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CHAPTER 9

BIOMOLECULES
All carbon compounds that we get from living tissue can be called as biomolecules
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Protein, nucleic acid, polysaccharide, lipids are macromolecule of more than 1000
Daltons(except lipid) and are present in acid insoluble pool
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Lipid molecular weight is nearly 800Da but present in acid insoluble fraction with
the protein , nucleic acid and polysaccharide as it is not soluble in water
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The main organic compounds includes carbohydrates, lipids, amino acids, proteins,
nucleotides, nucleic acids, hormones and vitamins
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1 INORGANIC SUBSTANCES
Salts, mineral ions and water are the important inorganic materials present in a cell
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In all body fluids there is a balance between the amounts of minerals present as ions
and in complexes
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minerals which occur in very small amounts, e
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, iron, copper, cobalt, manganese,
molybdenum, zinc, fluorine, iodine, and selenium
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The mineral elements required in large amounts are termed macronutrients and
include phosphorus, potassium, calcium, magnesium, sulphur and iron
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These are
manganese, cobalt, zinc, boron, copper and molybdenum
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 Calcium gives strength and rigidity to bones and teeth by getting deposited in
them along with phosphatesSo bone dust is used as fertiliser
 Magnesium also contributes to the rigidity of bones and teeth
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Shells of some
molluscs are burnt to yield lime (CaO)
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The deficiency of iron causes anaemiaand this is because of a failure in
2+
haemoglobin synthesis
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Cytochromes are heme-protein complexes acting as oxidizing agents
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Iodine occurs in mammals as inorganic iodine, protein-bound iodine of blood and
thyroid hormones
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Mineral elements present in trace amounts are mostly required for enzyme action
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 Mitochondria are rich in manganese
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Copper occurs in cytochrome oxidase
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 Sodium and potassium are responsible for the maintenance of extracellular
and intracellular fluids through the osmotic effects of the concentrations
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+
+
 Na and K ions are also responsible for the transmission of electrical impulses
in the nerve cells
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 Water
 Water is a best solvent in nature it forms the fluid matrix of protoplasm and all
constituents of protoplasm are its solute
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 Water is a tiny polar molecule and passes readily through the membranes
 Water contains two electronegative atoms of oxygen of two water molecules share
a hydrogen atom and become linked by hydrogen bondand thus several water
molecules form short-lived macromolecular aggregates known as
lattice
structure
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 To dissolve in water, a solute molecule must form hydrogen bonds with water

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molecules to join this lattice structure
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In aqueous body fluids, proteins and nucleic acids become folded and coiled to
assume specific 3-dimensional forms suitable for biological activity
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

Water ionizes to a small but significant extent into H+ and OH-, depending on
temperature
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

High latent heat of vapourisation of water causes elimination of excess heat
through evaporation which helps in maintaining the constant body temperature
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It is of two types
1
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For example the synthesis of cholesterol from
acetic acid, synthesis of proteins from amino acids
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Catabolism- All the degradation processes in which complex molecules
are converted into simples and energy is released in it are called
catabolism
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 It is also called as destructive metabolism
Turnover of biomolecules means that they are continuously being changed into
other biomolecules and are also made from other biomolecules simultaneously
in a living cell
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Often these simple molecules
assemble and form large and complex molecules, called macromolecules
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All macromolecules except lipids are formed by the process of polymerisation,
a process in which repeating subunits termed monomers are bound into chains of

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different lengths
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The large size and complex 3dimensional shape of macromolecules enables them to
function as structural components, molecular messengers, energy sources, enzymes,
nutrient stores and sources of genetic information
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It is represented by the empirical formula (CH2O)n , some carbohydrates contain
additional atoms of sulphur or nitrogen
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These molecules exist in a great variety of configurations
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

A monosaccharide is a simple polyhydroxy aldehyde or ketone molecule
containing 3–7 carbons (trioses,tetroses,pentoses, etc
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10
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

Monosaccharides and disaccharides are specified by combining a prefix that
describes some characteristics of the sugar with the suffix –ose
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

Glucose is the sugar form of fruits, and xylose a pentose sugar, derives its name
from the Greek word (xylon) for wood
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Fig
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1 Disaccharide molecules
Carbohydrate Bonds
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The subunits of disaccharide and polysaccharide are linked by means of
glycosidic bonds, in which carbon of one sugar unit is bound to carbon of
another suger unit through the oxygen atom
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Lactose is formed when galactose and glucose join by their (1) and (4) carbons
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Forming this bond, one carbon gives up its OH groups and the other loses the
hydrogen from its OH groups
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Three polysaccharides (starch, cellulose and glycogen) are structurally as well
as biochemically distinct, even though, all are polymers of the same
monosaccharide glucose
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The synthesis and breakage of each type of covalent bond requires a specific
enzyme
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10
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

The cell wall in plants and algae derives its strength and rigidity from cellulose
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

Cellulose is digested by only few bacteria and fungi
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

Agar, a common polysaccharide used for preparing solid culture media, is a
natural component of certain seaweeds It is made up of galactose and suphur
containing carbohydrates
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

Peptidoglycan is a polysaccharides (glycans) which are linked to peptide
fragments (a short chain of amino acids)
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

The cell envelope of gram negative bacteria also contains lipopolysaccharide, a
complex of lipids and polysaccharide
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The outer surface of many cells has a delicate ‘sugar coating’ composed of
polysaccharides bound to proteins and
is called as mucoprotein or
glycoprotein
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Many bacteria are coated by a protective polysaccharide capsule that contributes
to their infectiousness
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

Starch is the primary storage food of green plants, microscopic algae and some
fungi
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Lipids
The term lipid is derived from the Greek word lipos, meaning fat
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The main groups of compounds classified as lipids are monoglycerides, diglycerides,
triglycerides, phospholipids, steroids and waxes
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

Triglycerides are composed of a single molecule of glycerol bound to three fatty
acids (Fig
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3)
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Fatty acids are long chain hydrocarbon molecules with a carboxyl group (COOH)
at one end which binds to one of the OH groups of the glycerol, thus forming a
bond called ester bond
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The fat may be saturated or unsaturated
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10
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The structure of fatty acids is responsible for the physical nature of fats and oils
(liquid fats) which are greasy and insoluble
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In most cells for long term, triglycerides are stored in concentrated form as
droplets or globules
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Although phospholipids are similar to triglycerides in containing
glycerol and fatty acids, there are some significant differences
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10
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These lipids have both hydrophilic and hydrophobic regions due to a charge on
the phosphoric acid / alcohol ‘head’ of the molecule and lack of a charge on the
long ‘tail’ of the molecule (formed by the fatty acids)
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The way
lipids naturally assume single and double layered (bilayer) configuration makes
them a valuable component of the primary framework of cell membranes
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

The structure of lipid bilayer helps the membrane in functions such as selective
permeability and fluid nature
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The best known of these is the sterol called cholesterol (Fig
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5)
which reinforces the structure of the cell membrane in animal cells and in an
unusual group of cell-wall deficient bacteria called mycoplasmas
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

Prostaglandins are fatty acid derivatives found in trace amounts that function
in inflammatory and allergic reactions, blood clotting and smooth muscle
contraction
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10
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10
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10
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This material is typically pliable and soft when warm but hard and water resistant
when cold (e
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, paraffin)
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

Bacteria that cause tuberculosis and leprosy produce a wax (wax-D) that
contributes to their pathogenicity
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10
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The term protein was coined by Mulder and is derived from the Greek word
proteios meaning ‘of the first rank’
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The building blocks of proteins are amino acids, which exist in about 20 different
naturally occurring forms
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Essential elements in protein are C,H,O,N
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The variations among the amino acids occur at the R group, which is different in
each amino acidand imparts the unique characteristic to the molecule and to
the protein that contains it
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10
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Peptide usually refers to a molecule composed of a short chain of amino acids,
such as a dipeptide (two amino acids), a tripeptide (three) and a tetrapeptide
(four)
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It is often a smaller subunit of a protein
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The terms polypeptide and protein are often interchangeably used, though not all
polypeptides are large enough to be considered proteins
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10
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Just after the synthesis is completed, the protein folds into a specific three
dimensional form
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10
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e
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Primary protein structure is a straight chain of amino acids linked by peptide
bonds form primary structure of proteins and is the most unstable
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The first protein to have its primary structure determined was insulin
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This
causes the peptide to twist into a coiled configuration called the α-helix or many
peptide chains to fold into a flat, β-pleated sheet (Fig
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8b)
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Tertiary protein structure arises when the secondary level proteins undergo
further folding by additional bonds between functional groups, such as disulfide
bonds (between sulfur atoms on two different cysteins of protein molecule),
hydrophobic bond , Ionic bond, (Fig
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8c)
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e complex proteins in which more than one polypeptide forms a large multi unit
protein (Fig
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8d)
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10
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The Nucleic Acids
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Nucleic acid function as genetic material of the cell
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These were originally isolated from the cell nucleus and were also found in cells
with no defined nuclei (bacteria), and in viruses later
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Nucleotide is composed of three smaller units; a nitrogen base, a pentose (5
carbon sugar) and a phosphate
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10
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

There are two types of purines: adenine (A) and guanine (G),

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There are three types of pyrimidines: thymine (T), cytosine (C) and uracil (U)
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

The nitrogen base is covalently bonded to the sugar ribose in RNA, and to
deoxyribose (it has one oxygen less than ribose) in DNA
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

Thus, the backbone of a nucleic acid strand is a chain of alternating
phosphatesugar-phosphate-sugar molecules
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These bonds occur between complementry pairs of nitrogen
bases (Fig
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10)
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10
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The DNA strands, sometimes, are compared to a twisted ladder, with the sugarphosphate backbone representing the rails and the paired nitrogen bases
representing the steps
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The structure of DNA is intimately related to its function
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The three major types of RNA are important for protein synthesis
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ATP
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ATP is a nucleotide containing adenine, ribose and three phosphates, and is the
energy molecule of the cell
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10
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The presence of these high energy bonds makes it possible for ATP to store and
release energy for cellular chemical reactions
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ADP can be converted back to ATP when the third phosphate is restored, thereby
serving as an energy depot or energy currency
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10
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Catalyst are substances which influences the rate of a chemical reaction without
being used or altered at the end of the reaction
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Enzymes which are biocatalysts ,are synthesized by the living cell but retain their
catalytic activity after getting extracted from the cells
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Mostly enzymes are proteins but all proteins are not enzymes
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Prosthetic groups are metal compounds
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Certain organic compounds and inorganic ions are required for enzyme activity
whichare loosely bound to the enzyme and are called Co-factors
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Iron (Fe++) is a co-factor responsible for the catalytic action of catalase
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The active site serves as a ‘lock’ into which the reactant (commonly referred to as
the substrate) fits in like a key (Fig
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12)
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Substrate binding causes a lowering of the activation energy and allows the
reaction to proceed
Fig
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12 Enzyme action – lock and key mechanism

(Fig
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13)
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How fast do enzymes act?
Fig
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13 Activation energy

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A single molecule of the enzyme carbonic anhydrase, the fastest enzyme known,
hydrates 36 million (36 x 106) molecules of carbon dioxide per minute

The catalysed reaction is 10 million times faster than the non-catalysed reaction
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Optimum Temperature
 Enzymes generally function in a narrow range of temperature which usually
corresponds to the body temperature of the organism
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Activity declines both above and below the optimum
temperature
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 Food may be preserved for a long time in a frozen state because neither microbial
enzymes nor enzymes in the food can act at low temperatures to cause its
spoilage
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 For this reason, only a few cells can tolerate temperatures above 45oC
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Optimum pH
 Each enzyme shows its highest activity at a specific pH
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 Activity declines both above and below the optimum pH
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 Some digestive enzymes have their optimum in the acidic or alkaline range
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0
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5
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 A highly reactive enzyme-substrate complex is consequently produced
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Formation of the enzyme-substrate complex is essential for catalysis
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Effect of substrate concentration
 Increase in substrate concentration increases the activity of enzymes until all the
active sites of enzyme are saturated
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(Fig
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14)
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Fig
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14 Effect of substrate concentration on enzyme action
Inhibition of Enzyme Action
 Enzyme action can be inhibited in four different ways
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The other three ways in which enzymes can be inhibited are:
Fig
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15 Competitive inhibition of enzyme action
Competitive Inhibition
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In this type of inhibition ,the action of an enzyme may be reduced or inhibited in
the presence of a substance which closely resembles the substrate in its
molecular structure (substrate analogues)Such an inhibitor is called a
competitive inhibitor of that enzyme
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e
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, the inhibition of succinic dehydrogenase by malonate, which closely
resembles succinate in structure
Such competitive inhibitors are often used in the control of bacterial pathogens
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Non-competitive Inhibition
 In this type of inhibition , inhibitor substance can bind simultaneously to an
enzyme other than it’s active site and destroy the catalytic function of the enzyme
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 The inhibitor (cyanide) has no structural similarity with the substrate
(cytochrome c)
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Allosteric Modulation or Feedback Inhibition

 When product of biochemical reaction inhibits the enzyme action , it is known as
product inhibition or feedback inhibition
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 ; e
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, allosteric inhibition of hexokinase(allosteric enzymes)by glucose-6phosphate
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Nomenclature and classification
Enzyme commission of IUB-1961 divides all enzymes into 6 major classes and also
proposed an international code of 4 digits for each enzyme
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It involves three sub classes i)Oxidase ii)Dehydrogenase iii) Reductase
e
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- Cytochrome oxidase
II)Transferases: These enzymes transfer specific group from one substrate to another
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g
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E
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Proteases, Lipases, Carbohydrases
IV)Lyases: These enzymes split the substrate molecule without water and split the
specific covalent bonds without hydrolysis or water addition
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g
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VI) Ligases(Synthases): These enzymes covalently bind two substrates to form a large
molecule
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g
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10
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 A hormone is a substance that is synthesised in minute quantities in one tissue
and transported by circulatory system to another organ of the body
 The tissue or organ where they are produced are called effectors and those where
they act are called targets
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 The local hormones have specific local effects, for example, cholecystokinin
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g
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 The hormones are required in extremely small quantities and perform a variety
of regulatory functions like growth, vegetative and sexual development, cellular
oxidation,thermal regulation and the metabolism of carbohydrates, proteins and
fats
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
The plant hormones are known as ‘phytohormones’
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Auxins, gibberellins, cytokinins, abscisic acid (ABA), and ethylene are the five
major types of hormones found in plants
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 vitamin’s deficiency can leadto a specific set of disease symptoms that can be
cured by administration of that vitamin alone
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 These are classified on the basis of solubility as:
(a) Water Soluble Vitamins which include the B-complex group of vitamins, and
vitamin C (ascorbic acid)
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Citrus fruits are good
source of vitamin C
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g
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

These are present in food fats, e
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fatty meats, liver, dairy fats, yolks, vegetable
seed oils, etc
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