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11.9 BIOMOLECULES
Biochemistry: Science dealing with chemicals and physiochemical reactions found in living organisms and
their life processes.
Biomolecules: Chemicals or molecules present in the living organisms.
Cellular pool: Sum total of different types of biomolecules, compounds and ions present in a cell.
*Most abundant element in Earth crust and Human body = O2 (46% and 65% resp.)

True/Homogenous solution: Formed by crystalloids (1nm or less)

Colloidal/Heterogenous solution: Formed by colloids (1-100nm)
Biomolecules: Two types

INORGANIC ORGANIC
Minerals, gases, water Carbohydrates, lipids, amino acids, proteins,
enzymes, nucleotides, nucleic acids, vitamins etc.
Do not contain carbon and hydrogen together Possess carbon and hydrogen together

Chemical analysis of living tissue:

Living tissue (liver or vegetable) + Cl3CCOOH (Trichloroacetic acid)
Grind (In pestle and mortar)
Slurry
Filter
Filterate (Acid soluble pool) Retentate (Acid insoluble fraction)
Micromolecules (<1000D) Macromolecules (>10000D)
Include H2O, gases, minerals, sugars, amino acids, nucleotides
Carbohydrates Lipids Proteins Nucleic acids

CARBOHYDRATES
Organic substances having carbon, hydrogen and oxygen where hydrogen and oxygen occur in ratio of 2:1
 Upto 80% of dry weight of plants is carbohydrates.
 General formula Cn(H2O)n or (CH2O)n
 Also called saccharides because of their basic component which is sugar.
 May be monosaccharide, oligosaccharide and polysaccharide.
Monosaccharides: Which cannot be hydrolysed further into smaller components.
 CnH2nOn
 Trioses (3 carbon molecules) to heptoses (7C).
 Fructose (Sweetest sugar); also called fruit sugar or laevulose.
 Glucose – Blood sugar/Grape sugar/Dextrose/Corn sugar
Oligosaccharides: Formed by condensation of 2-9 manosaccharides
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 Linked with glycosidic bond.

 Disaccharides, trisaccharides etc.
 Sucrose - Commercial sugar/Cane sugar
- Glucose + Fructose
- Non reducing sugar
 Maltose - Malt sugar
- Reducing sugar
- Glucose + Glucose
 Lactose - Milk sugar
- Reducing sugar
- Glucose + Galactose

Reducing sugar Non reducing sugar

Have a free aldehyde or ketonic group. Free aldehyde or ketonic group absent.
Reduce Cu3+ ions of Bendicts or Fehlings Do not reduce
solution to Cu2+
E.g. All monosaccharides, maltose, lactose Sucrose, trehalose

Polysaccharides: Formed by polymerisation of large number of monosaccharides.

 Also called ‘Glycans’.
 Food – Starch, Glycogen (animal starch)
 Structural - Chitin (second most abundant organic molecule); polymer of acetyl glucosamine
- Cellulose (most abundant organic molecule); (Glucose)n; Cotton fibre = cellulose
- Tunicin (animal cellulose)
 Mucosubstances - Agar (D-galactose)
- Pectin, hemicelluloses, peptidoglycan (NAG + NAM)
 Inulin = Polymer of fructose

LIPIDS
Lipids are fatty acid esters of alcohol and related substances.
 Insoluble in water; soluble in non-polar organic solvents like ether, benzene, chloroform, acetone
etc.
Fatty acids: Organic acids having hydrocarbon chain that end in a carboxylic group (-COOH).
 Essential fatty acids → Linoleic, Linolenic, Arachidonic acids
 Two types of fatty acids

Saturated Unsaturated
- No double bound in carbon chain - Have double bonds
- Solid at room temperature - Liquid at room temperature

Lipids are of three types:

1. Simple – Formed of fatty acid and alcohol. E.g. Fats, Suberin
2. Compound – Possess additional group besides fatty acid and –OH
3. Derived – Either lipid like chemicals. E.g. Sterols
- or derivative of lipids. E.g. Terpenes
A. Neutral or true fats: Triglycerides formed by esterification of three molecules of fatty acids with one
molecules of trihydric alcohol, glycerol.
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o Pure fats – If three molecules of fatty acid are different

o Mixed fats – If two of them are similar. E.g. Butter
o Hydrogenation – Conversion of unsaturated into saturated
o PUFA – Oils with polyunsaturated fatty acids
- Called Polyunsaturates
B. Waxes: Fatty acid esters of long chain monohydric alcohols.
o Plant wax – In cuticle
o Animal wax – Cerumen (ear wax)
- Wax – D (by leprosy bacteria)
C. Cutin: Complex lipid
D. Suberin: Mixture of condensation products of glycerol and phellonic acid
E. Phospholipids: Are amphipathic (have both polar and non polar end). E.g. Lecithin
F. Lipoproteins – Composed of lipids and proteins
G. Terpenes – Lipid like hydrocarbons formed of isoprene (C5H8) units.
H. Prostaglandins – Derivatives of arachidonic acid
I. Steroids – Group of complex lipids that possess a ring system.
- E.g. Sterols (Cholesterol), Bile acids, sex hormones etc.
Formed in liver
Atherosclerosis – When deposited in arteries
Gall bladder stones – When deposited in gall bladder

AMINO ACIDS
Amino acids are organic compounds containing an amino acids and an acidic carboxylic group as
substituent on same carbon (α-carbon).
COOH
H2N C H
R
E.g. Glycine (simplest amino acid) i.e. COOH
H2N C H
H
There are total 20 types of amino acids in proteins.
Seven types (Based on structure and reaction):
1. Neutral – Glycine, Alanine, Valine, Leucine, Isoleucine *GALIV
2. Acidic – Glutamine, Asparagine, Glutamic acid, Aspartic acid *AAGG
3. Basic – Arginine, Lysine *BArLy
4. Sulphur containing – Cysteine, Methionine *CM
5. Alcoholic – Serine, Threonine *SeTh
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6. Aromatic – Phenylalanine, Tryptophan, Tyrosine *Ty Pher Try

7. Heterocyclic – Histidine, Proline *His Pr

ESSENTIAL AMINO ACIDS NON-ESSENTIAL AMINO ACIDS

Not synthesized in human body Can be synthesized by human body
Total – 7 Total – 13
Obtained from dietary proteins No need to be present in diet

Peptide formation:
 Amino acids condense to form peptides.
 Peptide or Amide bond (-NHCO-) link amino acids in dipeptides, tripeptides, oligopeptides or
polypeptides.

PROTEINS
Proteins are polypeptides. They are linear chains of amino acids linked by peptide bonds.
 Polymer of amino acids.
 Is heteropolymer.
 Collagen – Most abundant protein of animal world
 Rubisco – Most abundant protein of whole biosphere

Structure:
1. Primary: Description of basic structure of a protein.

 Sequence of amino acids and their positional information comes under primary structure.
 0.35 nm – Distance between two adjacent peptide bonds
 N terminal – Left end of protein
 C terminal – Right end of protein

2. Secondary structure: Development of new stearic relationships of amino acids present in the linear
sequence (1o structure).
Three type of secondary structures – α-helix, β-pleated, collagen helix
α-helix- Polypeptide chain is coiled spirally in right handed manner.
- Stabilized by hydrogen bonds.
β-pleated – Two or more polypeptide chains get inter-connected by hydrogen bonds in form of sheet.
Collagen helix- Generally three strands or polypeptides coiled around one another.
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- Coil is strengthened by forming of H2-bond between NH- of glycine and –CO of other two strands.
3. Tertiary structure: Bending and folding of various types to form spheres, rods or fibres.

 Tertiary structure gives the protein a three dimensional conformation.

 Stabilized by several type of bonds:
o Hydrogen bonds
o Ionic bonds
o Covalent bonds
o Vander Waal’s interactions
 Denaturation - Degrading of tertiary structure
- By high temperature, pH changes, heavy metal salts
 Renaturation - Reestablishment of tertiary structure.
- By chemicals, low temperature.
4. Quarternary structure: Assembly of more than one polypeptide which act as subunits in a multimeric
protein.

 Different subunit chains pack together to give the quaternary conformation.

 E.g. Haemoglobin (4 polypeptides; 2α, 2β)
*GLUT-4: Enables glucose transport into cells

*Sweet proteins – Brazzein

NUCLEOTIDES
It is a condensation product of three chemicals - A pentose sugar
- Phosphoric acid
- A nitrogen base
It is the basic unit of nucleic acid.
Pentose sugar in nucleotides – Two types i.e. Ribose (C5H10O5) & Deoxyribose (C5H10O4)
Nitrogen base are of two types – Purines (Adenine and Guanine) – 9 membered
- Pyrimidines (Cytosine and Thymine), Uracil – 6 membered
Nucleoside = Nucleotide – Phosphoric acid
Higher nucleotides: Nucleotides having more than one phosphate group.

 Occur in free state

 Are high energy carriers.
 E.g. ATP, GTP, GDP etc.
 ATP – Discovered by Karl Lohmann (1929)
 ADP + 8.9 KCal mol-1 (or 8900 calories) → ATP
 AMP + 6.5 KCal mol-1 → ADP

NUCLEIC ACIDS
These are polynucleotides; are long chain macromolecules formed by end to end polymerisation of large
number of nucleotides.
Two types i.e. DNA (Deoxyribonucleic acid) & RNA (Ribonucleic acid)
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PROKARYOTIC DNA EUKARYOTIC DNA

DNA occurs freely inside cytoplasm Not free
Consists of single molecule Has several different molecule
Generally circular Linear
Introns are rare Cistron often contains introns
GC > AT AT > GC

DNA: Formed by cross linking of three chemicals - Phosphoric acid

- Deoxyribose sugar
- Nitrogen base

 Have four type of nitrogenous bases - Adenine

- Guanine
- Cytosine
- Thymine
 The two strands are antiparallel (5’→3’), (3’→5’)
o Template/minus/antisense → Act as template of RNA synthesis
o Non template/plus/sense → Not act as template
 Denaturation - Separation of two strands of DNA
- Due to high temperature, pH etc
 Palindromic DNA – Areas in DNA duplex where sequence of nucleotides is same but opposite in
two strands.

*Term DNA was given by Zacharis

*DNA content – C value in pictograms

*A human cell has 5.6 pg of DNA

RNA: Single strand or chain of a number of ribonucleotides.

 Characterised by presence of RIBOSE SUGAR & URACIL

 Formed through transcription.
 Three main types – rRNA, mRNA, tRNA

*Genetic RNA discovered by Conrat (1957)

1. Ribosomal RNA (rRNA):

 Most abundant RNA; constituent of ribosomes.

 Lies coiled in between and over the protein molecules.

2. Transfer RNA (tRNA):

 Also called soluble or sRNA.

 Smallest RNA
 Nitrogen bases of its some nucleotides get modified result in coiling of single stranded tRNA into L
shaped or clover shaped form.
o Half of nucleotides get paired to produce paired stems.
o Five regions remain unpaired - Amino acid binding site
- Anticodon
- TᴪC loop
- DHU loop
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- Extra arm
- Extra arm
 Anticodon – Made of three nitrogen bases for recognition and attaching to codon of mRNA
 AA binding site - Lies at 3’ end opposite to anticodon
- Also recognition site of tRNA
 TᴪC loop - Contains pseudouridine
- Binding site for ribosomes
 DHU loop - Contains dihydrouridine
- Binding site for amino acyl synthetase enzyme
 Extra arm - Lies between TᴪC loop and anticodon.
- Exact role not known

Function: Is adapter molecule which is meant for transferring amino acids to ribosomes for synthesis of
polypeptides.

3. Messenger RNA (mRNA): It brings instruction from DNA for the formation of particular type of
polypeptide (Instructions present as genetic code).

 mRNA has methylated region at 5’ terminus which functions as a cap for attachment with ribosome.
 Cap is followed by an initiation codon (AUG)
 Then followed by coding region.
 Then termination codon (UAA, UAG, UGA)
 Then small non-coding region and poly A area at 3’ end.

It carries coded information for translation into polypeptide formation.

CONCEPT OF METABOLISM
Dynamic state of body constitution: Flow of metabolites through metabolic pathway has a definite state
and direction. This metabolic flow is called the dynamic state of body constituents.

“There is no uncatalyzed metabolic conversion in living systems”.

Metabolism: It is the sum total of all chemical reactions occurring in an organism.

Turn over: Rate at which new biochemicals are being formed from others while they are themselves being
changed into others.

E.g. Amino acids → Amine + CO2

Metabolic pathway: It is a multistep interlinked series of enzyme catalyzed biochemical reactions in which
product of one reaction generally become substrate for the next.

Anabolic: Formation of more complex structure from a simple structure. E.g. Acetic acid becomes
cholesterol

Catabolic: Degradation of complex to simple. E.g. Glucose becomes lactic acid

ENZYMES
Enzymes - Biomolecules with catalyzing power

- E.g. Proteins, ribozymes

 Enzymes are highly selective unlike catalyst.

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 Increase rate of reaction many thousand fold.

GENERAL RULE OF THUMB: Rate of chemical reaction doubles or decreases by half for every 10oC
rise or fall.

Regulation of biochemical pathways:

 Enzymes have allosteric sites away from active sites. Presence of activator or inhibitor on these sites
switches the enzyme on or off.
 Feedback mechanism – Here the excess final product act as inhibitor for allosteric site leads to
inactivation of enzyme.

THE LIVING STATE:

Living systems always tends to maintain non equilibrium steady state by use of energy mostly, because no
work can be carried out in equilibrium.

METABOLITES:

Primary metabolites: Biochemicals required for basic metabolic processes.

 Produced in large quantities that can be easily extracted from plants.

 These are part of basic molecular structure of the cell.
 E.g. Carbohydrates, fats, proteins, nucleic acids etc.

Secondary metabolites: Organic compounds which are not involved in primary metabolism and have no
direct function in growth and development of plants.

 Produced in small quantities.

 Not part of basic molecular structure of cell.
 E.g. Rubber, gums, morphine, caretonoids, antibiotics, pigments, scents, spices, flavonoids etc.

Functions of secondary metabolites:

1. Help in pollination, seed dispersal by attracting animals.

2. Used in defence by plants.
3. Used in making drugs, insecticides, flavours, scents etc.

Types:

Isoprenoids (or terpenes); Branched chain unsaturated hydrocarbon. E.g. Rubber, steroids, essential oils
(lemon grass oil)

N2 containing: Alkaloids (Morphine, codeine), Glycosides (compound formed from a simple sugar and
another compound by replacement of hydroxyl group in sugar molecule)

Phenolic: Lignin – 2nd abundant polymer on earth after cellulose

Tannins – Derived from Gallic acid

Coumarins – Help in blood thinning, antifungicidal; making perfumes

Aflatoxins – Aspergillus flavus (damage liver)

ENZYMES
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These are commonly proteinaceous (globular) substances which are capable of catalysing chemical reactions
of biological origin without themselves undergoing any change.

 Anselme Payen – first to discover enzyme (Diastase) in 1833.

 Also called biocatalysts.
 Term enzyme was first coined by Kuhne (1878)
 Buchner extracted first enzyme (Zymase).
 Except proteins there are some nucleic acids that behave like enzymes, these are called
“RIBOZYMES”. E.g. 23S rRNA in bacteria
 Substrate: The biochemical which is acted upon by an enzyme is known as substrate.
 Active site: Part of enzyme that takes part in catalysing biochemical reaction is called active site.

CHEMICAL NATURE OF ENZYME:

Two types i.e. Simple and conjugate

SIMPLE ENZYME: Enzyme which is wholly made of protein. E.g. Pepsin, trypsin, urease

CONJUGATE ENZYME: Enzyme which is formed of two parts i.e. Apoenzyme and cofactor

 Apoenzyme: Protein part

 Cofactor: Non protein part either organic or inorganic:
 Organic cofactor:
o Coenzyme – Organic; Loosely bound
o Prosthetic group – Organic; Firmly bound
 Inorganic cofactor:
o Are mainly ions.
o Act as activators
o E.g. Zn for carboxypeptidase

Apoenzyme + Cofactor = Holoenzyme

APOENZYME COENZYME

Protein part of holoenzyme Non protein organic group attached to apoenzyme to

form holoenzyme

Large in size Small in size

Does not help in group transfer Takes part in group transfer

Not heat stable Heat stable

PROSTHETIC GROUP COENZYME (COFACTOR)

Non protein group attached firmly to an apoenzyme Non protein group attached loosely to an apoenzyme

Require a single apoenzyme for picking up and Require different apoenzyme for picking up and
transferring a group transferring a group

E.g. Heme in peroxidise and catalase E.g. NAD+, NADP+ (Both contain vitamin Niacin)
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Coenzymes: These are mostly water soluble vitamins, B, C. E.g. Thiamine, Riboflavin etc.

Inorganic cofactors: Includes ions of variety of minerals. E.g. Ca+, Fe2+, Fe3+, Cu2+, Zn+ (for
carboxypeptidase)

Active site: Area of the enzyme which is capable of attracting and holding particular substrate molecules by
its specific charge, size and shape so as to allow the chemical change.

 Very selective and specific

CLASSIFICATION:
1. Oxidoreductases: -Takes part in oxidation and reduction.

- Are of three types – Oxidases, dehydrogenases, reductases

- E.g. Nitrate reductase

2. Transferases: - Transfer a group from one molecule to another.

- E.g. Glutamate pyruvate transaminase

- Group transfer does not occur in free state

3. Hydrolases:- Catalyse hydrolysis of bonds like ester, ether, peptide, halide etc.

- Break down larger molecules into smaller

- E.g. Sucrase, Lactase etc

4. Lyases: - Cause cleavage, removal of groups without hydrolysis.

- E.g. Aldolase

5. Isomerases - Cause rearrangement of molecular structure to effect isomeric changes

- E.g. Mutase, Isomerase

6. Ligases (Synthetases) - Catalyze bonding of two chemicals with the help of energy.

- E.g. Pyruvate carboxylase

FACTORS INFLUENCING ENZYME ACTIVITY

1. Temperature:

 Active within a narrow range of temperature.

 Optimum temperature: Temperature at which enzyme shows its
highest activity. E.g. 37oC
 Inactive below minimum temperature and beyond maximum
temperature.
 Low temperature preserves enzyme in temporary inactive state.
 High temperature destroys enzymatic activity.

2. Optimum pH:
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 Enzyme is most effective at an optimum pH.

 A rise or fall in pH reduces enzyme activity.

3. Concentration of substrate:

 With increase in concentration of substrate, the velocity of enzyme reaction

rises at first.
 Reaches a maximum velocity (Vmax) at a certain concentration of
substrate (Because all enzyme molecules are occupied now).
 Michaelis constant (Km): Mathematical derivation or constant which
indicates substrate concentration at which chemical reaction
catalyzed by an enzyme attains half of its maximum velocity.
 Km generally lies between 10-1 to 10-6 M

CONCEPT OF ACTIVATION ENERGY

External supply of energy that is needed for the start of chemical reaction is called activation energy.

 Energy barrier of the reactant molecules is overcome with help of activation energy.
 Increase kinetic energy of system.
 Function of enzyme here: Enzyme lowers the activation energy required for a reaction.

Proenzyme - Inactive precursor of an enzyme.

- Also called zymogen

Allosteric enzymes: These are enzymes which have separate areas for
different types of modulators that alter the conformation of active site to
make enzyme effective or ineffective.

Modulator - Activator – Makes active site operational

- Inhibitor – Makes active site unavailable for substrate

Isoenzymes: The multiple molecular forms of an enzyme occurring in the same organism and having a
similar substrate activity are called isozymes.

Same activity but differs in activity optima and inhibition.

INHIBITION OF ENZYME ACTION

Reduction of a stoppage of enzyme activity due to presence of adverse conditions
or chemicals is called enzyme inhibition.

Competitive inhibition: Inhibition of enzyme activity by the presence of chemical

which is similar in structure to substrate that competes with the substrate for
binding to the active site of enzyme.

E.g. Inhibition of succinic dehydrogenase by malanate

Mode of enzyme action: - Lock and key hypothesis – Emil Fischer (1894)
- Induced fit theory – Koshland (1959)