Prokaryotic Cell.

All the prokaryotic cells consists of the following parts in common

i. Capsule (or Slime Layer). A thick polysaccharide layer outside of the cell wall
whose roles are;-

 Used for sticking cells together.

 Used as a food reserve.
 Used for protection against desiccation and chemicals, and
 Used for protection against phagocytosis.

ii. Cell Wall. Made of murein, which is a glycoprotein

There are two kinds of cell wall, which can be distinguished by a Gram stain, these are;-
 Gram positive bacteria have a thick cell wall and stain purple, and
 Gram negative bacteria have a thin cell wall with an outer lipid layer and stain
pink.
iii. Cell membrane. Made of phospholipids and proteins, like eukaryotic membranes.

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iv. Cytoplasm. Contains all the enzymes needed for all metabolic reactions, since there
are no organelles
v. Ribosomes. These are smaller (70s) type.
vi. Nucleoid. The region of the cytoplasm that contains DNA, which is not surrounded by
a nuclear membrane. Nucleoid contains a circular molecule of DNA which is the cells
genetic material, or genome.
vii. Mesosome. A tightly-folded region of the cell membrane containing all the
membrane-bound proteins required for respiration and photosynthesis.
viii. Flagellum. A rigid rotating helical-shaped tail used for propulsion.

Diagram: a typical structure of a prokaryotic cell.

Characteristics of Prokaryotic cells

i. They have no well organized nucleus

ii. They lack nuclear membrane
iii. They have 70s ribosome and free
iv. Respiration take place in folding of the cell surface called mesosome
v. Cell division is by simple fission
vi. No spindle are formed during cell division because their lack centrioles
vii. Many of them under goes anaerobic respiration
viii. They are small cell in size

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Eukaryotic Cell

Eukaryotic originated from two Greek words which are “Eu”- true and “karyo”- nucleus

Therefore Eukaryotic cell is defined as the cell whose nuclear material is bounded by
nuclear membrane.

Eukaryote is an organism with true nucleus. Eukaryotic cell contain a large number of
organelles. Organelle is a distinct part of a cell which has a particular structures and
functions.

Differences between prokaryotic and eukaryotic cells

S/no Prokaryotic cell Eukaryotic cell

i. Nucleus material are not enclosed by Nucleus material are enclosed by nuclear membrane
nuclear membrane
ii. Contains few organelles Contains many organelles

iii. No membrane bounded organelles such Has membrane bounded organelles

as chloroplast and mitochondria
iv. DNA is circular, without proteins and DNA is linear, associated with proteins to form
lies free in cytoplasm chromatin and enclosed in nucleus
v. It contains 70s ribosome (smaller) It contains 80s ribosome (larger)

vi. Have mesosomes for respiration Have mitochondria for respiration

vii. Have small size of about 0.2-2.0  m in Have larger size of about 10-100  m in diameter
diameter
viii. Always present in unicellular organisms Often contained in multicellular organisms

ix. No cytoskeleton always has a cytoskeleton

x. Cell division is by binary fission cell division is by mitosis or meiosis

Types of Eukaryotic cell

There are two different types of Eukaryotic cell namely;-

i. Plant cell and

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ii. Animal cell

Basically plant cells are very similar to animal cells but plant cells have more structures than
animal cells. The organelles and structures which are common to both plant and animal cells
are:-

 Plasma membrane
 Nucleus
 Mitochondria
 Endoplasmic reticulum
 Golgi apparatus

The chief differences between animal and plant cells are the presence of cell wall,
chloroplast and a large vacuole in plant cells.

Figure; Diagram of an Animal cell

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Figure; The diagram of a Plant Cell

The differences between plant cell and Animal cell

Components of Eukaryotic cell and their functions

Cell Wall

This is the semi-rigid external covering of the cell of the plant cell made up of cellulose and
micro fibrils.

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Both plant cells and fungi are surrounded by a relatively rigid wall which is secreted by
living cell (the protoplast) within. The plant cell wall differs in chemical composition from
that of fungi:-

 Plant cell wall contains cellulose.

 Fungi cell wall contains chitin.

The wall formed during cell division of plants is called the primary wall which is later
thickened to become a secondary wall.

Structure of plant cell wall

 It is not continues as it contains tin pore called plasmodesmata which join one
protoplast to another
 It consists of cellulose fiber of microfibrils which form the frame work of the cell
wall.
 The cell wall matrix consists of polysaccharide of pectin, hemicelluloses and rigin.
 The 60%-70% by mass of the cell wall is water which can move freely through
free space in the cell wall.
 The adjacent cell walls are separated by the middle lamella which is composed of
sticky gel-like magnesium and calcium salts of pectin.
 The cell wall has the great tensile strength and limited elasticity.

Functions of the Cell Wall,

i. It provides mechanical and skeletal support for individual cells and for the plant as a
whole.
ii. It allows the movement of water through it and along it due to presence of
plasmodesmata
iii. It prevents the cell from bursting when exposed to a dilute solution.
iv. It acts as water proofing layer when impregnated with lignin
v. It acts as a food reverse such as seed cell wall store hemicelluloses
vi. It reduce water loss since it contain a coating of waxy cutin
vii. The presence of microfibrils in the cell wall limits and helps to control cell growth and
shape.
viii. It protects the internal delicate parts of the cell from damage.
ix. The cell walls of root endodermal cells are impregnated with suberin that forms a
banner to water movements.

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x. It acts as a major pathway for the movement of water (apoplast).

The Plasma Membrane (Cell membrane)

Is an extremely thin structure surrounds the cell, separating its contents from the
surroundings and controlling what enters and leaves the cell.

Structure of the cell membrane.

 The membrane is made up of phospholipid bilayer with some proteins floating on the
surface of phospholipids bilayer ( peripheral or extrinsic protein), other extend into it
(intergral protein) and some extend completely across the membrane (transmembrane
protein)
 Phospholipid consists of polar heads made up by phosphate group and non polar tails
made of fatty acid.
 The ‘hydrophilic’ head is a polar molecule and have an affinity to water (hydrophilic
i.e. water loving) and the ‘hydrophobic’ tail is non-polar and do not mix with water
(hydrophobic i.e. water hating).
 Some protein and lipids have short branching carbohydrate chain like antennae
forming glycoprotein and glycolipids respectively
 Cholesterols are embedded between the phospholipids giving the dynamic nature of
the membrane.

Diagram: The structure of the plasma membrane

Plasma membrane Models

Different scientist explained the structure of the plasma membrane and they come out with
different model of the structure of the membrane including;-

1. Daniel- Dauson Model of the Structure of the Membrane.

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In 1940’s Daniel and Dauson proposed that all the plasma membrane consist of lipid
layer coated with protein molecules as continuous layer.

 The two scientists proposed the structure of the cell membrane as bilayer of the
phospholipids coated with protein molecule on both surface.
 The model regard the cell membrane as being static with several pore and the
protein layer is continuous
 The model insisted on the existence of glycoproteins, glycolipids and
cholesterol in the phospholipid bilayer.
 The phospholipids have got two ends, the polar head molecule which posses
great affinity to water (hydrophobic) and the non polar tail which does not
have any affinity to water.

2. The Fluid Mosaic Model or Singer and Nicolson Model.

In 1972, J Singer and G. Nicholas put forward the “Fluid Mosaic Model” of membrane
structure in which a mosaic protein molecules floats in a fluid lipid bilayer. They modified
Daniel –Davson model and put forward the fluid mosaic model of membrane structure as
follows;-

 This model suggested that cell membrane is mainly composed of

phospholipids, cholesterol, proteins, and carbohydrates.
 This model proposed that membrane is made up of phospholipid bilayer coated
by protein in both sides but the protein does not form a continuous layer as
proposed by Daniel and Dauson.
 Each phospholipid molecule has a head that is attracted to water (hydrophilic:
hydro = water; philic = loving) and a tail that repels water (hydrophobic: hydro
= water; phobic = fearing).
 The protein molecules are either partially (peripheral protein) or wholly
embedded (integral protein) in the phospholipids bilayer.
 The model suggests that the peripheral protein molecule float on the
phospholipids bilayer as a fluid, hence fluid mosaic model.

Note; The fluid mosaic model states that membranes are composed of a phospholipids
bilayer with various protein molecules floating around within it.

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Function of the cell membrane.

i. It separates the contents of the cell from their external environment in animal cell.
ii. Protect the internal organelles of the cell from damage.
iii. It controls the exchange of material between the cell and its external environment. (i.e.
it allows some material to pass through and retain other permanently).
iv. It acts as receptor site for recognizing stimulus such as hormone, enzymes, and
neurotransmitters coming into the cell.
v. It acts as the site for metabolic reactions such as energy production in mitochondria
and also enzymes attached to the plasma membrane.
vi. In some cell the membrane forms pinocytotic vesicles which aid in removing
unwanted material from the cell.
vii. Some membrane carries out phagocytosis where it capture foreign particle (protection
against disease).
viii. It contains glycoprotein which acts as cell identity markers, hence enables the cell to
recognize other cells and to behave in an organized way.

Adaptation of the membrane to its function.

a. Presence of hydrophilic pores which aid the exchange of material between the cell and
external environment.
b. Microvillus present in animals’ cell membrane offer a large surface area for
absorption
c. Ability to form pinocytotic and phagocytotic vessels ensures the ability of protecting
the cell against disease causing agents.
d. Presence of glycoprotein molecule which act as receptor site to detect the foreign
materials.
e. Protein present in the membrane gives the cell its identification.
f. The fluid nature of the membrane makes easy for materials to pass through it.

Membrane Components and their function

i. Phospholipids

 It gives the basic structural support of the membrane.

ii. Glycolipids

 Involved in cell- cell recognition

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 Acts as receptor site for chemical signals such as hormones and enzymes

iii. Glycoproteins

 Act as cell receptor sites, where hormones and drugs bid.

 They are involved in cell signaling in the immune system.

iv. Proteins

 Gives the structural support to the membrane

 Assist the transport of materials across the membrane
 Give specificity of the cell.

v. Cholesterol

 Increase the flexibility of the cell membrane

 Makes the membrane more stable and
 Prevents the membrane from solidifying when your body temperature is low.

Transport across the membrane.

Substances need in a cell or unwanted substances pass through the membrane to enter or
leave the cell. They do so in a number of ways where some of these processes require no
energy while others require energy.

Methods of transport across the membrane

There are two processes through which different materials move in and out across the
membrane which are:-

1. Active transport which includes phagocytosis, pinocytosis and exocytosis.

2. Passive transport which includes diffusion and osmosis,

Active Transport

This is a movement of molecules across cell membranes against concentration gradient.

When a substance is transported from a low concentration to a high concentration that is
uphill against the concentration gradient, energy has to be used.

Types of Active transport across the membrane

There are two active process involving the bulk transport of material across the membrane
which are;-

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i. Endocytosis
ii. Exocytosis

1. Endocytosis

Is the movement of materials into the cell across the membrane occurring by an unfolding
or extension of the cell surface membrane to form a vacuole. The vacuole is the fluid filled
membrane bound sac

Types of Endocytosis

There are two type of endocytosis which are

a) Phagocytosis ( cell eating) and

b) Pinocytosis (cell drinking)

Phagocytosis

Is the transport of material in the cell in the sold form. Phagocytosis is sometimes called
“cell eating” because it takes in sold materials. The specializing cells in this process are
called phagocyte or phagocytic cells.

For example the destruction of bacteria by white blood cells by the process of phagocytosis .
Once within the cell, enzymes produced by the lysosomes of the cell destroy the bacteria, as
shown below

Diagram: Phagocytosis

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Pinocytosis (cell drinking)

Is the transport of material in the cell in the liquid form. The cell specializing in this process
is called pinocytes.

Note; the vesicles formed are very small known as micropinocytotic vesicles, in this case the
process is known as micropinocytosis. E.g. Human egg cells obtain the food /nutrient from
the surrounding follicle cells by pinocytosis process.

2. Exocytosis

Is the movement of materials out of the cell through the cell membrane. Therefore substances
formed in the cell are moved through the plasma membrane into the fluid outside the cell (or extra-cellular
fluid) by the process known as exocytosis. It occurs in all cells but is most important in secretory cells such
as cells that produce digestive enzymes and nerve cells.

2. Passive Transport

Passive transport is a movement of molecules or ions and other substances across cell
membranes along or down the concentration gradient.

The main kinds of passive transport are

i. Diffusion and
ii. Osmosis

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Diffusion

Is the net movement of material from the area of their high concentration to the area of low
concentration down the concentration gradient. The concentration gradient is the
difference of concentration between the two areas.

Types of diffusion

a) Simple diffusion

Is the passive movement of solute from the region of high concentration to the region of low
concentration until the concentration of the solute is uniform throughout.

A few substances can diffuse directly through the lipid bilayer part of the membrane. The
only substances that can do this are lipid-soluble molecules such as steroids, or very small
molecules, such as O2 and CO2.

b) Facilitated diffusion

This is the transport of substances across a membrane by trans-membrane protein molecules

that are embedded within the membrane. The transport proteins tend to be specific for one
molecule, so substances can only cross a membrane if it contains the appropriate protein.

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Osmosis

Is the movement of water molecules from the region of high water potential to the region of
low water potential through a partially permeable membrane.

Or Osmosis is the passage of water molecules from a region of their high concentration to a
region of their low concentration through a semi- permeable membrane.

Water Potential is a measure of the water molecule potential for movement in a solution. It
is measured in units of pressure (Pa, or usually kPa), and the rule is that water always moves
by osmosis from less negative to more negative water potential. 100% pure water has water
potential = 0, which is the highest possible water potential, so all solutions have water
potential < 0 (i.e. a negative number), and you cannot get water potential > 0.

A cell with large negative water potential will draw in water from less negative potential,
but this depends on other factors, such as solute potential (ψs) and pressure potential (ψp).

Thus; ψw= ψs +ψp

Cells and Osmosis.

The osmotic concentration (or OP) of the solution that surrounds a cell will affect the state of
the cell, due to osmosis. There are three possible concentrations of solution to consider:

 Isotonic solution a solution of equal OP (or concentration) to a cell

 Hypertonic solution a solution of higher OP (or concentration) than a cell
 Hypotonic solution a solution of lower OP (or concentration) than a cell

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The effects of these solutions on cells are shown in this diagram:

Effects of osmosis in a living cell

i. What happens if a plant cell is placed in hypotonic solution such as pure water?

 Water will tend to move from the solution into the cell due to osmosis and the
cell becomes turgid or swell. But plant cell does not burst due to the presence of
cell wall, which exert inward force or turgor pressure.

ii. What will happens to the animal cell when is placed in hypotonic solution?

 Water will enter the cell and cause it to expand until it burst, unlike the plant
cell due to lack of cell wall.

iii. Explain what happens and why when the animal cell and plant cell are placed into
the hypertonic solution (solution with lower water potential).

The Cytoplasm
This is the jelly-like substance composed of mainly water and variety of cell organelles
found between the cell membrane and nucleus. The cytoplasm makes up most of the "body"
of a cell and is constantly streaming.

Functions of the cytoplasm

i. It is a site of metabolic activities such as glycolysis

ii. Act as a store of vital chemicals

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iii. Site for synthesis of some biochemical molecules such as fats, proteins, carbohydrates,
nucleotides and coenzymes.
iv. It facilitates the intracellular distribution of nutrients and metabolites
v. It assists the exchange of materials between the organelles

Components of the Cytoplasm

The cytoplasm is mainly composed of the following;-

i. Cytosol or intracellular fluid

ii. Cell inclusions,
iii. Organelles and
iv. Microfilaments and microtubules

a) Cytosol

This is a clear jelly-like fluid that composed mainly of water in which various molecules are
dissolved or suspended. These molecules include proteins, fats and carbohydrates as well as
sodium, potassium, calcium and chloride ions. Many of the reactions that take place in the
cell occur in the cytosol.

b) Cell inclusions

These are large particles of proteins, fat, carbohydrates and melanin that have been produced
by the cell. They are often large enough to be seen with the light microscope.

c) Organelles

These are structures with characteristic appearances and specific “jobs” in the cell. Most
cannot be seen with the light microscope but only by the electron microscope. The main
organelles in the cell are the nucleus, ribosome, endoplasmic reticulum, mitochondrion,
chloroplast Golgi complex and lysosomes. The cell organelles in the cell work as organs in
the body of an organism.

Types of cell organelles

There are two types of cell organelles

i. Membranous organelles
ii. Non membranous organelles

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Membranous Organelles

These are the organelles in the cell which are bound by unit membranes similar to the cell
membrane. Following are the membrane-bound organelles, which can be recognized in a
generalized eukaryotic cell.

1. Nucleus

Nucleus means “core” is the oval spherical organelle.

This is largest organelle, found in all eukaryotic cells only, except the mature phloem sieve
tube element and red blood cell have no nucleus.

Structure of the nucleus.

 It is surrounded double membranes known as nuclear envelopes with nuclear pores.
 The nuclear pores which allow exchange of material between the nucleus and
cytoplasm
 The outer membrane is continuous with the rough endoplasmic reticulum.
 The matrix of the nucleus is called nucleoplasm which contains chromatin and
nucleolus.

 The chromatin materials are coiled DNA bounded by protein called histones. There
are two types of chromatin in the nucleus, these are:

i. Heterochromatin – Tightly coiled and continues to stain intense.

ii. Euchromatin – The looser coiled and more scattered chromatin during the
interphase.

 The nucleoplasm contains dissolved phosphate, ribose sugar, protein, nucleotide and
chromosomes.

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 Cytology and Biochemistry notes for A-Level students

Function of Nucleus

i. The nucleus controls the development and all activities of the cell hence is known as
control centre.
ii. It store genetic information hence determines the character of an individual

iii. It carries the instructions for synthesis of proteins in the nuclear DNA.
iv. It synthesis the ribosomal RNA by nucleolus.
v. The nuclear membrane is covered by ribosome which are involve in the protein
synthesis
vi. It is the source of information that govern the morphology of a cell

Note; the shape, size, position, and chemical composition of the nucleus vary from cell to
cell but they perform the same functions which are

i. To control the cell activities and

ii. To retain the organism’s hereditary material the chromosomes

Qn; Explain the structural adaptations of the nucleus to its function.

2. Mitochondria

Mitochondria (sing. mitochondrion) are oval or rod shaped organelles scattered throughout
the cytoplasm. Mitochondria are called “power stations” of the cell because it is the site
where energy is made by “burning” food molecules like glucose. This process is called
cellular respiration.

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Figure; Diagram of a Mitochondrion

Structures of Mitochondrion

 This is a sausage-shaped organelle (8µm long), and is where aerobic respiration takes
place in all eukaryotic cells.
 Mitochondria are surrounded by a double membrane, the outer membrane is simple,
while the inner membrane is highly folded into cristae (sing. crista), which give it a
large surface area.
 Cristae increase the surface area for respiration since it provided abundant space for
enzymes attachment such as ATPase.
 The space enclosed by the inner membrane is called the matrix, and contains small
circular strands of DNA, 70s ribosomes, food granules and phosphate granules.

Note; Distribution of mitochodria depend much on the location and function of the cell, a
large number of mitochondria are found in active cells which are involve in high energy
consumption such as brain, liver ,spinal cord, nerve cell, sperm cell and skeletal muscles
cells.

Functions of mitochondrion

i. It is centre for aerobic respiration that is site for energy production

ii. It is involve in protein synthesis due to the presence of ribosome inside of it
iii. Mitochondrion is involved in storage of genetic material due since they posses DNA
iv. The matrix of mitochondrion is the site of Krebs cycles and where fatty acids are
oxides.

Adaptation of mitochondrion to its function

i. The inner membrane is folded inward to from cristae which increase the surface area
for enzyme attachment.
ii. They have cristae which are site for electron transport chain (ETC).
iii. The permeability of the outer membrane allows some material to enter or leave the
mitochondrion.
iv. They have DNA for genetic information storage.
v. They posses ribosomes for protein synthesis.

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3. Plastids

Plastids are ovoid or spherical shaped organelles found in plant cells and in certain
unicellular organism like algae. They are surrounded by two membranes which form an
envelope. There are three main types of plastids, these are:

i. Chloroplast
ii. Chromoplast and
iii. Leucoplast

The chloroplast

This is a plastid which found mainly in leaves and green part of the plant which contain
chlorophyll and carotenoid pigments.

Chloroplast is surrounded by double membrane the outer membrane and inner membrane
which forms the chloroplast envelope. Chloroplasts are where photosynthesis takes place, so
are only found in photosynthetic organisms (plants and algae)

Structure of the chloroplast

 This is oval shaped organelles of protoplasm which is surrounded of the double

membrane, the outer and inner membrane.
 It consists of many flattened fluid filled sacs called thylakoids which form stocks
called grana.
 Between one grana and the other there is a membrane called intergranal lamella.
 The internal system membrane is suspended in an aqueous matrix called stroma which
contains protein, circular DNA, starch grains and lipid globules.

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 The thylakoids contain chlorophyll which is responsible for absorbing energy from the
sunlight and convert it to chemical energy

Function of chloroplast

i. It is the site of photosynthesis reaction ,producing sugar from water and carbon
dioxide using solar energy
ii. It captures and converted solar energy into chemical energy due presence of
chlorophyll.
iii. Production of ATP, NADPH2 and evolution of oxygen through the process of
photolysis of water

Adaptation of chloroplast to its role

a) Presence of grana increase the surface area of photosynthesis reaction to take place
b) Presence of pores in the membrane ensures the exchange of the material between the
chloroplast and the surrounding.
c) Presence of pores on the membrane facilitates the absorption of light and carbon
dioxide gas.
d) Presence of enzyme such as RuBisCO and PEPC which facilitate photosynthesis
reaction.

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Symbiotic nature of chloroplast and Mitochondrion

This is explained by Endosymbiotic or Symbiogenesis theory. The endosymbiotic theory

explains the origin of eukaryotic cells from prokaryotes. It states that “several key organelles
such as mitochondria and chloroplasts of eukaryotic cell originated as symbiosis between
separate single-celled organisms”.

According to this theory, mitochondria and plastids (e.g. chloroplasts), and possibly other
organelles, represent formerly free-living bacteria that were taken inside another cell as an
endosymbiont, around 1.5 billion years ago.

Molecular and biochemical evidence suggest that the mitochondrion developed from
proteobacteria and the chloroplast from cyanobacteria.

Evidence for Endosymbiotic Theory

This theory is supported by following observations:

i. New mitochondria and chloroplast are formed only through a process similar to binary
fission.
ii. Both mitochondria and chloroplast contain single circular DNA that is different from
that of the cell nucleus and similar to that of bacteria.
iii. They have 70s type ribosomes like those found in bacteria.
iv. Mitochondria and chloroplasts DNA, RNA, ribosomes, chlorophyll (for chloroplasts),
and protein synthesis is similar to that for bacteria
v. Both mitochondria and chloroplasts have transport proteins called porins found in the
outer membranes, similar to that found in bacterial cell membrane.
vi. Mitochondria and chloroplasts are similar in size to bacteria, 1 to 10 microns .
vii. Both mitochondria and chloroplasts have double phospholipid bilayers which have
arisen by endocytosis and been engulfed and surrounded by the surface membrane.

Qn; What are the Similarities between mitochondrion and chloroplast and bacterial cell.

2. Chromoplasts

These are plastids containing mainly red, orange or yellow pigments which are commonly
known as carotenoids. They are non-photosynthetic pigments which are found mainly in
fruits and flowers. In the flower their bright color attracts insects and birds for pollination
and seed dispersal.

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Functions of chromoplast

a) They facilitates insect pollination

b) They insure seed dispersal
c) They indicates the ripe of fruits

3. Leucoplasts
These are colorless plastids which have no pigments. They are numerous in storage organs
such as roots, seeds and young leaves where they store food. Examples of leucoplasts
include:

a) Amyloplast store starch e.g. potato root.

b) Lipidoplast store oil and fat
c) Proteoplast stores protein e.g. beans seeds

4. Golgi apparatus
These bodies were named after the discovery by a scientist called Camillo Golgi (1898).

The Golgi apparati are bodies composed of membrane-bound flattened sacs called cisternae
and are associated with vesicles called golgi vesicles.

They are manufactured by rough and smooth endoplasmic reticulum.

There is normally only one golgi apparatus in each animal cell but in plant cell are more than
one, the collection of golgi bodies is known as dictyosome. Golgi apparati are most located
in the secretory cells such, neurons and small in muscle cell.

The Golgi apparatus is particularly well developed in cells that produce secretions, e.g.,
pancreatic cells producing digestive enzymes and hormones.

Diagram A Golgi body

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Functions of the Golgi apparatus

i. Used in modifying, sorting and packaging of proteins for secretion.

ii. It transports proteins from the RER to the cell membrane for export.
iii. It is involved in the transport of lipids around the cell.
iv. They are concerned in the creation of lysosomes
v. They are used in the production of glycoproteins such as mucin which is a
source of mucus.
vi. Involved in the production of enzymes such as digestive enzymes of
pancreas.

5. Endoplasmic Reticulum (E.R)

This is a network of membranes that form channels throughout the cytoplasm from the
nucleus to the plasma membrane. The system of membrane form parallel flattened sacs
called cisternae

Types of Endoplasmic reticulum (E.R)

Depending on the presence of ribosomes on the membrane of the tubules there are two types
of E.R

i. The rough E.R this is the one whose the surface is covered with ribosome and
ii. The smooth E.R this is the one whose surface is not covered with ribosome

Smooth Endoplasmic Reticulum (SER).

Series of membrane channels involved in synthesizing and transporting materials, mainly

lipids, needed by the cell.

Rough Endoplasmic Reticulum (RER).

Similar to the SER, but studded with numerous ribosome, which give its rough appearance.
The ribosome synthesize proteins, which are processed in the RER (e.g. by enzymatically
modifying the polypeptide chain, or adding carbohydrates), before being exported from the
cell via the Golgi body.

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Functions of E.R

i. It provide the large surface area for chemical reaction

ii. RER concerned with the transportation of proteins which are synthesized by ribosome
of its surface.
iii. The smooth E.R is concerned with synthesizes of lipid from fatty acid and glycerol
iv. The smooth E.R also makes steroids hormones such as corticosteroid, testosterone,
progesterone and estrogen.
v. It collect and store synthesized material such as protein ,lipids and steroid
vi. It provide skeleton structure of cell or maintain cellular shape such as smooth
endoplasmic reticulum of the rod cell in the retina of the eye
vii. Provide a path ways for transport of material in the cell.

Note; when there damage to a cell result in increase formation of RER in order to produce
more protein necessary for the cell repair.

Diagram: Rough endoplasmic reticulum

6. Lysosomes
These are simple spherical sacs derived from the Golgi vesicles of the Golgi bodies. They
are bounded by a single membrane and contain a mixture of digestive enzymes (hydrolytic
enzymes) such as protease, nuclease and lipase which break down proteins, nucleic acids
and lipids respectively.

 The enzymes contained within lysosomes are synthesized on rough E.R and
transported to the Golgi apparatus.
 Golgi vesicles containing the processed enzymes later bud off to form the lysosomes.
 Lysosomes are particularly abundant in animal cells, in plant cells the large central
vacuoles may act as lysosome.

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Functions of Lysosome

1. It digests the materials taken in by endocytosis such as bacteria since it

contains digestive enzymes by the process known as autophagy.
2. They remove unwanted structure or damaged macromolecules within or outside the
cell by autolysis.
3. They destruct the worn-out cells by releasing its contents and themselves are being
digested.
4. The disappearance of the tail of the tadpole during metamorphosis of frog is due to
autolysis by lysosomes.
5. They fuse with a feeding vacuole to digest its contents.

Definition of some terms.

Autolysis is the self digestion of a cell by releasing the contents of lysosome within the cell.
For this reason, lysosomes sometimes called ‘suicide bags’ or ‘self breaking down’.

Autophagy is the process by which unwanted structures within the cell are engulfed and
digested within lysosome.

How the lysosomes function

The hydrolytic enzyme of the lysosomes is released when unwanted structure in or out of the
cell of the cell is to be digested and removed. However the lysosome burst and releases its
contents.

Biological Effects of Lysosomes

i. They cause fertilization in which the sperm nucleus and the egg nucleus.
ii. They cause meat deterioration
iii. They cause a gradual return of the uterus to its normal size after birth
iv. They digest foreign bodies such as bacteria and worm out organelles.
v. They facilitate the metamorphosis in amphibians and insect.
vi. They assist the digestion of food store of the endosperm in the germinating
seeds
vii. They can change the normal cells into cancerous cells.
viii. They cause disappearance of an unexercised muscles

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7. Peroxisomes (Micro bodies).

These are spherical organelles bounded by a single membrane commonly found in
eukaryotic cells.

They are believed to be derived from endoplasmic reticulum.

The peroxosimes containing the powerful enzymes known as oxidative enzymes such as
Catalase enzyme

Eg: catalase which catalyses the decomposition of hydrogen peroxide to water and oxygen.
Catalase enzyme
i.e H2O2 2H2O + O2

Hydrogen peroxide as a byproduct of certain cell oxidation reaction is very toxic and
therefore must be eliminated immediately.

Liver is an organ which deals with neutralization of toxic substances (detoxification

function), it contains large number of peroxisomes. In plants peroxisomes are site of the
glycolate cycle (photorespiration).

Roles of peroxisome

i. It release the catalase enzymes which calalyse the decomposition of hydrogen

peroxide into water and oxygen.
ii. The peroxisome of the leaves offer protection against any physiological attack in
the leaves.

7.2.0.1 Non-membranous Organelles

These are organelles, which generally do not contain membranes, such as ribosomes,
cytoskeletons, centrioles, cilia, and flagella.

8. Ribosomes
These are very small organelles made up of protein and ribonucleic acid (ribosomal R.N.A)
from nucleoli.

These are the smallest and most numerous of the cell organelles, and are the sites of protein
synthesis. Ribosomes are either found free in the cytoplasm, where they synthesize proteins
for the cell's own use, or they are found attached to the rough endoplasmic reticulum, where
they make proteins for export from the cell.

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Ribosomes occur in both prokaryotic and eukaryotic cells. The ribosmes of prokaryotic cells
are distinctly smaller (70’s ribosomes type) than those of eukaryotic cells (80’s ribosomes
type).

Each ribosome consists of two units, small sub-unit and large sub-unit. When several
ribsomes occur along a common strand of mRNA, the whole structure is known as
Polyribosomes or Polysomes.

Diagram: structure of ribosome

9. Centrioles.
Centriole is a small cylindrical structure that is composed of groupings of microtubules
arranged in a 9 + 3 pattern. The pattern is so named because a ring of nine microtubule
"triplets" are arranged at right angles to one another.
Centrioles are found in animal cells only.
During cell division the centrosomes replicate and move apart so that each new cell has its
own centrosome.
Plant cells have the equivalent of a centrosome but it does not contain centrioles.

Diagram: structure of a centriole

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Functions of Centrioles

i. It controls the separation of chromatids or chromosomes by a sliding motion.

ii. It helps to organize the assembly of microtubules during cell division.
iii. They are source of cilia and flagella such as centrioles called basal bodies.

10. Vacuole

A vacuole is fluid filled sac bounded by a single membrane. These are membrane-bound
sacs containing water or dilute solutions of salts and other solutes.

 Animal cell have small or temporary vacuoles such as food vacuole but plant cells
have one large permanent vacuole that fills most of the cell.
 Plant cell vacuoles are filled with cell sap surrounded by a membrane called tonoplast,
and are very important in keeping the cell rigid, or turgid.
 The cell sap is a watery fluid containing water, sugar, organic acids, mineral salts,
pigments and toxic substances.

Functions of Vacuole

1. It maintains the hydrostatic pressure of the cell.

2. They are responsible for colors in flowers, fruits, buds and leaves since it contains
pigments.
3. The vacuole sometimes contains hydrolytic enzymes and act as lysosomes break down
complex molecules.
4. It stores nutrient and non-nutrient chemicals such as calcium oxalate, alkaloids and
tannins which offer protection from consumption by herbivores.
5. Vacuole acts as a food storage organelle.
6. It provides structural support the plant cell.

11. Cytoskeleton

Cytoskeleton is a series of intercellular network of protein fibers extending throughout all

eukaryotic cells. The cytoskeletons help a cell with shape, support, and movement.

Cytoskeleton has three main structural components:-

i. Microfilaments ,
ii. Intermediate filaments and
iii. Microtubules.

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The cytoskeleton mediates movement by helping the cell move in its environment and
mediating the movement of the cell's components. This is because each fiber has a
corresponding motor protein that can move along the fibre carrying a cargo such as
organelles, chromosomes or other cytoskeleton fibres. These motor proteins are responsible
for such actions as:

 Chromosome movement in mitosis,

 Cytoplasm cleavage in cell division,
 Cytoplasm streaming in plant cells,
 Cilia and flagella movements,
 Cell crawling and
 Muscle contraction in animals.

Roles of cytoskeletons

i. They are used for cell structural support

ii. Used in transportation of materials in a cell and motility of a cell.
iii. They gives the cell its shape,
iv. They are used for holding all the organelles in position.

12. Cilium and Flagellum.

Flagella and cilia are organelles that project from the surface of cells but are connected to a
basal body just below the plasma membrane.

 They are made up of 2 central singlet microtubules and 9 pairs of peripheral

microtubules. This is called 9 + 2 arrangement of microtubules.
 Flagella in prokaryotic cells do not have the 9+2 arrangement.

Differences between Cilia and Flagellum

i. Flagella are long structures, and cilia are short structures.

ii. One cell normally contains one flagellum or 2 flagella, but a large number of cilia are
present in a cell.
iii. Both cilia and flagella are surrounded by a unit membrane.

Functions

1. They are used for movement of the cell or unicellular organisms

2. They contain enzymes that produce energy to move a cell, e.g. sperm or paramecium.

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3. They are used for feeding, e.g. feeding current generated by paramecium in its oral
groove.
4. They are used to sense the environment, e.g: sensory hair cells.
5. They used to remove mucus that has trapped dust particles in respiratory track.

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1.2 Biochemistry
Biochemistry is the study of chemical processes that take place in living organisms.

The principal types of molecules present in the body of an organism are;-

i. Water
ii. Carbohydrates
iii. Lipids
iv. Proteins and
v. nucleic acids

Many of these molecules are complex molecules called polymers, which are made up of
monomer subunits.

1.2.1 Water
Water molecules are charged, with the oxygen atom being slightly negative and the
hydrogen atoms being slightly positive.

These opposite charges attract each other, forming hydrogen bonds. Hydrogen bonds are
weak, long distance bonds that are very common and very important in biology.

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Biological significance of water

About 80% of the mass of living organisms is water, and almost all the chemical reactions of
life take place in aqueous solution.

Water has a number of important properties essential for life. Many of the properties below
are due to the hydrogen bonds in water.

i. Universal Solvent.

Because it is charged, water is an excellent solvent for polar substances. Polar molecules
such as salts, sugars and amino acids dissolve readily in water and so are called hydrophilic
("water loving"). Non-polar molecules such as lipids do not dissolve in water and are called
hydrophobic ("water hating").

ii. High Specific heat capacity.

Water has a specific heat capacity of 4.2 J g-1 °C-1, which means that it takes 4.2 joules of
energy to heat 1 g of water by 1°C. This is unusually high and it means that water does not
change temperature very easily. This minimizes fluctuations in temperature inside cells.

iii. High heat of evaporation.

Water requires a lot of energy to change state from a liquid to gas, and this is made use of as
a cooling mechanism in animals (sweating and panting) and plants (transpiration). As water
evaporates it extracts heat from around it, cooling the organism.

iv. Density and freezing properties.

Water is unique in that its solid state (ice) is less dense that the liquid state, so ice floats on
water. As the air temperature cools, bodies of water freeze from the surface, forming a layer
of ice with liquid water underneath. This allows aquatic ecosystems to exist even in sub-zero
temperatures.

v. High surface tension and Cohesion.

Water molecules "stick together" due to their hydrogen bonds, so water has high cohesion.
This explains why long columns of water can be sucked up tall trees by transpiration without
breaking. It also explains surface tension, which allows small animals to walk on water.

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vi. Water as a reagent.

Water is biologically significant as an essential metabolite, which is it participates in the

chemical reactions of metabolism. In particular, it is used as a source of hydrogen in
photosynthesis and as a reagent in hydrolysis reactions.

Functions of Water in living organism

i. Reagent in photosynthesis and hydrolysis reaction

ii. Translocation of inorganic ions and organic compounds in plants
iii. Body cooling by evaporation, such as sweating and panting in animals, and
transpiration in plants.
iv. A vital chemical constituent of living cells.
v. Transport in blood vascular system, lymphatic system and excretory system in
animals
vi. Seed germination
vii. Osmoregulation
viii. Lubrication and
ix. Solvent and medium for diffusion

1.2.2 Carbohydrates
These are organic compounds which contain only carbon, hydrogen and oxygen elements.
As the name implies carbohydrates are the hydrates of carbon this means that hydrogen and
oxygen are present in the same proportions as in water that is 2:1.

Most carbohydrates obey the formula CX (H2O) Y where x and y are variable numbers.

General Properties of Carbohydrates

i. They are chemically composed of carbon, hydrogen and oxygen elements.

ii. They are hydrates of carbon.
iii. All are aldehydes or ketones
iv. All contains several hydroxyl groups
v. They conforms with a general formula of Cx (H2O)y.

Functions of Carbohydrates

i. They release energy when oxidized such as glucose

ii. Used for energy storage e.g. starch and glycogen
iii. Used in structural support such as cellulose in plant cell and chitin in Fungi and
arthropods

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iv. They are used in nucleic acid synthesis such as ribose is the constituent of RNA and
deoxyribose of DNA.
v. Are used in synthesis of coenzymes e.g. ribose involves in the formation of NAD and
NADP.
vi. Some are used in enzyme synthesis such as ribulose bisphosphate is made from
ribulose sugar.

Classification of Carbohydrates

There are three classes of carbohydrates includes

1) Monomers (monosaccharides),
2) Dimmers (disaccharides) and
3) Polymers (polysaccharides), as shown in this diagram:

1. Monosaccharides

These are the simplest sugar unit with a general formula of (CH2)n where n is between 3 and
7 . Examples of monosaccharides include glucose (dextrose), fructose, galactose, and ribose.

Monosaccharides are categorized into three category according to the number of carbon
having

i. n=3 C3H6O3 Triose sugar (this are less common)

ii. n=5 C5H10O5 Pentose sugar such as ribose and deoxyribose. Thus

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iii. n=6; C6H12O6 Hexose sugar such as glucose, fructose (also called the fruit
sugar because are found in fruits, honey, and the sole sugar in bull and human
semen. It is the sweetest of sugars). and galactose (is naturally found in milk,
tomatoes and many fruits and vegetables). Although all three share the same
molecular formula, but different structural formulae since the arrangement of
atoms differs in each case.

The open and cyclic structures of three common hexose sugars are shown below

Glucose Galactose Fructose

The most common and important monosaccharide is glucose, which is a six-carbon sugar. Its
formula is C6H12O6. Glucose forms a six-sided ring and the six carbon atoms are numbered
as shown below.

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Depending on the position of the hydroxyl at the carbon number one there two isomers of
glucose namely;-

 α –glucose;- this is glucose in which the hydroxyl group on carbon atom 1 projects
below the ring and
 β- glucose;- this is the one in which the hydroxyl group on the carbon atom 1 projects
above the ring as shown below

Physical properties of Monosaccharide

i. They are usually colorless in colour,

ii. They are water-soluble,
iii. They are crystalline solids
iv. They have a sweet taste.

Chemical properties of Monosaccharide

i. Reduce Benedict solution or Fehling solution from blue copper II sulphate to brick red copper I.

Thus; Cu2+ + e- Cu+

Blue solution Brick-red precipitate

ii. They reduce ammonical silver nitrate to metallic silver

iii. Aldoses are oxidized to form acid and are reduced to form alcohol

2. Disaccharides

Disaccharides are formed when two monosaccharide, usually hexoses, combine together by
means of chemical reaction known as condensation reaction, which involves the formation
of a molecule of water (H2O). The bond formed when two monosaccharide combine together
is called glycosidic bond. This bond is normally formed between carbon atoms 1 and 4 of
neighbouring units and hence it’s known as a 1, 4 bond or 1, 4 linkage.

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There are three common disaccharides:

i. Maltose (or malt sugar) is the molecule which is made up of glucose and glucose. It is
formed during digestion of starch by amylase, because this enzyme breaks starch
down into two-glucose units.

The condensation reaction of two glucose molecules to form the disaccharide maltose.

Condensation reaction is the reaction between two molecules in which water is evolved.
Because the bond formed is between carbon number 1 of one molecule and carbon number 4
of the other molecule it is called a 1-4 glycosidic bond.

This kind of reaction, where water is evolved, is called a. The reverse process, when bonds
are broken by the addition of water (e.g. in digestion), is called a hydrolysis reaction.

ii. Sucrose (or cane sugar) is the molecule made up of glucose and fructose. It is
common in plants because it is less reactive than glucose, and it is their main transport
sugar. It's the common table sugar that you put in tea.

Glucose + Fructose Sucrose

The structure of the sucrose

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iii. Lactose (or milk sugar) is formed from condensation reaction between galactose and
glucose. It is found only in mammalian milk, and is the main source of energy for
infant mammals.

The structure of Lactose.

Chemical Properties o Disaccharide

i. They are hydrolyzed using strong dilute acids like hydrolic acid (HCl) or
sulphuric acid (H2SO4) upon boiling to form monosaccharides.
Eg;
 Maltose + H2O HCl/H2SO4 Glucose + Glucose
 Sucrose + H2O HCl/ H2SO4 Glucose + Fructose
 Lactose + H2O HCl/ H2SO4 Glucose + Galactose
ii. Lactose and maltose can reduce copper II sulphate in Benedict solution/
Fehling’s solution to cupper I oxide, but sucrose does not.
This is because during their formation they retain their aldehyde groups
capable of reducing the copper II to cupper I oxide. Sucrose do not retain the
aldehyde group, hence sucrose does not reduce copper II sulphate to Copper
I unless it hydrolysed to form monosaccharides.

3. Polysaccharides

Polysaccharides are long chains of many monosaccharides joined together by glycosidic

bonds.

Roles of polysaccharides

 They are food and energy stores such as starch and glycogen.
 Used as structural materials such as cellulose

Qn; Explain why polysaccharides are used as storage molecules.

ANS;

 They have large size that make them more or less soluble in water, hence they
exert no osmotic or chemical influence in a cell
 They fold into compact shapes and

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 They are easily converted to sugars by hydrolysis when needed

Types of Polysaccharides

There are three important polysaccharides.

i. Starch

Starch is a polymer of glucose. It is a major storage polysaccharide in plants. It is insoluble

and forms starch granules inside many plant cells.

Qn; why starch is used as a storage polysaccharide?

Ans; Because starch being insoluble does not change the water potential of a cell, so does
not cause the cells to take up water by osmosis.

Starch is not a pure substance, but is a mixture of amylose and amylopectin.

 Amylose is simply poly-(1-4) glucose, so is a

straight chain. In fact the chain is floppy, and it
tends to coil up into a helix.

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 Amylopectin is poly (1-4) glucose with about 4%

(1-6) branches. This gives it a more open molecular
structure than amylose.

Both amylose and amylopectin are broken down by the enzyme amylase into maltose,
though at different rates.

Note, Amylopectin is less stable compared to amylose, because it has many ends, hence it
can be broken more quickly than amylose by amylase enzymes.

ii. Glycogen

This is the polymer of glucose similar in

structure to amylopectin but found in animals,
hence is known as animal’s starch. It is poly
(1-4) glucose with 9% (1-6) branches. It is
made by animals as their storage
polysaccharide, and is found mainly in muscle
and liver. Because it is so highly branched, it
can be broken down to glucose for energy
very quickly.

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iii. Cellulose

This is a polymer of (1-4) β- glucose only found in plant cells and it’s a main component of
cell walls. It differs from starch as it contains beta-glucose, in which the hydroxyl group on
carbon 1 sticks up. This means that in a chain alternate glucose molecules are inverted.

The α1-4 glucose polymer in starch coils up to form granules while the β1-4 glucose polymer in cellulose
forms straight chains.

Several chains of cellulose are linked together by hydrogen bonds to form cellulose microfibrils as shown
below. These microfibrils are very strong and rigid, and give strength to plant cells.

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Note; the beta-glycosidic bond in cellulose cannot be broken by amylase, but requires a
specific cellulose enzyme. The only organisms that possess a cellulase enzyme are bacteria,
ruminants and termites whose diet is mainly cellulose, they have mutualistic bacteria in their
guts so that they can digest cellulose.

Uses of cellulose

iii. A component of cell wall in plants

iv. Used in production of industrial products such as nylon, cellophase and
plastics.
v. Used in production of cellulose nitrate which are important in making film
and explosives.
vi. Used in industry for making writing materials such as papers
vii. Used in fibrils production such as cotton.

Other polysaccharides include:

iv. Chitin (poly glucose amine), found in fungal cell walls and the exoskeletons of
insects.

v. Pectin (poly galactose uronate), found in plant cell walls.

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vi. Agar (poly galactose sulphate), found in algae and used to make agar plates.
vii. Murein (a sugar-peptide polymer), found in bacterial cell walls
viii. Lignin (a complex polymer), found in the walls of xylem cells, is the main component
of wood.

1.2.3 Lipids
Lipids are organic compounds composed of the carbon, hydrogen and oxygen elements but
the ratio of H: O is not as in water.

 Each lipid molecule has less oxygen compared with carbohydrate molecules.
Therefore are rich in C-H (hydrogen-carbon bond).
 Lipids are immiscible in water and therefore are said to be hydrophobic (water
hating).
 They are only soluble in organic solvents like ethanol, acetone and ether.
 Lipids are formed from condensation of alcohol (glycerol) and fatty acids.

Types of Lipids

There are the two types of lipid which are;

i. Fats; these are lipids which are solid at room temperature.

ii. Oil; these are lipids which are liquid at room temperature.

Classification of lipids

1. Triglycerides

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Triglycerides are commonly called fats or oils. They are made of glycerol and fatty acids.

a) Glycerol; this is a small, 3- carbon molecule with three hydroxyl groups.

i.
b) Fatty acids; these are long molecules with a polar hydrophilic “head” and a non-polar hydrophobic
"tail". The hydrocarbon chain can be from 14 to 22 CH2 units long. The hydrocarbon chain is
sometimes called an R group, so the formula of a fatty acid can be written as R-COOH

Types of Fatty acid

There are two types of fatty acid depending on the presence or absence of double bonds,
namely

1. Saturated fatty acid

These are fatty acids without carbon-carbon double bonds in the hydrocarbon chain. They
are saturated fatty acid with hydrogen. These fatty acids form straight chains, and have a
high melting point.

2. Unsaturated fatty acid

These are fatty acid with carbon-carbon double bonds in the hydrocarbon chain. These fatty
acids form bent chains, and have a low melting point. Fatty acids with more than one double
bond are called poly-unsaturated fatty acids (PUFAs).

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Therefore the triglyceride molecule is obtained by joining one glycerol molecule and three
fatty acid molecules. One molecule of glycerol joins together with three fatty acid molecules
to form a triglyceride molecule.

Note; the following;

 Triglycerides that contain saturated fatty acids have a high melting point and tend to
be found in warm-blooded animals. At room temperature they are solids (fats), e.g.
butter, lard.
 Triglycerides containing unsaturated fatty acids have a low melting point and tend to
be found in cold-blooded animals and plants. At room temperature they are liquids
(oils), e.g. fish oil, vegetable oils.

2. Phospholipids

Phospholipids have a similar structure to triglycerides, but with a phosphate group in place
of one fatty acid chain.

Phospholipids have a polar hydrophilic "head" (the negatively-charged phosphate group) and
two non-polar hydrophobic "tails" (the fatty acid chains).

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3. Waxes

Waxes are formed from fatty acids and long-chain alcohols. They are commonly found
wherever waterproofing is needed, such as in leaf cuticles, insect exoskeletons, birds'
feathers and mammals' fur.

4. Steroids

Steroids are small hydrophobic molecules found mainly in animals. They include:

 Cholesterol , which is found in animals cell membranes to increase stiffness

 Bile salts, which help to emulsify dietary fats
 Steroid hormones such as testosterone, oestrogen, progesterone and cortisol
 Vitamin D, which aids Ca2+ uptake by bones.

Roles of lipids in the body

1. Protection ; fats surrounds and covers the delicate organs such as heart and kidney
2. Insulation; fats under the skin prevents heat loss
3. Energy storage; They yield more energy per unit mass than other compounds so are
good for energy storage.
4. Source of water; A lipid such as fat is a source of water during harsh conditions,
since the oxidation of fat yield high amount of water compared to other respiratory
substrates. That is

 1 gram of protein = 0.4g of water

 1 gram of carbohydrate =0.55 g of water
 1 gram of fat = 1.07g of water

5. Structural support; phospholipids and cholesterol are important components of cell

membranes.

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6. Regulation; steroid hormones such as estrogen and testosterone which regulate many
physiological processes.
7. Fat-soluble vitamins perform a variety of functions.

 Vitamin A forms retinol, which is necessary for seeing in the dark.

 Vitamin D promotes calcium uptake by the small intestine.
 Vitamin E promotes would healing
 Vitamin K is necessary for the synthesis of proteins responsible for blood
clotting.

Test for lipids

i. Fat turn red when the red stain called Sudan III is added to them.

 If olive oil is added to water and shaken up to form emulsion and then few
drops of Sudan III added the whole solution goes pinky red on standing the
oil separate out and red colour is only present in the oily layer.

ii. They are stained black precipitation when boiled with Osmic acid, this is because is
because fat reduce the osmium tetraoxide to black metal osmium.
iii. A drop of lipid on a dry white piece of paper will cause it to be transparent.

1.2.4 Proteins
Proteins are organic food substance consisting of carbon, hydrogen, oxygen and nitrogen
elements and sometimes are added with sulphur (S) and phosphorus (P). They are mainly
made of monomers called amino acid, joined together by peptide bonds.

Every protein consists of about 20 kinds of amino acids. Plants produce all their amino acids
using nitrates obtained from the soil but animal obtain their amino acid from their diet and
some are made in their body and such amino acid are called non-essential amino acid.

In animals 12 out of 20 are non-essential amino acid and the remain 8 are essential amino
acid which are obtained ready made from the diet.

1.2.4.1 Amino acids.

Amino acids are made of the five elements C H O N S. The general structure of an amino
acid molecule is shown below. There is a central carbon atom (called the "alpha carbon"),
with four different chemical groups attached to it:

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i. a hydrogen atom (H)

ii. a basic amino group(-NH2)
iii. an acidic carboxyl group(-COOH) and
iv. a variable "R" group (or side chain)

Properties of Amino Acids

Amino acids are so-called because they have both amino group (-NH2) and acid group (-
COOH), which have opposite charges. The amino group is basic and positively charged
while carboxylic group is acidic and negatively charged. A compound that has both acidic
and basic properties is referred to as amphoteric.

In Amino acid there is an internal transfer of a hydrogen ion from the -COOH group to the -
NH2 group to leave an ion with both a negative charge and a positive charge. This is called a
zwitterion.

A zwitterion is a compound with no overall electrical charge, since it contains two opposite
parts which are positively and negatively charged.

The charge on the amino acid changes with pH:

LOW PH (ACID) NEUTRAL PH HIGH PH (ALKALI)

charge = +1 charge = 0 charge = -1

It is these changes in charge with pH that explain the effect of pH on enzymes. A solid,
crystallized amino acid has the uncharged structure.

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However this form never exists in solution, and therefore doesn't exist in living things.

Polypeptides Formation

Amino acids are joined together forming peptide bond between the amino group and the
carboxylic group of the adjacent amino groups. The reaction is a condensation reaction since
it involves the formation of water molecule as shown below;

Note; when two amino acids are joined together a dipeptide is formed, three amino acids
form a tripeptide and many amino acids form a polypeptide.

NH3-Gly — Pro — His — Leu — Tyr — Ser — Trp — Asp — Lys — Cys-COO-
+

In a polypeptide there is always one end with a free amino (NH2) (NH3 in solution) group,
called the N-terminal, and one end with a free carboxyl (COOH) (COO in solution) group,
called the C-terminal.

Bonds in Polypeptide Molecules

In polypeptide molecule there are several amino acids which can form various bonds and
interaction such as;

i. Hydrogen bonding

Hydrogen bond is the bonds that occur between hydrogen atom and highly electronegative
atoms with lone pairs such as oxygen and nitrogen.

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This occur when the hydrogen of the amino group is attracted towards the electronegative
oxygen or nitrogen atom, such as the O of a C=O group or the N of an NH2 group

ii. Ionic bonding

This bonding occurs between the carboxylic group (COO-) and the amino group (NH3+) of
the adjacent amino acids in the same polypeptide chain. This bond is very weak and may be
broken easily when the pH is altered.

iii. Disulphide bonding

A disulfide bond is a covalent bond, usually derived by the coupling of two thiol groups
(SH). The linkage is also called an SS-bond or disulfide bridge. The overall connectivity is
therefore C-S-S-C.

Disulfide bonds in proteins are formed between the thiol groups of cysteine residues. This
bond can form between different polypeptide chains or in the same chain forming a coil.

Cystine is composed of two cysteines linked by a disulfide bond (shown here in its neutral form).

iv. Hydrophobic interactions

These are the interactions between alkyl groups of adjacent amino acid in the polypeptide
chain. Alkyl groups are water hating molecules they tend to move in ward away from water
causing inward folding of the molecule and hence hydrophobic interaction.

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1.2.4.2 Structure of Protein

The structure of proteins is classified into four basic structures namely primary, secondary,
tertiary and quaternary.

1. Primary Structure

This is the sequence of amino acids in the polypeptide chain, so is not really a structure at
all. However, the primary structure does determine the rest of the protein structure. Finding
the primary structure of a protein is called protein sequencing.

2. Secondary Structure

This is the most basic level of protein folding or bending of polypeptide chain caused by the
hydrogen bonds between amino acids. The secondary structure is held together by hydrogen
bonds between the carboxyl groups and the amino groups in the polypeptide backbone. The
two secondary structures are the α-helix and the β-sheet.

The α -helix. The polypeptide

chain is wound round to form a
helix. It is held together by
hydrogen bonds running parallel
with the long helical axis. There
are so many hydrogen bonds that
this is a very stable and strong
structure. Helices are common
structures in biology.

The β-sheet. The polypeptide

chain zig-zags back and forward
forming a sheet held together by
hydrogen bonds.

3. Tertiary Structure

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This is the 3 dimensional structure formed by the folding up of a whole polypeptide chain.
Every protein has a unique tertiary structure, which is responsible for its properties and
function.

For example the shape of the active site in an enzyme is due to its tertiary structure. The
tertiary structure is held together by several bonds between the R groups of the amino acids
in the protein, and so depends on what the sequence of amino acids is.

There are three kinds of bonds involved;

i. Hydrogen bonds, which are weak.

ii. Ionic bonds between R-groups with positive or negative charges, which are
quite strong.
iii. Sulphur bridges - covalent S-S bonds between two cysteine amino acids,
which are strong.

4. Quaternary Structure

This is the number and arrangement of multiple folded protein subunits in a multi-subunit
complex. This structure is found only in proteins containing more than one polypeptide
chain. The individual polypeptide chains are usually globular, but can arrange themselves
into a variety of quaternary shapes.

For example Haemoglobin, the oxygen-carrying protein in red blood cells, consists of four
globular subunits arranged in a tetrahedral (pyramid) structure. Each subunit contains one
iron atom and can bind one molecule of oxygen

These four structures are not real stages in the formation of a protein, but are simply a
convenient classification that scientists invented to help them to understand proteins. In fact
proteins fold into all these structures at the same time, as they are synthesized.

The final three-dimensional shape of a protein can be classified as globular or fibrous.

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globular structure fibrous (or filamentous) structure

The vast majority of proteins are globular, including enzymes, membrane proteins,
receptors, storage proteins, etc. Fibrous proteins look like ropes and tend to have structural
roles such as collagen (bone), keratin (hair), tubulin (cytoskeleton) and actin (muscle). They
are usually composed of many polypeptide chains. A few proteins have both structures: the
muscle protein myosin has a long fibrous tail and a globular head, which acts as an enzyme.

Structure of Proteins
There are four structural levels of organization to describe the complex macromolecule, protein based on the degree
of complexity of the molecule. They are Primary Structure, Secondary structure, Tertiary structure and Quaternary
structure.

Primary Structure of Protein

 Primary structure of protein is the linear sequence of amino acids that make up the polypeptide chain.
 this sequence is given by the sequence of nucleotide bases of the DNA in the genetic code.
 The amino acid sequence determines the positioning of the different R groups relative to each other.
 The positioning determines the way the protein folds and the final structure of the molecule.

Secondary Structure of Protein

 The linear, unfolded structure of polypeptide chain assumes helical shape to produce the secondary
structure.
 The secondary structure refers to the regular folding pattern of twists and kinks of the polypeptide chain.
 The regular pattern is due to the hydrogen bond formation between atoms of the amino acid backbone of
the polypeptide chain.
 The most common types of the secondary structure are the alpha helix and the ß pleated sheet.

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Tertiary Structure of Protein

 Tertiary structure of proteins is the three dimensional structure formed by the bending and twisting of the
polypeptide chain.
 The linear sequence of polypeptide chain is folded into compact globular structure.
 The folding of the polypeptide chain is stabilized by weak, noncovalent interactions.
 These interactions are hydrogen bonds and electrostatic interactions.
 Hydrogen bonds are formed when hydrogen atom is shared with two other atoms.
 Electrostatic interactions between charged amino acid chains.
 Electrostatic interactions are between positive and negative ions of the macromolecules.
 Hydrophobic interactions, disulphide linkages and covalent bonds also contribute to tertiary structure.

Quaternary Structure of Protein

 Some proteins contain more than one polypeptide chains, this association of polypeptide chains refers to
the quaternary structure.
 Each polypeptide chain is called a subunit.
 The subunits can be same or different ones.
 Example: Haemoglobin the oxygen carrying component of blood is made up of two polypeptide chains, one
with 141 amino acids and the other is a different type of 146 amino acids.

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1.2.4.3 Classification of Proteins

1. Fibrous Proteins

These are proteins with a primary structure of regular repetitive sequence forming a long
chains.
These proteins are insoluble in water as they contain many hydrophobic amino acids.

Their polypeptide chains form long filaments or sheets, where in most cases only one type
of secondary structure, that repeats itself, is found.
Here are some examples.

 Fibroin; It is produced by spiders and insects.

 Collagen; They are found in different tissues and organs, such as tendons and the
organic matrix of bone,
 α-Keratins; They constitute almost the entire dry weight of nails, claws, beak,
hooves, horns, hair, wool, and a large part of the outer layer of the skin.
 Elastin; This protein provides elasticity to the skin and blood vessels.

They have primarily mechanical and structural functions, providing support to the cells as
well as the whole organism.

2. Globular Proteins

These are proteins with irregular sequence of amino acids in their polypeptide chain. They
have tertiary or quaternary structure and Most of the proteins belong to this class.
They have a compact and more or less spherical structure, more complex than fibrous
proteins.

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They are generally less stable and soluble in water.

They perform metabolic roles as they act as:

 enzymes;
 hormones;
 membrane transporters and receptors;
 transporters of triglycerides, fatty acids and oxygen in the blood;
 immunoglobulins or antibodies;
 grain and legume storage proteins.

Examples of globular proteins are myoglobin, hemoglobin, and cytochrome.

Haemoglobin

Comparison Between Fibrous and Globular Protein

Fibrous Protein Globular Protein

Repetitive regular sequence of amino acid Irregular amino acid
Actual sequence may vary slightly between Sequence highly specific and never varies
two example of the same protein between two example of the same protein
Polypeptide chain form long parallel strands Polypeptide strands form folded into spherical
shape
Length of chain may vary into two example Length always be identical into two example
of protein of protein
Stable structure Relatively unstable structure
Insoluble in water Soluble form colloidal solution
Structural and support function Metabolic functions
Example include collagen and keratin Example include enzymes and some
hormone (insulin) and haemoglobin

3. Conjugated Protein

These are proteins which contain one or more non-protein portion (prosthetic group). These
proteins are sometimes also called heteroproteins.

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Three examples are glycoproteins, chromoproteins, and phosphoproteins.

 Glycoproteins
They are proteins that covalently bind one or more carbohydrate units to the
polypeptide backbone such as mucin

 Chromoproteins
they are proteins that contain colored prosthetic groups. Typical examples are
hemoglobin and myoglobin, which bind, respectively, one and four heme groups.
 Phosphoproteins
They are proteins that bind phosphoric acid to serine and threonine residues. Example
egg york which contain phosphoric acid.

1.2.4.4 General Characteristics of Proteins

1.2.4.5 Roles of Proteins

Classification of Proteins and Their Functions

Class of Function in the body Examples

Protein
Structural Provide structural -Collagenis in tendons and cartilage
components. -Keratinis in hair, skin, wool, and nails.

Contractile Move muscles Myosin and Actin contract muscle fibers.

Transport Carry essential substances -Hemoglobin transports oxygen.
throughout the body -Lipoproteins transport lipids.

Storage Store nutrients. -Casein stores protein in milk.

-Ferritin stores iron in the spleen and liver.
Hormone Regulate body metabolism -Insulin regulates blood glucose level and
nervous system.
-Growth hormone regulates body growth.
Enzyme Catalyze biochemical -Sucrase catalyses the hydrolysis of sucrose.
reactions in the cells. -Trypsin catalyses the hydrolysis of proteins.

Protection Recognize and destroy Immunoglobulins stimulate immune

foreign substances. responses.

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1.2.5 Nucleic Acids

Nucleic acids are large biomolecules, essential for all known forms of life.

Nucleic acids, which include

 DNA (deoxyribonucleic acid) and

 RNA (ribonucleic acid), are made from monomers known as nucleotides.

Each nucleotide has three components:

o a 5-carbon sugar,
o a phosphate group, and
o a nitrogenous base.

If the sugar is deoxyribose, the polymer is DNA and if the sugar is ribose, the polymer is
RNA.

Roles of Nucleic Acid

 They function in encoding genetic information.

 Transmitting genetic information via protein synthesis and
 Expressing genetic information

Types of nucleic acids

i. Deoxyribonucleic Acid (DNA)
This is a double stranded molecule composed of four types of deoxyribonucleotide bases
(adenine (A), cytosine (C), guanine (G), and thymine (T)).

Chemical nature of DNA

The DNA is composed of the following;
a) Phosphate group, which is derived from phosphoric acid and gives the acidic nature
the DNA molecules
b) Pentose sugar, the five carbon sugar which is known as deoxyribose
c) Nitrogenous bases, of which there are four types includes adenine (A), cytosine (C),
guanine (G), and thymine (T).
d) Hydrogen bonds, which holds the complementary paired bases in the two strands of
DNA.
e) Phosphodiester covalent bonds, which links one nucleotide to another in the DNA
strand.

ii. Ribonucleic acid (RNA)

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This is a linear molecule composed of four types of smaller molecules called ribonucleotide
bases (adenine (A), cytosine (C), guanine (G), and uracil (U)). RNA is synthesized from
DNA by an enzyme known as RNA polymerase during a process called transcription and
is mainly found in the cytoplasm although some of it are found in the nucleus

Chemical nature of RNA

The RNA is chemically composed of the following
• Ribose sugar, the five carbon sugar
• Phosphate group, this is derived from phosphoric acid and it gives the acidic
nature of the molecule.
• Nitrogenous bases, these include adenine, guanine, cytosine and uracil.
• Phosphodiester bonds between one nucleotide to another in the strand.
Ribonucleic acid (RNA) functions in converting genetic information from genes into the
amino acid sequences of proteins.

Types of RNA
The three universal types of RNA include
i. Messenger RNA, which acts to carry genetic sequence information between DNA
and ribosomes, directing protein synthesis.
ii. Ribosomal RNA, which is a major component of the ribosome, and catalyzes
peptide bond formation.
iii. Transfer RNA, which serves as the carrier molecule for amino acids to be used in
protein synthesis, and is responsible for decoding the mRNA

1.3 ENZYMOLOGY
This is the branch of biology which deals with the study of enzymes

1.3.1 Concept of enzymes

Enzymes are biological catalysts which speed up the rate of metabolic reactions in organism
and itself remain unchanged at the end of the reaction.

All enzymes are globular proteins with a specific tertiary shape. The part of the Enzyme that
acts a catalyst is called the active site. The active site of an enzyme is complementary to
the substrate it catalyses.

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Enzymes as catalyst

i. They cause increase in the velocity of a chemical reaction without being themselves
used up.
ii. A very small amount of enzyme can affect the transformation of large amount of
substrate.
iii. They catalyze the reversible reactions
iv. Does not add any energy to the system
v. The presence of enzyme does not alter the nature and proportions of the final product.

Some examples of Enzymes are:

 Lactase: Breaks down lactose into glucose and galactose.

 Catalase: Breaks hydrogen peroxide down into water and oxygen.
 Glycogen synthase: Catalyses the formation of glycosidic bonds between
Glucose molecules.
 Trypsin; Breaks down protein to peptide
 ATP-ase: Breaks down ATP into ADP, producing energy.

Roles of Enzymes

Enzymes are used for a wide variety of purposes, such as in

1. Metabolism
i. Used in digestion of food substances
ii. Used in protection against Pathogens, where they destroy invading
microorganisms.
2. Industries
3. Medicine

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1.3.2 Mechanism of enzymes action

When an enzyme and substrate are mixed the following sequence of event occur

a. The surface of the substrate molecule come close with the surface of the enzyme
b. A temporary intermediate compound known as enzyme substrate complex is formed.
c. The substrate molecule is transformed into product
d. The transformed substrate molecule (product) move away from the surface of the
enzyme molecule.

The Lock-and-key Hypothesis of enzyme action

This is a model that shows how enzymes catalyze substrate reactions. It states that “the
shape of the active sites of enzymes is exactly complementary to the shape of the substrate”.

When a substrate molecule collides with an enzyme whose active site shape is
complementary, the substrate will fit into the active site and form Enzyme-Substrate
Complex.

According to this model, it is possible for an enzyme to catalyse a reverse reaction.

The Induced-Fit Hypothesis

A more recent model, which is backed up by evidence, and is widely accepted as

describing the way enzymes work, is the Induced-Fit Hypothesis.

It states that “the shape of active sites are not exactly complementary, but change
shape in the presence of a specific substrate to become complementary”.

 When a substrate molecule collides with an enzyme, if its composition is specifically

correct, the shape of the enzyme's Active Site will change so that the substrate fits

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into it and an Enzyme-Substrate Complex can form. The reaction is then catalysed
and an Enzyme-Product Complex forms.

How Enzymes Work

Most reactions in a cell require very high temperatures to get going, which would destroy
the cell. Enzymes work by lowering the Activation Energy of a reaction.

The Activation Energy of a reaction is lowered by putting stress on the bonds within a
molecule, or by holding molecules close together. This increases the likelihood of a
reaction, and so lowers the energy required to begin it.

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1.3.3 Properties of enzymes

i. They are biochemical catalyst

ii. They catalyze reversible reactions
iii. They are globular protein in nature
iv. They remain unchanged at the end of the reaction
v. Are highly specific to the substrate they catalyse. That is usually enzyme catalyze
only single reaction.
vi. They lower the activation energy of the reaction as they catalyze
vii. Have specific site called active site where the substrate attaches.
viii. Quantitative efficiency (i.e. small amount of enzyme can transfer a large number of
substrate to react).

1.3.4 Factors affecting the rate of enzyme action

The rate of enzyme activities

The activity of an Enzyme is affected by its environmental conditions. Changing these

alter the rate of reaction caused by the enzyme. In nature, organisms adjust the conditions
of their enzymes to produce an Optimum rate of reaction, where necessary, or they may
have enzymes which are adapted to function well in extreme conditions where they live.

1. Temperature

Increasing temperature increases the kinetic energy that molecules possess. In a fluid, this
means that there are more random collisions between molecules per unit time.

 Since enzymes catalyse reactions by randomly colliding with Substrate molecules,

increasing temperature increases the rate of reaction, forming more product.

 As temperature increases, more bonds, especially the weaker Hydrogen and Ionic
bonds, will break as a result of this strain. Breaking bonds within the enzyme will
cause the Active Site to change shape.

 This change in shape means that the Active Site is less complementary to the shape
of the Substrate, so that it is less likely to catalyse the reaction. Eventually, the
enzyme will become denatured and will no longer function.

 As temperature increases, more enzymes' molecules' Active Sites' shapes will be

less complementary to the shape of their Substrate, and more enzymes will be
denatured. This will decrease the rate of reaction.

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 In summary, as temperature increases, initially the rate of reaction will increase,

because of increased Kinetic Energy. However, the effect of bond breaking will
become greater and greater, and the rate of reaction will begin to decrease.

 The temperature at which the maximum rate of reaction occurs is called the enzyme's
Optimum Temperature. This is different for different enzymes. Most enzymes in the
human body have an Optimum Temperature of around 37.0 °C.

2. pH - Acidity and Basicity

 pH measures the acidity and basicity of a solution. It is a measure of the Hydrogen

Ion (H+) concentration, and therefore a good indicator of the Hydroxide Ion (OH-)
concentration. H+ and OH- Ions are charged and therefore interfere with Hydrogen
and Ionic bonds that hold together an enzyme, since they will be attracted or
repelled by the charges created by the bonds. This interference causes a change in
shape of the enzyme, and importantly, its active site.

 Different enzymes have different Optimum pH values. This is the pH value at

which the bonds within them are influenced by H+ and OH- Ions in such a way that the
shape of their Active Site is the most complementary to the shape of their
Substrate. At the Optimum pH, the rate of reaction is at an optimum.

 Any change in pH above or below the Optimum will quickly cause a decrease in
the rate of reaction, since more of the enzyme molecules will have Active Sites
whose shapes are not (or at least are less) Complementary to the shape of their
Substrate.

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 Small changes in pH above or below the Optimum do not cause a permanent

change to the enzyme, since the bonds can be reformed. However, extreme changes
in pH can cause enzymes to Denature and permanently lose their function.

 Enzymes in different locations have different Optimum pH values since their

environmental conditions may be different. For example, the enzyme Pepsin
functions best at around pH2 and is found in the stomach, which contains
Hydrochloric Acid (pH2).

3. Enzyme Concentration

 Changing the Enzyme and Substrate concentrations affect the rate of reaction of an
enzyme-catalysed reaction. Controlling these factors in a cell is one way that an
organism regulates its enzyme activity and so its Metabolism.

 Changing the concentration of a substance only affects the rate of reaction if it is the
limiting factor: that is, it the factor that is stopping a reaction from preceding at a
higher rate.

 If it is the limiting factor, increasing concentration will increase the rate of

reaction up to a point, after which any increase will not affect the rate of reaction.
This is because it will no longer be the limiting factor and another factor will be
limiting the maximum rate of reaction.

 As a reaction proceeds, the rate of reaction will decrease, since the Substrate will
get used up. The highest rate of reaction, known as the Initial Reaction Rate is the
maximum reaction rate for an enzyme in an experimental situation.

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4. Substrate Concentration

Increasing Substrate Concentration increases the rate of reaction. This is because more
substrate molecules will be colliding with enzyme molecules, so more product will be
formed.

 However, after a certain concentration, any increase will have no effect on the rate
of reaction, since Substrate Concentration will no longer be the limiting factor. The
enzymes will effectively become saturated, and will be working at their maximum
possible rate.

5. Enzyme Concentration

 Increasing Enzyme Concentration will increase the rate of reaction, as more

enzymes will be colliding with substrate molecules.

 However, this too will only have an effect up to a certain concentration, where the
Enzyme Concentration is no longer the limiting factor. At very high enzyme
concentration the substrate concentration may become rate-limiting, so the rate stops
increasing

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6. Enzyme Inhibitors

Inhibitors inhibit the activity of enzymes, reducing the rate of their reactions. They are
found naturally, but are also used artificially as drugs, pesticides and research tools.
Enzyme Inhibitors reduce the rate of an enzyme catalysed reaction by interfering
with the enzyme in some way. This effect may be permanent or temporary.

Types of inhibitors

There are two kinds of inhibitors.

(a) A competitive inhibitor

This is the molecule that has a similar structure to that of normal substrate molecule,
and it can fit into the active site of the enzyme. It therefore competes with the
substrate for the active site, so the reaction is slower. Competitive inhibitors increase
KM for the enzyme, but have no effect on vmax, so the rate can approach a normal rate
if the substrate concentration is increased high enough. The sulphonamide anti-
bacterial drugs are competitive inhibitors.

(b) A non-competitive inhibitor

This is the molecule which is quite different in structure from the substrate molecule
and does not fit into the active site. It binds to another part of the enzyme molecule,
changing the shape of the whole enzyme, including the active site, so that it can no
longer bind substrate molecules.

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Non-competitive inhibitors therefore simply reduce the amount of active enzyme (just
like decreasing the enzyme concentration), so they decrease vmax, but have no effect
on KM.
Inhibitors that bind fairly weakly and can be washed out are sometimes called
reversible inhibitors, while those that bind tightly and cannot be washed out are called
irreversible inhibitors. Poisons like cyanide, heavy metal ions and some insecticides
are all non-competitive inhibitors.

i. Competitive Enzyme Inhibitors

This work by preventing the formation of Enzyme-Substrate Complexes because they have
a similar shape to the substrate molecule.

This means that they fit into the Active Site, but remain unreacted since they have a
different structure to the substrate. Therefore less substrate molecules can bind to the
enzymes so the reaction rate is decreased.

 Competitive Inhibition is usually temporary, and the Inhibitor eventually leaves the
enzyme. This means that the level of inhibition depends on the relative
concentrations of substrate and Inhibitor, since they are competing for places in
enzyme Active Sites.

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ii. Non-competitive Enzyme Inhibitors

These work not by preventing the formation of Enzyme-Substrate Complexes, but by

preventing the formation of Enzyme-Product Complexes. So they prevent the substrate
from reacting to form product.

 Usually, Non-competitive Inhibitors bind to a site other than the Active Site, called an
Allosteric Site. Doing so distorts the 3D Tertiary structure of the enzyme, such that
it can no longer catalyse a reaction.

 Since they do not compete with substrate molecules, Non-competitive Inhibitors are
not affected by substrate concentration.

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 Many Non-competitive Inhibitors are irreversible and permanent, and effectively

denature the enzymes which they inhibit. However, there are a lot of non-permanent
and reversible Non-competitive Inhibitors which are vital in controlling Metabolic
functions in organisms.

 Enzyme Inhibitors by organisms are used in controlling metabolic reactions. This

allows product to be produced in very specific amounts.

Enzyme Inhibitors in Metabolic Control

 Enzymes vastly increase the rate of a metabolic reaction, often by a factor of 10

million. This fact is essential to all life on earth, but it means that Enzyme activity
must be very tightly controlled, since uncontrolled reactions can be fatal.

 For example, in the disease 'multiple sclerosis', the immune system starts destroying
nerves by allowing destructive Enzymes to attack nerve cells, often resulting in
paralysis.

 Often a Metabolic Process is composed of many different reactions, each of which

is catalysed by a different Enzyme. These are reactions are called Metabolic
Pathways. For example, photosynthesis has a Metabolic Pathway.

 In many cases, the final product of a Metabolic Pathway acts as a Non-competitive

Inhibitor to one of the enzymes earlier along the chain. This means that the
Metabolic Process controls itself, since the more product gets produced, the more it
inhibits the pathway, and so the slower the process proceeds.

Enzyme Inhibitors as Metabolic Poisons

 Many poisons work by inhibiting the action of enzymes involved in Metabolic

processes, which disturbs an organism.

 For example, Potassium Cyanide is an irreversible Inhibitor of the enzyme

Cytochrome C Oxidase, which takes part in respiration reactions in cells. If this
enzyme is inhibited, ATP cannot be made since Oxygen use is decreased. This means
that cells can only respire Anaerobically, leading to a buildup of Lactic Acid in the
blood. This is potentially fatal.

 The poison Malonate binds to the Active Site of the enzyme Succinate Dehydrogenase
competing with Succinate, which is important in respiration.

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Enzyme Inhibitors as Medicines

 Some Enzyme Inhibitors can be used as Medicines in the treatment of conditions.

 For example, infection by viruses can be treated by Inhibitors to the viral enzyme
Protease, often competitive Inhibitors. This means that viruses cannot build new
protein coats and therefore cannot replicate.

Factors that Affect the Rate of Enzyme Reactions

1. Temperature

Enzymes have an optimum temperature at which they work fastest. For mammalian
enzymes this is about 40°C, but there are enzymes that work best at very different
temperatures, e.g. enzymes from the arctic snow flea work at -10°C, and enzymes
from thermophilic bacteria work at 90°C.
 Up to the optimum temperature the rate increases geometrically with temperature (i.e.
it's a curve, not a straight line). The rate increases because the enzyme and substrate
molecules both have more kinetic energy so collide more often, and also because more
molecules have sufficient energy to overcome the (greatly reduced) activation energy.

The increase in rate with temperature can be quantified as

a Q10, which is the relative increase for a 10°C rise in temperature. Q10 is usually 2-3
for enzyme-catalysed reactions (i.e. the rate doubles every 10°C) and usually less than
2 for non-enzyme reactions.
 The rate is not zero at 0°C, so enzymes still work in the fridge (and food still goes
off), but they work slowly. Enzymes can even work in ice, though the rate is
extremely slow due to the very slow diffusion of enzyme and substrate molecules
through the ice lattice.
 Above the optimum temperature the rate decreases as more and more of the enzyme
molecules denature. The thermal energy breaks the hydrogen bonds holding the
secondary and tertiary structure of the enzyme together, so the enzyme (and especially
the active site) loses its shape to become a random coil. The substrate can no longer
bind, and the reaction is no longer catalysed. At very high temperatures this is
irreversible. Remember that only the weak hydrogen bonds are broken at these mild
temperatures; to break strong covalent bonds you need to boil in concentrated acid for
many hours.

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 Cytology and Biochemistry notes for A-Level students

7. Allosteric Effectors

The activity of some enzymes is controlled by certain molecules binding to a specific

regulatory (or allosteric) site on the enzyme, distinct from the active site. Different
molecules can inhibit or activate the enzyme, allowing sophisticated control of the rate. Only
a few enzymes can do this, and they are often at the start of a long biochemical pathway.
They are generally activated by the substrate of the pathway and inhibited by the product of
the pathway, thus only turning the pathway on when it is needed

Enzymology

Enzymes are biological catalysts. They increase the rate of reactions by a factor of between
106 to 1012 times, allowing the chemical reactions that make life possible to take place at
normal temperatures. They were discovered in fermenting yeast in 1900 by Buchner, and the
name enzyme means "in yeast". As well as catalysing all the metabolic reactions of cells
(such as respiration, photosynthesis and digestion), they also act as motors, membrane
pumps and receptors.

Enzyme Structure

Enzymes are proteins, and their function is determined by their complex structure. The
reaction takes place in a small part of the enzyme called the active site, while the rest of the
protein acts as "scaffolding". This is shown in this diagram of a molecule of the enzyme
amylase, with a short length of starch being digested in its active site. The amino acids
around the active site attach to the substrate molecule and hold it in position while the
reaction takes place. This makes the enzyme specific for one reaction only, as other
molecules won't fit into the active site.

Many enzymes need cofactors (or coenzymes) to work properly. These can be metal ions
(such as Fe2+, Mg2+, Cu2+) or organic molecules (such as haem, biotin, FAD, NAD or
coenzyme A). Many of these are derived from dietary vitamins, which is why they are so
important. The complete active enzyme with its cofactor is called a holoenzyme, while just
the protein part without its cofactor is called the apoenzyme.

How do enzymes work?

There are three ways of thinking about enzyme catalysis. They all describe the same process,
though in different ways, and you should know about each of them.

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 Cytology and Biochemistry notes for A-Level students

1. Reaction Mechanism

In any chemical reaction, a substrate (S) is converted into a product (P):

SP

(There may be more than one substrate and more than one product, but that doesn't matter
here.) In an enzyme-catalysed reaction, the substrate first binds to the active site of the
enzyme to form an enzyme-substrate (ES) complex, then the substrate is converted into
product while attached to the enzyme, and finally the product is released. This mechanism
can be shown as:

E + S ES EP E + P

The enzyme is then free to start again. The end result is the same (S P), but a different route
is taken, so that the S P reaction as such never takes place. In by-passing this step, the
reaction can be made to happen much more quickly.

2. Molecule Geometry

The substrate molecule fits into the active site of the enzyme molecule like a key fitting into
a lock (in fact it is sometimes called a lock and key mechanism). Once there, the enzyme
changes shape slightly, distorting the molecule in the active site, and making it more likely
to change into the product. For example if a bond in the substrate is to be broken, that bond
might be stretched by the enzyme, making it more likely to break. Alternatively the enzyme
can make the local conditions inside the active site quite different from those outside (such
as pH, water concentration, charge), so that the reaction is more likely to happen.

It's a bit more complicated than that though. Although enzymes can change the speed of a
chemical reaction, they cannot change its direction, otherwise they could make "impossible"
reactions happen and break the laws of thermodynamics. So an enzyme can just as easily
turn a product into a substrate as turn a substrate into a product, depending on which way the
reaction would go anyway. In fact the active site doesn't really fit the substrate (or the
product) at all, but instead fits a sort of half-way house, called the transition state. When a
substrate (or product) molecule binds, the active site changes shape and fits itself around the
molecule, distorting it into forming the transition state, and so speeding up the reaction. This
is sometimes called the induced fit mechanism.

3. Energy Changes

The way enzymes work can also be shown by considering the energy changes that take place
during a chemical reaction. We shall consider a reaction where the product has a lower

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 Cytology and Biochemistry notes for A-Level students

energy than the substrate, so the substrate naturally turns into product (in other words the
equilibrium lies in the direction of the product). Before it can change into product, the

substrate must overcome an "energy barrier"

called the activation energy (EA). The larger the activation energy, the slower the reaction
will be because only a few substrate molecules will by chance have sufficient energy to
overcome the activation energy barrier. Imagine pushing boulders over a hump before they
can roll down hill, and you have the idea. Most physiological reactions have large activation
energies, so they simply don't happen on a useful time scale. Enzymes dramatically reduce
the activation energy of a reaction, so that most molecules can easily get over the activation
energy barrier and quickly turn into product.

For example for the catalase reaction (2H2O2 2H2O + O2) the activation energy is 86 kJ mol-1
with no catalyst, 62 kJ mol-1 with an inorganic catalyst of iron filings, and just 1 kJ mol-1 in
the presence of the enzyme catalase.

The activation energy is actually the energy required to form the transition state, so enzymes
lower the activation energy by stabilising the transition state, and they do this by changing
the conditions within the active site of the enzyme. So the three ideas above are really three
ways of describing the same process.

Classification of enzymes

They are classified according to the type of reaction

They are classified according to the type of reaction they catyse

HYDROLYSIS ENZYMES

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 Cytology and Biochemistry notes for A-Level students

These catylase decomposition of substrate by hydrolysis attacking specific linkage or the

catalyst the synthesis of complex substrate by condensation forging a certain linkage
forexample

i. Esterases

These enzymes attack organic ester spelitting them into two group one of which is normaly
an acid

Eg Lipase is spilting fat into alphatic acid and glycerol

ii. Phospholases is hydrolyse phodpholic acid ester such as hexos phosphate ,

glycophosphate and nucleotrades producing phosphoric acid acid and base

Carbohydrat

All carbohydrate catalyse various stages in hydrplysis of higher carbohydrate to the simple
sugar eg

Starch amylase to disaccharides

Inulin inulase fructose

Cellulose under cellulose cellobiose

Maltose under maltase to glucose and glucoles

Sucrose under sucrose to glucose and fructose

Cellobiose cellobiase to glucose

Lactase lactose glucose and galatose

iii. Protease

Enzyme which attack the Co old (peptide limkage) in protein

Eg Exopeptide attack terminal peptide link ( Co NH) this spilting of amino acid eg Erepsin

Eniopeptidase spilt protein molecule into smaller units protease , peptone and peptide

iv. Aminases

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 Cytology and Biochemistry notes for A-Level students

Enzymes which attack (C NH2) and R-NH2 linkage in non protein cpds .The NH or NH2
group is replaced by OH and amino liberated

These enzymes are importance in purine metabolism and in production of urea in these
animals which excretes it

Co(NH2) plus H2O under ureases 2NH3 plus CO2

2 Oxidalation – Reduction enzymes

Oxidation - loss of electrons
-addition of oxygen
-Removal of hydrogen
Reduction –gain of hydrogen
Addition of hydrogen
@Dehydrogenases
-Catylases the reaction involving the transfer of hydrogen from the substrate to the
hydrogen receptor
Lactic acid dehydragenases – oxidation of lactic acid to pyravic acid in animals tissues
Malic acid malic dehydrogesis oxaloacetic acid

B)Oxidases

They catalyse the reaction in the presence free oxygen

Eg Amino acid amino acid oxidases keto acid and NH3

Uric acid uric acid oxidase allantain in liver and kidney cytochrome oxidases in the
presence of oxygen in cuyochrome series where it release ATP

Peroxidases

Act an hydrogen peroxide or organic peroxide only the presence of a substrate which is
oxygen receptor

Common in all higher in plants and certain mammalian tissues especially spleen and lungs

A plus h2o peroxidases H2o Ao

Catalases

Present in all aerobic tissue break hydrogen peroxide into water and molecular o2 does not
depend in o2 cceptor

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 Cytology and Biochemistry notes for A-Level students

2h2o catalase 2H2O plus O2

Dropng of H2O in cut plant or animal tissues into O2 is involved

3)Enzymes attackimg the c-c linkage (DESMOLASES)

I. Carbohydrate – causes decarboxylation of keton acids
Eg
decarboxylate pyravic acids acetaldehyde and CO2 pyrovic carboxylate|
CH3COCOOH under pyravic CH3CHO plus CO2
Oxaloacetic acid to pyravic and Co2

NB;Decarboxylase – occur principally in animals tissue convert various

amino acid ito corresponding ammonia with evolution of CO2.

Madam Rehema TMS