UNIT I- A) Biomolecules

Biomolecule-Definition:

Biomolecules are complex organic molecules. These molecules form the basic
structural constituent of a living cell.

Living bodies are built up with biomolecules and responsible for their growth
and maintenance. Biomolecules are biologically important molecules are
grouped in to 4 classes (Carbohydrates, Proteins, Lipids and Nucleic acids).
Biomolecule is an organic molecule and especially a macromolecule (such as
carbohydrates,proteins, lipids or nucleic acids) in living organisms, as well as
small molecules such as primary metabolites, secondary metabolites and natural
products. All living forms bacteria, algae, plants and animals are made of
similar macromolecules that are responsible for life. All the carbon compounds
we get from living tissues can be called biomolecules. Biomolecules also called
as “Biomacromolecules”.

The sequence that relates biomolecules to living organism is,

Biomolecules Organelles Cells Tissues Organs Living Organism

Characteristics of Biomolecules:
1.Most of them are organic compounds.
2.They have specific shapes and dimensions.
3.Functional group determines their chemical properties.
4.Many of them are asymmetric.
5.Macromolecules are large molecules and are constructed from small building
block molecules.
6.Buiding block molecules have simple structure.
7.Biomolecules first gorse by chemical evolution.

Macromolecule:
Macromolecule means large molecules (Polymer) that one made up of smaller
building blocks (monomer). Polymers are made of monomer. Examples of
macromolecules includes carbohydrates, proteins, lipids and nucleic acids.
 Classification of Biomolecules

4 Major Types of Biomolecules and their monomers:

1.Carbohydrates-Monomer is Monosaccharide

2.Proteins-Monomer is “Aminoacid”

3.Lipids-monomer is “Glycerol and Fatty acid”

4.Nucleic acids-monomer is “Nucleotide”

Carbohydrates Lipids Proteins Nucleic acids

Made up of C,H,O Made up of C,H,O Made up of Made up of
(Short term energy (Long term energy C,H,O,N C,H,O,N,P
storage) storage) (Do not produce
energy)

Biolgical Function: Biological Function: Biological Function: Biological Function:

Main energy source Builds up Building and DNA store genetic
biomembranes repairing cells, information and
make up the RNA is essential for
majority of our protein synthesis
body; muscles, hair,
skin,nails etc.
Biological Example: Biological Example: Biological Example: Biological Example:
Sugar, Rice, Bread, Fats and oils, Wax Enzymes, Muscle, DNA, RNA, ATP
Potatoes Hair, Nails
Chemical Nature of Biomolecules

Chemical Nature of Carbohydrates:

Carbohydrates contain carbon, hydrogen and oxygen in a 1:2:1 ratio and have
the general formula (CH2O)n. Carbohydrates are poly hydroxy alcohols with a
aldehyde or keto functional group.
They come in variety of forms including:

 Monosaccharides-simple sugars consisting of 1 sugar monomer

e.g.Glucose
 Disaccharides-sugars consisting of 2 sugar monomers. e.g.Lactose
 Polysaccharides-sugars consisting of many sugar monomers. e.g.Starch
 Glycoproteins-a molecule made up of carbohydrates and proteins
 Glycolipids-a molecule made up of carbohydrates and lipids

Chemical Nature of Lipids:

Lipids are a group of water-insoluble compounds which includes fats, glycerol,

phospholipids, steroids, oils, etc. Types of lipids vary according to their
constituents. Fatty acids are simple lipids, made up of carboxyl group and a
variable group, R. They may be saturated or unsaturated fatty acids. Glycerols
are trihydroxy propane which combines with fatty acids to give triglycerides.
Some lipids consist of a phosphorus group along with the organic chain. Such
lipids are called phospholipids which are the constituent of the plasma
membrane.

Chemical Nature of Nucleic acids:

Nucleic acids are the genetic materials present in an organism, which include
DNA and RNA. They are the combination materials of nitrogenous bases, sugar
molecules and phosphate group linked by different bonds in a series of steps.
Our body consists of heterocyclic compounds like pyrimidines and purines.
These are nitrogenous compounds like adenine, guanine, cytosine, thymine and
uracil. When these bases bond with sugar chains, they form nucleosides.
Nucleosides, in turn, bond with the phosphate group to give nucleotides like
DNA and RNA.
Chemical Nature of Aminoacids:

Aminoacids are carbon-containing compounds where a carboxylic acid group

and the amino group are present at the two ends. Each aminoacid consists of
one central carbon surrounded by four substituents. These four substituents
include an amino group, carboxylic acid group, hydrogen and a variable group
represented by R. The variable group, R decides the nature and type of
aminoacid.

General Structure of Aminoacid:

Chemical Nature of Proteins:

The chemistry of amino acid side chains is critical to protein structure because
these side chains can bond with one another to hold a length of protein in a
certain shape or conformation. Charged amino acid side chains can form ionic
bonds, and polar amino acids are capable of forming hydrogen bonds.
 Biological Role of Biomolecules

Biological Role of Carbohydrates:

1. Carbohydrates act as storage molecules. For example they are stored as

starch in plants and as glycogen in animals.
2. D-Ribose and 2-deoxy-D-ribose are the constituents of RNA and DNA
respectively.
3. Cell walls of bacteria and plants are made up of cellulose. It may be of
interest to note the human digestive system does not have the enzymes
required for the digestion of cellulose but some animals do have such
enzymes.
 4. Some carbohydrates are also linked to many proteins and lipids. These
molecules are known as glycoproteins and glycolipids, respectively.
These molecules perform very specific functions in organisms.

Biological Role of Lipids:

1. Fats are main food storage compounds and serve as reservoir of energy.
2. Presence of oils or fats is essential for the efficient absorption of fat
soluble vitamins A,D,E and K.
3. Subcutaneous fats serve as biological insulator aganist excessive heat
loss.
4. Phospholipids are the essential component of cell membrane.
5. Steroids control many biological activities in living organisms.
6. Some enzymes require lipid molecules for maximum action.

Biological Role of Nucleic acids:

1. A DNA molecule is capable of self duplication during cell divisions. The

process starts with the unwinding of the two chains in the parent DNA.
As the two strands separate, each can serve as a master copy for the
construction of a new partner. This is done by bringing the appropriate
nucleotides in place and linking them together. Because the bases must be
paired in a specific manner (adenine to thymine and guanine to cytosine),
each newly built strand is not identical but complimentary to the old one.
Thus when replication is completed, we have two DNA molecules, each
identical to the original. Each of the new molecule is a double helix that
has one old strand and one new strand to be transmitted to daughter cells.
2. Another important function of nucleic acids is the protein synthesis. The
specific sequence of bases in DNA represents coded information for the
manufacture of specific proteins. In the process, the information from
DNA is transmitted to another nucleic acid called messenger RNA, which
leaves the nucleus and goes to the cytoplasm of the cell. Messenger RNA
acts as template for the incorporation of aminoacids in the proper
sequence in protein. The amino acids are brought to the messenger RNA
in the cell, by transfer RNA, where they form peptide bonds. In short it
can be said that DNA contains the coded message for protein synthesis
whereas RNA actually carries out the synthesis of protein.
Biological Role of Aminoacids:

Biological Role of Proteins:

1. Structural proteins: Keratin of hair and nails, collagen of bone

2. Catalytic proteins or Enzymes: Hexokinase, pepsin
3. Transport proteins: Hemoglobin, serum albumin
4. Hormonal proteins: Insulin, growth hormone
5. Contractile proteins: Actin, myosin
6. Storage proteins: Ovalbumin, glutelin
7. Genetic proteins: Nucleeoproteins
8. Defense proteins: Snake venoms, immunoglobulins
9. Receptor proteins: Hormones, viruses

UNIT I- B) Bioenergetics
Energy Rich Compounds-Definition:

Energy rich compounds are referred to as high energy bonds and is created in
the process of oxidative phosphorylation in mitochondria. Some energy rich
compounds are produced so that phosphate is transferred from ATP to another
molecule in the reaction which is catalysed by kinase and high energy is
preserved.

All nucleoside phosphates have nearly equal standard free energies of

hydrolysis.
High-E compounds (energy rich)-Greater or equal 7.3 kcal/mol
Low-E compounds (energy deficient)-Less than 7.3 kcal/mol
Energy rich molecule-The main purpose of these molecules is to transfer either
inorganic phosphate groups (Pi) or hydride (H-) ions. The inorganic phosphate
groups are used to make high energy bonds with many of the intermediates of
metabolism. These bonds can then be broken to yield energy, thus driving the
metabolic processes of life.

Function of high energy compounds:

1. Phosphate containing compounds are considered “high-energy” if they have

standard free energy for hydrolysis “ more negative than -20 to -25 KJ/mol.
2. High energy phosphate compounds are not used for long term energy storage.
They are temporary forms of stored energy, and are used to carry energy from
one reaction to another.

Best example for Energy-rich compound:

ATP-Adenosine Tri Phosphate Structure: ATP, a nucleotide composed of

adenine (nitrogenous base-mainly purine), ribose (pentose sugar) and three
phosphate groups.

Energy can be stored in the chemical bonds within the molecules in the cell, but
not all chemical bonds are equally energetic. Breaking the phosphate bond
releases a lot of energy. ATP has 2 high energy phosphate bonds and is the main
form of energy/universal currency in the cell.

Functions of ATP:

1. Universal Currency of the cell / Molecular currency of “intracellular

energy transfer”-Able to store and transport chemical energy within cells.
2. An activated nucleotide found in all living cells that acts as an energy
carrier
3. ATP serves as the mediator of biological energy transfer (it links the
energy yielding (exergonic) and energy requiring (endergonic) processes,
releasing energy for both anabolic and catabolic processes and being
recharged by energy generated from other catabolic reactions.
4. Common intermediate in many reactions and drives most biological
processes.

Examples of energy rich compounds other than ATP:

 1. GTP-Guanosine triphosphate
2. CTP-Cytidine triphosphate
3. UTP-Uridine triphosphate
4. Acetyl phosphate
5. Phosphoenol pyruvate
6. Diphospho glyceric acid

Classification of Energy Rich compounds/High Energy compounds

High energy compounds are mainly classified into 5 groups:

The bonds in the high energy compounds which yields upon hydrolysis are
called high energy bonds. Most of the high energy compounds contain
phosphate (except acetyl CoA) hence they are also called high energy phosphate
compounds.

1. Pyrophosphates/Phosphoanhydride phosphates
2. Enol phosphates
3. Acyl phosphates
4. Thiol phosphates
5. Guanido phosphates or Phosphagens

1.Pyrophosphates/Phosphoanhydride phosphates:

Phosphoanhydrides are formed between two molecules of phosphoric acid. The

energy bonds in pyrophosphates are acid anhydride bonds.

Example: ATP has two high energy diphosphate bonds-Phosphoanhydride

bonds.

Structure of Pyrophosphate: Bond is C-P-P

Function of Pyrophosphate: ATP serves as principle immediate donor of free

energy in most endergonic reactions. E.g.Active transport, muscle
contraction,transmission of nerve impulse.
2.Enolphosphates:

Enol phosphates is formed when phosphate group attaches to a hydroxyl group

which is bounded to a carbon atom having double bond.

Example: Phospho enol pyruate (PEP) , Bond is -CH=C-O~P

COO-

C-O~P

CH2

Function of Enolphosphate: It is formed in breakdown of glucose in

glycolysis.

This bond is energetically very high whose hydrolysis release 61 KJ/mole.

3.Acylphosphates:

Acylphosphates is formed by the reaction between carboxylic acid group and

phosphate group.

Example: 1,3-bisphospho glycerate (1,3-BPG), Bond is -C=O-O~P

O C1-OPO32-

H-C2-OH

C3H2OPO32-

Function of Acylphosphate: It is formed in glycolysis. This bond releases 49

KJ/mole of energy on hydrolysis.

4.Thiolphosphates:

Here high energy phosphate bond is absent. Instead high energy thioester bond
is present. Thioester bond results from the reaction between thiol and carboxylic
acid group.

Example: Acetyl CoA, Bond is -C=C-O~S-

CH3-C-SCoA

5.Guanidophosphates or Phosphagens:
The bond present in phosphagens is guanidine phosphates bonds. It is formed
by the attachment of phosphate group to guanidine group.

Example: Phosphocreatine (PC), Bond is –N~P

OH

HO-P-HN-C-N-CH2-COOH

O NH CH3

Function of Guanidophosphate: It is found in muscle cell and acts as reserve

of energy in tissues. It releases about 43 KJ/mole of energy on hydrolysis.
 Biological Significances of ATP
Structure of ATP:

Biological processes need energy. ATP is the energy source. ATP is the
biochemical way to store and use energy.

ATP is an adenine nucleotide bound to three phosphate, that is a lot of energy

stored in the bound between the second and third phosphate groups that can be
used to fuel chemical reactions. When a cell needs energy, it breaks this bond to
form ADP and a free phosphate molecule.

The phosphate ion is covalently bonded to each other through a bond is called
tilde bond, it is very high energy bond. If one bond breaks then 7.3 Kcal/mol
energy is released, which is used by cell to perform different functions. Thus it
is the energy liberating molecule present in living cells. It get converted in to
ADP and one inorganic phosphate molecule to produce energy that is utilized
by the functioning of the reaction.

Every cell contains ATP. This energy-rich molecule is present in the matrix of
both the cell and its nucleus.

Food is broken down in to glucose molecules. By burning glucose in the

mitochondria of cells, energy is released to make ATP from adenosine
diphosphate and free phosphate molecule. This process is called glycolysis. As
ATP molecules are used, more are generated in the mitochondria by adding a
phosphate group to the ADP molecule. This is a major part of kreb’s cycle. The
ATP molecule contains three phosphate groups linked together and bonded to a
molecule of adenine, which is also found in DNA. The chemical reaction of
cleaving off each phosphate group from ATP yields energy. The most important
bond is between the second and third phosphate groups. When additional energy
is needed, the cleaving of another phosphate group from ADP to yield
adenosine mono phosphate provides more energy; however, this reaction gives
off less energy than taking a phosphate off ATP. So we can say that ATP acts as
a human battery making it important for body building.
Energy is stored in the covalent bonds between phosphate groups, with the
greatest amount of energy (approximately 7 Kcal/mole) in the bond between the
second and third phosphate groups. This covalent bond is known as a
pyrophosphate bond.

ADP + Pi + Energy ATP (Gain/Store energy)

ATP-higher energy form (recharged battery)

ATP ADP + Energy + Pi (Expenditure/Release energy)

ADP-lower energy form (used battery)

ATP comes from three different biochemical systems in the muscle, in this
order.

1. Phosphagen system
2. Glycogen-lactic acid system
3. Aerobic respiration

Important biological significances of ATP:

The energy released from the hydrolysis of ATP is utilized for,

1. Mechanical-Muscle contraction
2. Transport work-Na-K+ ATPase pump
3. Biochemical work-Intial steps of glycolysis
4. Anabolic pathways-TAG, DNA, Protein synthesis
5. Detoxification-Urea cycle, formation of active metabolites like UDP
glucose
6. Metabolism-Synthesis of polysaccharides, aminoacids, DNA/RNA etc.
7. Active transport- Changes the shape of carrier proteins
8. Secretion-In the formation of the lysosomes necessary for exocytosis
9. Chemical reactions-A phosphate molecule from ATP can be transferred
to another molecule, makes it more reactive and lowers activation energy

Biological Significances of Cyclic AMP

Structure of Cyclic AMP:

Cyclic AMP, or 3’ 5’- cyclic adenosine mono phosphate is a second messenger
important in many biological processes. Cyclic AMP is a derivative of ATP and
used for intracellular signal transduction in many different organisms,
conveying the cyclic AMP dependent pathway.

Cyclic AMP as a second messenger:

The cell releases second messenger molecules in response to exposure to extra

cellular signaling molecules-the first messenger (Cyclic GMP, inositol tri
phosphate, diacyl glycerol and calcium).
 Synthesis of Cyclic AMP

1. Cyclic AMP is a second messenger i.e. synthesized from ATP by the

action of the enzyme adenylyl cyclase.
2. Binding of the hormone to its receptor activates a G-protein which, in
turn, activates adenylyl cyclase.
3. Using protein kinase A (PKA)- a cyclic AMP dependent protein kinase
that phosphorylates target proteins
4. Cyclic AMP binds a protein called CREB (Cyclic AMP response element
binding protein), and the resultant complex controls transcription of
genes. Examples of Cyclic AMP action-Adrenaline, Glucagon and LH.

Important biological significances of AMP:

1. Plays an important role as a second messenger in the mechanism of
secretion in many endocrine cells.
2. Key mediator of extracellular detection in a variety of signaling
pathways, including
 Glycogen metabolism
 Gene regulation
 Olfactory sensory regulation