Biomolecules

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2022, Aakash
Aakash BYJU'S.
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rights reserved
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 Key Takeaways
1 Biomolecules

Metabolites 2

3 Carbohydrates

Lipids 4

5 Nucleic Acids

Amino Acids and Protein 6

7 Metabolism

Enzymes 8

Summary
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 Components of Life

Components of life

Organic components Inorganic components

Elements
Biomicromolecules Biomacromolecules (Ca, Mg, etc)

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 Biomolecules

Biomolecules: Carbon containing compounds which form the basic

chemical structure of all life forms

Biomolecules

Micromolecules Macromolecules

● Small size  Large size

● Low mol wt.  High mol wt.
● 18 - 800 Daltons  >1000 Daltons
● Found in the acid soluble pool  Found in the acid insoluble pool
● E.g., Simple sugars, amino acids,  E.g., Complex carbohydrate, lipid,
nucleotides protein, nucleic acids

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 Metabolites
 Carbon content of a cell - Metabolite content
 Metabolites - Molecules that take part in metabolic reaction
 Metabolism : Sum total of all the chemical reactions occurring in the body

Metabolites

Primary metabolites Secondary metabolites

Involved directly in growth Produced for defence purposes
and stress responses
● Carbohydrates ● Coloured pigments - Carotenoids
● Lipids ● Alkaloids - Morphine
● Proteins ● Polymeric substances - Rubber,
Gums
● Nucleic acids
● Essential oils - Lemongrass oil
● Antibiotics, toxin, scents, spices etc

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 Carbohydrates

 Carbohydrates are the hydrates Aldehyde group

of carbon
Keto CH2OH
 Have carbon, hydrogen and CHO group
oxygen in the ratio 1:2:1 C O
H C OH
 Contain at least 3 carbon atoms
 Have multiple –OH groups OH C H OH C H

 General formula- Cn(H2O)n H C OH H C OH

 Can be aldehydes or ketones H C OH H C OH

 Can be classified based on the CH2OH CH2OH
number of monomeric units
 Saccharide = Sugar Glucose (C6H12O6) : Aldose Fructose (C6H12O6) Ketose

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 Carbohydrates

Types of carbohydrates

Monosaccharides Polysaccharides

E.g., glucose, fructose, E.g., glycogen, starch,

mannose, galactose, etc hyaluronic acid, cellulose, etc

Derived monosaccharides Disaccharides Oligosaccharides

E.g., deoxyribose, E.g., sucrose E.g., raffinose,

glucosamine, mannitol, etc stachyose, etc
 Monosaccharides
 Simplest carbohydrates  Glucose (universal sugar) ,
 Form the building blocks of larger fructose (fruit sugar), mannose,
carbohydrates galactose are hexoses

 Cannot be hydrolysed into smaller units

Monosaccharides

Trioses Tetroses Pentoses Hexoses

Have 3 carbon atoms Have 4 carbon atoms Have 5 carbon atoms Have 6 carbon atoms
H O O H O H CH2OH
C O C
H OH H OH
H H
H C OH H OH H OH H C
C OH H
OH OH
H OH
CH2OH CH2OH
C C
CH2OH
H OH
Glyceraldehyde Erythrose Ribose
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Glucose
 Derived monosaccharides
 Modified monosaccharides
 Deoxy sugar : e.g., deoxyribose
 Amino sugar : e.g., glucosamine
 Sugar acid : e.g., glucuronic acid, ascorbic acid
 Sugar alcohol : e.g., mannitol (present in brown algae)

5 5
HOCH2 OH HOCH2 OH
O O

4 C Deoxygenation 4 C
OH on Carbon 2 H H C 1 H H C 1 No OH on Carbon 2

H C C H H C C H
3 2 3 2
OH OH OH H

Ribose (C5) Deoxyribose (C5)

Constituent of DNA

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 Disaccharides
Examples:
● Polymers of monosaccharides with
Sucrose = Glucose +
2 monomeric units
Fructose
● Di = Two; Saccharide = Sugar unit
Lactose = Glucose +
● Two monosaccharide units join with
Galactose
a glycosidic bond

H20 +

Monosaccharide Monosaccharide Disaccharide

(Glucose) (Glucose) (Maltose)
 Oligosaccharides

 Oligosaccharides are the polymers of monosaccharides with 3 - 9 monomeric units.

 Monosaccharides unit are bound together by glycosidic bond.
 Depending on the number of monosaccharide molecules, there are different types of
oligosaccharides.
 E.g. - Raffinose with 3 monomeric units is referred to as a trisaccharide.
 Similarly, stachyose with 4 monomeric units is referred to as a tetrasaccharide.

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 Polysaccharides
 Polysaccharides are the polymers of monosaccharides with 10 or more monomeric units.
 They have a reducing end and a non-reducing end in their chemical structure.

Made up of same Polysaccharides Made up of different

monomeric units monomeric units

Homopolysaccharides Heteropolysaccharides

Structural Storage
Peptidoglycan Agar Hyaluronic acid
polysaccharides polysaccharides

Cellulose Chitin Starch Glycogen Inulin

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 Homopolysaccharides

Storage polysaccharides Structural polysaccharides

Starch
 Polymer of glucose
 Gives blue colour with iodine Cellulose
 Major reserve food in plants  Polymer of glucose
 Consists of amylopectin and  Forms structural part of plants
amylose (cell wall)
 Straight chain and unbranched
Glycogen  Cotton fibres contain 90% of
 Polymer of glucose cellulose
 Food reserve in animals
 Highly branched
 Stored in liver and muscles Chitin
 Polymer of N-acetyl-D-
glucosamine
Inulin  Form structural part of living
 Polymer of fructose organisms (exoskeleton of
 Not metabolised in human body arthropods)
 Stored in Dahlia, dandelion and  Complex polysaccharide
artichoke

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 Homopolysaccharides

Peptidoglycan Agar
 Component of bacterial cell wall, which is  Obtained from the red algae - Gelidium and
degraded by lysozyme Gracilaria

 Made of two different repeating units  Agar is a mixture of agarose and agaropectin
o N-Acetyl glucosamine (NAG)  Used as medium in labs
o N-Acetyl muramic acid (NAM)

Oligopeptide​
Hyaluronic acid
 Responsible for the toughness and flexibility of
cartilage and tendon
 Made of two different units
o D-glucuronic acid
o N-acetyl-D-glucosamine
NAG
NAM

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 Reducing Sugars
 Reducing sugars: Free aldehyde (CHO) H O CH2OH H O
C C
/ketone group (C=O) present C O
H C OH H C OH
 Benedict and Fehling’s test: reducing HO C H
HO C H
HO C H
sugars reduce the Cu2+ ions to Cu+ which H C OH
H C OH
HO C H
gives brick red colour H C OH
H C OH
H C OH
CH2OH
 All monosaccharides are reducing CH2OH CH2OH

sugars
Glucose Fructose Galactose

Monosaccharide
Add an equal
amount of
Benedict’s solution

About 2ml of test Heat in water bath Brick red

solution (glucose) precipitate
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 Non-Reducing Sugars

 Non-reducing sugars: No free aldehyde/ketone group

 All polysaccharides and sucrose are non-reducing
 Among disaccharides, only sucrose is non-reducing sugars

Non-reducing end Reducing end

CH2OH
CH2OH CH2OH CH2OH CH2OH
CH2OH
O O
O O O O H
H CH2OH
H H H H H H H H H
H H H H

H OH H OH H OH H H HO
OH O O
O OH HO OH H H
HO O

H OH H OH H OH H OH
H OH H
n
OH

Polysaccharide Disaccharide: Sucrose

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 Lipids

 Water insoluble organic compounds  They are insoluble in water

 Consists of carbon, hydrogen and  They are not polymeric like
oxygen polysaccharides (carbohydrates)
 Molecular weight is less than 800
daltons

Classification of lipids

Simple Compound Derived

Neutral/ True
Waxes Phospholipids Glycolipids Lipoprotein Chromolipids
fats

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 Simple Lipids
CH2 OH
 Simple lipids are esters (organic acid and alcohol R C OH
react to form esters) of fatty acids with various CH OH
alcohol. O
 Neutral or true fats are esters of fatty acids with CH2 OH
glycerol, called glycerides Glycerol Fatty acid structure
o Glycerol is an alcohol with three carbons, five O ester bonds O
hydrogens, and three hydroxyl (OH) groups
(Trihydroxypropane) H2C OHHO C R H2C O C R

o Fatty acids: Carboxylic acid with an R group O O

attached. R groups can be
HC OHHO C R HC O C R
■ Methyl (-CH3)
■ Ethyl (-C2H5) O

■ 1- 19 (-CH2) groups H2C OHHO C R H2C O C R

triglyceride
3H2O

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Esterification reaction
 Simple Lipids

Glycerides

Monoglycerides Diglycerides Triglycerides

Condensation of one Condensation of two Condensation of three

fatty acid and glycerol fatty acid and glycerol fatty acid and glycerol

C FA C FA C FA

C C FA C FA

C C C FA
Monoglyceride Diglyceride Triglyceride

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 Simple Lipids
Fatty acids
(Based on structure)

Saturated Unsaturated Essential fatty acids:

 Without a double bond
 Mostly solid at room
temperature
 Higher melting point
 With a double bond
 Mostly liquid at room
temperature
 Lower melting point
Cannot be
synthesised by the
body, so they must be
obtained from diet
E.g., Linoleate

OH
Non-essential fatty
O acids: Can be
Arachidonic
acid (20 Carbon synthesised by the
atoms) body
Palmitic acid (16 Carbon atoms)

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 Simple Lipids

Simple lipids
Fats Oils

Similarities Triglycerides Triglycerides

Solid at room Liquid at room

Fats and oils Waxes temperature temperature

Esters of fatty acids Esters of long chain Mainly from Mainly from plant
and glycerol fatty acids and fatty animal sources
E.g.,- Butter, ghee, alcohol sources
oils E.g.,- Bee wax
Differences
Relatively Relatively more
more unsaturated
saturated

High melting Low melting

point point
E.g., Ghee E.g., Oil

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 Compound Lipids
 Esters of fatty acids and  Additional groups could be phosphorus,
alcohol with additional proteins or sugar
groups
 Usually found in cell membrane

Compound lipids

Phospholipids Glycolipids Lipoproteins Chromolipids

 Phosphate group +  Glycolipid = fatty acid +  Contain lipids  Contains pigment
nitrogen choline + alcohol + carbohydrate (phospholipids) such as
fatty acid group and proteins carotenoids
 Major component of  Membranes are  E.g., Carotene and
 Found on the cell
cell membranes composed of vitamin A
membrane surface
proteins
 E.g., Lecithin  Help in cell recognition

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 Derived Lipids

 Lipids derived from simple or conjugated lipids CH3 CH3

 Steroids do not contain fatty acids yet have fat like CH3 CH3
properties
 Most common steroids are sterols CH3

 Complex in structure
HO
 E.g., Cholesterol
o Most common sterols Cholesterol
o Tetracyclic in nature
o Essential component of animal plasma membrane, also
synthesised in live
 E.g., Prostaglandins
o Derived from arachidonic acid
o Group of hormone which function as messenger
substance between the cell

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 Lipids

Functions of lipids

Long term energy storage

Protection against heat loss

(insulation)

Protection against physical shock

Protection against water loss

Chemical messengers
(hormones)
Major component of membranes
(phospholipids)

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 Nucleic Acids
● Nucleic acids are polymers ● Polymers of repeating units of
of macromolecules nucleotides (building blocks)

Monomers of
Nucleic acids Nucleotide nucleic acid

DNA RNA Pentose sugar Nitrogenous base Phosphoric acid

Deoxyribonucleic
Ribonucleic acid
acid
Nucleoside Phosphate
Nitrogenous
Pentose sugar base

Nucleotide
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 Nucleic Acids

Pentose sugar

 5-Carbon monosaccharide
 Central molecule in a nucleotide

RNA has ribose sugar DNA has deoxyribose sugar

Ribose Deoxyribose

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 Nucleic Acids

Heterocyclic Nitrogen-
Nitrogenous bases containing compounds

Purines Pyrimidines

Have double ringed structure Have single ringed structure

H H O H H O H O
N N
C H C H C C H
N H H
N C C H C C N
N C N
C N C N H
H C
H C
C C C C C C
C C C C H O
N N N H H O N
N H N N O N

H H H H H
H

Adenine (A) Guanine (G) Cytosine (C) Uracil (U) Thymine (T)
 In both DNA and RNA  In DNA, cytosine and thymine are found
 In RNA, cytosine and uracil are found

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 Nucleic Acids

Phosphodiester Bond
-
 Ester bond formed between
the phosphate group of one
nucleotide and hydroxyl
group of the sugar of the next
nucleotide
Phosphodiester  Connecting link between two
bond
- consecutive nucleotides

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 Double Helix Model
 Made up of two polynucleotide chains, existing as a double helix
 Two polynucleotide strands are joined together by hydrogen
bonds between purines and pyrimidines

Backbone of DNA
Antiparallel strands

5’ end - 5th carbon of pentose Sugar – phosphate Nitrogen bases facing

sugar is free backbone inside
3’ end - 3rd carbon of pentose
sugar is free Right-handed coiling Purines Pyrimidines

Each base pair strand Helix diameter 2 nm

turns 36 degree Complementary
Helical rise 0.34 nm
base pairing
Full turn involves 10 base pairs Helical pitch 3.4 nm
A T C G
Hydrogen bonds
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 5’ Double Helix Model
3’

0.34 nm 3’
5’
Minor
groove

Major
groove
3.4 nm

5’
3’
Phosphodiester H- Bonds
bond

3’ T A Forms two hydrogen bonds

5’ C G Forms three hydrogen bonds

2 nm
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 DNA
Forms of DNA
(with right handed coiling)

B - form A - form C - form D - form

● Usual DNA ● 11 base pairs per turn ● Like B-form ● Like B-form
● 10 base pairs ● Not perpendicular to the ● 9 base pairs ● 8 base pairs
per turn axis but slightly tilted per turn per turn

● DNA with left-handed coiling is called Z - DNA with 12 base pairs

Chargaff’s rule
● Concluded by Erwin Chargaff for ● (A+T)/ (G+C) constant for a given
DNA molecule species only
● (A + G) Purines = Pyrimidine (T + C) ● Equal proportion of deoxyribose
● A = T and G = C sugar and pentose sugar
 RNA
 Usually single stranded but sometimes double stranded
(Reovirus and Rice dwarf virus)
 Does not follow Chargaff’s rule

Forms of RNA

Messenger (m- RNA) Ribosomal (r- RNA)

Transfer/ soluble
(s- RNA, t- RNA)
 5% of total cellular RNA  80% of total cellular  10-15% of total cellular
RNA RNA

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 Amino Acids
Amino acids General structure: Four substituent
Amino acids are substituted methanes groups occupying the four valency
positions
Based on nature of R group there
are many amino acids. For e.g.,
Carboxyl group

COOH COOH COOH Amine group

H C NH2 H C NH2 H C NH2 H

H CH3 CH2 OH H O
H
Glycine Alanine Serine
N C C

H O
R=H R = CH3 R = CH2-OH
R

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 Classification of Amino Acids

Based on number of amine and carboxyl groups Based on the presence of aromatic ring

Acidic Basic Neutral Non-aromatic Aromatic

1 carboxyl and 2 1 carboxyl and 1 Have aromatic
2 carboxyl and 1
amine group amine group Have straight (benzene) rings E.g.,
amine group
E.g., lysine, E.g., valine, chains and no tyrosine,
E.g., glutamic
arginine and alanine and aromatic rings phenylalanine,
acid, aspartate
histidine glycine tryptophan

COOH H H O O O
H H H
H2N C COOH H2N C C OH H2N C C OH H2N C C OH
CH2 H2N C COOH
CH2
CH2 CH2 CH2
CH2 H
CH2

H2N C H CH2 Glycine

COOH CH2 HN

NH2
OH
Aspartic acid Lysine Phenylalanine Tryptophan Tyrosine
 Amino Acids

Amino acids Essential Non essential

Phenylalanine Proline

Valine Alanine
Essential Non-essential
Threonine Glycine
Obtained through
Synthesised by Tryptophan Glutamate
diet; body does
the body
not synthesise
Isoleucine Cysteine

Methionine Serine
Semi-essential amino acid:
Lysine
Synthesised very slowly by human
beings.

E.g., arginine and histidine

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 Amino Acids

Zwitterions:
 Molecule with one functional group having positive charge and the other
having negative charge
 Positive charge = Negative charge
 Net charge = Zero
 -NH2 is a strong base and can Amino acids Zwitterions
pick up protons (H+) from
Cation Zwitterion Anion
-COOH group
○ Due to this, NH2 acquires +
NH3
+
NH3 NH2
positive charge (NH3+ ) and - -

R C COOH R C COO R C COO

COOH acquires negative
H H H
charge (COO-)

Low pH pH Scale High pH

Different pH = Different states of amino acids

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 Proteins
● Polypeptides are linear chains of amino acids linked by peptide bonds.

● Polypeptides undergo modification to form proteins.

● Proteins are heteropolymers made by different amino acids.

● There are 20 types amino acids, a protein is a heteropolymer and not a homopolymer.

Amino acids Polypeptide Protein

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 Proteins

Formation of peptide bond

Amino acid 1 Amino acid 2 Amino acid 1 Amino acid 2

H O H O H O H O

N C H N C H N C N C H
H C O H C O H C C O

H H H H
R R R R
C-terminal N-terminal

Water molecule elimination Peptide bond

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 Proteins

Structure of proteins

Primary structure

Secondary structure
Complexity

Tertiary structure

Quaternary structure

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 Proteins

Primary structure
 Linear chain of amino acids
 Positional information
 N- Terminal : Free Amine group with alpha carbon
 C-Terminal : Free Carboxyl group with alpha carbon

C-terminal amino acid Amino acids

H O H O H O H O
N C N C N C N C H
H C C C C O

H H H
R H
R R R
N-terminal amino acid

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 Proteins
Secondary structure
 Folding of the polypeptide chain due to interactions between amino acids

Secondary structure

Alpha-helix Beta- pleated sheet

Polypeptide
Segments of
chain folds in the
polypeptide chain
form of right-
line up next to each
handed helices
other resembling
resembling a
pleated paper.
spring. E.g.,
α-helices E.g.,Fibroin β-sheets
Keratin

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Tertiary structure
 Three-dimensional structure
 Protein is folded upon itself
like a hollow woollen ball
 Biologically active
 E.g., Globular protein,
Myoglobin
Tertiary structure
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Proteins
Quaternary structure
 Two or more polypeptide chains
 Each chain = Subunit
 Arrangement of each folded polypeptide chains with
respect to each other determines the structure
 Adult human haemoglobin consists of 4 subunits
o two subunits of α type
o two subunits of β type
● E.g., Haemoglobin
Polypeptide 1
Polypeptide 2
Quaternary structure
 Types of Proteins
Simple
Conjugated proteins
proteins

Based on composition Collagen found Nucleoproteins (prosthetic group-

in the skin nucleic acid) e.g., Protamines.

Myosin found in Metalloproteins (prosthetic group-

the muscles metals) e.g., Ferritin.
Simple Conjugated
Insulin produced Chromoproteins (prosthetic
by the pancreas group-pigment) e.g. Cytochromes.
Protein part +
Composed of Non-protein Phosphoproteins (prosthetic
long chains Keratin found in
part group-phosphoric acid) e.g.,
of amino the hair
(Prosthetic Casein of milk.
acids group)
Lipoproteins (prosthetic group-
Egg albumin
lipids) e.g., Chylomicron.

Glycoproteins (prosthetic group-

Serum globulins
carbohydrates) e.g., Mucin.
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 Types of Proteins

Based on shape and structure

Fibrous Globular

 Form long and  Round or spherical

narrow fibers in shape
 Provide structural  Have multi-
Elastin found support functional role Ovalbumin
in the skin  Examples: Keratin,  Examples: found in egg
collagen, fibroin, Haemoglobin, whites
elastin insulin, ovalbumin

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 Types of Proteins
Based on function

Structural Nutrient Defence Catalytic

Examples: Examples: Examples:
Examples:
Elastin, keratin, Casein, and Enzymes such
Antibodies
collagen whey as trypsin

Contractile Regulatory Transport

Examples: Hormones
Examples:
Examples: (like insulin,
Haemoglobin and
Actin and myosin glucagon) and their
hemocyanin
receptors

Note:
Most abundant animal protein: Collagen
Most abundant protein in the biosphere: RuBisCO
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 Metabolism

Metabolism: All the chemical reactions occurring in a living organism

Metabolism

Anabolism Catabolism

 Biosynthetic pathways ● Breakdown or degradation pathway

 Endothermic ● Exothermic

Energy

Energy

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 ATP - Energy Currency

ATP

Triphosphate
Adenine Ribose

Absorb Release
energy energy

ADP

Diphosphate
Adenine Ribose

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 Metabolic Pathways

High energy Metabolic reactions

ATP Energy
bond are linked to other
Catabolic reactions release energy to

required reactions and are

not isolated
be used in an anabolic reaction

CH2 Adenine

Ribose Anabolic reactions

store energy released
from a catabolic
reaction

CH2 Adenine

Energy ADP
released Ribose

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 Metabolic Pathways
Pyruvic acid
NAD+
CO2 NADH

Acetyl - CoA
CoA Citric Acid (6C)
Metabolic pathways CAA
NAD+
can be cyclic (4C)
NADH
(E.g., Krebs cycle) CO2
NADH

NAD+
NAD+
NADH
FADH2 CO2

FAD

ADP +1P
ATP

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 Metabolic Pathways

Glucose
ATP
ADP
ATP
Unstable ADP
P P
Metabolic pathways Fructose-1, 6-bisphosphate
can be linear
P P
(E.g., Glycolysis) DHAP Glyceraldehyde - 3 -phosphate
NAD+D
All the DHAP will be
NADH
converted into
glyceraldehyde-3- ADP
phosphate ATP
ADP
ATP

Pyruvate

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 Living State

 Living organisms exists in steady state

 Living organisms = non-equilibrium steady state to be able
to perform work
 Biomolecules in steady state = Metabolic flux
 Metabolic flux : rate of turnover of molecules through a
metabolic pathway

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 Enzymes

 Enzymes are usually proteins and act as catalysts

Organic
(speed up a process or reaction without getting Inorganic
catalysts
consumed) also known as biocatalysts. catalysts
(Enzymes)
 Exceptions of enzyme (non-proteinaceous in nature)
o Ribozymes (RNA enzyme) Metal ions or
o Ribonuclease P (RNA enzyme) Proteins complex
molecules
 There are two types of catalysts: organic and inorganic.
 They are unused in reaction. Most of them
Work efficiently
are damaged
 They are highly specific in action due to the presence at high
at high
temperatures
of active site (Crevice or pocket for binding the temperatures
and pressures
substrate). (>40 degree
celsius)
 Enzymes isolated from thermophilic organisms shows
thermal stability even at 80-900C. Example:
Example:
Platinum,
Lipases,
palladium,
chymosin, etc.
etc.

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 Enzymes
Made up Enzymes Made up of
entirely of amino acids
amino acids. and a
For e.g., prosthetic
Simple Conjugated
“pepsin” group

 A coenzyme or metal ion that is very

Apoenzyme Cofactor tightly (covalently or noncovalently)
+
(Protein part) (Non-protein part) bound to the enzyme protein is called
a prosthetic group.
Biologically inactive Activates catalytic activity
 It is a type of the cofactor.
Holoenzyme = Apoenzyme + Cofactor  For example, in peroxidase and
catalase, which catalyse the
The complete, biologically active conjugated breakdown of hydrogen peroxide to
enzyme where both apoenzyme and cofactor are water and oxygen, haem is the
present is known as holoenzyme. prosthetic group and it is a part of
the active site of the enzyme.
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Prosthetic group
● Organic compound,
tightly bound with
apoenzyme
● For e.g., Haem ( present in
peroxidase, it catalyses
hydrogen peroxide)
Enzymes
Types of Cofactor (Non-protein part)
Coenzymes (Organic) Metal ion
● Organic compound, ● For e.g.; enzyme named carboxypeptidase
associated with is associated with zinc
apoenzyme for a short ● Form coordination bonds
period of time
○ with side chains at the active site
● For e.g., NAD and NADP, ○ one or more coordination bonds with
contain vitamin niacin the substrate
Zn tightly bound
carboxypeptidase
Niacin NAD+ Coordination
bond
 Chemical Reaction
Chemical reaction: Process of formation or breaking of bonds

Reactant 1 (Substrate 1) Reactant 2 (Substrate 2) Product (P)

 Rate of reaction: The amount of product formed per unit time

 Catalysed reactions proceed at rates vastly higher than that of uncatalysed one

Without catalyst:

H2CO3-
CO2 H2O
200 molecules

With catalyst:
carbonic
anhydrase
CO2 H2O H2CO3-
2,160,000,000 molecules
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 Chemical Reaction

Chemical Reaction

Endothermic Exothermic

Energy (heat) needed Energy (heat) released

E E
n n
e e Heat of reaction
r Products r Reactants
g g
y Reactants y Products

Progress of reaction Progress of reaction

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 Enzymes

Mechanism of action
Activation
energy:
Substrate (S) + Enzyme (E)
The difference in
free energy
between the
E-S Complex transition state
and that of
reactant
E-P Complex

Enzyme (E) + Product (P) Enzymes increase the rate of reaction by:
 Decreasing the activation energy
 Forming weak bonds with the substrate
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 Enzymes
Enzyme-Substrate complex:
Two important model have been proposed to describe the enzyme and substrate binding.

1. Lock and key model:

Substrates
 Proposed by Fischer
Product
 Enzymes have an active site at which the substrate Active Site
binds.
 The binding of substrate and active site can be
compared to a lock and key mechanism. Enzymes
Enzymes
 Every active site has a specific substrate which can
bind to it. Enzyme - Substrate
complex
2. Induced fit model:
 Proposed by Koshland
Active Site
 The enzyme changes shape on
substrate binding. S
 Enzymes have two groups + S
E E
○ Buttressing (for support)
○ Catalytic ( for catalysis)
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 Factors Affecting Enzyme Activity

Temperature pH
 High temperature : Denaturation ● Enzymes are sensitive to pH
 Low temperature : Temporary ● Rise or fall in pH : reduces enzyme activity
inactive state ● Optimum pH : maximum action

100%
30
Rate of reaction

active enzyme
Temperature

Percentage
1
increases activity 1 2

Optimum rate
20 Denaturation
2
decreases activity

0
0%
10 20 30 40 50 60
Temperature / C
o

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 Factors Affecting Enzyme Activity

Substrate concentration
 Low substrate concentration:
Low enzyme activity
VMax
 Optimum substrate
concentration: Maximum
enzyme activity
 Higher substrate concentration: ½ VMax
No change in maximum activity
 KM (Michaelis constant) :

reaction
Rate of
Indicates the substrate
concentration at which the
chemical reaction catalysed by Substrate
an enzyme attains half its KM concentration
maximum velocity (Vmax)

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 Factors Affecting Enzyme Activity

Inhibitors : Chemicals that shut off enzyme activity

Inhibitors

Non-competitive Competitive Allosteric modulation

Binds to the enzyme at

Resembles the sites other than active
Changes the shape of substrate
active site such that site
substrate is not able Competes with Low molecular
to bind substrate for active site weight substance

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 Inhibitors

Competitive inhibitors

 Effect on Vmax: Decreases

 Effect on Km: Increases for a given substrate
 In the presence of competitive inhibitor more substrate is needed to achieve 1/2 Vmax
 Examples:
o Max inhibition of
alcohol dehydrogenase
Fumarate
by ethanol in +
methanol poisoning Enzyme
Enzyme Succinate Succinate-
o Sulpha drugs for folic acid enzyme complex
synthesis in bacteria
No
o Inhibition of succinic product
dehydrogenase by is formed
malonate and oxaloacetate. Enzyme Malonate Malonate-
enzyme complex

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 Inhibitors

Non-competitive inhibitors

 Effect on Vmax: Decreases

 Effect on Km: Remain same
 Increased substrate levels will not be able to reverse the inhibitor’s action since the
inhibitor is not in direct competition with the substrate
 Examples: Cyanide kills an animal by inhibiting cytochrome oxidase

Normal
Substrate
Non competitive
Inhibitor

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 Inhibitors

Allosteric modulation

 Also known as feedback inhibition

 After binding, they can increase or decrease the enzyme action
 Examples:
o Allosteric inhibition of hexokinase by glucose 6- phosphate
o Phosphofructokinase activated by ADP and inhibited by ATP
o Inhibition of threonine deaminase by isoleucine

Normal
Substrate

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 Classification and Nomenclature
of Enzymes
Enzyme Function Example
Catalyses oxidation-reduction reactions
Oxidoreductase Dehydrogenase
Ared Box Aox Bred

Catalyses transfer of groups between molecules

Transferases Transaminase
A-B C A B-C

Catalyses breaking of bonds by adding water

Hydrolases Proteases
A-B H2O A-H B-OH

Catalyses breaking of bonds without using water

Lyases Aldolase
A=B HX A-X B-H

Catalyses the switch between isomers

Isomerases Isomerase
AB BA

Catalyses joining of molecules by forming bonds

Ligases Ligase
A B ATP A-B ADP

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 Summary

Metabolites

Primary metabolites Secondary metabolites

NH2
R OH
O O
N N Pigments
OH H3C HO
Carotenoids, Anthocyanins, etc.
H2N OH
n N Alkaloids Morphine, Codeine, etc
OH N
OH OH
Mono Terpenoids Monoterpenes, Diterpenes, etc.
Amino acids Fatty acids Nucleobases
saccharides
Essential oils Lemongrass oil, etc,
Nucleotides Toxins Abrin, Ricin

Complex Lectins Concanavalin A

Proteins Lipids carbohydrate Nucleic acids
Drugs Vinblastine, Curcumin, etc

Polymeric Rubber, gums, cellulose

substances

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 Summary

Types of carbohydrates

Monosaccharides Polysaccharides

Derived monosaccharides Derived monosaccharides Oligosaccharides

Classification of lipids

Simple Compound Derived

Neutral/
Waxes
True fats Phospholipids Glycolipids Lipoprotein Chromolipids
 Summary

Amino acids
Amino acids

Essential Non essential

Essential Non-essential Phenylalanine Proline

Valine Alanine
Obtained through
Synthesised by
diet; body does
the body Threonine Glycine
not synthesise
Tryptophan Glutamate

Semi-essential amino acid: Isoleucine Cysteine

Synthesised very slowly by human Methionine Serine

beings.
Lysine

E.g., arginine and histidine

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 Summary

Nucleic acids

Monomers of
Nucleic acids Nucleotide nucleic acid

DNA RNA Pentose sugar Nitrogenous base Phosphoric acid

Deoxyribonucleic
Ribonucleic acid
acid
Nucleoside Phosphate
Nitrogenous
Pentose sugar base

Nucleotide
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 Summary

Double helix model

Backbone of DNA
Antiparallel strands

5’ end - 5th carbon of pentose Sugar – phosphate Nitrogen bases facing

sugar is free backbone inside
3’ end - 3rd carbon of pentose
sugar is free Right-handed coiling Purines Pyrimidines

Each base pair strand Helix diameter 2 nm

turns 36 degree Complementary
Helical rise 0.34 nm
base pairing
Full turn involves 10 base pairs Helical pitch 3.4 nm
A T C G
Hydrogen bonds
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 Summary

Forms of DNA
(with right handed coiling)

B - form A - form C - form D - form

● Usual DNA ● 11 base pairs per turn ● Like B-form ● Like B-form
● 10 base pairs ● Not perpendicular to the ● 9 base pairs ● 8 base pairs
per turn axis but slightly tilted per turn per turn

Forms of RNA

Messenger Ribosomal Transfer/ soluble

(m- RNA) (r- RNA) (s- RNA, t- RNA)
 Summary

Types of proteins

Based on shape and structure

Fibrous Globular

Based on function

Structural Nutrient Defence Catalytic

Contractile Regulatory Transport

 Summary

Inhibitors

Non-competitive Competitive Allosteric modulation

Binds to the enzyme at

Resembles the sites other than active
Changes the shape of substrate
active site such that site
substrate is not able Competes with Low molecular
to bind substrate for active site weight substance

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