Biomolecules

All the carbon compounds that we get from living body can be called
Biomolecules.

Amino acids
Amino acids are organic compounds containing an amino group and an acidic
group as substituents on the same carbon i.e., the - Carbon. Hence, they
are called

- amino acids.

There are four substituent groups occupying the four valency positions. These
are hydrogen, carboxyl group, amino group & a R group.
Based on nature of R group there are many amino acids. However, those which
occur in proteins are only of 20 types.
In glycine, R group is hydrogen, in alkine, R group is methyl, in serine it is
hydroxy methyl etc.
COOH
H C NH2
H

COOH
H C NH2
CH3

COOH
H C NH2
CH2 OH

Glycine
Alanine
Serine
The chemical and physical properties of amino acids are essentially of the amino,
carboxyl & the R functional groups.
Based on number of amino & carboxyl groups, there are acidic (glutamic acid),
basic (lysine) and neutral (valine) amino acids.
Similarly, there are aromatic amino acids like tyrosine, phenylalanine, tryptophan
etc.
A particular property of amino acid is the ionizable nature of NH 2 & -COOH
groups.

Hence in solutions of different pHs, the structure of amino acids changes.

R
NH2 C COOH
H
Covalent form

NH3+ - C COOH
Zwitter ionic form

Lipids
Lipids are generally water insoluble.
They are made up of fatty acids. A fatty acid has a carboxyl group attached to
an R group. (R is an alkyl group).
Eg: palmitic acid, Arachidonic acids.
Fatty acids can be saturated (C C) or Unsaturated ( C = C )
Another simple lipid is glycerol which is trihydroxy propane. Many lipids have
both glycerol & fatty acids. They can be monoglycerides, diglycerides &
triglycerides.
Lipids are categorised into oils & fats depending on their melting points. Fats
are solids at room temp & oil are liquids at room temp.
Some lipids are associated with phosphorus and are called phospholipids. They
are found in cell membrane. Eg. Lecithin.

Nitrogen bases
Nitrogen bases are organic compounds with heterocyclic rings and found in
nucleic acids. Eg: Adenine, guanine, cytosine, Thymine, Uracil.
Nitrogen bases when attached to sugar, are called nucleosides & when
nucleosides are attached to phosphate group, they are called as nucleotides.
Adenosine, guanosine, cytodine, thymidine, uridine are nucleosides.
Adenylic acid, Guanylic acid, Thymidylic acid, Guanylic acid, cytidylic acid &
ridylic acid are nucleotides.
DNA & RNA function as genetic material.
Adenine & guanine are called purines & cytosine, Thymine & uracil are called
pyrimidines.

Primary & Secondary Metabolites.

The general biomolecules are called metabolites or primary metabolites.
Eg: Amino acids, sugurs etc.
There are some other organic compounds which are useful to human welfare
are called secondary metabolites. Eg: Rubber, drugs, pigments, toxins,
alkaloids etc.
Biomacromolecules
Chemical compounds found in living organisms whose molecular weight is less
than 1000 daltons (Da) are called simply biomolecules or micromolecules.
Chemicals compounds found in living organisms whose molecular weight is more
than 1000 daltons are called macromolecules or biomacromolecules.
Eg: Acid insoluble fractions (protein, nucleic acids, polysaccharides, lipids)
The molecular weight of lipid is less than 800 Da. So lipids are not strictly
macromolecules.
Proteins
Proteins are linear chains of amino acids linked by peptide binds. (polypeptides)
As there are 20 types of amino acids a protein is heteropolymer & not a
homopolymer.
Some example for amino acids are alanine, cysteine, proline, tryptophan, lysine
etc.
There are two types of amino acids. (i) Essentail (ii) Nin-essential amino acids,
depending on whether they are prepared by our body or not.
Some important functions of protein are transport nutrients across cell memrane,
antibodies, hormones, enzymes etc.
Collagen is the most abundant protein in animal and Ribulose biphosphate
carboxylase oxygenase (Rubisco) is the most abundant protein in the whole of
the biosphere.
Polysaccharides
Polysaccharide is an example for acid insoluble pellet made up of long chain of
sugars. (monosaccharides). Eg: cellulose is a homopolymer of glucose.
In a polysaccharide chain, the right end is called reducing end & the left, nonreducing end.

 Starch forms helical structure & thus, can hold I2 molecules. The starch I2 is
blue in colour. Cellulose does not contain complex helical structure & hence
cannot hold I2.
Plant cell wall, cotton fibre, paper contain cellulose.
There are more complex polysaccharides in nature. They have building blocks
like amino-sugar & chemically modified sugars.
(eg: glucosamine, N-acetyl galactosamine etc).
Exoskeleton of arthropuda has complex polysaccharides called chitin. These
complex polysaccharides are heteropolymers.
Nucleic Acids
It is another nacromolecule of acid insoluble fracton. They are oplymer of
nucleotides (polynucleotides)
A nucleotide has heterocyclic nitrogen bases, a monosaccharide & a phosphate
group(phospharic acid).
In DNA, deoxyribose sugar is present & in RNA, ribose sugar is present.

Structure of proteins.
The arrangement of amino acids in a sequence is called primary structure of
protein.
A protein is imagined as a line. The left end represented by the first amino acid
called N-terminal amino acid. The right end represented by the last amino acid
called C-terminal amino acid.
A protein chian does not exist as an extended rigid rod. It is folded in the form of
a helix. The folded form of helix forms secondary & teritiary structure, thus
it gives 3 dimensional view of protein.
Some proteins are an assembly of more than one poly peptide or subunits. This
is known as quaternary structure of protein.
Adult human haemoglobin consists of 4 subunits. Two of these are identical to
each other. Hence, two subunits of type & two subunits of type
together constitute the human haemoglobin (Hb).

Nature of Bond Linking Monomers in a Polymer.

In a polypeptide or a protein, amino acids are linked by a peptide bond which is
formed when the carboxyl (-COOH) group of one amino acid reacts with the
amino (-NH2) group of the next amino acid with the elimination of a water
molecule (dehydration)
In a polysaccharide the individual monosaccharides are linked by a glycosidic
bond. This bond is also formed by dehydration. This bond is formed between two
carbon atoms of two adjacent monosaccharides.
In a nucleic acid a phosphate molecule links the 3 | - carbon of one sugar of one
nucleotide to the S| - carbon of the sugar of next nucleotide. The bond between
the phosphate and hydroxyl group of sugar is an ester bond. As there is one
such ester bond on either side, it is called phophodiester bond.
The secondary structure of DNA is explained by watson & crick. This model
says that DNA exists as a double helix.
The two starnds of polynucleotides are antiparallel i.e., run in the opposite
direction.
The backbone is formed by the sugar-phospate sugar chain. The nitrogen bases
are projected more or less perpendicular to this backbone but face inside.
A & G of one strand compulsorily base pairs with T & C, respectively (i.e.,
purine with pyrimidine) (complementary base pairs)
There are two hydrogen bonds between A & T and 3 hydrogen bonds between G
& C.
Each strand appears like a helical ladder.
Each base pair represents each step of the ladder.
At each step starnd turns 360. One full turn of the helical strand involve ten steps
or ten base pairs & the length will be 34A0. Thus, the distance between any two
successive base pair is 3.4A0.
Dynamic state of body constituents-concept of metabolism.
Biomolecules have turn over. That means, they are constantly being changed
into some other biomolecules & vice versa. This breaking & making takes place
through chemical reactions. All these chemical reactions are together called as
metabolism. But majority of these reactions do not take place in isolation,
instead, series of linked reactions called pathoways. These pathways are linear
or circular. These pathways are linear or circular. These pathways criss-cross

each other. This flow of biomolecules or metabolites is called dynamic state of

body constituents.
In such metabolic reactions, every chemical reaction is a catalysed reaction. The
catalysts that participate in chemical reactions of living systems are called
enzymes or biocatalysts.
Metabolic Basis for living
Metabolic pathway can be constructive (anabolism) or destructive
(catabolism).
Anabolic pathway consumes energy & catabolic pathway releases energy.
Formation of protein from amino acid is anabolic pathway & glycolysis is catabolic
pathway.
The energy released during catabolism is stored in chemical bond. E.g., ATP
(Adenosine triphosphate).
The living state
Any physical or chemical process moves spontaneously to equilibrium (Nonsteady state). The steady state is non-equilibrium state.
According to physics, systems oat equilibrium cannot perform work. As living
organisms work continuously, they should not reach equilibrium. Thus, the living
state is a non-equilibrium steady-state.
Thus, to prevent equilibrium, there should be energy input & it is achieved by
metabolism.
Without metabolism there cannot be a living state.
Enzymes
Almost all enzymes are proteins. There are some nucleic acids that behave like
enzymes. They are called ribozymes.
An enzyme like any protein has a primary, secondary & tertiary structure.
Due to folding pattern, enzyme forms crevices or pockets called active site,
in which the substrate fits. They are active areas for Catalysis.
Inorganic catalysts work efficiently at high temperature but enzymes get
damaged.
However, enzymes isolated from thermophilic organisms (hot vents &Sulphur
springs), retain their catalytic power even at high temperature thus, enzymes of
such organisms have thermal stability.

Chemical reactions
A chemical reaction is a process in which reactants are converted into products.
Ba(OH)2 + H2SO4
BaSO4 + 2H2O
Reactants
Products
Rate of reaction refers to the amount of products formed per unit time.
p
p
Rate = t or t
As a general rule, rate of a reaction doubles for every 10oC rise in temperature
But, catalyzed reactions proceed at very high rate.
CO2 reacts with water to form carbonic acid. About 200 molecules of H2CO3is
formed in an hour but in presence of a catalyst carbonic anhydrase, 600000
molecules are formed in every second.
In different conditions different products are possible e.g.,
I. Glucose
lactic acid (Anaerobic)
II. Glucose
pyruvic acid (Aerobic)
III. Glucose
Alcohol (Fermentatics)
Mechanism of enzyme catalysis
A reaction takes place when the reacting molecules collide. However, products
are formed only if the colloiding molecules possess a definite amount of energy
called threshold energy.
In the reacting system, the difference between the threshold energy & the
average energy of the molecules is called activation energy.
If this difference (activation energy) is large an alternate path for the reaction
such that activation energy is lowered. Thus, the reaction becomes faster.
During enzyme catalysis, the substrate binds to the active site of the enzyme to
form a complex.
E+S
ES ( Enzyme substrate complex )
The enzyme-substrate complex breaks into products releasing the enzyme and
the free enzyme is ready to bind to another molecule of substrate.
ES
P+E
(Product)

Factors affecting Enzyme activity

 Theactivity of an enzyme can be affected by a change in the condition which can

change the tertiary structure of theprotein. The following are the factors that
affect enzyme activity.
Temperature & pH
Each enzyme shows its highest activity at a particular temperature & pH called
the optimumtemperature & optimum pH. Low temperature makes the
enzymes temporarily inactive & high temp. destroys enzymatic activity
because proteins are denature by heat.
Concentration of substrate
As the concentration of substrate increases, the activiry of the enzyme also
increases, but soon it reaches a mazimum and thereafter any rise in
concentration of the substrate will not cause any effect. This is because,after
saturation, there will not be any free enzyme molecules to bind with the
substrate.
Inhibitor
Inhibitors are the substances that inhibits the activity of enzymes, when the
inhibitor closely resembles the substrate in its molecular structure, it is known
as competitive inhibitor. Such inhibitor competes with the substrate for
binding site of the enzyme. So, substrate cannot bind & the enzyme action
declines e.g., inhabitation of succinic dehydrogenase bymalonate which
closely resembles the substrate succinate. Such competitive inhibitors are often
used in the control of bacterial pathogens.
Classification and Nomenclature of Enzymes
Enzymes are classified into 6 major groups as follows.
I.

Oxidoreductases (dehydrogenases)
Catalyse oxidation-reduction reactions

II.

Transferases
Catalyse transfer of a group between a pair of substrates Eg.- Kinase

III.

Hydrolases
Catalyse hydrolytic reactions. Eg.- Proteases
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IV.

V.

VI.

Lyases
Catalyse removal of group from substrate & leave double bonds.
X

XY+C=C

Eg.-Hydrases

Isomerases
Catalyseinterconversion of isomers. Eg.- epimerase
Ligases
Catalyse the linking together of two compound. Eg.-DNA ligase.

Nomenclature
Enzymes are named after the substrates on which these act, by adding the
suffix-asewith the substrate. Eg.- Lipase (lipid), sucrose (sucrose) ets.
Co-factors
For the proper functioning of certin enzymes, these must be associated with
small non protein compounds calledco-factors. Here, protein part of enzyme is
called apoenzyme. There are 3 kinds of co-factors.
I.

Prosthetic group
they are organic compounds that are tightly bound to the apoenzyme.
For e.g., In Peroxide, thatcatalyse breakdown of hydrogen peroxide,
haem is the prothetic group.

II.

Co-enzymes
They are organic compounds that bind to apoenzyme is only transient,
(association only during catalysis) E.G- Vitamins.
Co-enzyme nicotinamideaderisedisucleotide (NAD) & NADP contain the
vitamin niacin (B5)

III.

Metal ions
Metal ions form co-ordination bond with the active site of enzymes. E.gzinc is co-factor for carboxypeptidase.

Assignment
1. Describe the important properties of enzymes.

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