STC 222-1

UNESC
CO‐NIGERIA TTECHNICAL & VOCATIONAAL
EDUCATTION REVITALLISATION PRO
OJECT‐PHASEE II
NATTIONALL DIPLO
OMA IN
SCIENCE LA
ABORA
ATORY TTECHNO
OLOGY

BIIOCHEEMIST

TRY
CO
OURSE C
CODE: STTC222

YEAR II‐ SSE MESTTER II
TH
HEORY
V
Version 1: D
December 2008
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TABLE OF CONTENTS
WEEK 1: MOLECULAR ORGANIZATION OF THE LIVING CELLS………………………………………….3
WEEK 2: THE IMPORTANCE OF WATER AND THE CONCEPT OF THE PH AND BUFFER………13
WEEK 3: CARBOHYDRATES……………………………………………………………………………………………..25
WEEK 4: PROPERTIES, STRUCTURES AND REACTIONS OF MONOSACCHARIDES………………28
WEEK 5: STRUCTURES AND USES OF DISACCHARIDES AND POLYSACCHARIDES……………..44
WEEK 6: NATURE, BIOLOGICAL AND INDUSTRIAL IMPORTANCE OF LIPIDS…………………….51
WEEK 7: NATURE, BIOLOGICAL AND INDUSTRIAL IMPORTANCE OF LIPIDS…………………….61
WEEK 8: STRUCTURE, PROPERTIES AND FUNCTIONS OF PROTEINS……………………………….69
WEEK 9: CLASSIFICATION OF AMINO ACIDS AND THEIR STRUCTURES……………………………72
WEEK 10: STRUCTURE AND BEHAVIOUR OF PROTEINS…………………………………………………89
WEEK 11: NATURE OF ENZYMES …………………………………………………………………………………..96
WEEK 12: DISTINCTIVE FEATURESOF ENZYMES………………………………………………………………97
WEEK 13: CLASSIFICATION OF ENZYMES…………………………………………………………………………99
WEEK 14: FACTORS AFFECTING ENZYME ACTIVITIES……………………………………………………..101
WEEK 15: VITAMINS……………………………………………………………………………………………………….103
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WEEK 1. THE MOLECULAR ORGANIZATION OF LIVING CELLS

1.0 Introduction
Biochemistry is the science concerned with the chemical basis of life (Gk bios “life”). Biochemistry is
therefore concerned with the entire spectrum of life forms, from relatively simple viruses and
bacteria to complex human beings. The cell is the structural unit of living systems. Thus,
biochemistry can also be described as the science concerned with the study of the chemical
constituents of living cells, the reactions and processes they undergo. By this definition, biochemistry
encompasses, chemistry and molecular biology.
The major objective of biochemistry is the complete understanding, at the molecular level, of all of
the chemical processes place within living cells. To achieve this objective, biochemists have sought
to isolate the numerous molecules found in cells, determine their structures and their functions.
some of the biochemical techniques employed for these purposes include the following
Centrifugation: Differential, Ultracentrifugation.
• Chromatography: Paper; exclusion, ion exchange; affinity; thin‐layer; gas‐liquid; high‐
pressure liquid; gel filtration.
• Dialysis: Ultrafiltration, Electrodialysis.
• Electrophoresis: Paper; high‐voltage; agarose; cellulose acetate; starch gel; polyacrylamide
gel;
SDS‐polyacrylamide gel.
• Salt fractionation: eg, precipitation of proteins with ammonium sulfate
• Spectroscopy: Mass spectrometric, UV, visible, infrared, and NMR spectroscopy
• Radio‐Isotopy: X‐ray crystallography

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1.1 List of Cell Organelles
Cell
Cells are the structural and functional units of all living organisms. There are different types of Cells,
which vary enormously in size, shape and specialized functions. Living cells are divided into two
major classes: prokaryote that do not have a nucleus or internal membrane‐surrounded organelles
e.g. Escherichia coli cells and eukaryotes that have a defined nucleus and intracellular organelles
surrounded by membranes e.g. Cells of yeast, fungi, plants and animals. Each organelle has a specific
role to play in cell activities.Cell Organelles include: Nucleus, nucleolus, Plasma membrane,
ribosomes, mitochondria, endoplasmic reticulum, Golgi complexes, and lysosomes. It also include
peroxisomes and cytosol, Plant cells also contain vacuoles and chloroplasts. Also present in the
cytoplasm of many cells are granules or droplets containing stored nutrients such as starch and fat
(Fig 1.1).
Abbreviations:
BM, basement membrane
ER, rough endoplasmic

reticulum
(with ribosomes attached;

smooth
ER is depicted nearer the

nucleus
and on the right side of the

cell.)
DI, deep indentation of

plasma
membrane
GI, glycogen granules
Gap, space ~10-20 nm

thick
between adjacent cells
4

M, mitochondrion
Mb, microbody
L, lysosome
D, desmosome
TJ, tight junction
Mv, microvilli
C, cillium
SG, secretion granule
V, vacuole
Nu, nucleolus
G, Golgi apparatus
CW, cell wall (of a plant)
Ct, centrioles
P, plasmodesmata
N, nucleus
Cp, chloroplast
St, starch granule
FIGURE 1.1 The “average” eukaryotic cell. This composite drawing shows the principal organelles of both animal and
plant
1.2 Centrifugation
Centrifugation Is a method for separating liquids of different specific gravities or for separating
suspended colloidal particles according to particle‐size fractions by centrifugal force using special
rotating devices called centrifuges. When the centrifugation techniques are devised to used a high
centrifugal force (i.e.high speed), it is referred to as ultra centrifugation. One of the major uses of
centrifugal methods in biochemistry is in the separation of cell organelles from tissue homogenates.
The use of centrifugal methods to separate cell organelles is also referred to as cell fractionation.
5

Both the density gradient centrifugation and differential centrifugation are used to separate sub‐
cellular organelles.
In a major advance in biochemistry, Albert Claude, Christian de Duve, and George Palade developed
methods for separating organelles from the cytosol and from each other—an essential step in
isolating biomolecules and larger cell components and investigating their structures and functions. In
a typical cell fractionation (Fig. 1.2), cells or tissues in solution are disrupted by gentle
homogenization. This treatment ruptures the plasma membrane but leaves most of the organelles
intact. The homogenate is then centrifuged; organelles such as nuclei, mitochondria, and lysosomes
differ in size and therefore sediment at different rates. They also differ in specific gravity, and they
“float” at different levels in a density gradient. Differential centrifugation results in a rough
fractionation of the cytoplasmic contents, which may be further purified by isopycnic (“same
density”) centrifugation. . In isopycnic centrifugation, a centrifuge tube is filled with a solution, the
density of which increases from top to bottom; a solute such as sucrose is dissolved at different
concentrations to produce the density gradient. When a mixture of organelles is layered on top of
the density gradient and the tube is centrifuged at high speed, individual organelles sediment until
their buoyant density exactly matches that in the gradient. Each layer can be collected separately.
In this procedure, organelles of different buoyant densities (the result of different ratios of lipid and
protein in each type of organelle) are separated on a density gradient. By carefully removing
material from each region of the gradient and observing it with a microscope, the biochemist can
establish the sedimentation position of each organelle and obtain purified organelles for further
study. For example, these methods were used to establish that lysosomes contain degradative
enzymes, mitochondria contain oxidative enzymes, and chloroplasts contain photosynthetic
pigments. The isolation of an organelle enriched in a certain enzyme is often the first step in the
purification of that enzyme.
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FIGURE 1.2 Representation of Sub cellular fractionation of tissue. (a) The large and small particles
in the suspension can be separated by centrifugation at different speeds, or (b) particles of different
density can be separated by isopycnic centrifugation

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Marker Enzyme
A marker enzyme is an enzyme that is localized in a sub‐cellular organelles and its location is
known and on the assay of the enzyme can be used as an aid in the isolation and purification of
sub‐cellular organelles. Examples as shown (table 2.1)
ORGANELLES MARKER ENZYME.
Nuclei DNA polymerase
Golgi apparatus Glycosyl tranferase
Mitochondria Monoamine oxidase (outer membrane)
Cytochrome C (inner membrane)
Lysosomes Acid phosphatase
Endoplasmic reticular Cytochrome B reductase and cytochromes B
Vesicles Glucose‐6‐phospharase.
Cytoplasmic membrane Na+‐K+ AT pase viral receptor
1.3 Cell Organelles and Their Functions
The plasma membrane defines the periphery of the cell, separating its contents from the
surroundings. It is composed of lipid and protein molecules that form a thin, tough, pliable,
hydrophobic barrier around the cell. It is a semi permeable membrane surrounding the protoplasm.
it selectively allow passage and some solute through it.
The cytoplasm (Fig. 1.3) is composed of an aqueous solution, the cytosol, and a variety of suspended
particles with specific functions. The cytosol is a highly concentrated solution containing enzymes
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and the RNA molecules that encode them; the components (amino acids and nucleotides) from
which these macromolecules are assembled; hundreds of small organic molecules called
metabolites, intermediates in biosynthetic and degradative pathways; coenzymes, compounds
essential to many enzyme‐catalyzed reactions; inorganic ions; and ribosomes, small particles
(composed of protein and RNA molecules) that are the sites of protein synthesis.
All cells have, for at least some part of their life, either a nucleus or a nucleoid, in which the
genome— the complete set of genes, composed of DNA—is stored and replicated. The nucleoid, in
bacteria, is not separated from the cytoplasm by a membrane; the nucleus, in higher organisms,
consists of nuclear material enclosed within a double membrane, the nuclear envelope. Cells with
nuclear envelopes are called eukaryotes (Greek eu, “true,” and karyon, “nucleus”); those without
nuclear envelopes—bacterial cells—are prokaryotes (Greek pro, “before”). It is the control center of
the cell, oval in shape the surrounding membrane has pores in it that allow the passage of of large
molecules like messenger RNA(mRNA), proteins and lipids etc. Present in the nucleus is the
nucleolus, chromosomes etc.
Chloroplast: Are found mainly in the green plants and is the site of the most fundamental of
biochemical reaction. Light energy is trapped and transformed into chemical energy and carbon
dioxide is also reduced to the level of sugars, while oxygen is given out as a by‐product.
Mitochondrial: they are rod or oval in shape organelles which are surrounded by two membranes,
an inner and outer membrane. The outer membrane is smooth, where as the inner membrane is
double folded into sheets or tubules known as Critae which extend into the internal space matrix of
the mitochondrion. These organelles are concerned with the chemical processes by which energy is
made available to cells in the form of molecules of adenosine tri‐phosphate (ATP). Most of the AT P
used by cells is formed in the mitochondrion. These the chemical reaction of this processes
consumed oxygen and carbon dioxide Mitochondrion therefore function as the major site of ATP
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production, oxygen utilization and CO2 formation. It contains enzymes of Krebs cycle and oxidative
phosphorylation.
Endoplasmic Reticulum: A double layered lipoprotein membrane. There two types;
Rough Endoplasmic Reticulum; appears rough because of some ribosome attached to it functions
actively in the synthesis of protein.
Smooth Endoplasmic Reticulum; is smooth because of the absence of ribosome. It is actively
involved in the synthesis of lipid. It also functions as storage for enzymes.
Lysosome; they are spherical or oval bodies surrounded by a single membrane which encloses a
densely staining granular matrix. Lysosome digest (break down) various complex substances, such as
bacteria and cellular debris that have been engulfed by the cell. They may also digest other cell
organelles that have been damaged and are no longer functioning normally. They are an especially
important part of the defense system of the body.
Golgi apparatus; this are located near the nuleos protein that are synthesized on the ribosomes
attached to the rough endoplasmic reticulum are transferred to the golgi apparatus. The golgi
apparatus during the passage of various protein through its lumen selectively sorts them into
vesicles and in some manner determine by the address to which each vesicle will be delivered.
Peroxisome; they are similar in structure to lysosomes being oval bodies enclosed by a single
membrane. The chemical composition of the peroxisome matrix (lumen) is however, quite different
from that of the lysosomes. Like mitochondrial, peroxisomes consumes oxygen, although in much
smaller amounts and this oxygen is used in various chemical reactions that are not associated with
ATP formation. This organelle can also destroy certain products of oxygen reactions which can be
quite toxic to cells specifically hydrogen peroxide.
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Centroles; are two small bodies, composed of nine fuse sets of micro‐tubules located in the cells
cytoplasm; participate in nuclear and cell division.
Microtubules; are tubular filaments in the cytoplasm, which provide internal support of cells, can be
rapidly assembled and to produce the movements of organelles within the cells.
Microfilaments; are rod like filament in the cytoplasm of most of cell. They can be rapidly assembled
and disassembled to allow a cell to change its shape.
Secretory Vesicles; it is a membrane bound vesicles produced by the golgi apparatus. It contains
proteins to be secreted by the cell.
1.4 Chemical Composition of cell
Water is the major component of living cells which is about 60‐70% total weight of the cell.The solid
material of the cell comprises the fatty compounds which are referred to as lipids. Plant such as
young leafy vegetable is found to contain 2–5% lipid on a dry weight basis. Even very lean meats
contain 10–30% lipid. The cell consists predominately of three groups of compounds:proteins,
nucleic acids, and carbohydrates. Most of the nitrogen present in tissues is found in the proteins
and the protein content is sometimes estimated in a young green plant to be 20–30% of the dry
matter may be protein, while The amount of nucleic acid in tissues varies from 0.1% in yeast and
0.5–1% in muscle and in bacteria to 15–40% in thymus gland and sperm cells. For diploid cells of the
body the DNA content per cell is nearly constant Although the solid matter of cells consists
principally of C, H, O, N, S, and P, many other chemicalelements are also present. Among the
cations, Na+, K+,Ca2+, and Mg2+ are found in relatively large amounts .Thus, the body of a 70 kg
person contains 1050 g Ca (mostly in the bones), 245 g K, 105 g Na, and 35 g Mg. Iron (3 g), zinc (2.3
g), and rubidium (1.2 g) are the next most abundant. Of these iron and zinc are essential to life but
rubidium is probably not. It is evidently taken up by the body together with potassium. The other
metallic elements in the human body amount to less than 1 g each, but at least seven of them play
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essential roles. They include copper (100 mg), manganese (20 mg), and cobalt (~5 mg). Others, such
as chromium (<6 mg), tin, and vanadium, have only
recently been shown essential for higher animals.156,157 Nickel, lead, and others may perhaps be
needed. Nonmetallic elements predominating are phosphorus (700 g in the human body), sulfur
(175 g), and chlorine (105 g). Not only are these three elements essential to all living cells but also
selenium, fluorine, silicon , iodine, and boron
APPROXIMATE CHEMICAL COMPOSITION OF A BACTERIAL CELL.
Component % of total weight no. of types of each molecule
Water 70 1
Inorganic ions 1 20
Sugar precursors 3 200
A. acid&; 0.4 100
Nucleotides &; 0.4 200
Lipids& 2 50
Other small molecule 0.2 200
Macro molecules (nuclei acid
Proteins& polysaccharide) 22 500

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WEEK 2 THE IMPORTANCE OF WATER AND THE CONCEPT OF THE PH
AND BUFFER.
2.1 Importance Of Water As A Major Cellular Component
Water is the most abundant substance in living systems, making up 70% or more of the weight of
most organisms. The first living organisms doubtless arose in an aqueous environment, and the
course of evolution has been shaped by the properties of the aqueous medium in which life began.
Water is the most important liquid in existence, made of hydrogen and oxygen covalently
bonded It occur naturally by sea water, underground /spring water, river, lake water e.t.c pure
water can be obtained by the process of distillation.
2.2 PHYSICAL PROPERTIES OF PURE WATER
A colourless, odourless and tasteless liquid Neutral to litmus with pH of 7.0 Density of 1.0g/cm3
at 4oC Freezing point of 0oC and boiling point of 100oC at lower pressure It turns white
anhydrous copper sulphate blue
2.3 Compartments of Water in Human Body
In the human body water is the most abundant and single constituent, it is estimate that
between 55 – 67% of the body weight of a normal human is water. Water distributed into
components i.e. there is intracellular water located within cell and extra cellular water which
include blood tissue and lymph. Water found in between cells (interstitial fluids) synod fluid
(between joints) gastro intestinal fluid e.t.c
A normal individual excretes 1.6‐ 2.5liters of water daily in urine, faeces, sweat and breathing
and all these needs to be replenish. This is done by drinking water, water in food and metabolic
reactions (metabolic water). Water balance is primarily maintained by the kidney, which in turn
is control by the kidney and the kidney is control by the Anti‐ diuretic hormones (vaso presin )
13

At cellular level water accounts for 60 % ‐85% of the mass of most kind of cells. it acts as a solvent
for small organic and inorganic molecules. In addition, it 's polar nature helps determines, the
irritation of polar and non polar groups in proteins molecules, thereby it influences enzyme surface
shape in a literally vital manner. The normal concentration of ions both in the intra and extra
cellular fluids is preserved by a balance between the intake of water and electrolyte in the diet and
the output in the excretion. Water is also involved widely as a medium for the transportation
of nutrients and metabolites and also in the maintenance of constant body temperature.
Water is the predominant chemical component of living organisms. Its unique physical properties,
which include the ability to solvate a wide range of organic and inorganic molecules, derive from
water’s dipolar structure and exceptional capacity for forming hydrogen bonds.
Water has a slight propensity to dissociate into hydroxide ions and protons. The acidity of aqueous
solutions is generally reported using the logarithmic pH scale

Water Is an Ideal Biological Solvent
A water molecule is an irregular, slightly skewed tetrahedron with oxygen at its center (Figure 3.1).
The two hydrogens and the unshared electrons of the remaining two sp3‐hybridized orbital occupy
the corners of the tetrahedron. The 105‐degree angle between the hydrogens differs slightly from
the ideal tetrahedral angle, 109.5 degrees. Ammonia is also tetrahedral, with a 107‐ degree angle
between its hydrogens. Water is a dipole, a molecule with electrical charge distributed
asymmetrically about its structure. The strongly electronegative oxygen atom pulls electrons away
from the hydrogen nuclei, leaving them with a partial positive charge, while its two unshared
electron pairs constitute a region of local negative charge. Water, a strong dipole, has a high
dielectric constant.
14

As described quantitatively by Coulomb’s law, the strength of interaction F between oppositely
charged particles is inversely proportionate to the dielectric constant of the surrounding medium.
The dielectric constant for a vacuum is unity; for hexane it is 1.9; for ethanol it is 24.3; and for water
it is 78.5.
Hydrogen Bonding Gives Water Its Unusual Properties
Water has a higher melting point, boiling point, and heat of vaporization than most other common
solvents (Table 2.1). These unusual properties are a consequence of attractions between adjacent
water molecules that give liquid water great internal cohesion. A look at the electronic structure of
the H2O molecule reveals the cause of these intermolecular attractions.
TABLE 2.1 Melting Points, Boiling Point, and Heat of Vaporization of Some Common Solvents
Each hydrogen atom of a water molecule shares an electron pair with the central oxygen atom. The
geometry of the molecule is dictated by the shapes of the outer electron orbitals of the oxygen
atom, which are similar to the sp3 bonding orbitals of carbon (see Fig.2.1a). These orbitals describe a
rough tetrahedron, with a hydrogen atom at each of two corners and unshared electron pairs at the
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other two corners (Fig. 2.1b). The H‐ O‐H bond angle is 104.5o, slightly less than the 109.50 of a
perfect tetrahedron because of crowding by the nonbonding orbitals of the oxygen atom.
Figure 2.1 Structure of the water molecule. The dipolar nature of the H2O molecule is shown by (a)
ball-and-stick and (b) space-filling models. The dashed lines in (a) represent the nonbonding orbital,
there is a nearly tetrahedral arrangement of the outer-shell electron pairs around the oxygen atom;
-
the two hydrogen atoms have localized partial positive charges (δ ) and the oxygen atom has a partial
-
negative charge (2 δ ). (c) Two H2O molecules joined by a hydrogen bond (designated here, and
throughout this book, by three blue lines) between the oxygen atom of the upper molecule and a
hydrogen atom of the lower one. Hydrogen bonds are longer and weaker than covalent H-O-H bonds
Water therefore greatly decreases the force of attraction between charged and polar species
relative to water‐free environments with lower dielectric constants. Its strong dipole and high
dielectric constant enable water to dissolve large quantities of charged compounds such as salts.
Water Interacts Electro statically with Charged Solutes
Water is a polar solvent. It readily dissolves most biomolecules, which are generally charged or polar
compounds. Compounds that dissolve easily in water are hydrophilic (Greek, “water‐loving”). In
contrast, non‐polar solvents such as chloroform and benzene are poor solvents for polar
biomolecules but easily dissolve those that are hydrophobic—non‐polar molecules such as lipids and
waxes (Fig 2.2).
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Water dissolves salts such as NaCl by hydrating and stabilizing the Na+ and Cl‐ ions, weakening the
electrostatic interactions between them and thus counteracting their tendency to associate in a
crystalline lattice. The same factors apply to charged biomolecules, compounds with functional
groups such as ionized carboxylic acids ( ‐COO‐), protonated amines ( NH3 +), and phosphate esters or
anhydrides. Water readily dissolves such compounds by replacing solute. Hydrogen bonds with
solute‐water hydrogen bonds, thus screening the electrostatic interactions between solute
molecules. Water is especially effective in screening the electrostatic interactions between dissolved
ions because it has a high dielectric constant, a physical property reflecting the number of dipoles in
a solvent. The strength, or force (F), of ionic interactions in a solution depends upon the magnitude
of the charges (Q), the distance between the charged groups (r), and the dielectric constant (£) of
the solvent in which the interactions occur:

Figure 2.2 Some Examples of Polar, Nonpolar, and Amphipathic Biomolecules (Shown as Ionic
Forms at pH 7)
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2.4 Physiological and laboratory buffers
The following are the buffers that are of Physiological and laboratory application and their pH
ranges
Buffer pH
• Acetic acid‐sodium acetate (3.5‐ 5.5)
• Mono and disodium phosphate (6‐8)
• Sodium Bicarbonate‐ carbonate (9‐11)
• Tris buffer (7‐9)
• Phosphate buffer (7‐9)
• proteins and
• Haemoglobin in the red blood cell

2.5 Buffer and their roles in resisting pH
A buffer is a solution of a particular pH that can resist pH change upon small addition of on acid or
alkaline. Buffers is in fact mixtures of weak acid and their salts or weak bases and their salts.
Some common buffer mixtures and their pH ranges includes: Acetic acid‐sodium acetate
(3.5‐ 5.5) Mono and di‐sodium phosphate (6‐8) Sodium Bicarbonate (9‐11)
Phosphate buffer (7‐9)
Life exist only within narrow limits of pH in man and other mammals, the plasma pH lies within a
very narrow limits of 7.35‐7.45 at normal body temperature. If for any pathological reason, the
pH should fall below 7.0 or above 7.8, death will surely occur as a result of acidosis coma.
Fortunately the pH is maintained by the following two important buffer systems. Phosphate Buffer;
this is important in intracellular fluid and is made up of a conjugate acid‐base pair which is a
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proton donor and its corresponding proton acceptor) i.e. H3PO4 as proton donor and HPO42‐ as
proton acceptor. Bicarbonate buffer; is the major buffer system in the blood system and it
consist of H2CO3 as proton donor and HCO3‐ as proton acceptor Other buffer systems include the
proteins and hemoglobin in the red blood cells The unique ability of buffer to result pH changes can
be explained by the common ion effect consider for example the acetate buffer

CH3COOH CH3COO‐ + H+
When excess hydrogen ion (H+) to this buffer system, they quickly combine with CH3COO‐ ion to
form CH3COOH until the original ( H+) concentration is maintained. Similarly lf base (proton
acceptor) enters the system and removes the H+ ion , more CH3COOH dissociate until the desired
level of (H+)is re‐established.
It is important to note, that buffers can resist pH changes but doesn’t mean that they can prevents
changes in the pH completely In fact all buffers will to some extent yield to pressure to change pH
as more and more of acid or base is added . The degree to which a buffer will resist or minimised
pH changes with addition of acid or base is known as buffer capacity.
2.6 pH
Water molecules have a slight tendency to undergo reversible ionization to yield a hydrogen ion (a
proton) and a hydroxide ion, giving the equilibrium

It is observed that the dissociation product of water as H+, free protons do not exist in solution;
hydrogen ions formed in water are immediately hydrated to hydroxonium ions (H3O+). Hydrogen
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bonding between water molecules makes the hydration of dissociating protons virtually
instantaneous:
2.7 The Ionization of Water Is Expressed by an Equilibrium Constant
The degree of ionization of water at equilibrium is small; at 25 °C only about two of every
109molecules in pure water are ionized at any instant. The equilibrium constant for the reversible
ionization of water is

In pure water at 25oC, the concentration of water is 55.5 M (grams of H2O in 1 L divided by its gram
molecular weight: (1,000 g/L)/(18.015 g/mol)) and is essentially constant in relation to the very low
‐
concentrations of H +and OH namely, 1 X 10‐7 M. Accordingly, 55.5 M can be substituted in the
equilibrium constant expression to yield
This, on rearranging, becomes
Where Kw designates the product (55.5 M) (Kw), the ion product of water at 25 °C
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‐
The value for Kw, determined by electrical‐conductivity measurements of pure water, is 1.8 X10 16 M
o
at 25 C. Substituting this value for Kw in Equation above gives the value of the ion product of
water:
‐ ‐
Thus the product [H+][OH ] in aqueous solutions at 250C always equals 1 X 10 14 M2. When there are
exactly equal concentrations of H_ and OH_, as in pure water, the solution is said to be at neutral
‐
pH. At this pH, the concentration of H+ and OH can be calculated from the ion product of water as
follows:
‐ ‐
As the ion product of water is constant, whenever [H+] is greater than 1X 10 7 M, [OH ] must become
less than 1X 10‐7M, and vice versa. When [H+] is very high, as in a solution of hydrochloric acid, [OH‐]
‐
must be very low. From the ion product of water we can calculate [H+] if we know [OH ], and vice
versa
pH is the negative logarithm to base 10 of [H+] concentration
pH = ‐log 10[H+]
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pH scale is a scale which shows the degree of acidity or alkanity of an aqueous solution numbered
‐
from 0.1 – 14. The pH Scale Designates the H+ and OH .
2.8 Calculation of pH
The ion product of water, Kw, is the basis for the pH scale. It is a convenient means of designating
‐ +
the concentration of H+(and thus of OH ) in any aqueous solution in the range between 1.0 M H and
‐
1.0 M OH . The term pH is defined by the expression
The symbol p denotes “negative logarithm of.” For a precisely neutral solution at 25 _C, in which the
concentration of hydrogen ions is 1.0 X10‐7 M, the pH can be calculated as follows:
Table The pH Scale
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1. What is the concentration of H+ in a solution of 0.1 M NaOH?

- ‐
2. What is the concentration of OH in a solution with an H+ concentration of 1.3 X 10 4M?

3: What is the pH of a solution whose hydrogen ion concentration is 3.2 X 10−4 mol/L?
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4: What is the pH of a solution whose hydroxide ion concentration is 4.0 X 10−4 mol/L? We first
define a quantity pOH that is equal to −log [OH−] and that may be derived from the definition of Kw:

24

WEEK 3 STRUCTURE, SOURCES, PROPERTIES AND FUNCTION OF
CARBOHYDRATES
3.1 Carbohydrates
Carbohydrates, otherwise known as Saccharides or sugars are class of biomolecules containing
mainly Carbon, Hydrogen and Oxygen and Sometimes other non‐metals.
They are Poly‐hydroxy aldehydes or Ketones and their derivatives or compounds which when
hydrolysed will yield Poly‐hydroxyl aldehydes or Ketones Many, but not all, carbohydrates have the
empirical formula (CH2O)n; some also contain nitrogen, phosphorus, or sulfur.
e.g.
FIGURE 3.1 Representative monosaccharide. (a) Two trioses, an aldose and a ketose.
The carbonyl group in each is shaded. (b) Two common hexoses. (c) The pentose
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components of nucleic acids. D-Ribose is a component of ribonucleic acid (RNA), and 2-
deoxy-D ribose is a component of deoxyribonucleic acid (DNA).
3.2 General properties of Carbohydrates
3.4 Sources of Carbohydrates
Carbohydrates are the most abundant biomolecules on Earth. Each year, photosynthesis converts
more than 100 billion metric tons of CO2 and H2O into cellulose and other plant products. Certain
carbohydrates (sugar and starch) are a dietary staple in most parts of the world, and the oxidation of
carbohydrates is the central energy‐yielding pathway in most non‐photosynthetic cells. Insoluble
carbohydrate polymers serve as structural and protective elements in the cell walls of bacteria and
plants and in the connective tissues of animals. Other carbohydrate polymers lubricate skeletal
joints and participate in recognition and adhesion between cells. More complex carbohydrate
polymers covalently attached to proteins or lipids act as signals that determine the intracellular
location or metabolic fate of these hybrid molecules, called glycoconjugates.
3.5 Uses of Carbohydrate
They serve as a primary source of metabolic energy.
Use as a source of C atom in the biosynthesis of other biomolecules.
It acts as the components of many structural and cellular secretory materials.
They also serve n the polymeric storage form e.g. Glycogen and Starch.
They used commercially in the thickening agents, stabilizers, sweeteners and also as water
retainers.
They are found naturally in gum and used industrially to make gum.
It is a major component in the exoskeleton of insects and in bacterial cell wall (Peptidoglycan).
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3.6 Classification of Carbohydrates
There are three major size classes of carbohydrates: monosaccharide, oligosaccharides, and
polysaccharides (the word “saccharide” is derived from the Greek sakcharon, meaning “sugar”).
3.7 Structural formular of different classes of Carbohydrates

Figure 3.2 Structural formula of mono, di and polysaccharides

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WEEK 4 STRUCTURE, SOURCES, PROPERTIES AND FUNCTION OF
MONOSACCHARIDES
4.1 Monosaccharide
Monosaccharide is another term for a simple sugar, such as glucose, which is not linked to any other
sugars. They are simplest unit that is not link to any unit.
Monosaccharides are the simplest sugars, having the formula (CH2O) n. The smallest molecules
usually considered to be monosaccharides are those with n = 3.
Monosaccharides can be categorized according to their value of 'n,' as shown below (Table 4.1)
Table 4.1
n Category Formular examples
3 Triose C3H6O3 Glyceraldehydes
4 Tetrose C4H8O4 Erythrose, threose, Erythrulose.
5 Pentose C5H10O5 Ribose
6 Hexose C6H12O6 Glucose, Galactose, Mannose
7 Heptose C7H14O7 Sedoheptane
8 Octose
Monosaccharides can exist as aldehydes or ketones and are called aldoses or ketoses, respectively.
For example, (Figure 4.2‐ 4.4) is the structures of glyceraldehyde, an aldo‐triose, and
dihydroxyacetone, a keto‐triose. Glyceraldehyde and dihydroxyacetone have the same atomic
composition, but differ only in the position of the hydrogens and double bonds. Moreover, they can
28

interconvert via an enediol intermediate (Figure 4.1). When the structures of molecules are related
in these ways, the molecules are called tautomers.

Tautomers
Figure 4.1
29

FIGURE 4.2 Aldoses and ketoses. The series of (a) D-aldoses and (b) D-ketoses having from three
to six carbon atoms, shown as projection formulas. The carbon atoms in red are chiral centers In all
these D isomers, the chiral carbon most distant from the carbonyl carbon has the same configuration
as the chiral carbon in D-glyceraldehyde. The sugars named in boxes are the most common in
nature.
30

Figure 4.3. D‐Aldoses containing three, four, five, and six carbon atoms D‐Aldoses contain an
aldehyde group (shown in blue) and have the absolute configuration of D‐glyceraldehyde at the
asymmetric center (shown in red) farthest from the aldehyde group. The numbers indicate the
standard designations for each carbon atom.
31

Figure 4.4. D ‐Ketoses containing three‐ four, five, and six carbon atoms The keto group is shown in
blue. The asymmetric center farthest from the keto group, which determines the D designation, is
shown in red.
4.2 Properties of Monosaccharides
• Stereo Isomerism in Monosaccharide
Stereo‐isomers are isomers in which the same atoms are bonded to one another, but their
orientation in shape differs only in the spatial arrangement of atoms or groups of atoms about a
central atom. Stereo‐Isomerism include; Geometric Isomerism, Conformational Isomerism and
optical Isomerism.
• Geometric Isomerism ( Cis and Trans isomers)
32

Figure 4.5 showed cis and trans isomers of the alkene 2-butene. This is an example of
geometrical isomerism in which the same bonds are present in a molecule, but are arranged
in a
different way.
• Conformational Isomerism (Staggered or Eclipsed Isomers)
Staggered isomer is the type of isomer in the circle represents the 2nd central atom on which 3
hydrogen atoms are attached. The central bond is twisted and the hydrogen atoms on the second
Carbon atom can be seen.
Eclipsed Isomers; is the type of isomer in which the 1st carbon atom tends to overlapped or covers
the one behind it, so that the Hydrogen atoms in front are almost covering the one behind.
• Optical Isomerism ;( L And D Isomers)
Optical Isomerism
Another, more subtle form of isomerism is optical isomerism, which is based on
the fact that some molecules can be mirror images of each other that are not super imposable, just
as left and right gloves, both placed palm down, cannot be superimposed on each other, although
placed palm to palm they are mirror images. Such isomers are known as optical isomers because in
the pure form they rotate plane‐polarized light either left or right. The d isomer rotates such light
right and is said to be dextrorotatory, whereas the l isomer rotates plane‐polarized light left and is
labeled levorotatory. The D and L isomers of the same compound are called enantiomers, and the
compounds that form enantiomers are said to be chiral.
Except for the property of rotating plane‐polarized light in opposite directions, the physical
properties of enantiomers of the same compound are identical. In addition, their chemical
properties are identical, except when they are acted upon by another chiral molecule. One such kind
33

of molecule consists of enzymes, large molecules of proteins that catalyze biochemical reactions.
Therefore, many biochemical reactions involve chiral molecules.
Chirality produced as a mixture of equal parts of D and L isomers, called a racemic mixture,

FIGURE 4.6 Three ways to represent the two stereoisomers of glyceraldehyde.
The stereoisomers are mirror images of each other. Bal and- stick models show the actual
configuration of molecules. By convention, in Fischer projection formulas, horizontal bonds project out
of the plane of the paper, toward the reader; vertical bonds project behind the plane of the paper,
away from the reader
In biological systems, the D ‐forms of sugar predominates as such the human body can only use the D‐forms of
the sugars.
Optical Activity of Compounds
Optical Activity as first observed Louis Pasteur(1843) (figure 4.7) is the phenomenon, that indicate
the capacity of certain compounds to interact with the plane polarized light and to rotate its plane
of polarization as a result of its asymmetrical property, such compound is said to be optically active.
By plane polarized light is when light energies are transformed by polarizer into a single plane rather
than a multiplicity of possible plane.
34

Figure 4.7 Louis Pasteur first discovered of optical activity.
The optical activity of a stereoisomer is expressed quantitatively by its optical rotation, the number
of degrees by which plane‐polarized light is rotated on passage through a given path length of a
solution of the compound at a given concentration. The specific rotation [α]D 250C of an optically
active compound is defined thus:
Interco version of D‐Glucose Forms
A solution of one stereoisomer of a given monosaccharide rotates plane polarized
light to the left (counter clockwise) and is called the levorotatory isomer, designated (‐); the other
stereoisomer rotates plane‐polarized light to the same extent but to the right (clockwise) and is
35

called the dextrorotatory isomer, designated (+). An equimolar mixture of the (+) and (‐) forms does
not rotate plane‐polarized light. The numbers of such optical isomers are determined by the number
of asymmetry centers. Thus molecule having one center will exist in 2 configurations corresponding
n
to D and L antipodes. In general term for "n" numbers of asymmetry center 2 optically active
isomers may be anticipated. Example, a compound with 5 asymmetry carbon atoms would have how
many possible stereo‐isomers?
Consider n = 5
2n = 25 = 32
4.3Epimer
Two sugars that differ only in the configuration around one carbon atom are called epimers; D‐
glucose and D‐mannose, which differ only in the stereochemistry at C‐2, are epimers, as are D‐
glucose and D‐galactose (which differ at C‐4) (Fig. 4.8).
FIGURE 4.8 Epimers. D-Glucose and two of its epimers are shown as projection
formulas. Each epimer differs from D-glucose in the configuration at one chiral center
(shaded red).
It is important to note that D‐Glucose and D‐ Mannose are not epimers because they differs with
more than one carbon atoms, at carbon 2 and 4.

36

ANOMERS
Isomeric forms of monosaccharides that differ only in their configuration about the hemiacetal or
hemiketal carbon atom are called anomers. The hemiacetal (or carbonyl) carbon atom is called the
anomeric carbon.
4.4 Close Ring Structure
For simplicity, we have thus far represented the structures of aldoses and ketoses as straight‐chain
molecules (Figs ). In fact, in aqueous solution, aldotetroses and all monosaccharides with five or
more carbon atoms in the backbone occur predominantly, (more than 90% of the cellular sugars) as
cyclic (ring) structures in which the carbonyl group has formed a covalent bond with the oxygen of a
hydroxyl group along the chain. The formation of these ring structures is the result of a general
reaction between alcohols and aldehydes or ketones to form derivatives called hemi‐acetals or
hemi‐ketals (Fig ), which contain an additional asymmetric carbon atom and thus can exist in two
stereo‐isomeric forms. For example, D‐glucose exists in solution as an intra‐molecular hemi‐acetal in
which the free hydroxyl group at C‐5 has reacted with the aldehydic C‐1, rendering the latter carbon
asymmetric and producing two stereo‐isomers, designated α and β (Fig. )
FIGURE Formation of hemiacetals and hemiketals. An aldehyde or ketone can react with an
alcohol in a 1:1 ratio to yield a hemiacetal or hemiketal, respectively, creating a new chiral center at
the carbonyl carbon. Substitution of a second alcohol molecule produces an acetal or ketal. When the
second alcohol is part of another sugar molecule, the bond produced is a glycosidic bond.
37

Haworth perspective formulas like those in Figure are commonly used to show the stereochem‐
istry of ring forms of monosaccharides. However, the six‐membered pyranose ring is not planar, as
Haworth perspectives suggest, but tends to assume either of two
“chair” conformations (Fig. ). that two conformations of a molecule are interconvertible without
the breakage of covalent bonds,
FIGURE Formation of the two cyclic forms of D-glucose. Reaction between the aldehyde group
at C-1 and the hydroxyl group at C-5 forms a hemiacetal linkage, producing either of two
stereoisomers, the _ and _ anomers, which differ only in the stereochemistry around the hemiacetal
carbon. The interconversion of _ and _ anomers is called mutarotation
38

Figure Furanose Formation. The open‐chain form of fructose cyclizes to a five‐membered ring
when the C‐5 hydroxyl group attacks the C‐2 ketone to form an intramolecular hemiketal. Two
anomers are possible, but only the α anomer is shown.
the hydroxyl group at C‐6 of L‐galactose or L‐mannose produces L‐fucose or L‐rhamnose,
respectively; these deoxy sugars are found in plant polysaccharides and in the complex
oligosaccharid
e components
of
glycoproteins
and
glycolipids
39

FIGURE Pyranoses and furanoses. The pyranose forms of Dglucose and the furanose forms of D‐
fructose are shown here as Haworth perspective formulas. The edges of the ring nearest the reader
are represented by bold lines. Hydroxyl groups below the plane of the ring in these Haworth
perspectives would appear at the right side of a Fischer projection (compare with Fig. 7–6). Pyran
and furan are shown for comparison
4.5 Mutarotation
The α and β anomers of D‐glucose interconvert in aqueous solution by a process called
mutarotation. Thus, a solution of α‐D‐glucose and a solution of β‐D‐glucose
eventually form identical equilibrium mixtures having identical optical properties. The process is
accelerated by enzyme Aldose mutarotase. If α‐D‐glucose in put into solution it undergo conversion
to β‐D‐glucose until equilibrium is established. The mixture containing 64% of β and 36% of α form
4.6General Reactions Of Moosaccharides
Oxidation Reaction
Oxidation of the carbonyl (aldehyde) carbon of glucose to the carboxyl level produces gluconic acid;
other aldoses yield other aldonic acids. Oxidation of the carbon at the other end of the carbon
chain—C‐6 of glucose,galactose, or mannose—forms the corresponding uronicacid: glucuronic,
galacturonic, or mannuronic acid. Bothaldonic and uronic acids form stable intramolecular esters
called lactones (Fig. 7–9, lower left). In addition to
these acidic hexose derivatives, one nine‐carbon acidic sugar deserves mention: N‐acetylneuraminic
acid (a sialic acid, but often referred to simply as “sialic acid”), a derivative of N‐acetylmannosamine,
is a component of many glycoproteins and glycolipids in animals. The carboxylic acid groups of the
acidic sugar derivatives are ionized at pH 7, and the compounds are therefore correctly named as
the carboxylates—glucuronate, galacturonate,

40

FIGURE Some hexose derivatives important in biology. In amino sugars, an ONH2 group replaces
one of the OOH groups in the parent hexose. Substitution of OH for OOH produces a deoxy sugar;
note that the deoxy sugars shown here occur in nature as the L isomers The acidic sugars contain a
carboxylate group, which confers a negative charge at neutral pH. D‐Glucono‐_‐lactone results from
formation of an ester linkage between the C‐1 carboxylate group and the C‐5 (also known as the _
carbon) hydroxyl group of D‐gluconate.
Reducing Agents
Monosaccharides can be oxidized by relatively mild oxidizing agents such as ferric (Fe3_) or cupric
(Cu2_) ion (Fig. 7–10a). The carbonyl carbon is oxidized to a carboxyl group. Glucose and other
sugarscapable of reducing ferric or cupric ion are called reducing sugars. This property is the basis of
Fehling’s reaction, a qualitative test for the presence of reducing sugar. By measuring the amount of
41

oxidizing agent reduced by a solution of a sugar, it is also possible to estimate the concentration of
that sugar.

FIGURE Sugars as reducing agents. (a) Oxidation of the anomeric carbon of glucose and other
sugars is the basis for Fehling’s reaction. The cuprous ion (Cu+) produced under alkaline conditions
forms a red cuprous oxide precipitate. In the hemiacetal (ring) form, C‐1 of glucose cannot be
oxidized by Cu2+. However, the open‐chain form is in equilibrium with the ring form, and eventually
the oxidation reaction goes to completion. The reaction with Cu2+ is not as simple as the equation
here implies; in addition to D‐gluconate, a number of shorter‐chain acids are produced by the
fragmentation of glucose. (b) Blood glucose concentration is commonly determined by measuring
the amount of H2O2 produced in the reaction catalyzed by glucose oxidase. In the reaction mixture,
a second enzyme, peroxidase catalyzes reaction of the H2O2 with a colorless compound to produce
a colored compound, the amount of which is then measured spectrophotometrically.
4.7Cyclic Hemi‐acetal or Ketal Formation
The carbonyl group (C=O) of an aldehyde or keton can react with the OH groups to form hemiacetal
or ketal
42

Esterification Reaction
Simple sugars condensed with organic acid to form esters and water only

R- COOH + HO-R → R – C –OR

I
OH

43

WEEK FIVE STRUCTURES AND USES OF DISACCHARIDES AND
POLYSACCHARIDES
Oligosaccharides consist of short chains of monosaccharide units, or residues, joined by
characteristic linkages called glycosidic bonds. The most abundant are the disaccharides, with two
monosaccharide units. Typical is sucrose (cane sugar), which consists of the six‐carbon sugars D‐
glucose and D‐fructose. All common monosaccharides and disaccharides have names ending
with the suffix “‐ose.” In cells, most oligosaccharides consisting of three or more units do not occur
as free entities but are joined to nonsugar molecules (lipids or proteins) in glycoconjugates.
Glycosidic Bond O‐glycosidic bond, which is formed when a hydroxyl group of one sugar reacts with
the anomeric carbon of the other (Fig. 7–11). This reaction represents the formation of an acetal
from a hemiacetal (such as glucopyranose) and an alcohol (a hydroxyl group of the second sugar
molecule)
Disaccharides
Disaccharides (such as maltose, lactose, and sucrose) consist of two monosaccharides joined
covalently by an O‐glycosidic bond Glycosidic bonds are readily hydrolyzed by acid but resist
cleavage by base. Thus disaccharides can be hydrolyzed to yield their free monosaccharide
components by boiling with dilute acid.
FIGURE Formation of maltose. A
disaccharide is formed from
two monosaccharides (here, two
molecules of D‐glucose) when an
44

OOH (alcohol) of one glucose molecule (right) condenses with the intramolecular hemiacetal of the
other glucose molecule (left), with elimination of H2O and formation of an O‐glycosidic bond. The
reversal of this reaction is hydrolysis—attack by H2O on the glycosidic bond. The maltose molecule
retains a reducing hemiacetal at the C‐1 not involved in the glycosidic bond.
.
FIGURE 7–12 Some common disaccharides. Like maltose in Figure 7–11, these are shown as
Haworth perspectives. The common name, full systematic name, and abbreviation are given for each
disaccharide
Polysaccharides Most carbohydrates found in nature occur as polysaccharides, polymers of medium
to high molecular weight.Polysaccharides, also called glycans, differ from each
45

other in the identity of their recurring monosaccharide units, in the length of their chains, in the
types of bonds linking the units, and in the degree of branching. Homopolysaccharides
contain only a single type of monomer; heteropolysaccharides contain two or more different
kinds (Fig. 7–13). Some homopolysaccharides serve as storage forms of monosaccharides that are
used as fuels; starch and glycogen are homopolysaccharides of this type. Other
homopolysaccharides (cellulose and chitin)
FIGURE 7–13 Homo‐ and heteropolysaccharides. Polysaccharides may be composed of one, two, or
several different monosaccharides, in straight or branched chains of varying length.
Amylose
Consists of long, unbranched chains polymer of D‐glucose residues connected by (α1 →4) linkages.
Such chains vary in molecular weight from a few thousand to more than a million. It represents
46

about 20 ‐30% of the natural occurring starch.it is water soluble and folds in helical formation. It
gives a dark blue coloration or complex with iodine
Amylopectin
Represent about 80% of natural starch. It is less soluble and has a branched structure due to the α1
→6 glycosidic linkage in addition to the normal α 1,4 glycosidic linkage. The branching is about 20 –
25% glucose residue. It gives a red‐ violet colour with iodine.
FIGURE 7–15 Amylose and amylopectin, the polysaccharides of starch. (a) A short segment of
amylose, a linear polymer of D‐glucose residues in (_1n4) linkage. A single chain can contain several
thousand glucose residues. Amylopectin has stretches of similarly linked residues between branch
points. (b) An (_1n6) branch point of amylopectin. (c) A cluster of amylose and amylopectin like that
believed to occur in starch granules. Strands of amylopectin (red) form doublehelical structures with
each other or with amylose strands (blue). Glucose residues at the nonreducing ends of the outer
branches are removed enzymatically during the mobilization of starch for energy production.
Glycogen has a similar structure but is more highly branched and more compact.
Starch
47

Contains two types of glucose polymer, amylase and amylopectin (Fig. 7–15). The former consists of
long, unbranched chains of D‐glucose residues connected by (_1 →4) linkages. Such chains vary in
molecular weight from a few thousand to more than a million. Amylopectin also has a high
molecular weight (up to 100 million) but unlike amylose is highly branched. The glycosidic linkages
joining successive glucose residues in amylopectin chains are (_1 →4); the branch points (occurring
every 24 to 30 residues) are (α1 → 6) linkages.
Glycogen
Glycogen is the main storage polysaccharide of animal cells. Like amylopectin, glycogen is a polymer
of (_1 →4)‐linked subunits of glucose, with (α1 →6)‐linked branches, but glycogen is more
extensively branched (on average, every 8 to 12 residues) and more compact than starch. Glycogen
is especially abundant in the liver, where it may constitute as much as 7% of the wet weight; it is also
present in skeletal muscle. In hepatocytes glycogen is found in large granules (Fig. 7–14b), which are
themselves clusters of smaller granules composed of single, highly branched glycogen molecules
with an average molecular weight of several million. Such glycogen granules also contain, in tightly
bound form, the enzymes responsible for the synthesis and degradation of glycogen. Because each
branch in glycogen ends with a nonreducing sugar unit, a glycogen molecule has as many
nonreducing ends as it has branches, but only one reducing end. When glycogen is used as an energy
source, glucose units are removed one at a time from the nonreducing ends. Degradative enzymes
that act only at nonreducing ends can work simultaneously on the many branches, speeding the
conversion of the polymer to monosaccharides. Why not store glucose in its monomeric form? It has
been calculated that hepatocytes store glycogen equivalent to a glucose concentration of 0.4 M. The
actual concentration of glycogen, which is insoluble and contributeslittle to the osmolarity of the
cytosol, is about 0.01 _M. If the cytosol contained 0.4 M glucose, the osmolarity would be
threateningly elevated, leading to osmotic entry of water that might rupture the cell (see Fig. 2–13).
Furthermore, with an intracellular glucose concentration of 0.4 M and an external concentration of
48

about 5 mM (the concentration in the blood of a mammal), the free‐energy change for glucose
uptake into cells against this very high concentration gradient would be prohibitively large.
Dextrans are bacterial and yeast polysaccharides made up of (_1 →6)‐linked poly‐D‐glucose; all have
(_1 →3) branches, and some also have (_1 →2) or (_1 →4) branches. Dental plaque, formed by
bacteria growing on the surface of teeth, is rich in dextrans. Synthetic dextrans are used in several
commercial products (for example, Sephadex) that serve in the fractionation of proteins by size‐
exclusion chromatography (see Fig. 3–18b). The dextrans in these products are chemically cross‐
linked to form insoluble materials of various porosities, admitting macromolecules of various sizes.
Homopolysaccharides Serve Structural Roles
Cellulose, a fibrous, tough, water‐insoluble substance, is found in the cell walls of plants, particularly
in stalks, stems, trunks, and all the woody portions of the plant body. Cellulose constitutes much of
the mass of wood, and cotton is almost pure cellulose. Like amylose and the main chains of
amylopectin and glycogen, the cellulosemolecule is a linear, unbranched homopolysaccharide,
consisting of 10,000 to 15,000 D‐glucose units. But there is a very important difference: in cellulose
the glucose residues have the _ configuration whereas in amylose, amylopectin, and glycogen the
glucose is in the _ configuration. The glucose residues in cellulose are linked by (_1 →4) glycosidic
bonds, in contrast to the (_1 →4) bonds of amylose, starch, and glycogen. This difference gives
cellulose and amylose very different structures and physical properties. Glycogen and starch
ingested in the diet are hydrolyzed by _‐amylases, enzymes in saliva and intestinal secretions that
break (_1 →4) glycosidic bonds between glucose units. Most animals cannot use cellulose as a fuel
49

source, because they lack an enzyme to hydrolyze the (_1 →4) linkages. Termites readily digest cellulose
FIGURE Cellulose breakdown by wood fungi. A wood fungusgrowing on an oak log. All wood
fungi have the enzyme cellulase, which breaks the ) glycosidic bonds in cellulose, such that wood is
a source of metabolizable sugar (glucose) for the fungus. The only vertebrates able to use cellulose
as food are cattle and other ruminants (sheep, goats, camels, giraffes). The extra stomach
compartment (rumen) of a ruminant teems with bacteria and protists that secrete cellulase.
50

WEEK 6. NATURE, BIOLOGICAL AND INDUSTRIAL IMPORTANCE OF
LIPIDS.
6.1. Definition of lipids.
Lipids are a class of biological molecules defined by low solubility in water and high solubility in non‐
polar solvent such as chloroform, ethyl ether, benzene, etc. Fats and their derivatives are collectively
known as lipids. As molecules that are largely hydrocarbon in nature, lipids represent highly reduced
forms of carbon and, upon oxidation in metabolism, yield large amounts of energy. Lipids are thus
the molecules of choice for metabolic energy storage. The biological functions of the lipids are as
diverse as their chemistry
The lipids found in biological systems are either hydrophobic (containing only non‐polar groups) or
amphipathic, which means they possess both polar and non‐polar groups. The hydrophobic nature
of lipid molecules allows membranes to act as effective barriers to more polar molecules.. Fats and
oils are the principal stored forms of energy in many organisms. Phospholipids and sterols are major
structural elements of biological membranes. Other lipids, although present in relatively small
quantities, play crucial roles as enzyme cofactors, electron carriers, and light absorbing pigments,
hydrophobic anchors for proteins, “chaperones” to help membrane proteins fold, and emulsifying
agents in the digestive tract, hormones, and intracellular messengers. The fats and oils used almost
universally as stored forms of energy in living organisms are derivatives of fatty acids.
6.2. Definition of fat as mono‐, di‐, and tri‐carboxylic esters of glycerides.
Neutral fats contain different types fatty acids, they are esters of glycerol. The number of fatty acids
can be used to classified as: monoglycerides, diglycerides, and triglycerides. The preferred term for
esters of glycerol (a trihydric alcohol) with fatty acids is now acylglycerols, although you will certainly
come across the synonym glycerides in other literature. Triacylglycerol, diacylglycerol and
monoacylglycerol will be used here for the specific compounds in which three, two or one of the
51

glycerol hydroxyl groups are esterified, rather than the older triglyceride, diglyceride and
monoglyceride.
6.3. Natural sources of fats.
Fats can be obtained from plant and animal sources. Butter and lard are examples of fat
from animal sources, while coconut oil, palm oil, olive oil, etc.
6.4. Lipids are Classified as Simple and Complex.
1. Simple lipids: Esters of fatty acids with various alcohols.
a. Fats: Esters of fatty acids with glycerol. Oils are fats in the liquid state.
b. Waxes: Esters of fatty acids with higher molecular weight monohydric alcohols.
2. Complex lipids: Esters of fatty acids containing groups in addition to an alcohol and a fatty
acid.
a. Phospholipids: Lipids containing, in addition to fatty acids and an alcohol, a phosphoric
acid residue. They frequently have nitrogen containing bases and other substituent’s, eg, in
glycerophospholipids the alcohol is glycerol and in sphingophospholipids the alcohol is
sphingosine.
b. Glycolipids (glycosphingolipids): Lipids containing a fatty acid, sphingosine, and
carbohydrate.
c. Other complex lipids: Lipids such as sulfolipids and aminolipids. Lipoproteins may also be
placed in this category.
3. Precursor and derived lipids: These include fatty acids, glycerol, steroids, other alcohols,
fatty aldehydes, and ketone bodies ( hydrocarbons, lipid‐soluble vitamins, and hormones.
52

Because they are uncharged, acylglycerols (glycerides), cholesterol, and cholesteryl esters
are termed neutral lipids.
6.5. Examples of members of classes of lipids.
Class Examples
Simple Squalene
Fatty acids, e.g.
palmitic acid
Stearic acid
Oleic acid
Lipid alcohols Cholesterol
Esters of lipid alcohols cholesterol esters
Neutral fats triglycerides, eg. tristearin
53

6.6 Structures of Named Saturated and Unsaturated Fatty Acids
Fig. 6.1 Structured of Named Saturated and Unsaturated Fatty Acid
6.7 Lipids Contain Even Number Fatty Acid
Naturally occurring fatty acids normally, but not exclusively, have straight even‐numbered
hydrocarbon chains. This is explained by their principal mode of biosynthesis from acetate
(2C) units.
6.8. Essential and Non‐Essential fatty acids
The word “essential” is usually used in nutrition , to refer to nutrients that must be provided
in the diet either because the body can not synthesize them at all or they are synthesized in
quantities not sufficient to meet the body’s requirement.Two fatty acids are essential for
human”s:linolenic and linoleic.Arachidonic acid becomes essential if its precursor,linoleic,is
missing in the diet.Dietary fat provides the essential fatty acids(EFA).Non‐Essential fatty
acids are those that can be synthesized in sufficient amount in the body,e.g.palmitic
acid,oleic acid,stearic acid.e.t.c.
54

6.9 General Chemical structure of mono‐, di‐ and triacyglycerols
Fig. 6.2 General Chemical structure of mono‐, di‐ and triacyglycerols
Fig. 6.3 Structures of acylglycerols and alkylglycerols. To emphasize the stereochemistry of the central
carbon atom, imagine that this carbon is in the plane of the paper. The groups linked by dotted lines
are to be thought of as behind, and those linked by solid lines in front of the plane of the paper. R
represents a long hydrocarbon chain.
6.10 General Chemical Structured of Named Triacylglycerols
Fig. 6.3 General Chemical Structured of Named Triacylglycerols
55

6.11 Structure of Mono‐, di‐, and triacylglycerol
Fig. 6.4 Structure of Mono‐, di‐, and triacylglycerol
6.12 Physical properties and uses of triaglycerides
• They are relatively insoluble in water.
• They do not have sharp melting points.i.e.their melting points are in ranges.
Triglycerides are often used for the making of soap, i.e.in saponification reactions.
Fatty acids
A fatty acid is composed of a long hydrocarbon chain (“tail”) and a terminal carboxyl group (or
“head”). The carboxyl group is normally ionized under physiological conditions. Fatty acids occur in
large amounts in biological systems, but rarely in the free, uncomplexed state. They typically are
esterified to glycerol or other backbone structures. Most of the fatty acids found in nature have an
even number of carbon atoms (usually 14 to 24) among the most biologically significant properties
of lipids are their hydrophobic properties. These properties are mainly due to a particular
56

component of lipids: fatty acids, or simply fats. Fatty acids also play important roles in signal
transduction pathways.
Fatty acids are either saturated (all carbon–carbon bonds are single bonds) or unsaturated (with one
or more double bonds in the hydrocarbon chain). If a fatty acid has a single double bond, it is said to
be monounsaturated, and if it has more than one,
polyunsaturated. Fatty acids can be named or described in at least three ways, as listed in the table
For example, a fatty acid composed of an 18‐carbon chain with no double bonds can be called by its
systematic name (octadecanoic acid), its common name (stearic acid), or its shorthand notation, in
which the number of carbons is followed by a colon and the number of double bonds in the
molecule (18:0 for stearic acid). The structures of several fatty acids are given in Figure 6.1. Stearic
acid (18:0) and palmitic acid (16:0) are the most common saturated fatty acids in nature.
57

Table6.2 Some naturally occurring straight chain saturated acids
58

Table6.3
Unsaturated fatty acids
Monoenoic (monounsaturated) fatty acids
Over one hundred naturally occurring monoenoic acids have been identified but most of these are
extremely rare. In general, the more common compounds have an even number of carbon atoms, a
chain length of 16‐22C and a double bond with the cis configuration. Often the cis bond begins at
the Δ9 position. Trans isomers are rare but do exist, one of the most interesting being trans‐3‐
hexadecenoic acid, a major fatty acid esterified to phosphatidylglycerol in the photosynthetic
membranes of higher plants and algae. The presence of a double bond causes a restriction in the
motion of the acyl chain at that point. Furthermore, the cis configuration introduces a kink into the
59

average molecular shape [Fig. 6.2]
while the trans double bond ensures that the fatty acid has an extended conformation and
properties nearer to that of an equivalent chain length saturated acid Because the cis forms
are less stable thermodynamically than the trans forms, they have lower melting points than the
latter or their saturated counterparts. The configuration of the double bonds in most unsaturated
fatty acids is cis. The double bonds in polyunsaturated fatty acids are separated by at least one
methylene group. The properties of fatty acids and of lipids derived from them are markedly
dependent on chain length and degree of saturation. Unsaturated fatty acids have lower melting
points than saturated fatty acids of the same length. For example the melting point of stearic acid is
69.6°C, whereas that of oleic acid (which contains one cis double bond) is 13.4°C. The melting points
of polyunsaturated fatty acids of the C18 series are even lower. Chain length also affects the melting
point, as illustrated by the fact that the melting temperature of palmitic acid (C16) is 6.5 degrees
lower than that of stearic acid (C18). Thus, short chain length and unsaturation enhance the fluidity
of fatty acids and of their derivatives.

60

WEEK 7.NATURE , BIOLOGICAL AND IMPORTANCE OF LIPIDS.
6.13.Equation for the hydrolysis of triglycerides.
6.14.Saponification.
Saponification
Acylglycerols can be hydrolyzed by heating with acid or base or by treatment with lipases. Hydrolysis
with alkali is called saponification and yields salts of free fatty acids and glycerol.
RCOOR1 + K+ + OH‐ → RCOO‐ + R1OH + K+
RCOO‐ K+ + H2O → RCOOH + K+ + OH‐
This is how soap (a metal salt of an acid de fat) was made by our ancestors. One method used
potassium hydroxide (potash) leached from wood ashes to hydrolyze animal fat (mostly
triacylglycerols). (The tendency of such soaps to be precipitated by Mg2+and Ca2+ ions in hard water
makes them less useful than modern detergents.) When the fatty acids esterified at the first and
third carbons of glycerol are different, the second carbon is asymmetric. The various acylglycerols
are normally soluble in benzene, chloroform, ether, and hot ethanol. Although triacylglycerols are
insoluble in water, mono‐ and diacylglycerols readily form organized structures in water owing to
the polarity of their free hydroxyl groups.
6.15.Definitions
Saponification number of fat is the number of mg (milligram)of KOH (potassium hydroxide) that can
be neutralized by the fatty acid content of 1g of fat. If a fat contains high molecular weight carbon
chain (C18 and above ) or a sterol the number will be small.
61

Iodine Number
A measure of the extent of the unsaturation in a fat that is equal to the number of grams of iodine
taken up by 100 g of fat. The greater the iodine number, the greater the extent of unsaturation in
the fat.
6.17.Hardening Of Oils.
oils are triglycerides that are rich in unsaturated fatty acids ,and are usually liquids at room
temperature.the addition of hydrogen to the unsaturated bonds converts them to saturated bonds
forming fats,this is known as hardening of oils.
Triacylglycerols
A significant number of the fatty acids in plants and animals exist in form of triacylglycerols (also
called triglycerides). Triacylglycerols are a major energy reserve and the principal neutral derivatives
of glycerol found in animals. These molecules consist of a glycerol esterified with three fatty acids
(Figure 6.1). If all three fatty acid groups are the same, the molecule is called a simple triacylglycerol.
Examples include tristearoylglycerol (common name tristearin) and trioleoylglycerol (triolein).
Mixed triacylglycerols contain two or three different fatty acids. Triacylglycerols in animals are found
primarily in the adipose tissue (body fat), which serves as a depot or storage site for lipids.
Monoacylglycerols and diacylglycerols also exist, but are far less common than the triacylglycerols.
Most natural plant and animal fat is composed of mixtures of simple and mixed triacylglycerols.
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FIGURE 6.1 ● Triacylglycerols are formed from glycerol and fatty acids.
Most natural fats, such as those in vegetable oils, dairy products, and animal fat, are complex
mixtures of simple and mixed triacylglycerols. These contain a variety of fatty acids differing in chain
length and degree of saturation. Vegetable oils such as corn (maize) and olive oil is composed largely
of triacylglycerols with unsaturated fatty acids and thus are liquids at room temperature. They are
converted industrially into solid.
Saponification
Acylglycerols can be hydrolyzed by heating with acid or base or by treatment with lipases. Hydrolysis
with alkali is called saponification and yields salts of free fatty acids and glycerol.
RCOOR1 + K+ + OH‐ → RCOO‐ + R1OH + K+
RCOO‐ K+ + H2O → RCOOH + K+ + OH‐
This is how soap (a metal salt of an acid de fat) was made by our ancestors. One method used
potassium hydroxide (potash) leached from wood ashes to hydrolyze animal fat (mostly
triacylglycerols). (The tendency of such soaps to be precipitated by Mg2+and Ca2+ ions in hard water
makes them less useful than modern detergents.) When the fatty acids esterified at the first and
third carbons of glycerol are different, the second carbon is asymmetric. The various acylglycerols
63

are normally soluble in benzene, chloroform, ether, and hot ethanol. Although triacylglycerols are
insoluble in water, mono‐ and diacylglycerols readily form organized structures in water owing to
the polarity of their free hydroxyl groups.
BIOMEDICAL IMPORTANCE
The lipids are a heterogeneous group of compounds, including fats, oils, steroids, waxes, and related
compounds, which are related more by their physical than by their chemical properties. They have
the common property of being (1) relatively insoluble in water and (2) soluble in nonpolar solvents
such as ether and chloroform. They are important dietary constituents not only because of their high
energy value but also because of the fat‐soluble vitamins and the essential fatty acids contained in
the fat of natural foods. Fat is stored in adipose tissue, where it also serves as a thermal insulator in
the subcutaneous tissues and around certain organs. Non‐polar lipids act as electrical insulators,
allowing rapid propagation of depolarization waves along myelinated nerves. Combinations of lipid
and protein (lipoproteins) are important cellular constituents, occurring both in the cell membrane
and in the mitochondria, and serving also as the means of transporting lipids in the blood.
Knowledge of lipid biochemistry is necessary in understanding many important biomedical areas, eg,
obesity, diabetes mellitus, atherosclerosis, and the role of various polyunsaturated fatty acids in
nutrition and health.
Properties of Lipids
When three fatty acids are esterified to glycerol, the resulting molecule is a fat (if solid at room
temperature) or oil (if liquid at room temperature). Fats which are rich in unsaturated fatty acids are
typically oils. Esterification of the fatty acids to make fats greatly diminishes the hydrophilic nature
of the polar end of the original fatty acid. Consequently, fats are very non‐polar and do not form
micelles readily. Some lipids, such as glycerol‐phospholipids and some sphingo‐lipids, have a very
non‐polar end containing a phosphate. These molecules readily form lipid bilayers and are important
in forming membranes surrounding cells (Figure 6.5). In this case, the polar portions face outwards,
64

towards water, and the non‐polar moieties associate with each other inside the bilayer. Another
class of lipids, called steroids, is a large group of molecules that includes cholesterol and is only
weakly amphiphilic due to few polar groups (Figure 10.9). Cholesterol is a prominent component of
lipid bilayers, but its bulky shape tends to disrupt the regularity of the membrane.

Figure 10.5: Phospholipids, membrane structure and the structure of Cholesterol

Phospholipids
Phospholipids are abundant in all biological membranes. A phospholipid molecule is constructed
from four components: fatty acids, a platform to which the fatty acids are attached, a phosphate,
and an alcohol attached to the phosphate (Figure 12.3). The fatty acid components provide a
hydrophobic barrier, whereas the remainder of the molecule has hydrophilic properties to enable
interaction with the environment. The platform on which phospholipids are built may be glycerol, a
3‐ carbon alcohol, or sphingosine, a more complex alcohol. Phospholipids derived from glycerol are
called phosphoglycerides. A phosphoglyceride consists of a glycerol backbone to which two fatty acid
chains (whose characteristics were described in Section 12.2.2) and a phosphorylated
alcohol are attached. In phosphoglycerides, the hydroxyl groups at C‐1 and C‐2 of glycerol are
esterified to the carboxyl groups of the two fatty acid chains. The C‐3 hydroxyl group of the glycerol
65

backbone is esterified to phosphoric acid. When no further additions are made, the resulting
compound is phosphati‐date (diacylglycerol 3‐phosphate)
Phosphatidic Acid
Phosphatidic Acid (also known as diacylglycerol‐3‐ phosphate) is formed by esterification of
glycerol‐3‐ phosphate with two fatty acids. Phosphatidic acid is an important intermediate in
synthesis of fats and glycerophospholipids. In fat synthesis, the phosphate from phosphatidic acid is
removed to form 1,2‐diacylglycerol and then a third fatty acid is esterified to yield triacyglycerol
(fat).
, the simplest phosphoglyceride Only small amounts of phosphatidate are present in membranes.
However, the molecule is a key intermediate in the biosynthesis of the other phosphoglycerides The
major phosphoglycerides are derived from phosphatidate by the formation of an ester bond
between the phosphate group of phosphatidate and the hydroxyl group of one of several alcohols.
The common alcohol moieties of phosphoglycerides are the amino acid serine, ethanolamine,
choline, glycerol, and the inositol.
66

Figure The structural formulas of phosphatidyl choline and the other principal phosphoglycerides
namely, phosphatidyl ethanolamine, phosphatidyl serine, phosphatidyl inositol, and diphosphatidyl
glycerol
Glycerophospholipid Degradation: One of the Effects of Snake Venoms
The venoms of poisonous snakes contain (among other things) a class of enzymes known as
phospholipases, enzymes that cause the breakdown of phospholipids. For example, the venoms of
the eastern diamondback rattlesnake (Crotalus adamanteus) and the Indian cobra (Naja naja) both
contain phospholipase A2, which catalyzes the hydrolysis of fatty acids at the C‐2 position of
glycerophospholipids. The phospholipid breakdown product of this reaction, lysolecithin, acts as a
detergent and dissolves the membranes of red blood cells, causing them to rupture. Indian cobras
kill several thousand people each year.
67

Plasmalogens are ether glycerophospholipids in which the alkyl moiety is cis- _, _-unsaturated (Figure 8.10).
Common plasmalogen head groups include choline, ethanolamine, and serine. These lipids are referred to as
phosphatidal choline, phosphatidal ethanolamine, and phosphatidal serine.
FIGURE 8.10 ● The structure and a space-filling model of a choline plasmalogen.
68

WEEK 8 STRUCTURE, PROPERTIES AND FUNCTIONS OF PROTEINS
7.1. Classifcation of Proteins
Proteins are macromolecules with high molecular weight. The term protein is derived from the
Greek word “Proteios” which means “of first rank of importance”. Protein consists of large number
of amino acids residues covalently linked together to form long un branched chain (poly peptide). In
proteins, different monomeric amino acids are bonded in a defined manner.
Generally, proteins can be classified into major groups, based on solubility as Globular Proteins and
Fibrous Proteins.
7.2. Sources of Protein
Natural sources of Proteins are animals and plants.Example of Animal sources include: collagen,
immunoglobulins, hormones, keratin, elastin, and myosin
Examples of plant sources include:casein,albumin,seed proteins of cereals.
7.3 Characteristic Properties of Globular And Fibrous Proteins
(a) Globular Proteins: These are soluble in water and they have spherical and compact
structure, they are biologically active and constitute a great majority of molecular species of
proteins in the living system. Structure wise, globular, proteins contains polar amino acids
“outside” and hydrophobic amino acids are “inside”. Examples of globular proteins include
enzymes, antibodies, hormones; e.t.c.
(b) Fibrous Proteins: They are insoluble in water composed of elongated filamentous chains
joined laterally by hydrogen bonds. They are physically tough, this is the bases for their roles
69

as structural elements in tissues e.g. α – keratin found in hair, nails, and skin collagen found
in muscles e.t.c.
7. 4 Functions of Proteins
Proteins can be classified according to their biological roles:
1. catalytic(enzymes)
2. Transport proteins,e.g.lipoproteins
3. Nutrient and storage proteins,e.g.casein,ovalbumin
4. structural protens,e.g. collagen, elastic, keratin .
5. Contractile or motile proteins,e.g. actin,myosin,resilin
6. Regulatory proteins,e.g hormones, DNA proteins
7. Defence proteins,e.g.immunoglobulins,fibrinogen,thrombin
7.5 Prosthetic Groups Of Protein
A prosthetic group is a tightly bound coenzyme that does not dissociate from the enzyme. It is a non‐
protein moiety of a complex protein.
7.6. Classification Of Proteins On The Basis Of Composition
Based on composition, proteins are classified as simple proteins and conjugated proteins. Simple
proteins contain only amino acid with no other group while conjugated proteins contain amino acids
plus some other chemical components. The non amino acid group is called its prosthetic group.
Conjugated protein prosthetic group Example
Hemoprotein Heme+amino acids Haemoglobin
70

Lipoprotein Lipid+amino acids β‐lipoprotein
Glycoprotein Carbohydrate + amino acids Immunoglobulin G
Flavorprotein Flavin nucleotide+ amino acids Succinate dehydrogenase
Phosphoprotein phosphate group +amino acids casein
Metalloproteins iron + aminoacids Ferritin
Calcium + amino acids calmodullin
Structure Of A Protein
A protein can be described as a chain of amino acids linked one to another by peptide bonds
between the carboxyl group of one amino acid and the α‐ amino group of the other amino acid.(CO‐
NH). These sequences of amino acids vary in number depending on the length of the polypeptide
chain.
7.8 General Structural Formular For α‐ Amino Acids

H
H2N ‐ C ‐ COOH
R
Where R is the side group, it varies from one amino acid to the other.

71

WEEK 9. CLASSIFICATION OF AMINO ACIDS AND THEIR STRUCTURES
8.1 Classification Of Amino Acids Based On Chemical Nature Of The Side Groups
Proteins are polymers, composed of covalently linked amino acids. The number, chemical nature and
sequential arrangement of amino acids in a protein determines, the distinctive structure and
chemical behaviour of that protein. Thus understanding the structure and properties of amino acids
is a pre‐requisite of how proteins function at the molecular level. About 20 amino acids are utilized
in protein biosynthesis.
The classification of amino acid are based on the chemical nature of the side groups as shown below:
1. Aromatic R Groups Phenylalanine, tyrosine, and tryptophan, with their aromatic side chains, are
relatively nonpolar (hydrophobic).
2. Polar, Uncharged R Groups The R groups of these amino acids are more soluble in water, or more
hydrophilic, than those of the nonpolar amino acids, because they contain functional groups that
form hydrogen bonds with water. This class of amino acids includes serine, threonine, cysteine,
asparagine, and glutamine.
3. Positively Charged (Basic) R Groups The amino acids in which the R groups have significant
positive charge at pH 7.0 are lysine, which has a second primary amino group at the έ position on its
aliphatic chain; arginine, which has a positivelycharged guanidino group; and histidine, which has an
imidazole group. Histidine is the only common amino acid having an ionizable side chain with a pKa
near neutrality. In many enzyme‐catalyzed reactions, am His residue facilitates the reaction by
serving as a proton donor/acceptor.
4. Negatively Charged (Acidic) R Groups The two amino acids having R groups with a net negative
charge at pH 7.0 are aspartate and glutamate, each of which has a second carboxyl group.
5. Nonpolar, Aliphatic R Groups The R groups in this class of amino acids are nonpolar and
hydrophobic. The side chains of alanine, valine, leucine, and isoleucine tend to cluster together
within proteins, stabilizing protein structure by means of hydrophobic interactions. Glycine has the
72

simplest structure. Although it is formally nonpolar, its very small side chain makes no real
contribution to hydrophobic interactions. Methionine, one of the two sulfur‐containing amino acids,
has a nonpolar thioether group in its side chain. Proline has an aliphatic side chain with a distinctive
cyclic structure. The secondary amino (imino) group of proline residues is held in a rigid
conformation that reduces the structural flexibility of polypeptide regions containing proline.
8.2 Hydrolysis of Proteins
Most biopolymers are inherently unstable with respect to cleavage to monomer units by reaction
with water. Hydrolysis can be catalyzed by protons, by hydroxyl ions, or by the protein‐hydrolyzing
enzymes Peptide bonds of proteins are hydrolyzed by either strong acid or strong base. Because acid
hydrolysis proceeds without racemization and with less destruction of certain amino acids (Ser, Thr,
Arg, and Cys) than alkaline treatment, it is the method of choice in analysis of the amino acid
composition of proteins and polypeptides.
8.3 Structural Formular Of Amino Acids in Their Various Classes

73

8.4. .D‐And L‐Isomers within Amino Acids.
Amino acids have asymmetric carbon atom that is four different chemical groups are linked to the
carbon atoms (except glycine because it has two hydrogen atom attached to the α – carbon). Amino
acids with asymmetric carbon atom exhibit stereoisomerism ( they have optical activity). Depending
on location of amino group, there are D and L – isomers of amino acids that can exist:

COOH COOH

H2N C H H C NH2

R R

74

L – isomer D‐ isomer
Most of the naturally occurring ‐amino acids are of the L‐configuration.
With only one exception (praline) amino acids, generally are carboxylic acids where the adjacent α –
carbon atom is also attached to an amino group, a H – atom and a side chain that determines the
types of amino acid.
H
NH2 ‐ C ‐ COOH
R
General structure of amino acid
H
H – N ‐ C ‐ COOH
CH2 CH2
CH2 PROLINE
ACID/BASE PROPERTY OF AMINO ACIDS
The presence of both α – amino and carboxyl group contributes interesting acid/basic properties in
amino acids, because of this they are amphoteric in nature, at neutral pH, amino acids are di‐polar,
rather than the de‐ionised state and this explains their high solubility in water.
ISO – ELECTRIC POINT
This is the pH at which an amino acid has zero net charge i.e. the number of positive charges are
exactly equal to the number of negative charges and the structural representative of that amino acid
at that pH is called the zwitter ion e.g. for alanine.
75

H

NH3 C COOH

CH3

Pka = 2.35 Pka = 9.69 H
H H

‐ NH2 C COO‐
NH
3 C COOH NH3+ C COO

CH3
CH3 CH3

Net charge ‐1

Net charge +1

Net charge = 0
Alkaline pH = 11

pH = 1 Neutral pH = 7
From the example above, it is clear that the ionization state of an amino acid varies with pH. In acidic
conditions; the COOH is un‐ionised, while the amino group is ionized, hence a net positive is the
result in acidic pH, while a net negative charge will be at alkaline pH.
The iso‐electric post is also referred to ISOTONIC POINT, and this can be calculated by averaging the
pka’s of the groups ionizing on either side of the zwitter ion. E.g.
Isotonic Point (PI) = Pka1 + Pka2
2
e.g for alanine as shown above
PI = 2.35 + 9.69
2
= 6.02
Which means that at pH 6.02, alanine exist in zwitter form.
76

The COOH and NH2 groups in the amino acid can be titrated against a base or an acid and each group
has it’s characteristic Pka value, which is the pH at which half. The group present would be
protonated (i.e. thin of H+) and the other half de‐protonated. Generally, acidic groups have low Pka
values and basic groups have high pka values as seen in alanine.

Pka = 9.69

H

NH2 C
COO_
CH3
Pka = 6.02
H
pH Pka = 2.35
COO_
H3N+ C
H
CH3
H 3N + C COOH

CH3

Equivalent of base added

Amino acids have ssymactric carbon atom (except glycerine because it has two hydrogen atom
attached to the α – carbon), as such they have optical activity. Depending on location of amino
group, there are D and L – isomers of amino acids that can exist; e.g. in Alanine.

COOH COOH

NH2 C H H C NH2

CH3 CH3

L – isomer D‐ isomer
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The D and L ‐, isomers are stereo isomers and are non – super imposable (i.e. one isomer cannot be
super imposed on the other no matter the angle of rotation). Stereo isomers that are non super
imposable mirror images of one another are termed as ENANTIOMERS. The stereo isomeric and the
enantiomeric properties of a compound gives it chirality, and this is due to the presence of an
asymmetric carbon atom.
CLASSES OF AMINO ACIDS
Amino acids are grouped on the basis of polarity and charge of the side chains into four classes:
(a) Non – Polar Amino Acids: These posses a non – polar hydrophobic side acid. Non‐polar
amino acid include glycine, alanine, valine, leucine, isoleucine, praline, phenyalanine,
methionine e.t.c.
(b) Neutral Polar Amino Acids: These have polar, but uncharged side chain which can engage in
hydrogen bonding through oxygen, nitrogen and di – sulphide bond to other polar residues
or to water molecules. They play vital roles in maintaining protein structure. Examples
include thio‐amino acid cysteine, hydroxylic amino acids, serine and threonine, aromatic
amino acids tryptophan, amino acids with an amide side chain like glutamine and
asparagines.
(c) Basic Amino Acids: They are positively charged side chains at physiological pH, e.g. lysine,
arginine and histidine.
(d) Acidic Amino Acids: These are a negatively side chain at physiological pH, they include
glutamic and aspartic acid. They have a second carboxyl group which is fully ionized. They
are also referred to as glutamate and asphartate to as emphasize their negatively charge at
physiological pH.
78

Neutral polar
Non‐polar
Basic Acid
‐ H ‐ CH2

(CH3)4 CH2

N
+
NH3 C
O O‐
Trypphan (Trp) w
Lysine (Lys) K Aspartic acid (Asp) D

CH2
‐ CH2 OH CH2

Glycine (Gly) G CH2
N C Tyrosine (Tyr) Y N
N
C
CH2 CH2 H
O
CH2 OH Histidine (His) H O ‐
CH2

Praline (Pro) P Serine (Ser) S Glutamic acid (Glu) E
CH2
CH2 SH (CH2)3
CH3
CH Valine (Val) V Cysteine (Cys) C NH CH
CH3 COOH
C N COOH
CH CH3
CH3
NH2
OH Carboxyl glutamic
CH CH2 CH3 Arginine (Arg) R
acid
Threonine (Thre) T
Isoleucine (Ile) I
O
CH3 CH2 CH2 C

CH CH
2
Asparagines (Asn) N
CH3
O
Leusine (Leu) L
NH2
CH2 CH2 C
CH2 CH2 CH3 Glutamine (Gln) G
Methionine (Met) M

CH2

Phenyl alanine (Phe) F

79

GENERAL REACTIONS OF AMINO ACIDS
Amino acids can undergo many chemical reactions, but only those of biological importance will be
discussed.
1. Ninhydrin Reaction: α – amino groups, when heated with a compound known as nihydrin

react to form a dark blue or purple complex. This reaction is sued to detect amino acids both
qualitatively (paper chromatography) and quantitatively (using amino acid analyzer).

O O O
C C C
OH O
C + kcat O C = N ‐ C +R–C
O
C
OH H N – C – COOH C
2
C O

Triketo hydrindene hydrate Diketohydrid amine
Note that praline gives a yellow derivative because of it’s cyclic R – structure
2. Reaction with densyl chloride: This is a more, sensitive reaction and is used to detect much
more smaller concentration of amino acids. It involves the reaction with dimethylamine
naphthalene – 5 – sustonyl chloride (commonly referred to as Donsyl chloride to give a
lightly florescent derivative.

CH3 – N – CH3 CH3 – N – CH3

O O O
O +
H
+ HCl
H2N ‐ C ‐ COOH

S O S O H
O O
R NH ‐ C ‐ COOH
80
Cl Amino acid
Dansyl chloride R

Dansylated Amino acid
FDNB (1 – fluoro – 2, 4 – Dinitro Benzen)
DENSYL CHLORIDE
This reaction is effectively used in the end group analysis of pepetides. The reaction with
polypeptides leads to the formation of densylated polypeptides. The acid hydrolysis of the
liberate the end terminal residue as a dansyl amino acid. This compound exhibit an intense
yellow fluorescence we enable the amino acid to be identify xmotographycally. This
procedure can enable identification of end group in materials as little as 100 pilo moles (1 x
10‐12mol).
3. Sangers Reaction: Amino group also undergo reaction with fluorodinitro benzene to give
yellow derivatives which is highly florescent

H
‐ NH2 + F NO2 ‐ N NO2 O
+ HF
O
NO2 NO2
Tjhuorodinitro benzene Dinitrophenylated A. acid
4. Formation of Peptide Bond: This is the most important reaction of amino acids from
biological point of view, in their ability to form peptide linkages. It is the reaction of the
amino group of one amino acid with the carboxyl group of another.

H H H H
O O

NH2 – C – C – OH + H – N – C – COOH NH2 – C – C – N – C – COOH + H2O

R2 R2
R1 R1 H

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Two amino acids linked by a peptide bond will give a dipeptide and 3 a tripeptide, while the
term polypeptide is commonly used for apolymer of more than 3 amino acids. Polymers with
molecular weight of 1000 – 1,000,000 are termed proteins. Peptide bonds can be broken
using water, acid or base.
LEVELS OF STRUCTURAL ORGANIZATION IN PROTEINS
There are 4 levels, termed as 1o, 2o, 3o and 4o i.e. primary, secondary, tertiary and duarternary
structures respectively. The 1st, 3 structural levels can exist in a protein made up of a single
polypeptide chain, where as the fourth involves the interaction of more than one polypeptides
within a multi chained protein molecules.
1o structure: This is simply the number and sequence of amino acids in a polypeptide. The covalent
peptide bonds is responsible for the bonding at this level of protein structure e.g. 1o structure of
vasopression is NH2 – Cys – Tyr – Phe – Gln, Aps – Cys – Pro – Arg – Gly – COOH.
2o structure: This refers to the amount of structural regularity contained in a polypeptide as a result
of hydrogen bonding between two peptide chains. These are of two types i.e., α – helix or β – sheets
(i) α – helix: This is a rod like structure, in it; the polypeptide chain is closely wrapped around a
helical axis. The tightly coiled polypeptide main chain forms the inner portion of the rod and
the side chains (R groups) extends on towards a helical array. The α – helix is stabilized by
intra molecular hydrogen bonds between amino and carboxyl groups. The carboxyl groups of
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each amino acid is hydrogen bonded to the amino group of the amino acid that is situated
about 4 residues (amino acids) ahead in the linear sequence. The stability of the α – helix
conformation can be destabilized by the presence of certain amino acids in the chain e.g.
bulky amino acids (stearic hindrance), electrostatic repulsion (from –ve charged amino acids)
e.t.c
(ii) β – plated sheets: Also stabilized by hydrogen bonds formed between neighbouring strands
of polypeptide chains through strong hydrogen bonds. Creating a corrugated sheet like
structure. If the adjacent strands in the β – sheets turns in the same direction, it is referred
to as parallel β – sheet and anti – parallel β – sheets is used for the reverse case.
3o Structure: This is the folding and curling of a polypeptide to produce a complex globular molecular
shape. The convolutions the polypeptide undergo is specified by a particular set and sequence of R –
groups in the molecule. These may be regions of α – helix, β – sheets and of randomly arrayed length
of amino acids. The integrity of this level of structure is maintain by weak, non covalent interactions
that include:
(a) Hydrophobic interaction
(b) Hydrogen bonds
(c) Electrostatic interactions
(d) Dipole dipole. Another covalent interaction that is extremely important in stabilizing the 3o
structure is the
(e) Disulphide bond or bridge
4o Structure: This refers to the interaction by two or more polypeptide chains to form a biologically
active protein. The responsible cohesive forces are usually the same as those involved in stabilizing
the 3o structure e.g. the enzyme phosphorylase is made up of two identical submits which associate
83

to form the active enzyme. Also haemoglobin is made up of 4 subunits, two α ‐ chains and 2 β –
chains. Generally, the 4o structure is maintain by specific interaction involving the concerned
polypeptide chains.
DENATURATION OF PROTEINS
Denaturation is a process whereby all physical bonds in a protein are broken up without the splitting
of any peptide linkages. Denaturation can also be partial, where certain aspect of the 2o and 3o
structures be broken down with others left intact. Partial or complete denaturation of proteins can
be accomplished by a variety of agents e.g. organic solvents will serve to break hydrophobic
interactions, acids/bases serve to break electrostatic linkages, while high concentration of urea can
break hydrogen bonds. Other physical agents used include heat, irradiation and surface tension.
Generally when a protein molecule has been denatured, it will precipitate i.e. the structure will
collapse and it comes out as a salt.
ENZYMES
Enzymes are organic catalysts, proteins in nature, which accelerate enormously the rate at which
chemical reactions occur and almost every reaction occurring in the cell is mediated by on enzyme.
Enzymes enable plants and animals to carry out metabolic reactions at temperatures between 20 –
40oC and at a pH of about 7. Similar reactions, if carried out in the laboratory will require very high
temperature and pressure, strong acids and bases and very complex and expensive machinery, but
the cells carry out such reactions with ease and under mild conditions using the catalytic power of
enzymes. Generally, the substance on which on enzyme act on is called the substrate and what is
form is the product.
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ACTIVE SITE
Experiments have linked reactions catalysed by enzymes to certain specific regions within the
enzyme. This specific region is called the active site, which is that portion of the enzyme molecule in
direct contact with the substrate during it’s transformation to product. It contains amino acids which
individually or as group participate in binding the substrate and on carrying out subsequent catalytic
reactions. The folding of the protein molecule can bring about well separated regions of amino acid
to be present at the active site; also at the active site may be some metals such enzymes are called
metallo enzymes. Generally the active site reactions in
- Substrate specificity
- Substrate binding
- Catalytic activity
Enzyme specificity: Enzymes are specific in the reaction they catalysed and this differentiates them
from other catalysts and is also probably, an important factor in the cells control of metabolic
activities or reactions. For e.g., the enzyme arginase catalyses the decomposition of L – arginine to
ornithine and urea, but it will not act on the D – isomer, glycosidases are usually specific in
hydrolyzing either α or β – glycosidic linkage while lipases or esterases are known to split almost all
ester bonds, thus representing the least specific enzymes.
NATURE OF ENZYMES
Certain proteins require the participatation of other non‐protein compounds to enhanced their
catalytic activities, as such an enzyme may have different parts:
85

(a) Co – enzymes: These are non‐ protein moiety of enzymes that are often necessary for
enzymatic activity. They are usually locked at or near the active site. They are of low
molecular weight and are easily separated from the protein by a mild procedure such as
dialysis; but there certain co‐enzymes called prothetic group which are permanently fixed to
the active site and are involved in catalytic activities, and these are not easily removed by
dialysis. Examples of co‐enzymes include many derivatives of vitamin A and other like
viotein, co‐enzyme A, thiamine pyrophosphate e.t.c.

(b) Apo enzyme: These are conjugate proteins that can only have catalytic activity when a non –
protein moiety co‐enzyme is attached to or is near it active site in combination with
substrate

(c) Holo – enzyme: These are enzymes made up conjugate proteins (Apo‐enzyme) that require
groups that are not amino acid (co‐enzyme) at the active sites for the enzyme to effectively
bind and catalysed the transformation of substrate to product e.g. the enzyme pyruvate
decarboxylase has biotin as co‐enzyme.
CLASSES OF ENZYMES
Based on the reaction they catalysed, enzymes are named and classified into 6 (six) groups:
Oxido – reductases: These add or substarte elections, O2 or H2 e.g. the oxidases and dehydrogenases
methyl and acyl group transgerase
Hydrolases: This splits a molecule into two by the action of water of enzymes acting on esters,
glycosidic or peptide bonds.
86

Lyases: This removes group non – hydrolytically, leaving a double bond or in reverse, add groups to a
double bond e.g. de‐carboxylase, aldolase ese
Isomerases: These brings about re – distribution of atoms or group of atoms within a molecule e.g.
epimerases, mutases e.t.c
Lipases: These link together two molecules, always at the expanse of a high energy compound
usually ATP, e.g. acetyl – COA synthetase.
FACTORS THAT AFFECTS ENZYME CATALYSIS
Temperature: Just as any normal chemical reaction; enzymatic reactions are increased with
increasing temperature, but at temperature above 50oC, the protein molecules becomes denatured,
thus the enzymes loses its activity optimum temperature is temperature of maximum velocity of
reaction.
pH: The net charge of an amino acid can be affected by pH. Generally, the activity of an enzyme
is evidently over a narrow range of pH and within the range, it has maximum activity at a particular
pH which is often called the optimum pH.
Substrate Concentration: With all other factors been equal, the concentrations of substrate and
enzyme will determine the rate of catalysis in a case where the concentration of the enzyme is kept
constant, rate of catalysis will depend on the substrate concentration until a certain optimum level,
then it will no longer affect the rate of catalysis.
87

Inhibitors: These are generally substances that reduces the rate of enzyme catalysis when added to
the reaction medium. They usually act by competing with the substrate for the active site.
88

WEEK 10. STRUCTURE AND BEHAVIOUR OF PROTEINS
9.1. Levels of Structural Organization in Proteins
The complexity of protein structure is best analyzed by considering the molecule in terms of four
organizational levels, these are Primary,. secondary, tertiary and quaternary structures (i.e. 1o, 2o,
3o and 4o) respectively.
Primary structure this is describes the number and sequence of amino acids in a polypeptide chain.
In proteins amino acid are covalently joined by
peptide bonds. e.g.Primary structure of vasopressin is NH2 – Cys – Tyr – Phe – Gln, Aps – Cys – Pro –
Arg – Gly – COOH.
Secondary structure: This refers to the regular arrangements of amino acids that are located near
to each other in the linear sequence. These arrangements are termed the secondary structure of the
polypeptide.The α – helix, β – sheet, and β‐ bend are example of secondary structure frequently
encountered in proteins.
(iii) α – helix: This is a spiral structure, consisting of a tightly packed, coiled polypeptide
backbone core with the side chains of the component amino acids extending outward from
the central axis. The α – helix is stabilized by extensive hydrogen bonds between amide
hydrogens and carbonyl oxygens that are part of the polypeptide backbone. The stability of
the α – helix conformation can be destabilized by the presence of certain amino acids in the
chain e.g. bulky amino acids (stearic hindrance), electrostatic repulsion (from –ve charged
amino acids) e.t.c
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Figure 9.1. Structure of α ‐ Helix
(iv) β – sheets:This is another form of secondary structure in which all of the peptide bond
components are involved in hydrogen bonding. The surfaces of β‐sheets appear"
pleated",and these structures are therefore called " β‐pleated sheets". β‐sheets are also
stabilized by hydrogen bonds which are perpendicular to the polypeptide backbone. A β –
sheet can be formed from two or more separate polypeptide chains or segments of
polypeptide chains that are arranged either parallel or anti parallel to each other.
90

Figure 9.2. Structure of β ‐ Sheets
Tertiary Structure: the primary structure of a polypeptide chain determines its tertiary structure.
Tertiary structure refers both to the folding of domains, and the final arrangement of domains in the
polypeptide. Domains are the fundamental functional and three‐dimensional structural units of a
polypeptide. Tertiary structure of proteins may be composed of a combination of α – helices and β
– strands or, mostly α – helices or β – strands.The integrity of this level of structure is maintained by
weak, non covalent interactions that include:
(f) Hydrophobic interaction
(g) Hydrogen bonds
(h) Electrostatic interactions
(i) Dipole dipole.
91

(j) Disulphide bonds

Myoglobin Immunoglobulin
Figure 9.3. Examples of tertiary structures of globular protein
Quaternary Structure: Many proteins consist of a single polypeptide chain, while others consist of
two or more polypeptide chains that may be structurally identical or totally unrelated. the
arrangement of these polypeptide subunts is call the Quaternary structure of the protein. If there
are two subunits,the protein is called "dimeric"; if three subunit, "trimeric"; if several subunits, "
multimeric". Subunits are held together by non‐ covalent interactions.
Figure 9.4. Examples of quaternary structures of haemoglobin
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9.2 Types of Interactions Involved In Structural Levels of Protein
a. Secondary structure
a. Hydrogen bonds
b. Tertiary structure
b. Hydrophobic interaction
c. Hydrogen bonds
d. Electrostatic (ionic) interactions
e. Dipole dipole.
f. Disulphide bonds
c. Quaternary structure
g. Hydrophobic interaction
h. Hydrogen bonds
i. Electrostatic (ionic) interactions

9.3 Examples of Proteins Illustrating the Structural Organization
a. Secondary structure
• α ‐ Helix
• β – Sheets
b. Tertiary structure
• Haemoglobin (α ‐ Helices)
• Immunoglobulin(β ‐ Strands)
• Triose phosphate Isomerase(combination of α – Helices and β ‐ Strands)
c. Quaternary structure
• Haemoglobin(four polypeptide subunits)

9.4. Denaturation of Proteins
Protein denaturation is the disruption of the biologically active conformation of a protein structure
leading to the loss of activity. Protein denaturation results in the unfolding and disorganization of
93

the protein's structure which are not accompanied by hydrolysis of peptide bonds. Denaturing
agents include heat organic solvents, mechanical mixing, strong acids or bases, detergents,
irradiation and surface tension e.t.c.
9.5. Denaturation May Be Reversible or Irreversible
Denaturation of proteins may, in rare cases, be reversible, in which case the protein refolds into its
original native structure when the denaturing agent is removed. However, most proteins, once
denatured, remain permanently disordered that is irreversible. Denatured proteins are often
insoluble and therefore precipitated from solution.
Figure 9.5 Denaturation of the intricate structure of a protein.
9.6 Protein precipitation at iso‐electric point
Protein as an amphoteric polyelectrolyte carries both positive and negative charges, whose ratio is
defined by the number of acidic and basic amino acids in the protein molecule. The charge on a
protein molecule is a factor of protein stability in solution, since it prevents the agglomeration of
94

protein particles and their precipitation. Each protein is characterized by a pH value at which the
sum of positive and negative charges on the protein is equal to zero. This states of proteins is
referred to as isoelectric point. At the isoelectric point, protein solutions are unstable and are prone
to easily deposit as a precipitate, especially in the presence of dehydrating agents (ethanol, acetone
and others).

95

WEEK 11. NATURE OF ENZYMES
10.1 ENZYMES
Enzymes are organic catalysts, proteins in nature, which accelerate enormously the rate at which
chemical reactions occur. Almost every reaction occurring in the cell is mediated by an enzyme.
Enzymes enable plants and animals to carry out metabolic reactions at temperatures between 20 –
40oC and at a pH of about 7.0. Similar reactions, if carried out in the laboratory will require very high
temperature and pressure, strong acids and bases and very complex and expensive machineries, but
the cells carry out such reactions with ease and under mild conditions using the catalytic power of
enzymes.
10.2 Definition of substrate
Generally, the substance on which an enzyme acts upon is called the substrate and what is form is
the product. Enzymes are highly specific, interacting with one or a few substrates.
10.3 Active Sites
Enzyme molecules contain a cleft called the active site. The active site is therefore that region of the
enzyme molecule where substrate transformation occurs. The active site contain amino acid side
chain that create a three‐dimensional surface complementary to the substrate.
Figure 10.1. Schematic representation of an enzyme binding a substrate molecule at the active site
96

WEEK 12. DISTINCTIVE FEATURESOF ENZYMES
10.4 General Characteristics of enzymes
• All enzymes are protein in nature. They increase the velocity of a chemical reaction and are
not consumed during the reaction they catalyze.
• Enzyme specificity: Enzymes are highly specific in the reaction they catalysed. Enzymes have
definite substrates they act upon . For example, the enzyme arginase catalyses the
decomposition of L – arginine to ornithine and urea, but it will not act on the D – isomer,
glycosidases are usually specific in hydrolyzing either α or β – glycosidic linkage while
esterases are known to split almost all ester bonds, thus representing the least specific
enzymes.
• Catalytic rate: most enzyme‐catalyzed reactions are highly efficient, proceeding from 103 to
108 times faster than un‐catalyzed reactions. Typically, each enzyme molecule is capable of
transforming 100 to 1000 substrate molecules into product each second. The number of
molecules of substrate converted to product per enzyme molecule per second is called the
turnover number.
• Directive effect: Enzyme activities can be regulated. That is enzymes can be activated of
inhibited so that the rate of product formation responds to the needs of the cell.
• Location within the cell: many enzymes are localized in specific organelles within the cell.
Such compartmentalization serves to isolate the reaction substrate or product from other
competing reactions, to provide a favourable environment for the reaction.
• Co‐factor: some Enzyme associate with a non‐protein co‐factor that is need for Enzymic
activity. Commonly encountered co‐factors include metal ions and organic molecules,
known as co‐enzyme. Holo – enzyme refers to the enzyme with its co‐factor. Apo‐enzyme
refers to the protein portion of the holo – enzyme. In the absence of the appropriate
97

cofactor, the apo‐enzyme typically does not show biological activity. A prosthetic group is a
tightly bound co‐enzyme that does not dissociate from the enzyme.
10.5 Examples illustrating the distinctive features
Distinctive features Examples
• Directeffect
Activation
Trypsinogen Trypsin
Inhibition
Pepsin Pepsinogen

• Specificity
Lipases act on ester bonds of lipids
Urease act on only urea
• Co‐factors
Metal ions; e.g. Zn2+, Fe2+
Organic molecules; Derivatives of Vitamins,
e.g. Coenzyme A, FAD, NAD+
• Localization of enzymes
Mitochondria Enzymes of TCA cycle, e.g.
Aconitase, Isocitrate dehydrogenase
Cytosol Enzymes of Glycolysis, e.g. Hexokinase,
Phoshoglucose Isomerase
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WEEK 13. CLASSIFICATION OF ENZYMES

10.6 CLASSES OF ENZYMES
The international union of biochemistry and molecular biology (IUBMB) developed a system of
nomenclature in which enzyme are classified into six major classes.
1. Oxidoreductases: catalyze oxidation‐reduction reactions, i.e. transfer of electrons.
2. Transferases: catalyze transfer of C, N or P‐containing groups, i.e. group transfer reactions.
3. Hydrolases: catalyze cleavage of bonds of water, i.e. hydrolysis reaction.
4. Lyases: catalyze cleavage of C‐C, C‐S, and certain C‐N bonds, .i.e. addition of groups to double
bonds by removal of groups.
5. Isomerases: catalyze racemization of optical or geometric isomers, i.e. transfer of groups within
molecules, to yield isomeric forms
6. Ligases: catalyze formation of bonds between carbon O, S, N coupled to hydrolysis of high‐energy
phosphates, i.e .formation of C‐C, C‐S, C‐O, C‐N bonds by condensation reactions coupled to ATP
cleavage.
10.7. List of Examples of Enzymes Belonging to Each Class
Class Examples
1.Oxidoreductase Dehyrogenases,oxidases
2.Transferases Methyl transferase, Transketolase,
Amino acyl transferase.
3. Hydrolases Esterases, Lipases, Phosphatases,
99

Nucleases.
4. Lyases Decarboxylases, Carbonic anhydrase
Aspartate ammonia Lyase,
5. Isomerases Racemases, Epimerases, Cis‐trans
Isomerases.
6. Ligases Pyruvate carboxylases.

100

WEEK 14. FACTORS AFFECTING ENZYME ACTIVITIES
10.8: Cofactors of enzymes
Some Enzyme associate with a non‐protein co‐factor that is need for Enzymic activity. Commonly
encountered co‐factors include metal ions (e.g. Zn2+, Fe2+) and organic molecules, known as co‐
enzyme (They are often derivatives of vitamins, NAD+,FAD, CoenzymeA). Holo – enzyme refers to the
enzyme with its co‐factor. Apo‐enzyme refers to the protein portion of the holo – enzyme. In the
absence of the appropriate cofactor, the apo‐enzyme typically does not show biological activity. A
prosthetic group is a tightly bound co‐enzyme that does not dissociate from the enzyme (e.g. the
biotin of carboxylases).
10.9 Factors Affecting Enzyme Action
Temperature: enzyme activity increases with increase in temperature, upto an optimum. Animal
enzymes generally have an optimum temperature of 40‐50oC, While plant enzymes have an
optimum 50 ‐ 60oC. For most s, the rate of activity normally increases from1‐3 times for every 10 oC
rise in temperature.
Substrate Concentration: For a given quantity of enzyme, the rate of enzyme activity (i.e. of the
velocity of the reaction) increases as the concentration of the substrates increases.
pH: as the pH increases enzyme activity increases, upto a certain maximum which is the optimal pH
for the enzyme. For most enzymes this is between 6.8 and 7.2, except for pepsin which is 1.5 to 2.5.
Enzyme concentration: enzyme Activity is directly proportional to enzyme concentration, at least at
the start of the reaction.
Inhibitors: they are substances that can diminish the velocity of an enzyme‐catalyzed reaction. There
are two main types of inhibitors; reversible and irreversible inhibitors
101

Activators: some enzymes may not be able to perform their catalytic function because they are
formed in an inactive form called a zymogen. Activation of the zymogen involves a limited hydrolysis
which either allows a subsequent formation of an active sites or removal of an inhibitory peptide.
10.10 Profiles of the effects of pH, temperature and
substrate concentration

Temperature or pH Substrate concentration
Temperature and pH effect Substrate concentration effect
Velocity
Enzyme concentration
10.11. Optimum pH and Optimum temperature
Optimum pH of an enzyme is the pH at which it shows maximum activity.
Optimum temperature of an enzyme is the temperature at which it shows maximum activity.
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WEEK 15. VITAMINS FOUND IN THE LIVING CELL
11.1 Importance of Vitamin Supplements
Vitamins are organic compounds required by the body in trace amounts to perform specific cellular
function. Vitamins may either not be synthesized at all by humans or may, be synthesized only at a
rate not consistent with normal health, and therefore must be supplied by the diet.
Traditionally, supplementation of vitamins in the diet was reserved for patients at risk for nutritional
deficiencies. For example vitamin supplements are often required for individuals consuming
modified diets, including weight reduction regimens, and strict vegetarian diets. Furthermore, some
normal physiologic conditions, for example pregnancy and lactation, may require vitamin
supplementation. Vitamin supplementation is now recommended for the general population for
normal health.
11.2 Water‐Soluble Vitamins
From the standpoint of nutrition, vitamins are divided into classes according to their solubility and
their functions in metabolism. The two classes are fat – soluble and water – soluble classes.
Water – soluble vitamins are the vitamins that are soluble in water.
11.3 General Functions Of Water Soluble Vitamins
Water soluble vitamins are water soluble and are precursors of coenzymes for the enzymes of
intermediary metabolism. They are nine in number namely; thiamine, riboflavin, niacin, biotin,
pantothenic acid, folic acid, cobalamin, pyridoxine, and ascorbic acid. The water soluble vitamins are
103

not toxic, and the amounts stored in the body are usually small. When ingested in excess of the
body’s needs, they are readily excreted in the urine.
11.4 List of Deficiency Diseases of Water Soluble Vitamins
Vitamins Deficiency diseases
Thiamine (vitamin B1) Beri‐beri
Riboflavin (vitamin B2) Dermatitis,
Cheilosis,
Glossitis
Pyridoxine (vitamin B6) Peripheral neuritis,
Anaemia
Niacin Pellagra
Biotin Exfoliative dermatitis,
Glossitis,
Loss of appetite
Nausea
Conjunctivitis
Pantothenic acid Burning feet
Folic acid growth failure
104

Megaloblastic anaemia
Cobalamin (vitamin B12) Pernicious anaemia
Ascorbic acid Scurvy
11.5 Definition of Fat – Soluble Vitamins
Fat‐soluble vitamins are only fat soluble. They are four in number, namely; vitamin A, D, E, and K.
11.6 General Functions and Deficiency of Fat ‐ Soluble Vitamins
Fat – soluble vitamins are released, and absorbed, and transported with fat of the diet. They are not
readily excreted in the urine, and significant quantities are stored in the liver and adispose tissue.
Each vitamin has its specific role/functions.
Vitamin A functions include aiding vision, growth, reproduction. Vitamin D is maintenance of plasma
calcium levels, vitamin E is an antioxidant, preventing non enzymic oxidation of cell components
while vitamin K plays a coenzyme role in the blood coagulation process.
Deficiency Diseases of Fat – Soluble Vitamins
Vitamin A Night blindness, Acne and Psoriasis
Vitamin D Rickets (in children),
Osteomalacia (in adults)
Vitamin E Defective lipid absorption
105

Vitamin K Hypoprothrombinemia
106

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UNESC

BM, basement membrane

ER, rough endoplasmic

(with ribosomes attached;

ER is depicted nearer the

and on the right side of the

DI, deep indentation of

GI, glycogen granules

Gap, space ~10-20 nm

between adjacent cells

TJ, tight junction

SG, secretion granule

CW, cell wall (of a plant)

St, starch granule

centrifugal force (i.e.high speed), it is referred to as ultra centrifugation. One of the major uses of

enzymes, mitochondria contain oxidative enzymes, and chloroplasts contain photosynthetic

hydrolysed will yield Poly‐hydroxyl aldehydes or Ketones Many, but not all, carbohydrates have the

empirical formula (CH2O)n; some also contain nitrogen, phosphorus, or sulfur.

3.2 General properties of Carbohydrates

FIGURE 4.6 Three ways to represent the two stereoisomers of glyceraldehyde.

b. Glycolipids (glycosphingolipids): Lipids containing a fatty acid, sphingosine, and

hydrocarbon chains. This is explained by their principal mode of biosynthesis from acetate

Glycerophospholipid Degradation: One of the Effects of Snake Venoms

FIGURE 8.10 ● The structure and a space-filling model of a choline plasmalogen.

glutamic and aspartic acid. They have a second carboxyl group which is fully ionized. They

CH2 CH2 CH3 Glutamine (Gln) G

1. Ninhydrin Reaction: α – amino groups, when heated with a compound known as nihydrin

the active site and are involved in catalytic activities, and these are not easily removed by

Figure 9.5 Denaturation of the intricate structure of a protein.

• Location within the cell: many enzymes are localized in specific organelles within the cell.

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