BIOMOLECULES

Are all living organisms AND non -living made of the same chemicals?

Analysis of living tissues and on a piece of earth’s crust – we

will get same list of compounds but amount will be vary
 Biomolecules
Biomolecules are molecules that occur naturally in living organisms.

The molecules required by living things to build body parts and maintain the
biochemical processes required for life functions

they contribute to the structure and function of cells

Any of numerous substances that are produced by cells and living organisms.

A molecules that are involved in the maintenance and metabolic processes of

living organisms.
 ANALYSIS CHEMICAL COMPOSITION
Living tissue + Trichloro acetic acid(Cl3CCOOH)

Grinding

Fitler through cheese cloth

FILTRATE RETENTATE

Acid soluble compounds Acid insoluble compounds

Purification

Analysis

Molecular formula and structure

All the carbon compounds that we get from living tissues can be
called ‘bio molecules and also contains
•Oraganic compound analysis
•Inorganic compound analysis

Inorganic compound analysis

Dried living tissue

Burn all the carbon compounds are oxidised to
gaseous form (CO2, water vapour) and are
Ash removed
Contains inorganic elements (like calcium,
magnesium etc). Inorganic compounds like
sulphate,phosphate, etc.,
 They include organic and inorganic compounds.

Elemental analysis: Hydrogen, Oxygen, Chlorine, Carbon etc.

Chemistry point of view:one can identify functional groups like

aldehydes, ketones, aromatic compounds, etc.

 Biological point of view: we shall classify them into amino acids,

nucleotide bases, fatty acids etc
HOW TO ANALYSE CHEMICAL COMPOSITION?

1. Filtrate 2. Retentate
(acid-soluble pool) (acid-insoluble fraction)
Contains Contains
Biomicromolecules. Biomacromolecules
(Molecular weight is less (Molecular weight is greater
than 1000 Dalton). than 1000 Dalton).
It represents the It contains molecules from
cytoplasmic composition. cytoplasm and organelles.
 Types of biomolecules
1 Micro molecules

 Micro molecules are known as monomers

 These are biomolecules having molecular weight less than 1000 Da.
 Biomicromolecules found in the acid soluble pool
 Ex. Amino acids, Lipids, Sugars Nitrogen bases.

2 Macro molecules
 Macromolecules are known as polymers
 These are biomolecules having molecular weight greater than 1000 Da.
 Biomicromolecules found in the retentate
 Ex. Proteins, Nucleic acids, Proteins
Primary and Secondary metabolites:
 These are biomolecules in living cells
metabolites.
 Primary metabolites are those which have
identifiable functions and play specific roles
in normal physiological processes. Eg. Amino
acids, nitrogenous bases, proteins and
nucleic acid.

Secondary metabolites are product of certain

metabolic pathways from primary metabolites.
 Pigments – anthocyanin, carotenoids
 Drugs – vinblastin, curcumin
 Alkaloids - morphine, codeine
 Essential oils – lemon grass oil
 Polymeric compounds - rubber gum,
cellulose, resins
 Amino acids
Amino acids are organic molecules used to build proteins.

Methane derivatives

All amino acids have a central carbon atom surrounded by a hydrogen atom,
a carboxyl group (COOH), an amino group (NH2), and an R-group.

It is the R-group or side chain that differs between the 20 amino acids.

Structure of a typical amino acid

 –NH2 & –COOH are attached to the same carbon atom (α-carbon). Therefore
they are called α-amino acids.
 The R group in amino acids could be
 a hydrogen -H (the amino acid is called glycine),
 a methyl group ie -CH3 (alanine)
 hydroxy methyl ie –CH2OH(serine), etc

Basic Acidic
R= H in Glycine:

R= CH3 in Alanine:

R= CH2-OH in Serine:
 Based on number of amino and carboxyl groups
amino acids are three types

Acidic amino acids (e.g., glutamic acid) -NH3<-COOH

Basic amino acids (lysine, Arginine-NH3>-COOH
Neutral amino acids (Glycine and serine) -NH3=-COOH

 Some amino acids are aromatic. E.g. tyrosine, phenyl

alanine and tryptophan.
 There are 20 types of amino acids that take part in
protein synthesis.
 Amino acids can also be classified as follows

ESSENTIAL AMINO ACIDS NON-ESSENTIAL AMINO ACIDS

They cannot be synthesized by the They can be synthesized by
body and should be supplied the body.
through diet.
E.g. Lysine, Leucine, Isoleucine, Ex.Glycine, Alanine,
Tryptophan etc. Serine.Arginine etc
 LIPIDS

•Lipids are generally water insoluble.

•Contain C, H & O but number of oxygen atoms is less.

•A fatty acid has a carboxyl group attached to an R group.

•The R group could be a methyl (–CH3), or ethyl (–C2H5) or higher number of –

CH2 groups (1 carbon to 19 carbons).
Ex.Palmitic acid has 16 carbons including carboxyl carbon.
Arachidonic acid has 20 carbon atoms including the carboxyl carbon
•Fatty acids could be
oSaturated(without double bond)
Ex.Palmitic acid, stearic acid
oUnsaturated (with one or more C=C double bonds).
Ex.Oleic acid
 Carboxylic acid is an organic compound that contains
an Carboxyl group attached to it,R-COOH is the general
formula). fatty acids are Carboxylic acids that contain
at least 4 carbon and they tend to have even
no of carbon atom,with aliphatic hydrocarbon
unbranched(mostly)chain attached.

A fatty acid is a long aliphatic hydrocarbon

chain(b/w C4 to C28) capped by a carboxyl
group (COOH).
Types of lipids
Simple lipids
Compound lipids
Derived lipids
 A. Simple Lipids

 These are formed of Fatty acids & alcohol like glycerol.

 Fatty acids are organic acids with a hydrocarbon chain (R-
group) ending in –COOH group. i.e. R-COOH.
 E.g. Palmitic acid has 16 carbons (CH3 - (CH2)14 - COOH or
C15H31-COOH) and Arachidonic acid has 20 Carbons.
 CH2-OH
Simple lipids |
CH-OH
|
Example for simple lipid is trihydroxy propane(Glycerol)
CH2-OH
Many lipids have both glycerol and fatty acids.
Fatty acids are esterified (ester bond) with glycerol to form fats or oils.
They can be then monoglycerides, diglycerides and triglycerides.

1 glycerol + 1 fatty acid = Monoglyceride

1 glycerol + 2 fatty acid = Diglyceride
1 glycerol + 3 fatty acid = Triglyceride

Here, R1, R2 and R3 are fatty acids

B. Compound lipids
 These are the esters of fatty acids and alcohol with additional groups.
 E.g. Phospholipids (fatty acids+ glycerol + phosphate). They are found in
cell membranes. E.g. Lecithin.

C. Derived lipids
These are the products of hydrolysis of simple lipids and compound lipids.
E.g. Cholesterol
Based on melting point
lipids are 2 types:

Fats
Higher melting point
Ex. Clarified butter

Oils
Lower melting point
Coconut oil
 3. SUGARS (CARBOHYDRATES)
Glucose and ribose picture

 Sugars are sweet and water soluble carbohydrates.

 Carbohydrates are the key source of energy used by the living organisms.

 They are formed of C, H and O in the ratio of 1:2:1

 General formula Cn(H2O)n

 Carbohydrates are absorbed as monosaccharides like simple Ex. glucose,

fructose, and galactose ( Monosaccharides cannot be further broken down
by hydrolysis and disaccharides such as sucrose, lactose, maltose, and
dextrin that can be hydrolyzed to two monosaccharides).
Polysaccharides can be broadly classified into two classes:

Homo-polysaccharides
Hetero-polysaccharides

Homo-polysaccharides – are made up of one type of monosaccharide units.

ex: Cellulose(polymer of glucose),

Starch (polymer of glucose),
Glycogen(polymer of glucose),
Inulin(polymer of fructose)
Storage polysacchrides
Structural polysacchrides
 •Starch(α -Glucose) are homopolymers of glucose

: Starch is the main storage polysaccharide of plants

It consists of two components: the linear and helical amylose and the branched
amylopectin.

Starch forms helical secondary structures and can hold I2 molecules(starch-I2 is

blue in colour)
 Glycogen
The carbohydrates are stored in animal body as glycogen. It is also known as animal
starch because its structure is similar to amylopectin and iis also found in yeast and
fungi.

It s right end is called the reducing end and the left end is called the non-reducing end.
 Cellulose(1-4 linkage β-Glucose)
Cellulose occurs exclusively in plants and it is the most abundant organic substance
in plant kingdom

Homopolymer of β glucose(1-4 beta glucose bond)

Cellulose does not contain complex helices and hence cannot hold I2
  Inulin -is a polymer of fructose

Fructose are linked by β(2,1) bonds

Diagrammatic representation
of a portion of glycogen
Hetero-polysaccharides – are made up of two or more types of
monosaccharide units. ex. Hyaluronic acid, Heparin

Complex polysaccharides in nature. They have as building blocks, amino-

sugars and chemically modified sugars (e.g., glucosamine, N-acetyl
galactosamine, etc.).

Exoskeletons of arthropods, for example, have a complex polysaccharide

called chitin.
Glycosidic bond in polysaccharides
 3. NUCLEIC ACIDS (DNA & RNA)
Nucleic acids are heteropolymer of nucleotides.
i.e., many nucleotides are linked to form polynucleotide.

Nucleic acids are 2 types:

 DNA (Deoxyribonucleic acid)
 RNA (Ribonucleic acid)
Nitrogen base + Sugar = Nucleoside

Adenine + Sugar = Adenosine

Guanine + Sugar = Guanosine
Cytosine + Sugar = Cytidine
Thymine + Sugar = Thymidine
Uracil + Sugar = Uridine
 4. NITROGEN BASES

• These are the nitrogen- containing cyclic compounds found in

nucleic acids.
• They are classified as follows:
 Nucleotides

Nitrogen base + Sugar + Phosphate = Nucleotide

Adenine + Sugar + Phosphate = Adenylic acid
Guanine + Sugar + Phosphate = Guanylic acid
Cytosine + Sugar + Phosphate = Cytidylic acid
Thymine + Sugar + Phosphate = Thymidylic acid
Uracil + Sugar + Phosphate = Uridylic acid
5’ 3’

3’ 5’
 Secondary structure of DNA (Watson-Crick model)

 Made of two polynucleotide chains.

 Sugar and phosphate forms the backbone and bases projected
to inside.
 Two chains have anti-parallel polarity.
 Two strands are held together by hydrogen bond present in
between bases.
 Adenine of one strand pairs with Thymine of another strand by
two hydrogen bonds and vice versa.
 Guanine of one strand pairs with Cytosine of another strand by
three hydrogen bonds a vice versa.
 Phosphoric acid attached to the 5’ OH of a nucleoside by Phosphodiester
linkage a corresponding nucleotide is formed. (Ribonucleotide or
deoxyribonucleotides depending on the sugar unit).
 Two nucleotides are joined by 3’-5’ Phosphodiester linkage to form dinucleotide.
 More than two nucleotides joined to form polynucleotide chain.
 Polynucleotide chain has a free phosphate moiety at 5’ end of sugar, is referred to as
5’ end
 In the other end of the polymer with 3’-OH group called 3’ end.
 The backbone of the polynucleotide chain is sugar and phosphate.
 Nitrogen bases linked to the sugar moiety project from the backbone.
 In RNA every nucleotide has an additional –OH group at 2’ of ribose.
 In RNA Uracil is found in place of thymine.
 5-methyl uracil is the other name of thymine
 A nitrogenous base is linked to the pentose sugar through a N-glycosidic linkage to form a
nucleoside,
 A purine comes opposite to a pyrimidine.This generates
approximately uniform distance between the two strands of the
helix.
 The two chains are coiled in a right – handed fashion.
 The pitch of the helix is 3.4 nm or 34 A0
 There are roughly 10 bp in turn.
 The distance between the bp in a helix is 0.34nm or 3.4 A0.
 The plane of one base pair stacks over the other in double helix.
 H-bond confers stability of the helical structure of the DNA.
 Central dogma of flow of genetic information: DNA→ RNA→
Protein.
These are biomolecules having molecular
weight greater than 1000 Da.

Proteins
Polysaccarides
Nucleic acids
 1. PROTEINS

 Proteins are heteropolymer of amino acids.

 They are polypeptides. i.e., linear chains of amino Structure
acids linkedofbya typical amino
peptide bonds.
 Peptide bond is formed when –COOH group of one amino acid reacts
with –NH2 group of next amino acid by releasing a molecule of water
(dehydration).
 Functions of protein
Some are hormones (e.g. Insulin), enzymes (e.g. Trypsin)

Acts as receptors (e.g. receptors of smell, taste, hormones).

Acts as antibodies to fight infectious organisms.

Acts as intercellular ground substance (e.g. collagen).

Transport nutrients across cell membranes (e.g. GLUT-4 enables

glucose transport into cell).

For growth and tissue repair.

Collagen is the most abundant protein in animal world

 Ribulose bisphosphate Carboxylase-Oxygenase

(RUBISCO) is the most abundant protein in the whole of
the biosphere.
STRUCTURAL LEVELS OF PROTEIN

– Primary structure
– Secondary structure
– Tertiary structure
– Quaternary structure
 PRIMARY STRUCTURE
N-terminal amino acid

N-terminal amino acid

It describes the sequence of amino acids, i.e. the positional information in a

protein.
Left end: First amino acid (N-terminal amino acid)
Right end: last amino acid (C-terminal amino acid)
 SECONDARY STRUCTURE

• A protein thread is folded in the form of a helix. Only right handed helices.
• E.g. Keratin, Fibroin (silk fibre).
 TERTIARY STRUCTURE

• Long protein chain is also folded upon itself like a hollow woolen ball.
• It gives 3-D view of protein.
• It is necessary for many biological activities of proteins.
• E.g. Myoglobin
 QUATERNARY STRUCTURE

• Some proteins are an assembly of more than one polypeptide or subunits.

• E.g. Haemoglobin has 4 subunits (2 α subunits & 2 β subunits).
Nature of bonds linking monomers
in a polymer
 Amino acids are linked by Peptide bonds
 Monosaccharides are linked by Glycosidic bond
 Nucleotides are linked by Phosphodiester bond between 3-
C of one nucleotide with
 5-C of another - Each helix of DNA contains 10 base pairs
with the length of 3.4 nm (34 Ao).
 Concept of Metabolism
 Biomolecules have turn over (because constantly changing from
one form to another) Chemical reactions are called metabolism.
Examples:
 Amino acids can be formed by the removal of amino group in a
nucleotide base.
 Hydrolysis of disaccharides – 2 monosacharides
 Linked chemical reactions are called Metabolic pathways, it is a
catalysed reaction by enzymes.
Metabolic pathways in living system:
 Anabolic pathways - making / constructing big molecules from
micromolecules (eg – photosynthesis)
 Catabolic pathways – breaking down of big molecules in to smaller
ones (eg – respiration)
 For both ATP is required (energy currency)
 The living state
 Blood glucose – should be 4.5 -5.0mM
 Hormones – in nanograms/mL
 System at equilibrium cannot perform work
 As living organisms work constantly, it is non equilibrium.
 Hence the living state is non equilibrium steady state to be
able to perform work.
 ENZYMES
All enzymes are proteins but all proteins are not enzymes.

Enzymes are specific. i.e. each enzyme has its own substrate.
Carbonic anhydrase is the fastest enzyme. It accelerates the following reaction
10 million times.

CO2 + H2O carbonic anhydrase H2CO3

In the absence of the enzyme, only 200 molecules of H2CO3 are formed in an
hour. In presence of carbonic anhydrase about 600,000 molecules are formed
per second
• In a multistep chemical reaction (metabolic pathway), each step is catalysed
by different enzymes.
• E.g. In glycolysis [Glucose (C6H12O6) → 2 Pyruvic acid (C3H4O3)] ten different
enzymes take part.

Rate of reaction = amount of product

formed/unit time.
i.e. δp/δt
 CHEMICAL REACTIONS

In a chemical reaction, there will be

breaking of bonds.
Ba(OH)2 + H2SO4 → BaSO4 + 2H2O
(Inorganic chemical reaction).
Starch + H2O → glucose
(Organic chemical reaction).

Rate of reaction = amount of product

formed/unit time.
i.e. δp/δt
 If the direction of the reaction is specified the rate can also be
called velocity.
 Temperature and other factors influence the chemical and
physical reactions.
 In many cases the rate doubles or decreases by half for every
100 C change in either forward or backward direction.
 NATURE OF ENZYME ACTION (CATALYTIC CYCLE)

 Substrate binds to the active site of enzyme (E+S).

 This induces some changes in enzymes so that the substrate is
tightly bound with active site of enzyme to form enzyme-
substrate complex (ES).
 The active site breaks chemical bonds of substrate to form
enzyme- product complex (EP).
 Enzyme releases the products and the free enzyme is ready to
bind to other molecules of the substrate (E+P).
 How do Enzymes Speed up a chemical Reaction?

 Activation energy is the additional energy required to start a chemical

reaction.
 In an exothermic or an endothermic (energy requiring) reaction, the
substrate has to go through a much higher energy state. It is called
transition state energy. Therefore, activation energy is the difference
between average energy of substrate and transition state energy.

 If the product (P) is at a lower energy level than the substrate

(S), the reaction is an exothermic reaction (spontaneous
reaction). It requires no energy (by heating) in order to form
the product.
 In a biochemical reaction, enzymes lower the activation
energy. As a result, speed of the reaction increases.
 Factors affecting enzyme activity

1. Temperature & pH
2. Concentration of the substrate
3. Presence of inhibitor
 1. Temperature & pH

 Enzymes show highest activity at

optimum temperature & pH.
Activity declines below and above
optimum value.
 At low temperature, enzymes
temporarily inactive.
 At high temperature, enzymes
destroy because proteins are Temperature
denatured by heat.

pH
 2. Concentration of substrate

 With the increase in substrate concentration, the velocity of enzyme

action rises at first and reaches a maximum velocity (Vmax).
 This is not exceeded by further rise in concentration because enzyme
molecules are fewer than the substrate molecules i.e. No free enzyme
molecules to bind with additional substrate molecules.
 3. Presence of inhibitor

The binding of specific chemicals (inhibitor) shuts off the enzyme activity. This is
called inhibition.

If the inhibitor is closely similar to the substrate, it is called competitive inhibitor.

It competes with the substrate for the binding site of the enzyme. As a result, the
substrate cannot bind and the enzyme action declines.
E.g. Inhibition of succinic dehydrogenase by malonate which is similar to the
substrate succinate.

Competitive inhibitors are used to control

bacterial pathogens.
 Classification & Nomenclature of enzymes
Oxidoreductases/dehydrogenases: Enzymes which catalyse oxidoreduction
between two substrates S and S’ e.g.,
S reduced + S’ oxidised ⎯ → ⎯ S oxidised + S’ reduced.

Transferases: Enzymes catalysing a transfer of a group, G (other than hydrogen)

between a pair of substrate S and S’ e.g.,
S - G + S’ ⎯ → ⎯ S + S’ - G

Hydrolases: Enzymes catalysing hydrolysis of ester, ether, peptide, glycosidic, C-C,

C-halide or P-N bonds.

Lyases: Enzymes that catalyse removal of groups from substrates by mechanisms

other than hydrolysis leaving double bonds.

Isomerases: Includes all enzymes catalysing inter-conversion of optical,

geometric or positional isomers.

Ligases: Enzymes catalysing the linking together of 2 compounds, e.g.,

enzymes which catalyse joining of C-O, C-S, C-N, P-O etc. bonds.
 Co-factors

 These are non-protein constituents bound to the enzyme to make the enzyme
catalytically active.
 Apo-enzyme: Protein portion of the enzyme.

Co-factor + Apoenzyme = Holoenzyme

(inactive) (active)

When the co-factor is removed from the enzyme, its catalytic activity is lost.