COURSE OUTLINE

1. Introduction to Biochemistry
2. Water and pH
3. Proteins
3.1 Definition
3.2 Functions
3.3 Structures
3.4 Amino Acids and peptide bonds
4. Enzymes
4.1 Definition
4.2 Types
4.3 Characteristics
4.4 Classification
5. Carbohydrates
5.1 Definition
5.2 Types
5.3 Structures
5.4 Functions
6. Nucleic Acids and its metabolism
6.1 Definition
6.2 Types
6.3 Structures
6.4 Functions
7. Lipid
7.1 Definition
7.2 Types
7.3 Functions
7.4 Structures
8. Metabolism of macromolecules(Research Assignment)

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 CHAPTER ONE
INTRODUCTION TO BIOCHEMISTRY
Biochemistry can be defined as the science concerned with the chemical basis of
life (Gk bios “life”). The cell is the structural unit of living systems. Thus,
biochemistry can also be described as the science concerned with the chemical
constituents of living cells and with the reactions and processes they undergo. By
this definition, biochemistry encompasses large areas of cell biology, of molecular
biology, and of molecular genetics.
Biochemistry is the science concerned with studying the various molecules that
occur in living cells and organisms and with their chemical reactions. Because life
depends on biochemical reactions, biochemistry has become the basic language of
all biologic sciences. Biochemistry is concerned with the entire spectrum of life
forms, from relatively simple viruses and bacteria to complex human beings. •
Biochemistry and medicine are intimately related. Health depends on a
harmonious balance of biochemical reactions occurring in the body, and disease
reflects abnormalities in biomolecules, biochemical reactions, or biochemical
processes.
The major objective of biochemistry is the complete understanding, at the
molecular level, of all of the chemical processes associated with living cells. To
achieve this objective, biochemists have sought to isolate the numerous molecules
found in cells, determine their structures, and analyze how they function.
The biochemistry of the nucleic acids lies at the heart of genetics; in turn, the use
of genetic approaches has been critical for elucidating many areas of biochemistry.
Physiology, the study of body function, overlaps with biochemistry almost
completely. Immunology employs numerous biochemical techniques, and many
immunologic approaches have found wide use by biochemists. Pharmacology and
pharmacy rest on a sound knowledge of biochemistry and physiology; in particular,
most drugs are metabolized by enzyme-catalyzed reactions. Poisons act on
biochemical reactions or processes; this is the subject matter of toxicology.
Biochemical approaches are being used increasingly to study basic aspects of
pathology (the study of disease), such as inflammation, cell injury, and cancer.
Many workers in microbiology, zoology, and botany employ biochemical
approaches almost exclusively.

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Advances in biochemical knowledge have illuminated many areas of medicine.
Conversely, the study of diseases has often revealed previously unsuspected
aspects of biochemistry. The determination of the sequence of the human genome,
nearly complete, will have a great impact on all areas of biology, including
biochemistry, bioinformatics, and biotechnology.
Biochemical approaches are often fundamental in illuminating the causes of
diseases and in designing appropriate therapies.
The judicious use of various biochemical laboratory tests is an integral component
of diagnosis and monitoring of treatment. A sound knowledge of biochemistry and
of other related basic disciplines is essential for the rational practice of medical and
related health sciences.

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 CHAPTER TWO
WATER AND PH
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. The manner in which water interacts with a solvated
biomolecule influences the structure of each. An excellent nucleophile, water is a
reactant or product in many metabolic reactions. 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. Bicarbonate and other buffers
normally maintain the pH of extracellular fluid between 7.35 and 7.45. Suspected
disturbances of acid - base balance are verified by measuring the pH of arterial
blood and the CO2 content of venous blood. Causes of acidosis (blood pH < 7.35)
include diabetic ketosis and lactic acidosis. Alkalosis (pH > 7.45) may, for example,
follow vomiting of acidic gastric contents. Regulation of water balance depends
upon hypothalamic mechanisms that control thirst, on antidiuretic hormone (ADH),
on retention or excretion of water by the kidneys, and on evaporative loss.
Nephrogenic diabetes insipidus, which involves the inability to concentrate urine
or adjust to subtle changes in extracellular fluid osmolarity, results from the
unresponsiveness of renal tubular osmoreceptors to ADH.
WATER MOLECULES FORM DIPOLES
A water molecule is an irregular, slightly skewed tetrahedron with oxygen at its
center (Figure 2–1). The two hydrogen and the unshared electrons of the remaining
two sp3 -hybridized orbitals 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
hydrogen. 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. As described
quantitatively by Coulomb’s law, the strength of interaction F between oppositely
charged particles is inversely proportionate to the dielectric constant ε of the
surrounding medium. The dielectric constant for a vacuum is unity; for hexane it is

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1.9; for ethanol it is 24.3; and for water it is 78.5. 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 MOLECULES FORMS HYDROGEN BONDS

An unshielded hydrogen nucleus covalently bound to an electron-withdrawing
oxygen or nitrogen atom can interact with an unshared electron pair on another
oxygen or nitrogen atom to form a hydrogen bond. Since water molecules contain
both of these features, hydrogen bonding favors the self-association of water
molecules into ordered arrays (Figure 2–2). Hydrogen bonding profoundly
influences the physical properties of water and accounts for its exceptionally high
viscosity, surface tension, and boiling point. On average, each molecule in liquid
water associates through hydrogen bonds with 3.5 others. These bonds are both
relatively weak and transient, with a half-life of about one microsecond. Rupture
of a hydrogen bond in liquid water requires only about 4.5 kcal/mol, less than 5%
of the energy required to rupture a covalent OH bond. Hydrogen bonding enables
water to dissolve many organic biomolecules that contain functional groups which
can participate in hydrogen bonding. The oxygen atoms of aldehydes, ketones, and
amides provide pairs of electrons that can serve as hydrogen acceptors. Alcohols
and amines can serve both as hydrogen acceptors and as donors of unshielded
hydrogen atoms for formation of hydrogen bonds.

COVALENT BONDS

The covalent bond is the strongest force that holds molecules together
.Noncovalent forces, while of lesser magnitude, make significant contributions to
the structure, stability, and functional competence of macromolecules in living
cells. These forces, which can be either attractive or repulsive, involve interactions

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both within the biomolecule and between it and the water that forms the principal
component of the surrounding environment.
pH
The term pH was introduced in 1909 by Sörensen, who defined pH as the negative
log of the hydrogen ion concentration: This definition, while not rigorous, suffices
for many biochemical purposes. To calculate the pH of a solution: 1. Calculate
hydrogen ion concentration [H+]. 2. Calculate the base 10 logarithm of [H+]. 3. pH
is the negative of the value found in step 2. For example, for pure water at 25°C,
Low pH values correspond to high concentrations of H+ and high pH values
correspond to low concentrations of H+. Acids are proton donors and bases are
proton acceptors. Strong acids (eg, HCl or H2SO4) completely dissociate into anions
and cations even in strongly acidic solutions (low pH). Weak acids dissociate only
partially in acidic solutions. Similarly, strong bases (eg, KOH or NaOH)—but not
weak bases (eg, Ca[OH]2)—are completely dissociated at high termediates, whose
phosphoryl group contains two dis sociable protons, the first of which is strongly
acidic pH.

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 CHAPTER THREE
PROTEINS
3.1 DEFINITION OF PROTEINS
The word protein is derived from Greek word “proteios” which means
primary. As the name shows, the proteins are of paramount importance for
biological systems. Out of the total dry body weight, ¾ th are made of proteins.
Proteins are used for body building, all the major structural and functional aspects
of the body are carried out by protein molecules. Abnormality in protein structure
will lead to molecular diseases with profound alterations in metabolic functions.
Proteins contain Carbon, Hydrogen, Oxygen and Nitrogen as the major components
while Sulphur and Phosphorus are minor constituents. Nitrogen is characteristics
of proteins. All proteins are polymers of Amino Acids.
Proteins are found in all living systems as structural components and as biologically
importance substances such as Hormones, Enzymes and pigments.
Proteins in our food can be divided into first class and second class proteins.
First Class Proteins: These are proteins which contains essential amino acids. These
are mainly of animal origin, Examples of foods which are first class proteins are lean
meat, fish, eggs, milk and cheese.
Second Class Proteins are mainly vegetables proteins which are found in vegetables
such as peas and beans.
Examples of Proteins includes:
 Insulin (a hormone)
 Haemoglobin (oxygen-carrying pigment in blood)
 Ribonuclease (an enzymes)
 Collagen (a muscle protein)

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3.2 FUNCTIONS OF PROTEINS
Proteins are the most versatile macromolecules in living systems and serve critical
functions in essentially all biological processes. They function as catalysts, they
transport and store other molecules such as oxygen, they provide mechanical
support and immune protection, they generate movement, they transmit nerve
impulses, and they control growth and differentiation.
Several key properties enable proteins to participate in such wide range of
functions.
1. Proteins are linear polymers built of monomers units called Amino Acids: The
function of protein is directly dependent on its three-dimensional structure.
Remarkably, proteins spontaneously fold up into three dimensional
structures that are determined by the sequence of amino acids in the protein
polymer. Thus, proteins are the embodiment of the transition from the one-
dimensional world of sequences to three-dimensional world of molecules
capable of diverse activities
2. Proteins contain a wide range of functional groups; these functional groups
include alcohols, thiols, thioethers, carboxylic acids, carboxamides, and a
variety of basic groups. When combined in various sequences, this array of
functional groups accounts for the broad spectrum of protein function. For
instance, the chemical reactivity associated with these groups is essential to
the function of enzymes, the proteins that catalyze specific chemical
reactions in biological systems.
3. Proteins can interact with one another and with other biological
macromolecules to form complex assembles: The proteins within these
assemblies can act synergistically to generate capabilities not afforded by the
individual components proteins. These assemblies include macromolecular
machines that carry out accurate replication of DNA, the transmission of
signals within cells and many other essential processes.
4. Some proteins are quite rigid, whereas other display limited flexibility; Rigid
units can function as structural elements in the cytoskeleton (the internal
scaffolding within cells) or in connective tissue. Part of proteins with limited
flexibility may act as hinges, springs and levers that are crucial to protein
functions, to assembly of proteins with one another and with other
molecules into complex units and to the transmission of information within
and between cells.
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3.3 STRUCTURE OF PROTEINS
Protein structure is the three-dimensional arrangement of atoms in an amino acid-
chain molecule. Proteins are polymers – specifically polypeptides – formed from
sequences of amino acids, the monomers of the polymer. A single amino acid
monomer may also be called a residue indicating a repeating unit of a polymer.
Proteins form by amino acids undergoing condensation reactions, in which the
amino acids lose one water molecule per reaction in order to attach to one another
with a peptide bond.
Protein structures range in size from tens to several thousand amino acids.[2] By
physical size, proteins are classified as nanoparticles, between 1–100 nm. Very
large protein complexes can be formed from protein subunits. For example, many
thousands of actin molecules assemble into a microfilament.
A protein usually undergoes reversible structural changes in performing its
biological function. The alternative structures of the same protein are referred to
as different conformations, and transitions between them are
called conformational changes.

Proteins have a well-defined structure. The structure of Proteins is much more

complex than that of simple organic molecules.
There are four levels of organization in proteins structures and they includes;
i. Primary Structure
ii. Secondary Structure
iii. Tertiary Structure
iv. Quaternary Structure
PRIMARY STRUCTURE OF PROTEIN:
The primary structure of a protein is the linear sequence of the side chains that are
connected to the protein backbone. In other words, the primary structure of
protein refers to the way in which the atoms of the protein molecule are joined to
one another by covalent bonds to form chains and cross-linkages between chains.
Each protein has a unique sequence of amino acid residues that cause it to fold into
distinctive shape that allows the protein to function properly. Examples of primary
structure is Human Insulin.

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SECONDARY STRUCTURE OF PROTEIN
Secondary Structure is defined as the process by which hydrogen bonding causes
protein chain to fold and align to produce orderly patterns.
Pauling (Nobel prize, 1954) and Corey described the alpha helix and beta pleated
sheet structures of polypeptides chains in 1951.

Types of Secondary Structure of Protein

There are two types of secondary structure and they includes;
i. The α Helix
ii. The β-pleated Sheet

The α Helix: The α Helix is a single protein chain twisted to resemble a coiled helical
spring.
The α Helix is held in this shape by hydrogen bonding interactions between amide
groups, with the side chains extending outward from the coil. The amount of α Helix
coiling in proteins is highly variable. The alpha helix is the most common and stable
conformation for a polypeptide chain. In proteins like hemoglobin and myoglobin,
the alpha helix is abundant, whereas it is virtually absent in chymotrypsin.
The alpha helix is a spiral structure. The polypeptide bonds form the backbone and
the side chains of amino acids extend outwards. The structure is stabilized by
hydrogen bonds between NH and C=O groups of the main chain.
The β-pleated Sheet: This is a sheet in which several protein chains lie side by side,
held by hydrogen bonds between adjacent chains.
The polypeptide chains in the beta-pleated sheet is almost fully extended. The
distance between adjacent amino acids is 3.5A. It is stabilized by hydrogen bonds
between NH and C=O groups of neighboring polypeptide segments.
The Beta – pleated sheet is the major structural motif in proteins like Silk Fibroin
(anti-parallel), Flavodoxin (parallel) and Carbonic anhydrase (both). Beta bends
may be formed in many proteins by the abrupt U-turn folding of the chain. Intra-
chain disulfide bridges stabilize these bends.
Example of the β-pleated sheet is found in protein of Silk.

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TERTIARY STRUCTURE OF PROTEIN
The tertiary structure of protein refers to the bending and folding of the protein
into a specific three-dimensional shape.
These structures can be grouped into four types of interactions between the R side
chains of the amino residues.
i. Disulfide Bridges
ii. Salt Bridges
iii. Hydrophobic Interactions
iv. Hydrogen Bonds

DISULFIDE BRIDGES: This can form between two cysteine residues that are close to
each other in the same chain, or between cysteine residues in different chains.
These bridges hold the proteins chain in a loop or some other 3D shape.

SALT BRIDGES: These are attractions between ions that result from the interactions
of the ionized side chains of acidic amino acids(- COO-) and the side chains of basic
amino acids (-NH3+).

HYDROGEN BONDS: Hydrogen bond can form between a varieties of side chain s,
especially those that contain;

-OH -NH2 C NH2

Hydrogen bonding also influences the secondary structure, but here the hydrogen
bonding is between R groups, while in secondary structures it is between the C=O
and NH portions of the backbone.

HYDROPHOBIC INTERACTIONS: These result from the attraction of non-polar

groups, or when they are forced together by their mutual repulsion of the aqueous
solvent. These attractions are particularly important between the benzene rings in
phenylalanine or tryptophan. This interaction is relatively weak, but since it acts
over large surfaces, the net effect is a strong interaction.

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QUATERNANRY STRUCTURE:
The arrangement of sub-units to form a larger protein is the quaternary
structure of the protein.
Each of the polypeptide sub-units has its own primary, secondary and
tertiary structure. When two or more polypeptide chains are held together by
disulfide bridges, salt bridges, hydrogen bond or hydrophobic interactions, forming
a larger protein complex.
Hemoglobin is made of four sub-units; two identical alpha chains containing
141AA’s and two identical beta chains containing 146 AA’s. Each subunit contain a
heme group located in a crevices near the exterior of the molecules.

3.4 AMINO ACIDS AND PEPTIDE BONDS

Peptides are amides formed by the interaction between amino groups and carboxyl
groups. The bond joining the α-amino group of one amino acid and the α-carboxyl
group of another amino acid is known as the PEPTIDE BOND or CO-NH Bridge.
Proteins are synthesized by polymerization of amino acids through peptide bonds.

No of Amino Acid Peptide Name

2 Dipeptide
3 Tripeptide
4 Tetrapeptide
5-9 Oligopeptide
10 – 50 Polypeptide
More than 50 Protein

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Amino acids are derivatives of carboxylic acids in which one hydrogen atom of the
alkyl group has been replaced by an amino group, -NH2. Amino acids are the basic
structural units of proteins with the general molecular formula.

The common property of all proteins is that they consist of long chains of α-amino
(alpha amino) acids. The general structure of α-amino acids is shown in the diagram
below. The α-amino acids are so called because the α-carbon atom in
the molecule carries an amino group (―NH2); the α-carbon atom also carries a
carboxyl group (―COOH).

The Carbon atom of the amino acid to which the functional group is attached is
known as the α-carbon.
In acidic solutions, when the pH is less than 4, the ―COO groups combine with
hydrogen ions (H+) and are thus converted into the uncharged form (―COOH). In
alkaline solutions, at pH above 9, the ammonium groups (―NH+3) lose a hydrogen
ion and are converted into amino groups (―NH2). In the pH range between 4 and

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8, amino acids carry both a positive and a negative charge and therefore do not
migrate in an electrical field. Such structures have been designated as dipolar ions,
or zwitterions (i.e., hybrid ions).
In neutral solution, amino acids are mainly in the form of dipolar ions called
ZWITTERIONS.

There are twenty naturally occurring amino acids of biological importance. All
proteins found in living organisms are combinations of these amino acids. Some
of these amino acids are known as essential amino acids because they cannot be
synthesized in our body. Thus, these amino acids must be present in our dietary
proteins. The Twenty Amino acids are as follow;

1. Arginine 16. Leucine

2. Alanine 17. Threonine
3. Asparagine 18. Tryptophan
4. Aspartic acid 19. Valine
5. Cysteine 20. Tyrosine
6. Glutamine
7. Glutamic acid
8. Glycine
9. Histidine
10.Isoleucine
11.Lysine
12.Methionine
13.Phenylalanine
14.Proline
15.Serine

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15
 CHAPTER FOUR
ENZYMES
4.1 ENZYMES
Enzymes are organic catalyst, usually proteinous in nature, which promotes or
speed up chemical changes in living cells but are not themselves used up in the
process. Enzymes accelerates metabolic reactions without changing their
composition in the process.

4.2 TYPES OF ENZYMES

There are two major types of enzymes. These are:
Intracellular Enzymes: These enzymes function inside the cells of living organisms.
Common examples are the enzymes that catalyze cell respiration inside the
mitochondria.
Extracellular Enzymes: these are enzymes which carry out their functions outside
the cells examples of the digestive enzymes.

4.3 CHARACTERISTICS OF ENZYMES

1. Remain chemically unchanged at the of a reaction
2. Are specific in action\one or a group of enzymes will act on specific
substrates.
3. Required in small quantities
4. Act best over a specific range of temperature / between 350- 400C.
5. They are denature/destroyed at high temperature/inactivated at very low
temperature
6. Act best at specific pH (either acidic or alkaline)
7. Their action is reversible.
8. Enzymes action is retarded by poison or inhibitors.
9. Some are inactive and require a co enzymes/agent to active them.
10.They can function outside the body of the organism that produces them.
11.Enzymes are protein in nature.

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4.4 CLASSIFICATION OF ENZYMES
The new method of classifying enzymes is based on the nature of chemical changes
brought about on a substrate. Such changes may involve oxidation in which case
the enzyme will be called an Oxidase.
It is important to note classification based on the substrate an enzyme works on,
e.g. Amylases for maltose, Proteases for protein or lipases for lipids are no longer
correct or biochemically acceptable.

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 CHAPTER FIVE
CARBOHYDRATES
5.1 CARBOHYDRATES
Carbohydrates are naturally occurring organic compounds containing
Carbon, Hydrogen and Oxygen with the hydrogen and oxygen present in the ratio
of 2:1 as in water. The general molecular formula of carbohydrate is C xH2yOy or
Cx(H2O)y.

5.2 CLASSES OF CARBOHYDRATE

Carbohydrate can be classified into two major groups namely:
a. Simple Sugar
b. Complex Sugar

SIMPLE SUGAR:
Simple sugars are crystalline, soluble in water and have a sweet taste. Structurally
they can be further divided into;
a. Monosaccharides
b. Disaccharides
MONOSACCHARIDES: These are simple sugars with three to six carbon atoms per
molecule. However, the most common and important of these are the ones
containing sic carbon atoms per molecules, the hexoses, e.g. glucose, fructose,
Galactose and mannose. All hexoses have the same molecular formula C6H12O6, but
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possess different spatial arrangements. Hexoses can exist both in the open chain
and cyclic form in solution. In solid, crystals, they exist in the ring form.
DISACCHARIDES: A disaccharide is derived from two molecules of
monosaccharides by the elimination of one molecule of water. The two component
monosaccharides which may be the same or different can be recovered by the
hydrolysis of the disaccharides.
Condensation
Monosaccharide + monosaccharide Disaccharide + Water
Hydrolysis
Most disaccharide are composed of two hexoses joined together by condensation.
They possess a general formula of C12H22O11.
C6H12O6 + C6H12O6 C12H22O11 + H2O

Monosaccharides Disaccharides C12H22O11 Common Name

Glucose + Fructose Sucrose Cane Sugar
Glucose + Glucose Maltose Malt Sugar
Glucose + Galactose Lactose Milk Sugar

COMPLEX SUGAR: Complex sugar are also known as polysaccharides. They are non-
crystalline, in-soluble and tasteless substances. They have very high relative
molecular masses and are polymers derived from monosaccharides.
POLYSACCHARIDES: These are a group of complex carbohydrates composed of
very long chains of monosaccharides linked together by condensation i.e. by the
elimination of one molecule of water for every bond formed between two
monosaccharides molecules.
Polysaccharide are polymers of hexoses and have a general molecular formula of
(C6H10O5)n where letter n shows a large number. Starch, Glycogen and cellulose are
polysaccharides.
Sources of Starch are Potatoes, Yam, Tapioca, Rice Millet, Wheat, Bread and
Cassava. These are plant starches. Glycogen is an animal starch produced and
stored in the liver and muscles. It is converted to glucose when the needs arises.
Cellulose is derived from vegetables and fruits. It forms the cell walls in most plant
cells.

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5.3 IMPORTANCE OF CARBOHYDRATES
a. When oxidized, they give energy and heat. The energy is used for
work while the heat is used to maintain body temperature in
hormoiothermic animals.
b. Excess carbohydrates are converted into glycogen thus acting as food
reserves only to be used when the need arises
c. Carbohydrates provide starting materials for the synthesis of
proteins, fats, oils and vitamins

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Examples of Monosaccharides

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 CHAPTER SIX
NUCLEIC ACIDS AND METABOLISM
DEFINITION OF NUCLEIC ACIDS
A nucleic acid is a chain of nucleotides which stores genetic information in
biological systems. They are naturally occurring chemical compound that is capable
of being broken down to yield phosphoric acid, sugars, and a mixture of organic
bases (purines and pyrimidines). Nucleic acids are the main information-carrying
molecules of the cell, and, by directing the process of protein synthesis, they
determine the inherited characteristics of every living thing.

TYPES OF NUCLEIC ACIDS

The two main classes of nucleic acids are deoxyribonucleic acid (DNA) and
ribonucleic acid (RNA).

 DNA is the master blueprint for life and constitutes the genetic material in all
free-living organisms and most viruses.
 RNA is the genetic material of certain viruses, but it is also found in all living
cells, where it plays an important role in certain processes such as the making
of proteins.

FUNCTIONS OF NUCLEIC ACIDS

 Nucleic Acid is responsible for the synthesis of protein in our body
 RNA is a vital component of protein synthesis.
 Loss of DNA content is linked to many diseases.
 DNA is an essential component required for transferring genes from parents
to offspring.
 All the information of a cell is stored in DNA.
 DNA fingerprinting is a method used by forensic experts to determine
paternity. It is also used for the identification of criminals. It has also played
a major role in studies regarding biological evolution and genetics.

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 COMPONENTS OF NUCLEIC ACIDS
Nucleic acids are long chainlike molecules composed of a series of nearly identical
building blocks called nucleotides. Each nucleotide consists of a nitrogen-
containing aromatic base attached to a pentose (five-carbon) sugar, which is in turn
attached to a phosphate group.
Nucleotides are the subunits of nucleic acids, bonded together in dehydration
synthesis reactions to form long polynucleotide chains. Each nucleotide, however,
is itself composed of three smaller subunits: a five-carbon (pentose) sugar, a
phosphate group attached to one end of the sugar, and a nitrogenous base
attached to the other end of the sugar.

 Nitrogenous bases
A nitrogenous base is an organic molecule that contains the element nitrogen
and acts as a base in chemical reactions. The basic property derives from the lone
electron pair on the nitrogen atom.
The nitrogenous bases are nitrogen-containing molecules of two kinds: pyrimidines
and purines. The pyrimidines contain a single ring of carbon and nitrogen, whereas
the purines have two such rings. Adenine (A), guanine (G), cytosine (C), thymine (T),
and uracil (U). A and G are categorized as purines, and C, T, and U are collectively
called pyrimidines. All nucleic acids contain the bases A, C, and G; T, however, is
found only in DNA, while U is found in RNA.

 Adenine is often represented by the capital letter A. In DNA, its

complementary base is thymine. The chemical formula of adenine is C5H5N5.
In RNA, adenine forms bonds with uracil.

Adenine and the other bases bond with phosphate groups and either the
sugar ribose or 2'-deoxyribose to form nucleotides. The nucleotide names
are similar to the base names but have the "-osine" ending for purines (e.g.,

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 adenine forms adenosine triphosphate) and "-idine" ending for pyrimidines
(e.g., cytosine forms cytidine triphosphate).

 Guanine is a purine represented by the capital letter G. Its chemical formula

is C5H5N5O. In both DNA and RNA, guanine bonds with cytosine. The
nucleotide formed by guanine is guanosine.
 Thymine is also known as 5-methyluracil. Thymine is a pyrimidine found in
DNA, where it binds to adenine. The symbol for thymine is a capital letter T.
Its chemical formula is C5H6N2O2. Its corresponding nucleotide is thymidine.
 Cytosine is represented by the capital letter C. In DNA and RNA, it binds with
guanine. Three hydrogen bonds form between cytosine and guanine in the
Watson-Crick base pairing to form DNA. The chemical formula of cytosine is
C4H4N2O2. The nucleotide formed by cytosine is cytidine.
 Uracil may be considered to be demethylated thymine. Uracil is represented
by the capital letter U. Its chemical formula is C4H4N2O2. In nucleic acids, it is
found in RNA bound to adenine. Uracil forms the nucleotide uridine.
In DNA and RNA, nitrogenous bases are bonded by Hydrogen bonds.
 In DNA, Adenine is bonded to Thymine by 2 — Hydrogen bonds. Guanine is
bonded to Cytosine by 3– Hydrogen bonds.
 In RNA, Adenine is bonded to Uracil by 2 — Hydrogen bonds. Guanine is
bonded to Cytosine by 3- Hydrogen bonds.

 Sugars
This is typically a 5 carbon sugar i.e. a pentose. These sugars form a bond with the
phosphate groups also present in nucleotides. The pentose sugar in DNA (2′-
deoxyribose) differs from the sugar in RNA (ribose) by the absence of a hydroxyl
group (―OH) on the 2′ carbon of the sugar ring. Without an attached phosphate
group, the sugar attached to one of the bases is known as a nucleoside.

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 Phosphate
Phosphate, chemical formula PO43-, is a chemical compound made up of one
phosphorus and four oxygen atoms. When it is attached to a molecule containing
carbon, it is called a phosphate group. It is found in the genetic material DNA and
RNA, and is also in molecules such as adenosine triphosphate (ATP) that provide
energy to cells.

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 DEOXYRIBONUCLEIC ACIDS
DNA is a polymer of the four nucleotides A, C, G, and T, which are joined through a
backbone of alternating phosphate and deoxyribose sugar residues. These
nitrogen-containing bases occur in complementary pairs as determined by their
ability to form hydrogen bonds between them. A always pairs with T through two
hydrogen bonds, and G always pairs with C through three hydrogen bonds.
The spans of A:T and G:C hydrogen-bonded pairs are nearly identical, allowing them
to bridge the sugar-phosphate chains uniformly. This structure, along with the
molecule’s chemical stability, makes DNA the ideal genetic material. The bonding
between complementary bases also provides a mechanism for the replication of
DNA and the transmission of genetic information.

THE STRUCTURE OF DNA

The DNA structure can be thought of like a twisted ladder. This structure is
described as a double-helix. It is a nucleic acid, and all nucleic acids are made up of
nucleotides. The basic building blocks of DNA are these nucleotides, and each
nucleotide is composed of three different components, such as sugar, phosphate
groups and nitrogen bases.
The sugar and phosphate groups link the nucleotides together to form each strand
of DNA. Adenine (A), Thymine (T), Guanine (G) and Cytosine (C) are four types of
nitrogen bases that make up the DNA. These 4 Nitrogenous bases pair together in
the following way: A with T, and C with G. These base pairs are essential for the
DNA’s double helix structure, which resembles a twisted ladder. The order of the
nitrogenous bases determines the genetic code or the DNA’s instructions.
Among the three components of DNA structure, sugar is the one which forms the
backbone of the DNA molecule. It is also called deoxyribose. The nitrogenous bases
of the opposite strands form hydrogen bonds, forming a ladder-like structure.

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DNA REPLICATION
DNA replication is the process by which a molecule of DNA is duplicated. When a
cell divides, it must first duplicate its genome so that each daughter cell winds up
with a complete set of chromosomes.

 Step 1: Replication Fork Formation

Before DNA can be replicated, the double stranded molecule must be “unzipped”
into two single strands. In order to unwind DNA, the interactions between base
pairs must be broken. This is performed by an enzyme known as DNA helicase. DNA
helicase disrupts the hydrogen bonding between base pairs to separate the strands
into a Y shape known as the replication fork. This area will be the template for
replication to begin.

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 DNA is directional in both strands, signified by a 5' and 3' end. This notation signifies
which side group is attached the DNA backbone. The 5' end has a phosphate (P)
group attached, while the 3' end has a hydroxyl (OH) group attached. This
directionality is important for replication as it only progresses in the 5' to 3'
direction. However, the replication fork is bi-directional; one strand is oriented in
the 3' to 5' direction (leading strand) while the other is oriented 5' to 3' (lagging
strand). The two sides are therefore replicated with two different processes to
accommodate the directional difference.
Replication Begins

 Step 2: Primer Binding

The leading strand is the simplest to replicate. Once the DNA strands have been
separated, a short piece of RNA called a primer binds to the 3' end of the strand.
The primer always binds as the starting point for replication. Primers are generated
by the enzyme DNA primase.

 Step 3: Elongation

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 Enzymes known as DNA polymerases are responsible for creating the new strand
by a process called elongation. There are five different known types of DNA
polymerases in bacteria and human cells. In bacteria such as E. coli, polymerase III
is the main replication enzyme, while polymerase I, II, IV and V are responsible for
error checking and repair. DNA polymerase III binds to the strand at the site of the
primer and begins adding new base pairs complementary to the strand during
replication. In eukaryotic cells, polymerases alpha, delta, and epsilon are the
primary polymerases involved in DNA replication. Because replication proceeds in
the 5' to 3' direction on the leading strand, the newly formed strand is continuous.
The lagging strand begins replication by binding with multiple primers. Each primer
is only several bases apart. DNA polymerase then adds pieces of DNA, called
Okazaki fragments, to the strand between primers. This process of replication is
discontinuous as the newly created fragments are disjointed.

 Step 4: Termination
Once both the continuous and discontinuous strands are formed, an enzyme called
exonuclease removes all RNA primers from the original strands. These primers are
then replaced with appropriate bases. Another exonuclease “proofreads” the
newly formed DNA to check, remove and replace any errors. Another enzyme
called DNA ligase joins Okazaki fragments together forming a single unified strand.
The ends of the linear DNA present a problem as DNA polymerase can only add
nucleotides in the 5′ to 3′ direction. The ends of the parent strands consist of
repeated DNA sequences called telomeres. Telomeres act as protective caps at the
end of chromosomes to prevent nearby chromosomes from fusing. A special type
of DNA polymerase enzyme called telomerase catalyzes the synthesis of telomere
sequences at the ends of the DNA. Once completed, the parent strand and its
complementary DNA strand coils into the familiar double helix shape. In the end,
replication produces two DNA molecules, each with one strand from the parent
molecule and one new strand.

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Replication Enzymes
DNA replication would not occur without enzymes that catalyze various steps in the
process. Enzymes that participate in the eukaryotic DNA replication process
include:

 DNA helicase - unwinds and separates double stranded DNA as it moves

along the DNA. It forms the replication fork by breaking hydrogen bonds
between nucleotide pairs in DNA.
 DNA primase - a type of RNA polymerase that generates RNA primers.
Primers are short RNA molecules that act as templates for the starting point
of DNA replication.
 DNA polymerases - synthesize new DNA molecules by adding nucleotides to
leading and lagging DNA strands.
 Topoisomerase or DNA Gyrase - unwinds and rewinds DNA strands to
prevent the DNA from becoming tangled or supercoiled.
 Exonucleases - group of enzymes that remove nucleotide bases from the end
of a DNA chain.
 DNA ligase - joins DNA fragments together by forming phosphodiester bonds
between nucleotides.
IMPORTANCES OF DNA

 DNA in the Field of Medicine: With the help of the DNA and genes, it is
possible to find the susceptibility of our body to different types of diseases.
This would help the doctors to develop the medicines required to enhance
our immunity system against the attack of those diseases. DNA has also
helped in the formulation of highly effective medicines to cure various deadly
diseases prevalent in our current world.

 DNA in the Field of Forensic Science: The law enforcement has become easier
with the discovery of DNA. Evidence against the suspects and criminals can
be collected with the help of DNA. The judiciary system nowadays relies on
the DNA fingerprint tests to determine a suspect’s involvement in a crime
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 scene. The other DNA samples collected from the crime scene like hair,
blood, etc., also help to prove a crime.

 DNA in the Field of Agriculture: DNA is used to increase the resistance of the
plants to various diseases, insects, and pests. Sometimes, genes from
bacteria are injected into the plants to resist the insects and pests. DNA helps
in the entire re-engineering of the plants and thus to produce viral proteins
necessary for them to survive in the current environmental condition.

 DNA in Animal Breeding: Information within the DNA facilitates the breeding
of animals with better resistance to the diseases. Crossbreed varieties of
animals could not have been possible to create without the help of genes
and DNA. The instructions on how the characteristics vary for each species
are contained in the DNA and this information is essential while cross-
breeding two different animals.

 DNA to Determine the Paternity of a Child: The paternity of a child can easily
be detected through a DNA. The legal cases pertaining to the paternity of a
child can be easily resolved by a DNA test. It helps a person to identify his /
her parents with scientific evidence.

RNA, abbreviation of ribonucleic acid, is a complex compound of high molecular

weight that functions in cellular protein synthesis and replaces DNA
(deoxyribonucleic acid) as a carrier of genetic codes in some viruses. RNA plays a
major role in protein synthesis as it is involved in the transcription, decoding,
and translation of the genetic code to produce proteins. RNA stands for ribonucleic
acid and like DNA, RNA nucleotides contain three components: A Nitrogenous Base,
Five-Carbon Sugar, and a Phosphate Group.

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 RNA consists of ribose nucleotides (nitrogenous bases appended to a ribose sugar)
attached by phosphodiester bonds, forming strands of varying lengths. The
nitrogenous bases in RNA are adenine, guanine, cytosine, and uracil, which replaces
thymine in DNA.

3.2. STRUCTURE OF RNA

There are multiple levels of structure in ribonucleic acid (RNA), which are described
as primary structure, secondary structure, tertiary structure, and quaternary
structure. The primary structure of RNA refers to its sequence of genetic
information units, called nucleotides. Its secondary structure is composed of the
pairs formed when nucleotides in the sequence bind to each other. Tertiary
structure is more complex still, encompassing the interactions between regions of
the secondary structure and throughout the entire molecule. Quaternary structure
applies only when multiple chains of RNA interact, and is any interactions or
structural changes that occur when these chains come together.

 Primary structure
Like DNA, RNA is a long polymer consisting of nucleotides. it is a single-stranded
helix. The strand has a 5′end (with a phosphate group) and a 3′end (with a hydroxyl
group). It is composed of ribonucleotides. The ribonucleotides are linked together
by 3′ –> 5′ phosphodiester bonds.
The nitrogenous bases that compose the ribonucleotides include adenine, cytosine,
uracil, and guanine, thus thymine in DNA is replaced by uracil in RNA, a different
pyrimidine. However, like thymine, uracil can form base pairs with adenine.
The sugar in RNA is ribose rather than deoxyribose as in DNA. The corresponding
ribonucleosides are adenosine, guanosine, cytidine and uridine. The corresponding
ribonucleotides are adenosine 5’-triphosphate (ATP), guanosine 5’-triphosphate
(GTP), cytidine 5’-triphosphate (CTP) and uridine 5’-triphosphate (UTP).

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  Secondary Structure
RNA secondary structure and deoxyribonucleic acid (DNA) double helices form in a
similar way, where nucleotides bind together into base pairs, giving the molecule
an overall structure. There are significant differences in the way RNA secondary
structure is formed, versus DNA double helices. In both RNA and DNA, cytosine
binds to guanine, but adenine binds to uracil, not thymine, in RNA. The secondary
structure of RNA is rarely a double helix; it forms a variety of specific loops, bulges,
and helix types that are aligned very differently than what is seen in DNA. RNA
secondary structure in general is more complicated, although not necessarily less
ordered, than DNA double helices.

3.3 TYPES OF RNA

In both prokaryotes and eukaryotes, there are three main types of RNA

 mRNA (messenger)
 rRNA (ribosomal)
 tRNA (transfer)

 Messenger RNA (mRNA)

Messenger RNA (mRNA) plays an important role in the transcription of DNA. It
accounts for about 5% of the total RNA in the cell and it’s the most heterogeneous

33
 of the 3 types of RNA in terms of both base sequence and size. It carries the genetic
code copied from the DNA during transcription in the form of triplets of nucleotides
called codons. Transcription is the process in protein synthesis that involves
copying the genetic information contained within DNA into an RNA message.
During transcription, certain proteins called transcription factors unwind the DNA
strand and allow the enzyme RNA polymerase to transcribe only a single strand of
DNA. DNA contains the four nucleotide bases adenine (A), guanine (G), cytosine (C)
and thymine (T) which are paired together (A-T and C-G). When RNA polymerase
transcribes the DNA into an mRNA molecule, adenine pairs with uracil and cytosine
pairs with guanine (A-U and C-G). At the end of transcription, mRNA is transported
to the cytoplasm for the completion of protein synthesis.
As part of post-transcriptional processing in eukaryotes, the 5’ end of mRNA is
capped with a guanosine triphosphate nucleotide, which helps in mRNA
recognition during translation or protein synthesis. Similarly, the 3’ end of an mRNA
has a poly A tail or multiple adenylate residues added to it, which prevent
enzymatic degradation of mRNA. Both 5’ and 3’ end of an mRNA imparts stability
to the mRNA.

 Ribosomal RNA (rRNA)

Ribosomal RNA (rRNA) is a component of cell organelles called ribosomes and
account for 80% of the total RNA present in the cell. rRNA directs the translation of
mRNA into proteins. A ribosome consists of ribosomal proteins and rRNA.
Ribosomes are typically composed of two subunits: the small ribosomal subunits,
which read the RNA, and the large subunits, which join amino acids to form a
polypeptide chain. Each subunit comprises one or more ribosomal RNA (rRNA)
molecules and a variety of ribosomal proteins (r-protein or rProtein. Ribosomal
subunits are synthesized in the nucleus by the nucleolus.
Ribosomes contain a binding site for mRNA and two binding sites for tRNA located
in the large ribosomal subunit. During translation, a small ribosomal subunit
attaches to a mRNA molecule. At the same time, an initiator tRNA molecule
recognizes and binds to a specific codon sequence on the same mRNA molecule. A
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 large ribosomal subunit then joins the newly formed complex. Both ribosomal
subunits travel along the mRNA molecule translating the codons on mRNA into a
polypeptide chain as they go. Ribosomal RNA is responsible for creating the peptide
bonds between the amino acids in the polypeptide chain. When a termination
codon is reached on the mRNA molecule, the translation process ends. The
polypeptide chain is released from the tRNA molecule and the ribosome splits back
into large and small subunits.

 Transfer RNA (tRNA)

Transfer RNA (tRNA) plays an important role in the translation portion of protein
synthesis. it is the smallest of the 3 types of RNA having about 75-95 nucleotides.
tRNAs are an essential component of translation, where their main function is the
transfer of amino acids during protein synthesis. Therefore they are called transfer
RNAs.
Each of the 20 amino acids has a specific tRNA that binds with it and transfers it to
the growing polypeptide chain. tRNAs also act as adapters in the translation of the
genetic (nucleotide) sequence of mRNA into specific proteins (amino acid
sequences). Therefore they are also called adapter molecules.
Transfer RNA is shaped like a clover leaf with three hairpin loops which is stabilized
by strong hydrogen bonds between the nucleotides. It contains an amino acid
attachment site (The 3′ end) on one end and a special section in the middle loop
called the anticodon site. The anticodon recognizes a specific area on mRNA called
a codon. A codon consists of three continuous nucleotide bases that code for an
amino acid or signal the end of translation. Transfer RNA along with ribosomes read
the mRNA codons and produce a polypeptide chain. The polypeptide chain
undergoes several modifications before becoming a fully functioning protein.

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 CHAPTER SEVEN
LIPIDS (FATS AND OIL)
FATS AND OILS
Fats are complex organic compounds containing carbon, hydrogen and
oxygen. They contain high proportion of carbon and hydrogen with little oxygen.
Fats are solid at room temperature while oils are liquid at room temperature. Liquid
fats are called oils. The end product of Fats and Oils is Fatty Acid or glycerol.

Fats are not soluble in water but soluble in solvents like kerosene, ether,
chloroform and benzene. Fats are found in both plants and animals. Oils can be
obtained from plants and animals fats by the process of heating (e.g. vegetable oils
from groundnut, coconut, melon, kernel and oil palm fruits). The oils can be
hardened into forms like butter by cooling, freezing and hydrogenation.

Fats and Oils belong to a general group of compounds known as Lipids. The
fatty acids commonly found in lipids are long chain alkanoic acids of the general
formula. RCOOH where R contains about 10 to 18 carbon atoms.
The terminal –COOH group is polar, hence the acid is able to dissolve in water. The
carboxylic acid group ionizes in water to a certain degree to form hydrogen ion and
the carboxylate ion. Fatty acids are thus weak acids.
RCOOH (aq) RCOO- (aq) + H+

The long alkyl group is non-polar, and so is not soluble in water.

Sources of Fats and Oils: Groundnut, groundnut oil, palm kernel, Soya bean oil,
Margarine, Butter, cheese, palm oil, fatty meat or fish, coconut oil, melons etc.

TYPES OF FATTY ACIDS

There are two types of Fatty acid and they include;
 Saturated Fatty Acids
 Unsaturated Fatty Acids
Saturated Fatty Acids: The saturated fatty acids have no double bonds in their
hydrocarbon chain
Unsaturated Fatty Acids: The unsaturated fatty acids have one or more double in
their hydrocarbon chain.
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Examples of Saturated and unsaturated fatty acids
IUPAC Name Old Source Molecular Formula
Name
Hexadecanoic Palmitic Palm oil CH3(CH2)14COOH
acid acids
Octadecanoic Stearic Animal fats CH3(CH2)16COOH
acid acid
Octadec-9- Oleic acid Peanut CH3(CH2)7=CH(CH2)7COOH
enoic acid oil,Olive oil
Octadeca- Linoleic Vegetable CH3(CH2)4CH=CHCH2CH=CH(CH2)7COOH
9,12-dienoic acid Oils
acid

IMPORTANCE OF FATS AND OILS

a. They act as insulator to nerves and cell membranes
b. When fats and oils are oxidized they give a great amount of energy and heat
to the body. They yield more energy than carbohydrates
c. Excess fats are stored under skin and around some organs like intestines,
eyes, gonads, kidney and heart. These stored fats help to keep the body
warm and protect vital organs

TEST FOR FATS AND OILS

Paper Test: A drop oil or melted fat on a piece of filter paper forms a translucent
grease spots.

Sudan III test: Shake a few cm3 of coconut oil with water. Then add 4 to 5 drops of
Sudan III stain. The oil is stained red. This is a specific test for fats and oils.

USES OF FATS AND OILS

Most fats are consumed as food. Oils are hardened into fats to make margarine.
Tallow (mutton fat) is used for making soaps.

37
Coconut oil and palm oil are used for making soaps and for cooking, while
groundnut oil and cotton seed oil are used only for cooking. Linseed oil is used for
making paints.

PROPERTIES OF FATS AND OILS

Fats have higher melting points because they are composed of a higher
proportion of esters of saturated fatty acids. Oils have lower melting points
because they are composed of a higher proportion of esters of unsaturated fatty
acids.
Any particular fat or oil is a complex mixture of propane-1, 2, 3-triol esters, its
properties depending mainly on the proportion of each constituent.

HYDROGENATION OF OIL
Oil can be changed into fat by hydrogenation. Margarine is made by this
process. Oils, usually from plants such as oil palm, groundnut and soya bean oil are
heated to about 1800C in the presence of finely divided nickel, and hydrogen is
bubbled in at about 5 atm. The hydrogen is added across the double bonds in the
unsaturated carbon chains in the oils. The hardened oil are then mixed with salt,
vitamins, skimmed mile and various fats to form margarine.

SAPONIFICATION
Hydrolysis of fats and oils with caustic alkali yields propane -1, 2, 3- triol and
the corresponding sodium and potassium salts of the component fatty acids. These
salts are the principal constituents of soap. This process is also known as
Saponification.
Saponification is simply defined as the process of making soap.

Fat or oil + caustic alkali Soaps + Propane 1, 2, 3- triol

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39