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Bio Chemistry
Core Unit #1 – Review and Introduction

• Tutorial 01: The Science of Chemistry

• Tutorial 02: Chemistry Review for Biochemistry
• Tutorial 03: Intoduction to Biochemistry
• Tutorial 04: Water
• Tutorial 05: Thermodynamics Principles

Core Unit #2 – Biomolecules

• Tutorial 06: Amino Acids, Peptides and Proteins

• Tutorial 07: All about Proteins
• Tutorial 08: Carbohydrates
• Tutorial 09: Lipids and Membranes
• Tutorial 10: Nucleic Acids

Core Unit #3 – Enzymology

• Tutorial 11: Enzyme: The Basic Concept

• Tutorial 12: Enzyme: The Kinetics and Catalysis

Core Unit #4 – Metabolism

• Tutorial 13: Introduction to Metabolism and Bioenergetics

• Tutorial 14: Glycolysis
• Tutorial 15: The Citric Acid Cycle
• Tutorial 16: Additional Pathways in Carbohydrate Metabolism
• Tutorial 17: Electron Transport and Oxidative Phosphorylation
• Tutorial 18: Photosynthesis
• Tutorial 19: Lipid Metabolism
• Tutorial 20: Amino Acid Metabolism
• Tutorial 21: Nucleotide Metabolism

Core Unit #5 – Information Pathway

Tutorial 22: DNA Structure and Replication

Tutorial 23: RNA Structure and Synthesis
Tutorial 24: Protein Biosynthesis

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The Science of Chemistry
What is chemistry?;

Chemistry is the study of matter, its properties and interactions. Some of the technologies which make use
of chemistry are computer chips, art supplies, medicines, power plants, plastics, alternative fuels etc.

Branches of chemistry

There are several subdivisions in chemistry. They are organic, inorganic, physical and analytical. In addition
to these four main, there are biochemistry, environmental, polymer, computational, organometallic, solid
state and many others.

Classification of matter and energy

Matter is anything that has mass and takes up space. Matter can be classified into pure substances and
mixtures. Pure substances are further classified into elements and compounds. Mixtures can be
homogeneous or heterogeneous. Energy is the ability to do work or cause changes. Energy is of two types:
Kinetic and Potential energy.

Determination of physical or chemical changes

Physical change is the one in which the chemical structure of the substances is not changed.
In chemical change, chemical structure of the substances is changed. There are several signs that may
indicate a chemical change has taken place. Ex: Gas production (bubbling). Physical property is the property
of matter that can be observed or measured without changing the matter chemically while chemical property
describes how a sample of matter reacts chemically with other matter.

Scientific processes

A hypothesis is an educated guess (prediction) and a theory can become a law if enough evidence is found.
There are common aspects of scientific experimentation like observations, questions, hypothesis formation,
experimentation, trend recognition, conclusion formation, communication and validation of results and
model formation.

How to study chemistry

Memorize basic information to save time later. Learn vocabulary quickly for understanding when it is used
later. Take each problem in steps. Connect each thing u learn with previous concepts. Keep up with the
work – chemistry builds on prior knowledge.

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Chemistry Review
Atomic and Molecular structure

An atom is made up of protons, neutrons and electrons. Protons are positively charged and they denote the
atomic number. Neutrons have no electrical charge. Protons and neutrons are present in the nucleus.
Electrons are negatively charged and present in the orbits surrounding the nucleus. Valence electrons are the
number of electrons in the outer shell. Organic acids are those that are derived from living organisms,
usually from metabolism. Esters are condensation products of carboxylic acids with the removal of water. .
Isotopes have same number of protons but different number of neutrons. Loss or gain of electrons is seen in
ions. Radicals have a single electron; there is no loss or gain of electrons in them. . Lewis structures are
drawn using the valence electron. Each pair of electrons makes one bond.

Types of carbon molecules

Carbon molecules are of four types: Stable neutral molecule, carbanion, carbocation and radical. A stable
neutral molecule has not gained or lost electrons, carbanion has gained electrons, carbocation has lost
electrons and radical is neutral and has a single electron.

Stereospecificity

Stereoisomers have the same atomic formula and connectivity but differ in the 3D position of the atoms.
Chiral carbon has four different groups attached.

Intramolecular bond interactions

Electronegativity is an atom’s ability to attract electrons. Bond polarity occurs when the bonding electrons
are not shared equally in a covalent bond. There are mainly two types of bonding, ionic and covalent. In
ionic bonding, transfer of electrons takes place. In covalent bonding, sharing of electrons occurs. It may be
either polar covalent bonding or non polar covalent bonding. Bond cleavage is of two types: hemolytic-
each fragment gets one electron, radicals are formed. Heterolytic – one fragment gets both electrons and the
other fragment gets no electrons, ions are formed.

Intermolecular forces

Intermolecular forces are of three types: London dispersion forces – between non polar molecules, dipole-
dipole forces between polar molecules, hydrogen bonding between molecules with OH, -NH or HF.

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Introduction to Biochemistry
Introduction

Living organisms should be able to transform matter and energy into different forms, show response to changes in
their environment and show growth and reproduction. All living organisms undergo changes due to large organic
compounds called macromolecules. Four main types of macromolecules control all activities. They are proteins,
carbohydrates, nucleic acids and lipids.

What is Biochemistry?

Molecules belong to different chemical groups based on their affinity for water. Hydrophobic groups – they can not
form hydrogen with water. Ex: Hydrocarbons. Hydrophilic groups – they are attracted to the charges within water.
They can form hydrogen bonds with water. Amphipathic groups – have both polar and non polar groups. Ex:
Hydrocarbon chain is non polar and carboxyl group is polar.

Biochemical compounds

There are four major classes of biochemical compounds - Carbohydrates, lipids, proteins and nucleic acids. In
carbohydrates, sugar units are connected together by ‘glycosidic bonds’. Lipids are insoluble in water but soluble in
organic solvents. All proteins are composed of amino acids which are connected by a peptide bond. There are 20
amino acids. Nucleic acids are composed of nucleotides.

Major types of biochemical reactions

Oxidation, reduction, hydrolysis, Phosphorolysis, Decarboxylation, deamination and transamination are the major
biochemical reactions. Oxidation is the loss of electrons. Reduction is the gain of electrons. Hydrolysis is the
chemical process in which a molecule is cleaved into two parts by the addition of a water molecule. Phosphorolysis
is the splitting of a bond by the addition of phosphoric acid to a compound. Decarboxylation is the loss of carbon
dioxide. Deamination is the removal of amino group. Transamination is the transfer of amino group from one
molecule to another.

Common Abbreviations

Abbreviations of amino acids, coenzymes, enzymes, nucleic acids have been listed.

How to study biochemistry

The various methods to study biochemistry are – summarize, forming a study group, question-answer sessions with
batch mates, practice drawing the biochemical structures to recollect during exams.
Introduction to Biochemistry

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Water
Weak interactions in aqueous systems

Water is a good solvent for polar solutes with which it forms hydrogen bonds. Non-polar compounds dissolve
poorly in water. They can not form a hydrogen bond with the solvent. Numerous weak non covalent interactions
influence the folding of macromolecules. The physical properties of aqueous solutions are strongly influenced by
the concentration of solutes. Ex: The tendency for water to move across a semi permeable membrane is the osmotic
pressure.

Ionization of water, weak acids and weak bases

Pure water is slightly ionized. pH is defined as the negative logarithm of the molar hydronium ion concentration.
An acid that ionizes completely in water is a strong acid. An acid which is partially ionized in water is a weak acid.
pk provides the measure of the ease of the dissociation of the proton. The lower the number the stronger is the acid.

Buffering against pH changes in biological systems

Buffers are aqueous systems that tend to resist in changes in pH when small amounts or acids or base are added. It
consists of a weak acid and its conjugate base. As an example a mixture of equal concentrations of acetic acid and
acetate ion is a buffer system. Every life form is extremely sensitive to slight pH changes. Human blood for
example needs to remain within the pH range of 7.38 to 7.42. The relationship between pH and pk is described by
Henderson – Hasselbach equation. It is used to calculate the pH of biological fluids. Two especially important
biological buffers are the phosphate and bicarbonate systems. The property of a solution that depends on the
concentration of a dissolved solute but not on its chemical identity is known as colligative properties. Substances
that do not ionize in water are non electrolytes. Vapor pressure, boiling point, freezing point and osmosis are
colligative properties.

Water as a reactant

Water is very often a direct participant in the chemical reactions of living cells. Formation of ATP from ADP and
inorganic phosphate is an example of a condensation reaction in which the elements of water are eliminated. Two
amino acid molecules are covalently joined through a peptide bond with a loss of water molecule.

Fitness of the aqueous environment for living organisms

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The high specific heat of water is useful to cells and organisms because it allows water to act as a ‘heat buffer’,
keeping the temperature of an organism relatively constant as the temperature of the surroundings fluctuates.

Thermodynamics for Biochemistry

Thermodynamics

It is the study of heat changes. Increased temperature increases molecular motion. Energy is the ability to do work.
Joules (J) and calories (cal) are the most common energy units. Energy can be transferred through work applying a
force over a distance.

Energy changes of physical and chemical processes

First law of thermodynamics states that energy can not be created or destroyed in physical or chemical changes.
Heat is the flow of energy from higher temperature particles to lower temperature particles.

Enthalpy, entropy and free energy

Enthalpy (H) takes into account the internal energy of the sample along with pressure and volume. Under constant
pressure, heat and enthalpy are the same. Enthalpy of reaction is the net energy change during a chemical reaction.
In endothermic reaction, the system takes in energy from the surroundings. ΔD is positive. In exothermic reaction,
the system gives off energy to the surroundings. Here, ΔH is negative. Heat capacity is the amount of energy that
can be absorbed by a particle, before the temperature increases. When changing between solids, liquids and gases,
the temperature does not change. Entropy is the randomness. Spontaneity occurs without outside intervention.
Second law of thermodynamics states that every spontaneous process has an increase in entropy of the universe.

Determining spontaneity of a process

Spontaneity occurs without outside intervention. Temperature can determine whether a process is spontaneous. Free
energy (G) relates temperature, enthalpy and entropy. Free energy is used to determine if the reaction is
spontaneous at a specific temperature.

Relating free energy and equilibrium

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A chemical reaction that can proceed in both directions is called a reversible reaction. A reaction is said to be at
equilibrium when the rate of the forward reaction equals the rate of the reverse reaction. It takes time to establish
equilibrium. The reactions continue to proceed in both directions, but at the same rate is said to be in dynamic
equilibrium. At thermal equilibrium, two objects at different temperatures, placed together will come to the same
temperature.

Amino acids, Peptides and Proteins

Structure, classification and nomenclature of amino acids

Amino acid refers to any compound containing an amino group and a carboxyl group. Amino acids are the basic
structural units of proteins. They contain an amino group and a carboxyl group. Chiral carbon has four different
types of atoms or groups attached to it. Most proteins are formed of 20 amino acids. Glycine is the simplest amino
acid. Usually, amino acids are coded with three letters. Ex: Alanine is coded as Ala. Amino acids are classified into
three categories: Aliphatic, aromatic and heterocyclic. Aliphatic amino acids are further classified into monoamino-
monocarboxylic, monoamino-dicarboxylic, diamino-monocarboxylic, sulphur containing carboxylic acids. In
neutral solution, amino acids are zwitterionic, with a positive charge on the nitrogen atom and a negative on the
carboxyl group. All amino acids have the same general structure except proline.

Formation and classification of peptides

Peptide bond is formed by dehydration. Two amino acid molecules can be covalently joined through a peptide bond
to yield a dipeptide. Peptide chain can be formed by the process of peptide bond formation between joining amino
acids. When there are a few amino acids in a chain, usually 10-20, its called an oligopeptide. When there are more
than 20, it is called a polypeptide.

Structure and function of proteins

Proteins are among the fundamental molecules of biology and are responsible for most of the complex functions
that make life possible. The amino acid sequence of a protein determines its 3D structure. There are 4 classes of
structure: Primary, secondary, tertiary and quaternary. Primary structure of proteins refers to linear number and
order of the amino acids present. The ordered array of amino acids in a protein confers regular conformational

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forms upon that protein. These conformations constitute the secondary structures of proteins. β- Sheets are either
parallel or anti parallel. α- helices and β sheet regions are connected by loop regions. Tertiary structure describes
the relationship of different domains to one another within a protein. Quaternary structure describes about proteins
containing several distinct polypeptide chains along with the non protein groups.

All about Proteins

Amino acids – Building blocks

All amino acids incorporated into proteins by organisms are in the L form. All amino acids have acidic and basic
functional groups. All amino acids except glycine have a chiral center. The pka for a functional group is the pH at
which acidic or basic groups on 50 % of the molecules in a solution are deprotonated.

3D structures and conformation

Proteins are complex structures. Average protein contains 300 amino acids. Average amino acid contains 8 heavy
atoms. Average structure contains 2400 atoms. X ray crystallography and NMR spectroscopy are the techniques
which allow getting atomic resolution pictures of proteins.

Protein folding

Protein molecules fold by interacting between atoms within the protein chains and by interacting between the
protein and the solvent. The forces involved are van der waals forces, disulphide bonds, hydrogen bonds,
electrostatic attraction, and hydrophobic interactions. Defect in primary structure of proteins may arise due to
mutations. Sickle cell anemia is a defect in the hemoglobin – a protein found in RBCs. Change in primary sequence
decreases protein solubility and protein aggregates. For a protein of n residues, there are 20n possible sequences. It
can fold into any pattern which is decided by its function.

Covalent backbone and sequence

Alpha helix is formed by hydrogen bonds. Backbone does not follow any actual bonds. They are used for structural
super impositions. Peptide bond has a partial double bond character

Protein functions

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Proteins are divided based on their functions. Ex: Collagen, fibrous protein is classified under structural proteins.
The globular proteins have a number of biologically important roles. Myoglobulin is present in the muscle and
hemoglobin in the RBC. Proteins act as biocatalyst – enzymes. They regulate metabolism too.

Carbohydrates
Carbohydrates and Classification

Carbohydrates are the most abundant biomolecules on earth. They have either an aldehyde or a keto group in
addition to many hydroxyl groups. Dihydroxyacetone is the simplest carbohydrate with a keto group.
Carbohydrates are defined as the polyhydroxy aldehydes or polyhydroxy ketones or substances that yield such
compounds on hydrolysis. The empirical formula of carbohydrates is (CH2O) n. Carbohydrates serve as energy
stores, structural elements and they are precursors for many organic compounds like fats and amino acids.
Carbohydrates are classified into four categories. Monosaccharides (simple sugars) containing a single polyhydroxy
aldehyde or ketone unit. Ex: Glucose. Disaccharides consist of two monosaccharides linked by glycosidic linkage.
Ex: Maltose. Oligosaccharides consist of three to twelve monosaccharides. Ex: Maltotriose which is a trisaccharide,
made up of three glucose units. Polysaccharides consist of more than twelve monosaccharides. Ex: Cellulose.

Monosaccharides

Monosaccharides with an aldehyde group are called an aldose sugar. Ex: Glucose and with keto group called ketose
sugar. Ex: Fructose. On the basis of number of carbon atoms, monosaccharides are classified as trioses, tetroses,
pentoses, hexoses and heptoses. Glyceraldehyde is an aldrotriose with a single asymmetric carbon atom. Fischer
projection of a molecule with asymmetric carbon is discussed. D and L glyceraldehdye are the mirror images of
each other, also called enantiomers. Monosaccharides exhibit isomerism. Glucose and fructose are aldose-ketose
isomers of one another. Glucose and mannose are epimers. They differ in configuration at the 2nd carbon of these
aldohexoses. Mostly monosaccharides occur in aqueous solution as aqueous ring. In the process, carbonyl group (-
CHO/-C=O) forms a covalent bond with oxygen of a hydroxyl group along the chain. The ring structure hemiacetal
is formed by the combination of an aldehyde and an alcohol group. The ring has six members and is called

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pyranose ring. Ex: α-D-Glucopyranose. With the ketose group, hemiketal is formed. The ring contains five
members and is called furanose ring. Ex: α-D-Fructofuranose. Anomerism is the process in which there is a creation
of asymmetric carbon, called anomeric carbon. Ex: α-D-Glucopyranose and β-D-Glucopyranose. Mutarotation is
the process in which cyclic α and β anomers produce equilibrium in a solution.
A constant source of blood glucose is compulsory for human life. Glucose is the preferred energy source of the
brain. Glycogen stored in muscle releases hexose units for glycolysis within the muscle itself. Glycogen in the liver
is concerned with export of hexose units for maintenance of the blood glucose, particularly between meals.
Monosaccharides are degraded by a process called glycolysis which takes place in cytosol and a series of reactions
in citric acid cycle in mitochondria. When one molecule of glucose is oxidized to carbon dioxide and water, 38
ATP molecules are generated. Reducing action of monosaccharides depends on the free anomeric carbon in their
molecules, which are capable of reducing cupric to cuprous ions and themselves get oxidized to sugar acids.
Oxidation of glucose gives rise to glucuronic acid. Two monosaccharides join covalently (glycosidic bond) when
hydroxyl group of one reacts with anomeric carbon of the other forming a glycoside. Deoxy sugars, amino sugars,
sugar acids and sugar alcohols are derivatives of monosaccharides.

Disaccharides

Maltose is a reducing disaccharide. It is made up of 2 glucose units linked by α (1-4) glycosidic linkage. Anomeric
carbon of second glucose residue is free. It is produced during starch digestion and it exhibits mutarotation. Lactose
is also a reducing disaccharide made up of one glucose and one galactose, linked by β (1-4) glycosidic linkage. It is
present in milk and exhibits mutarotation. Sucrose is a non-reducing sugar. It is composed of one glucose and one
fructose linked by α1- β2 glycosidic linkage. Anomeric carbon units are involved in linkage; hence no free
anomeric carbons are available.

Polysaccharides

Consist of repeating units of monosaccharides or their derivatives held together by glycosidic bonds. Ex: Starch,
Hyaluronic acid, homopolysaccharides contain only a single type of monosaccharide. Ex: Starch, glycogen,
cellulose, chitin. Starch is found in cereals, legumes, potatoes. Here, glucose is the monosaccharide unit. They are
made up of amylase and amylopectin with α (1-4) linage in linear structure of amylase and α (1-4) and α (1-6)
linkage in branched structure amylopectin. In cellulose, polymer of glucose is linked by β (1-4) glycosidic linkage.

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Cellulose is present in plant cell wall and functions as a dietary fiber. Glycogen is the main storage polysaccharide
in animals and is abundant in the liver. Glycogen is more extensively branched. Heteropolysaccharides are
composed of different types of monosaccharides or their derivatives. Mucopolysaccharides are known as
glycosaminoglycans. They are negatively charged large complexes. Ex: Hyaluronic acid, heparin, chondroitin
sulfate, dermatan sulfate, keratin sulfate etc. Glycoproteins mostly contain oligosaccharides which are tightly bound
to proteins. Ex: Immunoglobulins, mucin of stomach. They function as enzymes, hormones, receptors, structural
proteins, transport proteins. In proteoglycans, proteins are covalently bound with mucopolysaccharides. Found in
the bone, elastin and collagen.

Lipids and Membranes

Introduction
Lipids are heterogeneous compounds insoluble in water but soluble in organic solvents like chloroform. Biological
membranes are the organized assemblies of lipids and proteins with some amount of carbohydrates. Lipids are
mainly classified into storage lipids and membrane lipids.

Storage Lipids

Fatty acids are the components of storage lipids. Fatty acids are mainly classified into saturated (no double bond)
and unsaturated fatty acids (double bond present). Some of the polyunsaturated fatty acids are called essential fatty
acids. They are linoleic acid, linolenic acid and arachidonic acid. Fats are the esters of fatty acids with glycerol as
the alcohol. Simple fats contain same kinds of fatty acids in all three positions while mixed fats contain two or more
different fatty acids. Oils are fats but liquid at room temperature. Waxes are the esters of fatty acids with long chain
mono hydroxyl alcohol.

Membrane Lipids

Glycerophospholipids, sphingolipids and cholesterol are the membrane lipids. Glycerophospholipids contain
glycerol as the alcohol, fatty acids, a phosphate group and a nitrogenous or non-nitrogenous group. Lecithin,
cardiolipin, plasmalogens are some of the important glycerophospholipids. Sphingolipids are the derivatives of
sphingosine, which is an unsaturated amino alcohol. Sphingosine bonded with a fatty acid by amide linkage is
known as ceramide. Sphingomyelins are the common sphingolipids. Since they have a phosphate group, they are
known as sphingophospholipids. Cerebrosides are the simplest sphingoglycolipids, which have monosaccharides as
carbohydrate moiety. Gangliosides are the ceramide- oligosaccharide complexes. Cholesterol is a major component
of animal plasma membranes. It has a steroid nucleus. Cholesterol is the metabolic precursor of steroid hormones.

Lipid Aggregates

The sphere aggregates of amphipathic lipids are called micelles. In them, polar head groups are on the exterior and
nonpolar tails are in the interior. Lipid bilayer is the basic structure of cell membrane. Liposomes are the spherical
vesicles of lipid bilayer. They act as carriers for substances like drugs, proteins, enzymes, genes, etc to target
organs.

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Biomembranes

Plasma membrane envelops a cell. Moreover, the Subcellular organelles are membrane bound. Plasma membrane
has got several important functions since it has high selective permeability properties. In the fluid- mosaic model of
membrane, peripheral and integral membrane proteins are found.

Lipoproteins

They are lipid-protein complexes. The protein part is called apoprotein. They are classified based on density:
Chylomicrons, very low density lipoproteins, low density lipoproteins and high density lipoproteins.

Eicosanoids

They are derived from twenty carbon unsaturated fatty acids. They are mainly of two types: Prostanoids and
leukotrienes. Prostaglandins, prostacyclins and thromboxanes are called prostanoids. Prostaglandins are known as
local hormones due to their diverse physiological role.

Nucleic Acids

Introduction

Nucleic acids are polymers of ribonucleotides or deoxyribonucleotides and are associated with the nucleus of a cell.
DNA and RNA are the important nucleic acids found in the cells.

Structure

A nucleotide contains a nitrogenous base, phosphate group and sugar. An organic molecule containing a
nitrogenous base called purine or pyrimidine is present in nucleotide. Purines are adenine or guanine and
pyrimidines are cytosine, thymine or Uracil. Depending on the number of phosphate groups present in nucleotides,
they are known as nucleotide monophosphates, diphosphates or triphosphates.

Types of nucleic acids

There are two types of nucleic acids, deoxyribonucleic acid and ribonucleic acid.

DNA

DNA is a very long thread like molecule made up of a very large number of deoxyribonucleotides joined together.
DNA is a linear double stranded polymer made up of deoxyribonucleotides. Deoxyribonucleotide is made up of a
sugar called deoxyribose, a nitrogenous base and a phosphate group. DNA is located in the nucleus. Nucleotides are
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joined together by a phosphodiester bond in a condensation reaction. Double helix is formed when two strands are
joined together by hydrogen bonds. Double helix is anti parallel. Both the stands run in opposite direction and are
parallel to each other.

RNA

RNA is a linear polymer in which nucleotides are linked together by means of phosphodiester bridges. It does not
form a double helix like DNA. There are three different types of RNA: mRNA, tRNA and rRNA. Most RNA
molecules usually have secondary structure, consisting of stem and loop domains. mRNA is linear in structure,
variable in size, has a poly A tail and acts as a template for protein synthesis. tRNA has a clover leaf structure.
rRNA is large in size and is associated with protein. All the three types of RNA are associated in the production of
a protein.

Enzyme: Basic Concept

Enzyme structure

An enzyme is a protein that catalyzes a chemical reaction and a substrate is a molecule which is acted upon by an
enzyme. The substrate binds with the enzyme’s active site and the enzyme catalyzes the chemical reaction
involving the substrate. The active site is the location on the surface of the enzyme where the catalysis of chemical
reaction takes place. A Peptide bond is formed by amino acid condensation. Substrate is held by weak interactions
at the binding site of the enzyme. Reaction catalysis and product formation occurs at catalytic site of the enzyme.

Mechanism of enzyme action

Several steps of enzyme action results in the formation of products and eventually the enzyme is regenerated. In
lock and key hypothesis, enzyme holds the substrate as a lock holding the key. As per induced fit hypothesis, active
site expands and contracts on substrate interaction.

How enzymes Act as Biocatalysts

Activation energy is the amount of energy required to convert all the reacting substances from ground state to
transition state. It determines the rate of reaction. Enzymes work by lowering the activation energy. Lower the
activation energy, faster is the rate.

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Enzyme cofactors

Cofactor of an enzyme is the non-protein component and is essential for its catalytic activity. Coenzyme is a loosely
bound organic cofactor that is required for enzyme activity. Prosthetic group is a metal ion or an organic compound
that is covalently bound to an enzyme required for its activity. Activators are inorganic ions working as cofactors.
They are either loosely or firmly bound.

Enzyme properties

Enzyme specificity is the ability of an enzyme to discriminate among competing substrates for it. There are four
different types of specificity: Absolute, group, linkage, stereo chemical specificity.

Enzyme Catalysis and Kinetics

Enzyme catalysis

Enzymes act by lowering the activation energy. They do not change the equilibrium of the reactions. Enzyme binds
with the substrate to form an unstable complex which breaks up into products liberating enzymes. Lock and key
theory and induced fit theory explain the enzyme-substrate complex formation. Small region on the enzyme where
the substrate binds and catalysis takes place is called an active site. Enzymes are highly specific in their action.
Three types of enzyme specificity are well recognized: They are stereo specificity, reaction specificity and substrate
specificity. There are different mechanisms to explain enzyme catalysis. Different mechanisms are: acid base
catalysis, covalent catalysis and metal ion catalysis and transition state stabilization.

Enzyme kinetics

Various factors like concentration of substrate, pH and product concentration of products affect enzyme activity.
Michaelis-Menten kinetics is based on substrate concentration. When a graph is plotted for substrate concentration
[S] on x-axis and velocity [V] on the y axis, a rectangular hyperbola is obtained. A linear plot that is obtained by
rearranging the M-M equation is called Lineweaver-Burk plot or double reciprocal plot. Km value is the substrate
concentration at half maximal velocity of an enzyme catalyzed reaction. Enzymes having many subunits may not
strictly follow the M-M kinetics. Chemical substances which inhibit enzyme activity and reduce velocity of an
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enzyme catalyzed reaction are known as inhibitors. Enzyme inhibition is broadly classified into reversible and
irreversible inhibition. Reversible inhibition is further divided into competitive, non competitive and uncompetitive
inhibition. Suicide inhibition is a reversible inhibition.

Regulatory Properties of Enzymes

In each enzyme system, there is at least one enzyme that catalyzes the rate limiting reaction. It is known as a
regulatory enzyme. There are two major classes: Allosteric enzymes acting through reversible, non covalent
modulator. Enzymes regulated by reversible covalent modification. The allosteric sites are different from its active
site. Feedback inhibition is the best example for allosteric modulation. Localization of enzymes related to one
pathway partly in mitochondria and partly in cytosol is called compartmentation. Ribozymes are the enzymes made
of RNA.

Introduction to Metabolism and Bioenergetics

Introduction

Living organisms are not at equilibrium. They require a continuous influx of free energy to maintain order in a
universe where there is maximum disorder. Metabolism is the overall process through which free energy is acquired
and utilized by living systems to carry out their various functions. By coupling the exergonic (energy releasing)
reactions of nutrient oxidation and endergonic (energy consuming) reactions, they maintain the living state.
Metabolism is the overall process through which free energy is acquired and utilized by living systems to carry out
their various functions. Free energy is the most useful thermodynamic concept in biochemistry. A reaction can
occur spontaneously only if ΔG, the change in free energy is negative. The reactions are coupled by the shared
chemical intermediate. Energy is extracted from foodstuffs by three different stages.

In the first stage, large molecules of food are broken down into smaller units. No useful energy is liberated.

In the second stage, small molecules are degraded to a few simple units of metabolic importance like acetyl CoA.
Some amount of ATP is generated here.

In the third stage, final common pathways in the oxidation of fuel molecules are citric acid cycle and oxidative
phosphorylation. More than 90% ATP generation from degradation of food stuffs takes place in the third stage.

Universal carrier molecules

Processes involving the transfer of electrons are of immense biochemical significance. Oxidation-reduction

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reactions resemble other types of chemical reactions in that they involve group transfer. In Redox reactions, the
groups transferred are electrons which are passed from an electron donor to an electron acceptor. NADPH is the
major electron donor in reductive biosynthesis. NADH and FADH2 is the major electron carrier in the oxidation of
fuel molecules. Coenzyme A is the acyl group carrier which is an important molecule in metabolism.

Bioenergetics of phosphate compounds

ATP is the universal currency of free energy in biological systems. It is an energy rich molecule because its
triphosphate unit contains two phospho anhydride bonds. ATP on hydrolysis liberates a large amount of energy.
Creatine phosphate is a reservoir of high potential phosphoryl groups in the muscle which can readily transfer its
phosphoryl group to ATP.

Regulation of metabolic processes

Metabolism is regulated by controlling the amount of particular enzymes, catalytic activities and the accessibility of
substrates. Many reactions in metabolism are controlled by the energy status of the cell. Index of energy status is
the energy charge. An alternative index of the energy status is the phosphorylation potential. It depends on the
concentration of inorganic phosphate and is directly related to the free energy available from ATP.

Glycolysis
Release of energy from glucose

Glycolysis is the sequence of reactions that converts glucose into pyruvate with the concomitant production of a
relatively small amount of ATP. Glucose is the starting material and two molecules of pyruvate are the end
products of the pathway. Subcellular site of the pathway is the cytosol. Glycolysis is a linear pathway of ten
enzyme mediated steps.

Phases of glycolysis

Pathway has two phases: Energy investment phase and energy generation phase. Energy investment phase is also
called preparatory phase and consists of first five steps. Here the end product is glyceraldehyde - 3 – phosphate.
Energy generation phase is also known as payoff phase and consists of last five steps and end products are two
pyruvate molecules.

Energy yield from the pathway

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It can occur in presence or absence of oxygen. Altogether there are ten steps involved and in aerobic glycolysis net
ATP gain is 8 and the pyruvate enters the citric acid cycle, oxidized to CO2 and H2O.

Anaerobic glycolysis

Under anaerobic conditions, net ATP gain is 2 from substrate level phosphorylation. NADH gets accumulated
which is reoxidized via lactic acid and alcohol fermentation.

Sources of glucose for glycolysis

Glycogen, dietary disaccharides and monosaccharides also enter the glycolytic pathway, since they are the sources
of glucose.

The Citric Acid Cycle

TCA cycle

Cellular respiration

Cellular respiration is a process in which cellular energy is generated through the oxidation of nutrient molecules,
with oxygen as the ultimate electron acceptor.

Stages of cellular respiration

There are two stages of cellular respiration. In stage I, pyruvate is converted to acetyl CoA with the help of pyruvate
dehydrogenase complex by oxidative Decarboxylation. Coenzyme A activates acetyl group derived from pyruvate.
In stage II, acetyl CoA enters the TCA cycle and gets oxidized through 8 steps, generating ATPs.

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The Citric acid cycle

TCA cycle is a cyclic pathway and the subcellular site of the reaction is mitochondria in eukaryotes. Formation of
citrate, then, isocitrate, oxidation of isocitrate, oxidation of α ketoglutarate, conversion of succinyl CoA to
succinate, oxidation of succinate, hydration of fumarate, oxidation of malate to oxaloacetate. They are the 8 steps of
TCA cycle. Net ATP gain from one glucose molecule is 38.

Phases of reactions of citric acid cycle

Amphibolic pathway is the metabolic pathway used in both catabolism and anabolism. TCA cycle acts as an
amphibolic pathway since it is involved in both breakdown as well as synthesis of biomolecules. There are
Anaplerotic reactions which replenish the supply of intermediates in the citric acid cycle. Ex: Malate is formed from
pyruvate by the malic enzyme.

Additional Pathways in Carbohydrate

Metabolism
Carbohydrate Metabolism II

Pentose phosphate pathway

Pentose phosphate pathway (PPP) is a secondary pathway of glucose metabolism, primary being glycolysis.
Glucose enters PPP as glucose 6-phosphate. It occurs in the cytosol of tissues active in fatty acid biosynthesis.
Those tissues are liver, mammary and adrenal glands and adipose tissue. There are two phases in the pathway:
oxidative and non-oxidative. There are four steps involved in oxidative phase, during which glucose-6 phosphate
gets converted to ribose 5-phosphate. In the non-oxidative phase, transaldolase and transketolase enzymes catalyze
the reversible reactions for the regeneration of glucose 6-phosphate.

Glyoxylate cycle

Glyoxylate cycle is a variant of TCA cycle and occurs in bacteria and glyoxysomes of plants. It bypasses
decarboxylations of citric acid cycle and allows net synthesis of glucose from acetyl CoA.

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Gluconeogenesis

Gluconeogenesis is a process of biosynthesis of glucose from simpler non carbohydrate precursors such as
oxaloacetate or pyruvate. It is a universal pathway in animals, plants, microbes and fungi. It converts pyruvate to
glucose (reverse of glycolysis). The irreversible steps of glycolysis are circumvented by four key enzymes of
gluconeogenesis. They are pyruvate carboxylase, phosphoenol pyruvate carboxy kinase, fructose-1, 6-
bisphosphatase and glucose-6-phosphatase.

Glycogen synthesis

Glycogen synthesis takes place in the liver and muscle. All the enzymes of glycogen synthesis are located in the
cytosol. Activation of glucose takes place followed by the sequential addition of activated glucose units by glycogen
synthase. A brancher enzyme creates alpha 1-6 linkage.

Starch synthesis

Starch is synthesized in the chloroplasts of plants with the help of enzymes ADP-glucose phosphorylase and starch
synthase.

Disaccharide synthesis

Lactose is synthesized in lactating mammary glands of animals with the help of enzyme lactose synthase. Lactose is
made up of galactose and glucose. Sucrose is synthesized in plants.

Electron Transport and Oxidative

Phosphorylation
Introduction

The electron transport system is the place in the cell where electrons generated by oxidation are transferred. Passage
of the electrons through the system generates potential energy that is used to make ATP in oxidative
phosphorylation.

Components of electron transport chain

Components of ETC are arranged in the inner mitochondrial membrane involved in the process of electron
transport. In biological system, fuel molecules are oxidized by losing electrons, which are transferred through the

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carrier molecules like NAD and FAD. Finally electrons are donated to oxygen to reduce it to a water molecule.
Coenzyme Q is a respiratory electron carrier. Cytochromes are a group of heme containing proteins. The major
respiratory cytochromes are b, c and c1 and a or a3.

Electron Transport – Carriers and arrangement of carriers into complexes

Integral membrane proteins embedded in the inner mitochondrial membrane are arranged into complex I, II, III and
IV. They accept or donate electrons from preceding carrier to the following in sequence.

Pathway of Electron Transfer through the Carriers

I NADH dehydrogenase, II Succinate dehydrogenase, III CoQ – Cytochrome c oxidoreductase, and IV

Cytochrome oxidase are the four complexes. Electrons are transferred through these complexes. Through complex
I, III and IV, protons are pumped out of mitochondrial matrix creating proton gradient.

Proton Motive Force

Coupling of ATP synthesis to electron transfer via an electrochemical H+ gradient across a membrane is called
chemiosmosis. Energy from electron transport drives an active transport system which pumps protons out of the
mitochondrial matrix into inter- membrane space. An electrochemical gradient of protons is created, with a lower
pH value outside the inner mitochondrial membrane than inside. The protons on the outside have a thermodynamic
tendency to flow back in, so as to equalize pH on both sides of the membrane.

ATP Synthesis

When protons from inter-membrane space do flow back into the matrix, the free energy arising from the gradient is
used to drive the synthesis of ATP. ATP synthase also called complex V is the site where ADP is phosphorylated to
ATP.

Photosynthesis
Basic process of photosynthesis

Photosynthesis is a process where by energy from light is harvested and used to drive synthesis of carbohydrates
from carbon dioxide and water.

Physics of light

Quantum is the elemental unit of energy. Photon is a quantum of electromagnetic energy and it is particle of light.

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Chloroplast structure

Chloroplast is a plant subcellular organelle where photosynthesis takes place. Outer membrane of chloroplast is
permeable. Inner membrane encloses stroma. Thylakoid is flattened membrane surrounded vesicle. This is the place
where light reaction occurs. In stroma, fluid surrounding the thylakoids is the place where the dark reaction occurs.
Chlorophylls are the green pigments; they are present in the thylakoid membrane of chloroplast. They absorb deep
blue and red light. Secondary light absorbing pigments are called accessory pigments. They are carotenoids and
phycobilins. Photosystems are the light absorbing pigments of thylakoid membrane arranged in functional sets.

Light reaction and photophosphorylation

Photosystems are of two types: PS I P700, PS II P680. Components of photosystem I and II transfer the electrons
from water to NADP. Light is absorbed by these photosystems and electrons are transferred from water to NADP.
Photophosphorylation is a process where the light energy captured by the photosynthetic organisms is transformed
into the phosphate bond energy of ATP. During the transfer of electrons, ATP is synthesized. Electron flow is
cyclic. As a result oxygen is not released and ATP is formed as a result of proton gradient created by Cytochrome bf
pump.

Dark reaction – Calvin cycle

Second step of photosynthesis is called Calvin’s cycle and it is a dark reaction. There are two stages here, I and II.
In Stage I carbon dioxide is incorporated into 5 carbon ribulose bisphosphate. In stage II ribulose bisphosphate is
the regenerated.

Photorespiration

Photorespiration is the process wherein oxygen consumption occurs in illuminated temperature zone of plants under
high oxygen and low carbon dioxide. Oxygen is consumed and carbon dioxide is released. Moreover, ATP is
expended without benefit.

C4 pathway

C4 cycle is the pathway adopted by C4 plants to conserve the carbon dioxide released via photorespiration. It occurs
in mesophyll cells. Carbon dioxide is incorporated to form 4 carbon oxaloacetate.

Lipid Metabolism
Lipid digestion and absorption

Lipids play an important role in cell structure and metabolism. TAGs are the major storage form of energy.
Cholesterol is a component of cell membranes and precursor of steroid hormones. Lipid digestion occurs at lipid
water interfaces since TAG is insoluble in water and digestive enzymes are water soluble. Lipids are digested and
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absorbed with the help of bile salts. Products of lipid digestion aggregate to form mixed micelles and are absorbed
into the small intestine. Lipids are transported in the form of lipoproteins.

• Fatty acid oxidation

• Fatty acids have to be activated prior to their entry into mitochondrial matrix where the enzymes of β-
oxidation of fatty acids are located. Activated fatty acids are then transported from cytosol to the
mitochondrial matrix with the help of carnitine transporter. Total net yield of ATP per molecule of palmitic
acid is 129. Similarly oxidation of unsaturated and odd chain fatty acids also take place with additional
reactions. Β-oxidation in peroxisomes involves three enzymatic reactions. Minor pathways of oxidation
such as α-oxidation of branched chain fatty acids and ω-oxidation of medium and long chain fatty acids in
microsomes do take place in our body.

Ketone body metabolism

Ketone bodies are acetoacetate, β-hydroxy butyrate and acetone. Ketone bodies are synthesized in the liver but they
are utilized by extra hepatic tissues as fuels. Ketone bodies are accumulated in the blood if the rate of synthesis
exceeds the ability of extra hepatic tissues to utilize them. This leads to excess ketone bodies in blood, excretion of
ketone bodies in urine and smell of acetone in breath. All these three together are known as ketosis. In uncontrolled
diabetes mellitus and starvation, ketone bodies are formed.

Fatty acid biosynthesis

The enzymes of synthesis are located in the cytoplasm. Acetyl CoA is the source of carbon units and NADPH
provides reducing equivalents. ATP is the supplier of energy. Synthesis is not the reversal of oxidation. Dimer of
fatty acid synthase takes part in fatty acid synthesis. TAGs are synthesized from fatty acyl CoA and glycerol 3-
phosphate or dihydroxy acetone phosphate. TAG gets deposited in adipose tissue.

Cholesterol biosynthesis

80% of endogenous cholesterol is formed in the liver. Enzymes involved in the synthesis are partly located in the
endoplasmic reticulum and partly in the cytoplasm. Acetyl CoA is the precursor. HMG CoA, mevalonate,
isopentenyl pyrophosphate, squalene are some of the important intermediate compounds formed during cholesterol
synthesis. Cholesterol is transported in lipoprotein complexes. Elevation of lipids in blood leads to the deposition of
cholesterol on the arterial walls leading to atherosclerosis.

Eicosanoids

Prostaglandins are synthesized from arachidonic acid. Cycloxygenase enzyme catalyzes the reaction in which C20
fatty acid is converted to prostaglandins. Leukotrienes are also derived from arachidonic acid.

Synthesis of phospholipids and sphingolipids

Glycerol is the starting material in the synthesis of glycerophospholipids. CDP-diacylglycerol is the activated
intermediate of this pathway. Sphingolipids are synthesized from palmitoyl CoA and serine, initially to form
ceramide. Sphingomyelins and glycolipids are synthesized from ceramide. Various sphingolipids storage diseases
are resulted due to hereditary absence of hydrolytic enzymes.

Amino Acid Metabolism

Digestion of dietary proteins
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Digestion of dietary proteins starts in the stomach. Secretion of HCl activates formation of pepsin from pepsinogen
which hydrolyses peptide bonds of dietary proteins to release aromatic amino acids. Similarly, in the small intestine
digestion continues. Zymogens are activated for the breakdown of peptide bonds to release amino acids which are
absorbed into the small intestine.

Amino acid deamination

Transamination is a process by which amino group is transferred to the keto acid to yield the keto acid of the
original amino acid and a new amino acid, catalyzed by amino transferases. Glutamate is oxidatively deaminated in
the mitochondrion and release ammonia.

The Urea Cycle

This cyclic pathway takes place in the liver, partly in the mitochondria and partly in cytosol. There is interrelation
between urea cycle and citric acid cycle. Fumarate of the urea cycle is taken up by citric acid cycle. Carbamoyl
phosphate synthetase I is the regulatory enzyme.

Metabolic breakdown of individual amino acids

Catabolism of amino acids gives rise to the intermediate compounds of citric acid cycle. Alanine, serine, cysteine
and asparagine are converted to oxaloacetate. Glutamine, proline, arginine and histidine are converted to α-
ketoglutarate through glutamate. Succinyl CoA is a point of entry for non polar amino acids like methionine, valine
and isoleucine. Leucine is degraded to acetyl CoA and acetoacetate. Tryptophan, lysine, leucine, phenylalanine,
tyrosine and isoleucine donate their carbons to acetyl CoA. Various disorders of amino acid catabolism are
observed due to the defective enzymes. Tryptophan, tyrosine, glycine and glutamate are the precursors of some of
the biologically important compounds. Biotin, Tetrahydrofolate or S-Adenosyl methionine is the enzyme cofactors
in catabolism which transfer carbon compounds.

Amino acid biosynthesis

Nonessential amino acids are formed from intermediates of carbohydrate metabolism. Alanine is formed from
pyruvate and aspartate from oxaloacetate. Asparagine is formed from aspartate. Glutamate is formed from α
ketoglutarate and glutamine from glutamate. Glutamate is the precursor of proline and arginine. Cysteine is
synthesized from 3 – phosphoglycerate. During the process, serine is the intermediate compound which gives rise to
glycine.
Threonine is an essential amino acid. It is formed from β-aspartate. Methionine and lysine also have a common
precursor. Valine, Leucine and isoleucine are formed from pyruvate. Phenyl alanine, tyrosine and Tryptophan are
formed from phosphoenol pyruvate and erythrose – 4 – phosphate through the intermediate compound called
chorismate. Histidine originates from PRPP and ATP.

Nucleotide Metabolism

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Introduction

Nucleotides play a variety of important roles in all cells. They are the activated precursors of DNA and RNA. ATP,
an adenine nucleotide, is a universal currency of energy in biological systems. GTP is an essential carrier of
chemical energy. Adenine nucleotides are components of the coenzymes NAD+, NADP+, FMN, FAD and
Coenzyme A. UDP-Glucose in Glycogen synthesis and CDP-diacylglycerol in Phosphoglyceride synthesis are the
nucleotide derivatives that act as activated intermediates. Cyclic AMP is a ubiquitous mediator for the action of
many hormones. All cells can synthesize nucleotides from simple building blocks (de novo synthesis) or by the
recycling of pre-formed bases (Salvage pathway). Nucleotides are phosphate esters of pentoses in which a
nitrogenous base is linked to C1’ of the sugar residue. A nucleotide without the phosphate group is known as a
nucleoside. The major purine components of nucleic acids are adenine and guanine residues. The major pyrimidine
residues are those of Cytosine, Uracil and Thymine. Pyrimidines are bound to ribose through N 1 atoms.

Synthesis of purine ribonucleotides

IMP is synthesized from ribose 5-phosphate. There are 11 reactions in the formation of IMP. IMP is converted to
GMP and AMP with the help of ATP and GTP respectively. Nucleoside monophosphates are converted to
nucleoside diphosphates by base specific monophosphate kinases. Purine nucleotide synthesis is regulated by
feedback inhibitor – AMP, GMP and IMP. An important regulatory factor is the availability of PRPP. Salvage
pathway for purines is observed in RBC and the brain. Free purines are salvaged by APRTase and HGPRTase
enzymes

Synthesis of pyrimidine ribonucleotides

Pyrimidine ring is synthesized as free pyrimidine and then it is incorporated into the nucleotide. 6 reactions are
involved in the synthesis of UMP. UDP and UTP are synthesized from UMP with the help of ATP. CTP is formed
by adding an amino group from glutamine. Pyrimidine can also be salvaged using PRPP. In orotic aciduria,
excretion of large amount of orotic acid is observed. It results from the deficiency of either orotate phospho ribosyl
transferase or OMP decarboxylase.

Formation of deoxyribonucleotides

Ribonucleotide reductase catalyzes the synthesis of deoxyribonucleotide. The reductant is NADPH. Thioredoxin
transfers electrons from NADPH for reduction of 2’-OH of ribose. dTMP is formed by thymidylate synthase by
methylation of deoxy uridine monophosphate.

Degradation of nucleotides

Nucleotides of a cell undergo continuous turnover. Purines are catabolized and the end product is uric acid. Gout is
a disease characterized by elevated levels of uric acid in body fluids. Sodium urate crystals are precipitated in the
joints and soft tissues to cause painful arthritis. In Lesch-Nyhan syndrome, HGPRT deficiency occurs, leading to
excessive uric acid production through PRPP accumulation. Gout is treated by allopurinol administration. Animal
cells degrade pyrimidine nucleotides to their component bases by dephosphorylation, deamination and glycosidic
bond cleavages to give rise to carbon dioxide, ammonia, β-alanine and β-amino isobutyrate.

Nucleotide Coenzymes

Nucleotides are the components of many enzyme cofactors. Adenosine is a part of their structure in a variety of
enzyme cofactors serving a wide range of chemical functions. Coenzyme A is synthesized from pantothenic acid
and ATP.

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DNA Structure and Replication

Structure of DNA

Purine and pyrimidine nucleotides are the building blocks of DNA. Adenine specifically binds to thymine with 2

hydrogen bonds and cytosine specifically binds to guanine with three hydrogen bonds. Hydrogen bond is a type of

attractive intermolecular force that exists between two partial electric charges of opposite polarity. Two strands of

DNA are anti parallel with major and minor grooves.

DNA replication

The process of making an identical copy of a section of duplex DNA, using existing DNA as template for the

synthesis of new DNA strands. DNA undergoes semi conservative nature of replication. There are three steps in the

replication process: Initiation, elongation and termination. Initiation always begins at the origins of replication, it is

bidirectional with most genomes and priming is with RNA. Elongation has three steps: unwinding of DNA,

relieving of torsional stress and polymerization of poly nucleotide chain. One strand of DNA is made continuously

while the other strand is synthesized in fragments.

Functions and structures of DNA replication enzymes

Many enzymes are involved in DNA replication such as topoisomerase, helicase, primase, DNA polymerase and

ligase. Topoisomerases relax the super coiling of DNA, helicases unwind double strand of DNA, primases

synthesize a primer, DNA polymerases add and read proof new bases and ligases link the added bases.

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RNA Structure and Synthesis

Structure of RNA

Ribonucleic acids are made up of nitrogenous bases such as adenine, Uracil, guanine and cytosine, ribose sugar and
phosphate group. RNA is normally single stranded which can have a diverse form of secondary structures. tRNA
shows secondary and tertiary structure.

Types of RNA

mRNA represents about 5-10% of cellular RNA. It contains the sequence of bases coding for a particular amino
acid sequence in a polypeptide chain. tRNA represents about 15-20% of cellular RNA. Each tRNA molecule is
specific for one amino acid. There is an enzyme for each amino acid which recognizes the amino acid and its
specific tRNA and joins the two together. The specific joining of tRNA to amino acid is the only place where the
genetic code is realized. rRNA represents about 70-80% of cellular RNA. It is associated with specific set of
ribosomal proteins. It functions as non-specific ‘workbench’ for the assembly of polypeptides. Many copies of
genes coding for rRNA are located in nucleolar organizer regions of certain chromosomes.

RNA synthesis

RNA synthesis occurs in both prokaryotes and eukaryotes. There are three steps to RNA synthesis: Initiation,
elongation and termination. In the initiation step, RNA polymerase binds to gene regulatory elements. In the
elongation step, RNA polymerase unwinds DNA duplex next to a gene. RNA is transcribed 5’ to 3’ from the
template of 3’ to 5’. Termination in eukaryotes is by cleavage and polyadenylation.

RNA polymerase

RNA polymerase searches DNA for initial site. It unwinds a short stretch double helical DNA to produce a single
stranded DNA template from which it takes instructions. Also selects the correct ribonucleotide and catalyzes the
formation of phosphodiester bond and detects the termination signals which specify where a transcript ends. RNA
polymerase interacts with activated and repressor proteins that modulate the rate of transcription initiation over a
wide dynamic range. In prokaryotes, only one type of RNA polymerase is present. It transcribes mRNA, tRNA and
rRNA. Eukaryotes possess three RNA polymerases: RNA polymerase I, II and III.

Post transcriptional controls/ RNA splicing

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mRNA undergoes significant processing within the nucleus prior to transport to cytoplasm: by removal of non
coding into internal sequences called introns. It undergoes modification of the 5’ base and an addition of adenine to
3’ end (poly A tail) takes place. RNA splicing is a process that removes introns and joins exons in a primary
transcript.

Protein Biosynthesis
RNAs involved in protein biosynthesis

Information flow in the cell: DNA is transcribed to mRNA which is translated (decoded as) into Protein. Protein

biosynthesis takes place in the ribosomes. A series of ribosomes (poly ribosome) can simultaneously translate the

same eukaryotic mRNA molecule. tRNA brings specific amino acid to ribosome and mRNA carries the genetic

information to protein. Codons that encode the same amino acid often differ only by their third base. The binding of

the third base is less stringent than the other two. Because of this wobble, one tRNA can pair with multiple mRNA

codons.

Process of protein biosynthesis

There are signal sequences before the real coding sequence at the translation initiation sites. Amino acid activation

is catalyzed by amino acyl-tRNA synthetase and couples it to its corresponding tRNA. Anti codon in tRNA

molecule forms base pairs with the appropriate codon on the mRNA. In the initiation step, initiation factors are

involved. Initiation factor is the protein that promotes the proper association of ribosomes with messenger RNA. In

the elongation step, incorporation of an amino acid into a protein takes place. As a result, polypeptide chain is

grown. Termination is the last stage in protein biosynthesis.

Quality control and chaperones

If at all, a wrong amino acid is added, tRNA synthetase removes the incorrectly attached amino acid through

hydrolytic editing. There are protein molecules called chaperones that catalyze the correct folding of other proteins

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within the cell. They also help in preventing aggregation. The hsp70 family of molecular chaperones helps in

correct folding after synthesis.

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