Biomolecules - Notes | Class 11 | Part 1: Bio-

micromolecules
bankofbiology.com/2020/07/biomolecules-notes-class-11-part-1-bio.html

9. BIOMOLECULES

Biomolecules are chemical compounds found in living organisms. 

They include organic and inorganic compounds.
ANALYSIS OF CHEMICAL COMPOSITION IN A TISSUE

Grind a living tissue (vegetable or piece of liver etc.) in trichloroacetic acid

(Cl3CCOOH) to get thick slurry.
Strain this through a cheesecloth or cotton to get 2 fractions such as filtrate (acid-
soluble pool) and the retentate (acid-insoluble fraction).
The filtrate contains biomicromolecules (biomolecules having molecular weight
less than 1000 Dalton).
The retentate contains biomacromolecules (biomolecules having molecular
weight higher than 1000 Dalton).

Analysis of inorganic compounds

Weigh a living tissue (wet weight) and it is dried (dry weight) to evaporate water.
It is fully burnt to oxidize all carbon compounds to gaseous form (CO2 & water
vapour). It forms ash.
The ash contains inorganic elements (Ca, Mg, Na, K etc.) & inorganic
compounds (SO42-, PO43-, NaCl, CaCO3 etc.).

Comparison of Elements in Non-living & Living Matter

Element % Weight of

Earth’s crust Human body

Hydrogen (H) 0.14 0.5

Carbon (C) 0.03 18.5

Oxygen (O) 46.6 65.0

Nitrogen (N) Very little 3.3

Sulphur (S) 0.03 0.3

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 Sodium (Na) 2.8 0.2

Calcium (Ca) 3.6 1.5

Magnesium (Mg) 2.1 0.1

Silicon (Si) 27.7 Negligible

BIOMICROMOLECULES (MICROMOLECULES OR BIOMOLECULES)

Molecular weight of micromolecules found in the acid soluble pool ranges from 18 to
800 Dalton (Da). The acid soluble pool represents the cytoplasmic composition.
They include amino acids, sugars, nitrogen bases, lipids etc.
 

1. AMINO ACIDS

They are the compounds formed of an amino group (-NH2), an acid group (-
COOH), H & a variable group (R).
–NH2 & –COOH are attached to the same carbon atom (α-carbon). So, they are
called α-amino acids.
They are substituted methanes.

20 types of amino acids are used for protein synthesis. They include
Acidic amino acids: e.g. Glutamic acid, Aspartic acid.

Basic amino acids: e.g. Lysine, Arginine.

Neutral amino acids: e.g. Valine.

Some amino acids are aromatic. E.g. tyrosine, phenyl alanine and tryptophan.

Amino acids are 2 types:

Essential amino
acids: They cannot be synthesized by the body and should be
supplied through diet. E.g. Lysine, leucine, isoleucine, tryptophan etc.
Non-essential amino acids: They can be synthesized by the body. E.g. Glycine,
alanine, serine, arginine etc.

In amino acids, –NH2 & –COOH have ionizable nature. So, structure of amino acids
changes in solutions of different pH.

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If both –NH2 & –COOH are ionized, it is called Zwitterion.

2.
LIPIDS

Water insoluble. 

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

Types of lipids

a. Simple lipids: 

These are formed of Fatty acids and alcohol such as glycerol.

Fatty acids are lipids 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.

Fatty acids are 2 types:

Saturated fatty
acids: They have no double or triple bonds between carbon
atoms. E.g. Palmitic acid, Stearic acid (C17H35COOH) etc.
Unsaturated Fatty acids: They have one or more C=C bonds. E.g. Oleic acid
(C17H33COOH), Arachidonic acid (C19H31COOH) etc.

Structure of glycerol (trihydroxy propane):

CH2-OH
|
CH-OH
|
CH2-OH

Fatty acids are esterified with glycerol through ester bond forming monoglycerides,
diglycerides & triglycerides.
1 glycerol + 1 fatty acid
→ Monoglyceride
1 glycerol + 2 fatty acid → Diglyceride
1 glycerol + 3 fatty acid → Triglyceride

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Based on melting point, lipids (triglycerides) are 2 types:
Fats: Higher melting point.
Oils: Lower melting point.

b.Compound lipids: 
These are the esters of fatty acids and alcohol with additional groups.
E.g. 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.

3. SUGARS (CARBOHYDRATES)

Sugars are sweet and water-soluble

carbohydrates.

They are formed of C,

H and O in the ratio of 1:2:1.

4. NITROGEN BASES

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These are the nitrogen containing cyclic compounds found in nucleic acids. 
They are 2 types:

a. Purines: Includes Adenine (A) & Guanine (G).

& Uracil (U).
b. Pyrimidines: Includes Cytosine (C), Thymine (T)

Nitrogen base + Sugar → Nucleoside

Adenine     +     Sugar     →   
 Adenosine
Guanine     +     Sugar     →   
 Guanosine
Cytosine     +     Sugar     →     Cytidine
Thymine     +     Sugar     →   
 Thymidine
Uracil         +     Sugar     →     Uridine

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

Nucleotides are heterocyclic

compounds. 
Nucleic acids (DNA & RNA) are
made up of nucleotides.
============

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Biomolecules - Notes | Class 11 | Part 2: Bio-
macromolecules
bankofbiology.com/2020/07/biomolecules-notes-class-11-part-2-bio.html

9. BIOMOLECULES

BIOMACROMOLECULES (MACROMOLECULES)

These are biomolecules having molecular weight greater than 1000 Da. They include 
Proteins
Polysaccharides
Nucleic acids 

Their molecular weight is 10,000 Da and above.  

Acid insoluble fraction (macromolecular fraction) includes macromolecules from

cytoplasm and organelles.

Lipid is not strictly a macromolecule as its molecular weight does not exceed 800 Da. But
it comes under acid insoluble fraction because many lipids are arranged into structures
like cell membranes. When a tissue is grinded, cell membranes are broken and form water
insoluble vesicles. They cannot be filtered along acid soluble fraction.
 

Average
composition of cells Water 70-90 %

Protein 10-15%

Carbohydrates 3%

Lipids 2%

Nucleic acids 5-7%

Ions 1%

1. PROTEINS

Proteins are heteropolymer

of amino acids.

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 They are polypeptides. i.e., linear chains of amino
acids linked by 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 proteins
For growth and tissue repair.
Transport nutrients across cell membranes. E.g. GLUT-4 enables glucose transport
into cell.
Acts as intercellular ground substance. E.g. collagen.
Acts as antibodies to fight infectious organisms.
Acts as receptors. E.g. receptors of smell, taste, hormones.
Some are hormones (e.g. Insulin), enzymes (e.g. trypsin), pigments (e.g.
hemoglobin) etc.

Most abundant protein in animal world: Collagen.

Most abundant protein in the biosphere: Ribulose bisphosphate carboxylase -
oxygenase (RuBisCO).

Structural levels of protein

Primary structure: It describes the sequence of amino acids, i.e. the positional
information in a protein.
Secondary structure: Here, one or more polypeptide chains are folded in the
form of a helix. It has only right-handed helices. E.g. Keratin, Fibroin (silk fibre).
Tertiary structure: Here, helical polypeptide chain is further folded like a hollow
woolen ball. It gives 3-D view. Tertiary structure is necessary for many biological
activities of proteins. E.g. Myoglobin, enzymes.
Quaternary structure: Here, more than one polypeptide chains form tertiary
structure and each chain functions as subunits of protein. E.g. Haemoglobin. It has
4 subunits (2 α subunits and 2 β subunits). 

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 2. POLYSACCHARIDES (COMPLEX
CARBOHYDRATES)

These are polymers of sugars (monosaccharides). E.g.

Starch (homopolymer of glucose)

Cellulose (homopolymer of glucose)

Glycogen (homopolymer of glucose)
Inulin (homopolymer of fructose)

There are complex polysaccharides formed of amino-sugars (e.g. glucosamine, N-acetyl

galactosamine etc.).

Chitin is the homopolymer of N-acetyl glucosamine. It is seen in exoskeleton of

arthropods and fungal cell wall.

Glycosidic bond in polysaccharides: It is the bond formed when individual

monosaccharides are linked between 2 carbon atoms by dehydration.

Starch forms helical secondary structure. It can hold iodine molecules in the helical
portion giving blue colour.

Cellulose has no complex helices and so cannot hold iodine.

Diagrammatic representation of a portion of glycogen

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 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) and RNA (Ribonucleic
acid).
 

Secondary structure of DNA 

(Watson - Crick Double

Helix Model)

There are more than a dozen forms of DNA such as A, B, C, D, E, Z etc. 

DNA consists of 2 polynucleotide strands arranged antiparallelly as a double
helix.
In DNA, a nucleotide consists of nitrogen base, deoxyribose sugar and
phosphate group.
Backbone (strands) of DNA is formed by the sugar-phosphate-sugar chain.
Steps are formed of Nitrogen base pairs.
Nitrogen bases include Adenine (A), Guanine (G), Thymine (T) and
Cytosine (C). Uracil absent.
A pairs with T (A=T) by 2 hydrogen bonds.
G pairs with C (G≡C) by 3 hydrogen bonds.
A phosphate molecule links the 3’-carbon of the sugar of one nucleotide to the 5’-
carbon of the sugar of the next nucleotide. The bond between the phosphate and –
OH group of sugar is an ester bond. As there is one such ester bond on either side, it
is called phosphodiester bond.
The bond between sugar and nitrogen base is called N-glycosidic bond.

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In B-DNA:

-    One full turn of helical

strand has 10 steps (10 base pairs).

-    Length of one full turn = 34

Å (i.e. 3.4 Å for each step).

-    At each step, the strand

turns 360 (3600 for a full turn).

============

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Biomolecules - Notes | Class 11 | Part 3: Metabolism
bankofbiology.com/2020/07/biomolecules-notes-class-11-part-3.html

9. BIOMOLECULES

METABOLISM

All the biochemical reactions taking place inside a living system together constitute
metabolism. E.g. 

Removal of CO2 from amino acids to form amine.

Removal of amino group in a nucleotide base.
Hydrolysis of a glycosidic bond etc.

The intermediate products of metabolic reactions are called Metabolites.

Flow of metabolites in metabolic pathway has a definite rate & direction like automobile
traffic. This metabolite flow is called dynamic state of body constituents.

Metabolites are 2 types:

Primary metabolites:
They have identifiable functions in physiological processes
and necessary for life. E.g. amino acids, sugars, nucleic acids, lipids, vitamins etc.
Secondary metabolites: They are not directly involved in normal growth,
development or reproduction. They are found in plant, fungal and microbial cells.
E.g.
Pigments: Carotenoids, Anthocyanins etc.
Alkaloids: Morphine, Codeine etc.
Terpenoids: Monoterpenes, Diterpenes etc.
Essential oils: Lemongrass oil etc.
Toxins: Abrin, Ricin etc.
Lectins: Concanavalin A.
Drugs: Vinblastine, curcumin etc.
Polymeric substances: Rubber, gums, cellulose etc.

In metabolism, there is a series of linked multistep chemical reaction called metabolic

pathways. It is 2 types:

Anabolic (Biosynthetic) pathway Catabolic pathway

Simpler
molecules form complex structures Complex
molecules become simple
(Constructive process). structures (destructive process).

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 It consumes
energy. It releases
energy.

E.g. acetic acid becomes cholesterol,

assembly E.g.
glucose becomes lactic acid
of amino acids to protein, photosynthesis etc. (glycolysis), respiration etc.

The energy released through catabolism is stored in the form of chemical bonds. When
needed, this bond energy is utilized for biosynthetic, osmotic and mechanical works.

The most important energy currency in living system is the bond energy in adenosine
triphosphate (ATP).

THE LIVING STATE

In organisms, the metabolites are present in different concentrations. E.g. Blood

concentration of glucose in a normal person is 4.2 - 6.1 mmol/L. Concentration of
hormones is nanograms/mL.

Systems at equilibrium cannot perform work. As living organisms work continuously,

they cannot reach equilibrium. i.e. “The living state is a non-equilibrium steady-state to
be able to perform work”.

Living process is a constant effort to prevent falling into equilibrium. This is achieved by
energy input obtained from metabolism. So, no living state without metabolism.

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Biomolecules - Notes | Class 11 | Part 4: Enzymes
bankofbiology.com/2020/07/biomolecules-notes-class-11-part-4.html

9. BIOMOLECULES

ENZYMES

Enzymes are biological catalysts which influence the speed of biochemical reactions. 
All enzymes are proteins but all proteins are not enzymes.

Enzymes are specific. i.e. each enzyme has its own substrate.
Ribozymes: Nucleic acids (RNA) that behave like enzymes.

Enzymes form tertiary structure (3D) with some crevices (pockets) called ‘active site’
into which the substrate fits.
Chemical Reactions

Chemical compounds undergo two types of changes:

Physical change: A change in shape or state of
matter without breaking bonds.
E.g. ice melts into water, water becomes vapour.
Chemical change (chemical reaction): In this, bonds are broken and new
bonds are formed. It may be organic or inorganic reaction. E.g.

Rate of a physical or chemical process =

Amount of product formed per unit time.
i.e. δp/δt.

velocity if the direction is
Rate is called
specified.

Rates of physical and chemical processes are influenced by factors such as temperature.
Generally, rate doubles or decreases by half for every 10°C change in either direction.

Rate of enzyme catalysed reactions is very high. E.g. Carbonic anhydrase is the fastest
enzyme. It accelerates the following reaction 10 million times.

In the absence of enzyme, only 200 molecules of

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

Nature of enzyme action (catalytic cycle) 

Enzyme acts with substrate like a lock & key model action. 
It includes the following steps:

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 The substrate binds to the active site of enzyme (E+S).
This induces some changes in enzyme 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).
The enzyme releases the products and the free enzyme is ready to bind to other
molecules of the substrate (E+P).

This pathway goes through some

unstable transition state structures.

How do Enzymes Speed up a chemical Reaction? 

(Concept of activation energy)

Activation energy is the

additional energy required to start
a chemical reaction.
In an exothermic or endothermic
reaction, the substrate must 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) 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 

a) Temperature and pH 

Enzymes show highest activity at optimum temperature & pH. Activity declines below and
above optimum value.

At low temperature, enzyme temporarily inactive.

At high temperature, enzymes destroy because proteins are denatured by heat. 

Inorganic catalysts work at high temperature & pressure. But enzymes get damaged at
high temperature (> 40° C).

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Thermophilic organisms have enzymes
which are stable at high temperature (up
to 80-90° C).

b) 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.
c) Presence of Inhibitor 

The binding of specific chemicals

(inhibitor) shuts off the enzyme activity.
This is called inhibition.

The inhibitor closely similar to the

substrate 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. Malonate is similar to the substrate
succinate. So, it inhibits succinic dehydrogenase in the following reaction.

Competitive inhibitors are used to

control bacterial pathogens.

Classification and nomenclature of enzymes

Oxido-reductases / Dehydrogenases: Catalyze oxido-reduction b/w two

substrates.

S reduced + S’ oxidized → S oxidized + S’ reduced

Transferases: Catalyze transfer of a group (other than hydrogen).

S-G + S’ → S’-G + S
Hydrolases: Catalyze hydrolysis of ester, ether, peptide, glycosidic, C-C, C-halide
or P-N bonds.
Lyases: Catalyze removal of groups by mechanisms other than hydrolysis leaving
double bonds.

X-C-C-Y → X-Y + C=C

Isomerases: Catalyze inter-conversion of optical geometric or positional isomers.
Ligases: Catalyze the linking of 2 compounds together. E.g. enzymes catalyzing
joining of bonds like C-O, C-S, C-N, P-O etc.

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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.

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

Co-factors are 3 types:

Prosthetic group:
Organic. Tightly bound to apoenzyme. E.g. Haem. It is a part
of the active site of peroxidase and catalase. These enzymes catalyze breakdown of
H2O2 to water & O2.
Co-enzymes: Organic. Transient binding to apoenzyme. Many co-enzymes contain
vitamins. E.g. nicotinamide adenine dinucleotide (NAD) and NADP contain
niacin.
Metal ions: They form co-ordination bonds with side chains at active site and one
or more co- ordination bonds with the substrate. E.g. Zn is a cofactor for
Carboxypeptidase.

============

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