Biomolecules

Analysis Of Chemical Composition: For this, a living tissue is taken. The tissue is
ground in trichloroacetic acid (Cl3CCOOH); by using pestle and mortar. The slurry is
then filtered through a cloth. The filtrate contains acid-soluble pool and the retentate
contains acid-insoluble fraction. Organic compounds are found in the acid-soluble pool,
while inorganic substances are found in acid-insoluble fraction.
Biomolecules: All the carbon compounds which are obtained from living tissues are
called biomolecules.
AMINO ACIDS:
Amino acids are organic compounds which contain an amino group and an acidic group
as substituents on the same carbon, i.e. -carbon. Due to this, they are called -amino
acids. The amino acids are substituted methanes. There are four substituent groups
which occupy the four valency positions. These groups are; hydrogen, carboxyl group,
amino group and a variable group; called R group. The nature of the R-group governs a
particular type of amino acids.
However, there are only 21 types of amino acids which occur in proteins. The R-group
in these proteinaceous amino acids could be of various types. The amino, carboxyl and
the R functional groups decide the chemical and physical properties of an amino acid.
Amino acid with a hydrogen is called glycine, one with a methyl group is called alanine,
one with hydroxyl methyl group is called serine, etc. Based on the number of amino and
carboxyl group, the amino acids can be acidic, basic or neutral. A particular feature of
amino acid is the ionizable nature of NH 2 and COOH groups. Hence, structure of
amino acids changes in solutions of different pH.
LIPIDS:
Lipids are usually insoluble in water. Lipids can be simple fatty acids and some lipids
have phosphorous and phosphorylated organic compounds in them. Lipids; containing
phosphorus; are called phospholipids. A fatty acid has a carboxyl group attached to an
R group. The R group can be a methyl or ethyl or higher number of CH 2 group (1 carbon
to 19 carbons).
Fatty acids could be saturated or unsaturated. Many lipids have both glycerol and fatty
acids. In this case, the fatty acids are found esterified with glycerol. They can be
monoglycerides, diglycerides and triglycerides. On the basis of melting points, they can
be termed as fats and oils. Oils have lower melting points while fats have higher melting
points.

There are a number of carbon compounds; with heterocylic rings; found in living
organisms. Some of them are nitrogenous bases, e.g. adenine, guanine, cytosine, uracil
and thymin. When a nitrogenous base is attached to a sugar, it is called a nucleoside,
e.g. adenosine, guanosine, thymidine, uridine and cytidine. If a phosphate group is also
found esterified to the sugar then they are called nucleotides, e.g. adenylic acid,
thymidylic acid, guanylic acid, uridylic acid and cytidylic acid.
Primary Metabolites: Metabolites which have identifiable functions are called primary
metabolites. They play known key roles in normal physiological processes. All the
primary metbaolites are found in animal cells.
Secondary Metabolites: There are certain metabolites about which we do not have
enough information to suggest their role in physiological processes. Such metabolites
are called secondary metabolites. Secondary metabolites are not found in animal cells.

Mircomolecules: Biomolecules with molecular eights less than one thousand Dalton are
called micromolecules or simple as biomolecules.
Biomacromolecules: Biomolecules with molecular weights more than one thousand
Dalton are called biomacromolecules. These are found in the acid-insoluble fraction.
Proteins
Protein is a polymer of amino acids. Based on similar or different monomers repeating
in a protein, it is classified as homopolymer and heteropolymer. When same monomer
is repeated in the protein, it is called homopolymer. When different monomers are
present in the protein, it is called heteropolymer.
Essential Amino Acids: Some amino acids are essential for our health. But our body
does not make them and they need to be supplemented through diet. Such amino acids
are called essential amino acids. Collagen is the most abundant protein in the animal
world. Ribulose biphosphate Carboxylase-Oxygenae (RUBISCO) is the most abundant
protein in the whole biosphere.

POLYSACCHARIDES
The long chains of sugars are called polysachharides. If a polysaccharide is made up of
similar monosaccharides, it is called homopolymer, e.g. cellulose. If a polysaccharide is
made up of different monosachharides, it is called heteropolymer.
The right end of a polysaccharide chain is called the reducing end and the left end is
called the non-reducing end.
Starch forms helical secondary structures. Starch can hold I 2 (iodine) molecules in
helical portion. Cellulose does not contain complex helices and hence cannot hold I 2 .
In a polysaccharide chain, the right end is called the reducing end and the left end is
called the non-reducing end. Starch forms helical secondary structures. In fact, starch
can hold I2 molecules in the helical portion.
NUCLEIC ACIDS
A nucleic acid is composed of nucleotide. There are three chemically distinct
components in a nucleotide. One of them is a heterocyclic compound, the second is a
monosaccharide and the third is phosphoric acid or phosphate.
The heterocyclic compounds; present in nucleic acids are the nitrogenous bases, viz.
adenine, guanine, uracil, cytosil and thymine. Adenine and Guanine are substituted
purines, while uracil, cytosil and thymine are substituted pyrimidines.
Based on the presence of purine or pyrimidine, the heterocyclic ring is called purine and
pyrimidine. Polynucleotides contain either ribose sugar or 2 deoxyribose sugar. If ribose
sugar is present then the nucleic acid is called ribonucleic acid (RNA). If deoxyribose
sugar is present then the nucleic acid is called deoxyribose nucleic acid (DNA).
STRUCTURE OF PROTEINS
Primary Structure: The sequence of amino acids is called the primary structure of a
protein. The left end is represented by the first amino acid, while the right end is
represented by the last amino acid. The first amino acid is also called N-terminal amino
acid. The last amino acid is called C-terminal amino acid.

Secondary Structure: The protein is not a linear chain of amino acids rather the chain
would bend at some places and even form helices. Regularly repeating local structures
gives secondary structure to protein.
Tertiary Structure: The overall shape of a protein molecule; and the spatial relationship
of the secondary structures to one another; is called tertiary structure of protein. In other
words, the various folds which give three dimensional appearances to protein form its
tertiary structure.
Quaternary Structure: The manner in which the individual folded polypeptides are
arranged with respect to each other is called quaternary structure of protein.
Biomolecules
NATURE OF BOND LINKING MONOMERS IN A POLYMER
Glycosidic Bond: Certain type of functional group which joins a sugar molecule to
another group is called glycosidic bond. Another group may or may not be another
carbohydrate.

Peptide Bond: A chemical bond formed between two molecules; when the carboxyl
group of one molecule reacts with the amine group of another molecule; is called
peptide bond (amide bond). A molecule of water is released during this reaction. This is
a dehydration synthesis reaction and usually occurs between two amino acids. This is
also known as a condensation reaction. The resulting CO NH bond is called a peptide
bond. The resulting molecule is called an amide. The four atom functional group C
(=O)NH is called an amide group or a peptide group.

Phospho-diester Bond: A group of strong covalent bonds between a phosphate group

and two other molecules over two ester bonds is called a phosphor-diester bond.
Phosphodiester bonds make the backbone of the strands of DNA and hence are central
to all life on Earth. In DNA and RNA, the phosphodiester bond is the linkage between
the 3 carbon atom of one sugar molecule and the 5 carbon atom of another.

DYNAMIC STATE OF BODY CONSTITUENTS CONCEPT OF METABOLISM

Metabolism: All the biomolecules are constantly being changed into some other
biomolecules and also made from some other biomolecules. The turnover of
biomolecules takes place continuously. All these reactions are together called
metabolism.
Anabolism: When a complex biomolecule is synthesized from simple biomolecules
through a biological process, the process is called anabolism. Energy is utilised during
anabolism.
Catabolism: When a complex biomolecule is disintegrated to produce simple
biomolecules through a biological process, the process is called catabolism. Energy is
released during catabolism.
Metabolic Pathway: Metabolites are converted into each other in a series of linked
reactions. Such a series of linked reactions is called metabolic pathway. Every chemical
reaction in the metabolic pathways is a catalysed reaction. The metabolic pathways are
either linear or circular. These pathways crisscross each other; which means there are
traffic junctions. But the interlinked metabolic traffic is very smooth and no single mishap
has been reported for healthy conditions.
The Living State: All living organisms exist in a steady state; characterized by
concentrations of each of the biomolecules. The steady state is a non-equilibrium state.
It can be said that the living process is a constant effort to prevent falling into
equilibrium. Without metabolism, there cannot be a living state.

Biomolecules
ENZYMES
An enzyme is a catalyst which is utilised in metabolic reactions. Almost all enzymes are
proteins.
"Lock and Key" Model: The lock and key model was suggested by Emil Fischer in 1894.
Emil Fischer postulated that both the enzyme and the substrate possess specific
complementary geometric shapes that fit exactly into one another. This model explains
the specificity of enzyme. But this model fails to explain the stabilization of the transition
state which an enzyme achieves.
Induced Fit Model: This is the most accepted model and is a modification over the lock
and key model. The induced fit model was proposed by Daniel Koshland in 1958.
According to this model, since enzymes are rather flexible structures; the active site is
continually reshaped by interactions with the substrate when the substrate interacts with
the enzyme. In some cases, the substrate molecule also changes shape slightly when it
enters the active site. The active site continues to change until the substrate is
completely bound. The final shape and charge is determined at this point of enzymesubstrate reaction.
There are many differences between enzyme catalysts and inorganic catalysts.
Inorganic catalysts work efficiently at high temperatures and high pressures, enzymes
get damaged at high temperatures (above 40C). But enzymes which are isolated from
thermophilic organisms show thermal stability.
Mechanisms of Enzymatic Actions

Enzyme lowers the activation energy by creating an environment in which the

transition state is stabilized.

Enzyme lowers the energy of the transition state by creating an environment with
the opposite charge distribution to that of the transition state. But an enzyme
does this without distorting the substrate.

Enzyme provides an alternative pathway.

Enzyme reduces the reaction entropy charge by bringing substrates together in

the correct orientation to react.

Increase in temperatures speeds up reactions. But if the enzyme is heated too

much, its shape deteriorates and it regains it shape only when the temperature
comes back to normal. Some enzymes work best at low temperatures, e.g.
thermolabile.

The catalytic cycle of an enzyme action can be described in the following steps:
1. The substrate binds to the active site of the enzyme, fitting into the active site.
2. The binding of the substrate induces the enzyme to alter its shape, fitting more
tightly around the substrate.
3. The active site of the enzyme breaks the chemical bonds of the substrate and the
new enzyme- product complex is formed.
4. The enzyme releases the products of the reaction and the free enzyme is ready
to bind to another molecule of the substrate.
Factors Affecting Enzyme Activity
Temperature and pH: Enzymes usually function in a narrow range of temperature and
pH. Each enzyme shows its highest activity at optimum temperature and optimum pH.
Beyond that range, the activity declines. Low temperature preserves the enzyme
temporarily in inactive state, while high temperature destroys the enzyme.
Concentration of Substrate: The velocity of enzymatic action at first rises with an
increase in substrate concentration. But the velocity of reaction does not rise once it
reaches a maximum velocity (Vmax). This happens because there are fewer molecules
of enzyme and no free enzyme molecule is left to bind with the additional substrate
molecules.
Effect of Inhibitor: When the inhibitor closely resembles the substrate and inhibits the
activity of an enzyme, it is known as competitive inhibitor. Because of its close structural
similarity with the substrate, the inhibitor competes with the substrate for the binding site
on the enzyme. Such competitive inhibitors are often used in the control of bacterial
pathogens.
Classification and Nomenclature of Enzymes
Enzymes are divided into 6 classes each with 4-13 subclasses and named accordingly
by a four-digit number.
Oxidoreductases/dehydrogenases: Enzymes which catalyse oxidoreduction between
two substrates S and S.
Transferases: Enzymes catalysing a transfer of a group, G (other than hydrogen)
between a pair of substrate S and S.
Hydrolases: Enzymes catalysing hydrolysis of ester, ether, peptide, glycosidic, C-C, Chalide 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
In many cases, non-protein constituents are bound to the enzyme which makes the
enzyme catalytically inactive. Such non-protein constituents are called cofactors. In
such cases, the protein portion of the enzyme is called the apoenzyme. There are three
kinds of cofactors, viz. prosthetic groups, co-enzymes and metal ions.
Prosthetic Groups:
Prosthetic groups are organic compounds. They are distinguished from other cofactors
in that they are tightly bound to the apoenzyme. For example, in peroxidase and
catalase, which catalyze the breakdown of hydrogen peroxide to water and oxygen,
haem is the prosthetic group and it is a part of the active site of the enzyme.
Co-enzymes:
Co-enzymes are also organic compounds but their association with the apoenzyme is
only transient. A co-enzymes association; with apoenzyme; usually occurs during the
course of catalysis. Moreover, co-enzymes serve as co-factors in a number of different
enzyme catalyzed reactions. The essential chemical components of many coenzymes
are vitamins, e.g., coenzyme nicotinamide adenine dinucleotide (NAD) and NADP
contain the vitamin niacin.
Metal Ions: A number of enzymes require metal ions for their activity. Such metal ions
form coordination bonds with side chains at the active site and at the same time form
one or more cordination bonds with the substrate, e.g., zinc is a cofactor for the
proteolytic enzyme carboxypeptidase. Catalytic activity is lost when the co-factor is
removed from the enzyme which proves that they play a crucial role in the catalytic
activity of the enzyme.