BIOMOLECULES

All organisms are made of chemical compounds.

The carbon compounds in the living organisms are called Biomolecules.
1. Chemical Analysis
• Grind the living tissue in Trichloroacetic acid (Cl3COOH) to obtain
thick slurry.
• Slurry is filtered through cheese cloth to obtain 2 fractions.
1) Filtrate – acid soluble fraction (contain micro-biomolecules)
2) Retentate – acid insoluble fraction(contain
macrobiomolecules)

2. Ash analysis of Inorganic compounds

• This is a destructive technique
• Living tissue is dried to evaporate all water and remaining material
gives its dry weight.
• The dried material is burnt.
• All organic will be removed leaving ash.
• Ash contains many inorganic elements like Ca, Mg, S, P.
3. Amino Acids
• Amino acids are the building blocks of proteins.
• Amino acid are organic compounds containing C, H, O, N.
• Structure
Amino acid posses
* an amino group (NH2)
* a carboxyl group (COOH) on the same α carbon (α-alpha
so they are called as α-Amino acid)
* A hydrogen atom and a side chain R group is also present.
 *
• Amino acids are called substituted methane because it has a
variable side chain R.
eg: glycine, where R=H

Alanine, where R=CH3

Serine, where R=CH2-OH

 • Amino acids are Amphoteric compounds because they contain
both basic and Acidic (Carboxyl) group.
Based on this, amino acids are of 3 types:
a) Basic amino acids
Contains 2 amino group and 1 carboxyl group.
eg: Lysine
b) Acidic Amino Acids
Contains 1 amino group and 2 carboxyl group.
c) Neutral Amino Acids
Contains 1 amino group and 1 carboxyl group.
eg: Valine.
4. Ionizable nature of Amino Acids
The structure of amino acids changes into Zwitter ion in solutions of different
pH.

This structure internally transfers a hydrogen ion from COOH group to

amine group leaving a positive charge in the amine group and negative
charge in carboxylic group.

• Human body has 20 amino acids, which is divided into:

Essential Amino Acids (11 in number)
 Amino acids that are not synthesized in our body and is required
in our diet. eg: Alanine, Tyrosine, Valine.
Non-essential Amino Acids (9 in number)
Amino acids which are synthesized in our body and is not
required in our diet. eg: Serine, aspartic Acid
5. Lipids
• Lipids are insoluble in water
• They are soluble in Benzene and Chloroform.
• Lipids are esters of fatty acids with various alcohols.
• Based on melting point, lipids are of 2 types:
Fats
Solid form of lipids at room temperature.
Oils
Liquid form of lipids at room temperature (they have low melting
point, so remains as oil in winter, eg: Gingelly Oil)
• Basic units of lipids are fatty acids.
• Fatty Acids are organic acids with a hydrocarbon chain ending in a
carboxyl group.
• Carboxylic group (COOH group) is attached to an R-group. This R-
group may be Methyl (CH3), Ethyle (C2H5)
• Fatty acid may contain 1-19 carbon atoms
16 carbon atoms: Palmitic Acid
20 carbon atoms: Arachidonic Acid
Based on the number of bonds in their carbon chain, fatty acids are of 2 types:
Triglycerides
When 3 fatty acids are attached to a single glyceride molecule in a fat is
called Triglycerides.
Phospholipids
Lipids containing phosphorous are called phospholipids. Phospholipids
found in the cell membrane is Lecithin.
6. Carbon Compounds with Heterocyclic Rings
• Nitrogen bases are carbon compounds with Heterocyclic rings.
eg: Adenine, Guanine, Thymine, Cytosine, Uracil.
• Nucleosides are nitrogen bases attached to a sugar.
eg: Adenosine, Guanosine, Thymidine, Uridine, Cytidine.
• When the phosphate group is attached to nucleosides, they are
called Nucleotides.
eg: Adenylic Acid, Guanylic Acid, Uridylic Acid, Thymidylic acid,
Cytidylic Acid.

7. Metabolites
Organic biomolecules are called Metabolites, they are classified into 2:
a) Primary Metabolites
Biomolecules which involve directly in the normal growth,
development and reproduction in organisms. They are found in all
the cell type.
eg: Sugar, Amino Acids, Fatty Acids, Glycerol.
b) Secondary Metabolites
Biomolecules which are not directly involved in the normal
growth, development and reproduction in organisms,
They are found in plants, fungus and microbial cells. Produced for
defense purposes.
eg: Pigments, Alkaloids, Essential Oils, Toxins, Drugs.
 They have ecological importance and are useful to Human welfare.
• Some secondary Metabolites.
Pigments : Carotenoids, Anthocyanins
Alkaloids : Morphine, Codeine
Terpenoids : Monoterpenes, Diterpenes
Essential oils: Lemon grass oil
Toxins : Abrin, Ricin
Lectins : Concanavalin A
Drugs : Vinblastine, Curcumin
Polymer : Rubber, gums, cellulose.
Substance
8. Biomacromolecules
• Large size biomolecules having molecular weight more than 10000
Dalton are called Biomacromolecules
• They are found in acid insoluble fraction it includes
Polysaccharides, Proteins, Lipids, Nucleic acids.
• Molecular weight of lipids does not exceed 800 Daltons but it
comes under insoluble fractions because lipids are arranged into
structures like cell membranes. They are broken and form vesicles
which are water insoluble that is lipids are not strictly
macromolecules.
Polysaccharides
• long chains of sugar.
• Basic units are monosaccharides.
• Homopolymer: polysaccharides made of same type of monosaccharides.
eg: cellulose, Starch
• Heteropolymer: Polysaccharides made of different type of
Monosaccharides.
eg: Peptidoglycans, Pectin
• Starch is the store house of energy in plants.
• In a polysaccharide chain, right end is called Reducing end and left end is
called Nonreducing end.
Cellulose
• Cellulose is a Homo-polymer
• Found in the plant cell wall.
 • Cellulose does not contain Helices and hence cannot hold Iodine.
• Cotton fiber is a cellulose.
• Starch form Helical structures and hold iodine molecules and gives Blue
colour.

Chitin
Complex polysaccharides found in exoskeleton of Arthropods and in the
cell wall of Fungi.
Inulin
It is a polymer of fructose (sugar in fruits)

Proteins
Proteins are polypeptides and heteropolymers.
Some proteins and their functions
Collagen Intercellular ground substance
Trypsin Enzyme
Insulin Hormone
Antibody Fights infectious agents
Receptor Sensory reception
(Smell, taste, Hormones)
GLUT-4 Enables glucose transport into cells
RuBisCo
Ribulose Bisphosphate Carboxylase Oxygenase RuBisCo is the most abundant
protein in the Biosphere.
Collagen
Collagen is the most abundant protein in the animal kingdom.

STRUCTURE OF PROTEINS
Structure of proteins are described at 4 levels:
a) Primary Structure
• Amino acids are arranged linearly.
• They are joined by peptide bonds.
• Primary structure gives the positional information in a protein
molecule.
• First amino acid in a protein is called N terminal amino acid (left
end) and the last amino acid is called C terminal amino acid (right
end).

b) Secondary Structure
• When the protein thread is folded in the form of a helix.
• It forms only right-handed helix.
• Other regions are folded into other forms.
• eg: Beta- plated sheets of Silk fiber.
 c) Tertiary Structure
• The long protein chain is folded upon itself like hollow woollen ball
which gives rise to the Tertiary structure.
• Tertiary structure gives a 3-dimensional view to the protein which
is necessary absolutely for many biological activities.
• eg: Myoglobin of muscles

d) Quaternary Structure
• Some proteins are an assembly of more than one polypeptide or
subunits and the manner in which the individual folded
polypeptides are arranged with respect to each other gives the
Quaternary structures.
• eg: Human Haemoglobin is a protein with 4 subunits (2 alpha
subunits+2 Beta subunits)

NATURE OF BOND
a) Peptide Bond
• Bond formed between 2 amino acids.
b) Glycosidic Bond
• Bond formed between 2 monosaccharides.
c) Ester Bond
• Bond formed between Phosphate and sugar.
 d) Phosphodiester Bond
• Bond formed between 2 nucleotides.
Nucleic Acid
• They are long polymer of nucleotides.
• 2types:
RNA – Ribonucleic Acid
DNA – Deoxyribonucleic Acid
Structure of Polynucleotide Chain
• The nucleotide has 3 components:
a) Nitrogenous Base
b) Pentose Sugar
c) Phosphate group
• Nitrogen base: Purines, Pyrimidines
Purines: Adenine, Guanine
Pyrimidines: Cytosine, Thymine, Uracil
• Cytosine is common in DNA and RNA.
• Thymine present in DNA.
• Uracil present in RNA at the place of Thymine.
9. Structure of Nucleic acid
• Proposed by Watson and Crick (1953)
• DNA exist as double Helix that is each DNA is made of 2 strands
• 2 Strands are anti-parallel to each other that is they run in opposite
direction.
• Backbone of DNA is formed by Sugar Phosphate Sugar chain.
• Nitrogenous Base are Projected perpendicular to this Backbone but
face inside.
• Adenine Base pairs with Thymine by 2 hydrogen bonds (A=T)
• Guanine Base pairs with Cytosine by 3 hydrogen bonds (G=C)
• Each strand appears like a helical staircase and nitrogenous base
pairs form the steps of DNA.
• AT each step, the strand turns 36o. Length of one full turn/ gyre is
34Ao/3.4mm.
• One full turn of the strand has 10 steps or ten base pairs, so the
distance between 2 base pairs is 3.4Ao/0.34mm
• Diameter of a DNA molecule is 20Ao/2nm
[Link] of Metabolism
• Sum total of all chemical reaction in our body is called metabolism.
• It involves 2 processes:
a) Catabolism (Destructive process)
b) Anabolism (Constructive process)
• All metabolic reactions take place through metabolic pathway.
• Flow of metabolites has a definite rate and direction. This
metabolic flow is called the Dynamic state of body constituents.
• Each metabolic reaction is catalyzed by catalyst. The catalyst is
also called proteins.
• These proteins with catalytic power are called Enzymes.
[Link] Bases for Living
• Anabolic Pathway
Some metabolic reaction leads to the formation of complex
structure from simple structure.
eg: Formation of complex cholesterol from simple acetic acid.
• Catabolic Pathway
Some metabolic reactions lead to the conversion of complex
structure into simpler forms.
eg: Breaking of glucose into simple lactic acid.
• Anabolism consumes energy, catabolism releases energy.
• Living organism have to trap this energy which is liberated during
degradation and store it as chemical bond.
• Most important form of energy is called ATP (Adenosine
Triphosphate).
[Link] living state
There is a continuous flow of biomolecules in the metabolic pathway is called
metabolic flux.
System at equilibrium cannot perform work. Living state is a non-equilibrium
steady state to be able to perform work.
[Link]
• Enzymes are biological catalyst and are synthesized by living cells.
They influence the speed of biochemical reactions.
• All enzymes are proteins but all proteins are not enzymes.
• Enzymes are specific i.e each enzymes has its own substrate.
• Ribozymes are nucleic acids that behave like enzymes.
 • Enzymes form tertiary structure (3D) with some crevices (pockets)
called active site into which the substrate fits.

Cofactor
• Some enzymes have a non-protein constituent called co-factor bound to
the enzyme to make it catalytically active.
• Protein part of the enzyme is called Apoenzyme

• Three types of co-factors:

a) Prosthetic Group
They are organic compounds tightly bound to apoenzyme.
eg: Haem
b) Co-enzyme
They are organic compounds loosely bound to the apoenzyme.
eg: NAD, FAD
c) Metal ions
They are inorganic ions.
Eg: Zn+ is a co-factor of carboxypeptidase.
Q. Difference between Enzyme Catalysts and inorganic catalyst.
Ans: Enzymes catalysts differ from inorganic catalyst
• Inorganic catalysts work efficiently at high temperature and pressure.
• Enzyme catalysts get damaged at high temperature and pressure.
• Enzyme isolated from thermoacidophile organisms retains their catalytic
power even at high temperature (80o- 90o) that is they show thermal
stability.
[Link] Reaction
• Chemical compounds undergo 2 types of changes.
Physical Change – change in shape and in state of matter without
breaking of bonds.
Chemical Change- constitutes the breakdown of bonds and
formation of new bonds during transformation.
• Rate of physical or chemical process refers to the amount of
product formed per unit time i.e.

Delta (uppercase Δ, lowercase δ or 𝛿)

• General rule of Thumb is that rate of a reaction doubles or
decrease by half for every 10oC change in either direction.
• Catalyzed reaction proceeds at higher rates than uncatalyzed
reactions.
eg: Carbonic acid formation
* 200 molecules per hour in the absence of enzyme.
* 6,00,000 molecules per sec in the presence of carbonic
anhydrase enzyme.
eg: In Glycolysis,
glucose molecule breaks down to from pyruvic acid through
ten catalyzed steps.
Glucose converts to lactic acid in muscles under anerobic condition.
Glucose converts to ethanol during fermentation.
[Link] of Enzyme Action
 • Metabolic conversion of a substrate into a product is called a Reaction.
• The chemical which is converted into a product is called a substrate.
• When a substrate binds to the active site of the enzyme (ES) Enzyme
substrate complex is formed
• ES complex is transient (temporary) phenomenon
• A new structure of the substrate called EP (enzyme product) is formed.
• After breaking of the bond, product is released from the active site.

[Link] of Activation energy

• All chemical reaction has a potential energy barrier that must be
overcome before the substrates are converted into end products.
So, the substrate molecules must be given sufficient energy to
enter the reactive state called Transition state, which lies at the
apex of the energy barrier.
✓ A transition state is in which a molecule is no longer a substrate but not
yet a product. All chemical reactions must go through the transition
state to form a product from a substrate molecule. It has more free
energy in comparison to the substrate or product; thus, it is the least
stable state.
✓ There fore activation energy is the difference between average energy
of substrate and transition state energy.
• The minimum amount of energy required to bring the substrate
molecules of one mole in the reactive form is called Activation
Energy.
 ✓ The Y axis represents – the potential energy
✓ The X axis represents – the progression of the reaction
✓ Ther is an energy difference between ‘S’ and ‘P’. If ‘P’ is at a lower level
than ‘S’ the reaction is exothermic. One need not supply energy to form
the product.
✓ Whether it is exothermic/spontaneous reaction or endothermic / energy
requiring reaction the ‘S’ has to go through high energy state or
transition state.
✓ The difference in average energy content of ‘S’ from that of its transition
state is called activation energy.
[Link] Affecting Enzyme Activity
The tertiary structure of a protein can be affected by temperature, pH,
concentration of substance.
a) Temperature
• Enzymes show highest activity at optimum
temperature.
• At lower temperature enzymes are preserved to
inactive state.
• At high temperature enzymes are denatured.

b) pH
• enzymes are sensitive to pH.
• Enzymes show highest activity at optimum pH.
• At high and low pH, activity of enzyme decreases.
 c) Concentration of Substrate
• Increase in substrate concentration, increase the rate
of reactions up to a level. This is because more and
more active sites of the enzyme molecules active
sites of the enzyme molecules are occupied by the
substrate molecules.
This continues till all active sites are occupied called
Saturation of Enzymes.
• Further increase in substrate will no increase, the rate
of reaction. This stage of maximum velocity of
chemical reaction is called Vmax .

[Link] of Enzymes Action

• When the binding of the chemicals, shuts of enzyme
activity this process is called inhibition.
• The chemicals which inhibit the enzyme action is
called inhibitor.
• When the inhibitor closely resembles the substrate in
its molecular structure and inhibits the activity of
enzyme → Competitive Inhibitor.
This inhibition competes with the substrate for the
active site of the enzymes. The substrate cannot bind
and the enzyme action declines.
[Link] of Enzymes
In 1961, the enzymes commission of International Union of
Biochemistry (IUB) proposed the classification of enzymes.
According to this system, enzymes are classified into 6 major classes:
a) Oxidoreductases
Catalyzes oxidation – reduction reactions.
b) Transferase
Transfer of functional group
c) Hydrolases
Catalyzes the hydrolases of various bonds
eg: Peptide Bond
d) Lyases
Breaking of Bonds other than hydrolyses and oxidation.
e) Isomerases
Catalyzes isomerization, interconversion of optical or
positional isomers.
f) Ligases
Catalyzes linking together of 2 compounds