NOTE

B I O L O G Y

BIOMOLECULES
TYPES OF PROTEINS AND ENZYMES

Key Takeaways

• Types of proteins on the basis of:

Composition
○ ○ Shape and structure ○ Function

• Catalysts
• Enzymes
○ Types of enzymes ○ Cofactors ○ Mechanism of enzyme action

Prerequisites

Structure of Proteins - Four Levels

Primary structure Secondary structure Tertiary structure Quaternary structure

Proteins

• Proteins are macro (large-sized) biomolecules.

• They are polymers of amino acids joined together by peptide bonds.
• They maintain the structure and function of body tissues and regulate biological processes.

Types of proteins

• Proteins can be divided into different types based on their following features:
○ Composition ○ Shape and structure ○ Function

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Conjugated - They are made up of proteins and a non-protein

part known as the prosthetic group.

(a) Phosphoprotein - Protein + Phosphorus.

E.g., Casein protein in milk.
(b) Glycoprotein - Protein + Carbohydrate.
E.g., Mucin protein in the saliva.
(c) Nucleoprotein - Protein + Nucleic acid (DNA/RNA).
E.g., Ribosome.
Proteins (Based on
Composition) (d) Lipoprotein - Proteins + Lipids. E.g., High density
lipoproteins (HDL) found in blood.
(e) Chromoprotein - Proteins + Pigments.
E.g., Carotenoids found in carrots.

(f) Metalloprotein - Proteins + Metals. E.g., Haemoglobin

in blood which contains iron.

Simple - They are made of only amino “acids. No other

components are present.

(a) Collagen - Present in the skin

(b) Myosin - Present in muscles
(c) Insulin - Produced by pancreas pancreas
(d) Keratin - Present in hairs

Fibrous
• Fibrous proteins, also known as scleroproteins, are generally
elongated and fibrous in nature.
• They act as structural support because they are strong and
insoluble in water.
• Examples: Elastin found in the skin, keratin, collagen, fibroin
Proteins (Based on
Shape and Structure)
Globular
• Globular proteins are relatively compact and spherical in
shape.
• They perform multifunctional roles. They can be hormones,
transporters, defence proteins, and also structural proteins.
• Examples: Ovalbumin found in egg whites, haemoglobin,
insulin, immunoglobulins (antibodies).

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Catalytic
Catalyst is a substance that when added to a reaction, speeds
up or catalyses the reaction without getting consumed itself.

Types of catalysts
Inorganic Organic
• Examples • Examples
○ Platinum ○ Rhodium ○ Biological enzymes
like trypsin and pepsin

Defence
• Defence proteins the body protect against pathogens and
infectious agents.
• Example:
○ The antibodies produced by the immune system are also
made up of proteins. It traps infectious agents.

Transport
• Transport proteins help in moving materials from one place to another.
• Example:
Proteins (Based ○ Haemoglobin helps in the transport of oxygen and carbon
on Biological dioxide.
Function)
Regulatory
• Regulatory proteins, like hormones, regulate the physiological
activities of the organism.
• Examples:
○ Insulin and glucagon regulates blood sugar levels. Angiotensin

regulates blood pressure.

Nutrient
• Nutrient proteins provide nutrients to the body and act as building
blocks for many tissues.
• Examples:
○ Casein and whey

Contractile
• Contractile proteins help in the contraction of muscle tissues.
• Example:
○ Actin and myosin proteins present in muscles help in
muscle contractions.

Structural
• Structural proteins maintain the shape of the cell, and are also an
important part of the connective tissues.
• Example:
○ Collagen present in the skin.

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Enzymes

• Enzymes are biological catalysts that speed up the rate of a biochemical reaction.
• The rate of the reaction is the amount of the product formed per unit time.
• Examples of enzymes: Trypsin and pepsin

Structure of enzymes

• Majority of enzymes are proteins. The only exception is a class of catalytic RNAs, that are
known as ribozymes.

Primary structure

It is the amino acid sequence of the protein that is joined

together by peptide bonds.

Enzyme (Structure) Secondary structure

The polypeptide chain folds upon itself to form an alpha helix or

a beta-pleated structure that isstabilised by hydrogen bonds.

Tertiary structure

• The polypeptide with a secondary structure that further folds

upon itself to form a compact 3D structure.
• Crevices or pockets are made during this folding.

Active sites

• The active sites are the regions where a substrate binds with the enzyme.
• The crevices or pockets that are formed by the folding of the polypeptide chain in the
tertiary structure function as the binding sites.
• The active sites are specific to the substrate. They confer specificity to the enzymes.

Difference between inorganic catalysts and enzymes

Inorganic catalysts Enzymes

• Metal ions • Proteins

• Work efficiently at high temperatures
• Work efficiently at high pressure
○ Example: Platinum in the catalytic
converter of automobiles.
• Get damaged at high temperatures
○ Exception:Exception: Enzymes in the
organisms found in hot vents and
sulphur springs.
○ Stable up to 80°–90°C

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○ Example: Taq polymerase isolated from

Thermus aquaticus (bacteria residing in
hot (springs)

Catalytic converter

Automobile engine Taq polymerase

Thermus aquaticus
• Get damaged at high pressures
• Examples: Chymosin, trypsin, lipases, etc.

Examples of enzymes

Enzyme: RuBisCO
Location: Plants
Function: Carbon fixation
RuBisCO

Enzyme: Amylase
Location: Wheat
Function: Starch digestion
Amylase plays a role in the baking of bread

Enzyme: Chymosin
Location: Rennet
Function: Coagulation of milk
Chymosin plays a role in cheese formation

Enzyme: Alcohol dehydrogenase

Location: Yeast
Function: Fermentation
Alcohol dehydrogenase plays a role
in wine production

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Enzyme: Lipases
Location: Laundry detergent
Function: Removal of oil stains
Lipases are an important part
of laundry detergent

Enzyme: Microbial peroxidases

Location: Microbes
Function: Removal of toxic compounds
Peroxidases are an important part of waste
water management systems

Did you know?

Lactose Intolerance

• Lactose is the main carbohydrate in milk products.

• Lactase enzyme digests lactose.
• People having lactose intolerance are unable to produce lactase enzyme.

Nausea, vomiting

Diarrhea

Symptoms

Stomach ache Individuals suffering from lactose

intolerance must not consume:

Flatulence

Milk Cheese Ice cream

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Types of enzymes

Enzyme

Simple Conjugated

Simple enzymes consist of Conjugated enzymes are made up of

only amino acids (protein). amino acids and a non-protein group.

Apoenzyme Cofactor
(biologically inactive) (Non-protein part)

Holoenzyme = Apoenzyme + cofactor

Cofactors

It is the non-protein part of a conjugated enzyme that makes it catalytically active.

Types of cofactors

Prosthetic group Coenzymes Metal ions

• Organic or inorganic • Organic compounds • Inorganic compounds

compounds • Transiently or temporarily • Required for enzyme
• Tightly bound to the bound to the apoenzymes activity
apoenzyme • Mostly compounds of • Forms coordination bonds
• Part of the active site of vitamin B complex with the side chains at the
the enzymes. • Examples: Coenzyme active site and with
• Examples: Peroxidase NAD and NADP from substrate
and catalase niacin • Examples: Zinc
carboxypeptidase and
carbonic anhydrase

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Mechanism of the action of enzymes

• Enzymes catalyse biochemical reactions.

Chemical reaction

• It is the process of the formation or the breaking of bonds, resulting in a chemical change.

Reactant 1 Reactant 1
+ Product (P)
(Substrate 1) (Substrate 1)

• The substances that go into the chemical reaction are known as reactants or substrates.
• The substances that are produced at the end of the reaction are known as products.

Types of chemical reactions

Endothermic reactions
• A reaction is endothermic when it absorbs heat.
• In an endothermic reaction, the potential energy of the
reactant is lower than the potential energy of the product.
• There is a gain of energy during the reaction (Energy is
required for this reaction).

Chemical Reactions

Energy Products

Reactants Heat of reaction

Progress of reaction

Exothermic reactions
• A reaction is exothermic when it releases heat.
• It involves the loss of energy.
• In an exothermic reaction, the potential energy of the reactant
is higher than the potential energy of the product.
• It involves a loss of energy (Energy is released during the
reaction).

Heat of reaction
Energy Reactants

Products

Progress of reaction

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Transition state

• For a chemical reaction to happen, certain bonds are broken or made.

• The formation or the breaking of the bonds requires the atom to bend or deform.
• The state of the bent or the deformation is known as the transition state or the intermediate
product.

Reactant 1 Reactant 2 Intermediate

+ Product (P)
(Substrate 1) (Substrate 2) product

• The chemical energy of the transition state is higher than the combined chemical energy of
both the reactants.

Activation energy

• To achieve the state of transition, energy is required.

• The difference in the average energy content of the substrate (S) from that of the transition
state is known as activation energy.
• It energy is the energy required to initiate a chemical reaction.

Activation Activation
energy energy

Energy Products Energy Reactants

Reactants Products

Endothermic reaction Exothermic reaction

• Enzymes play a critical role in decreasing the activation energy of the reaction.

Without
Used enzyme

A+B With
(Reactants) enzyme
Energy Time

Released
AB (Product)

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Enzyme-substrate reaction

• The substrate binds to the active site of the enzyme by weak interactions (non-covalent
bonds and weak covalent bonds).

Substrate Substrate
Enzyme Enzyme

Active Site Active Site

• The active site of the enzymes forms weak reversible bonds with the substrate.
• The collective energy released during the formation of large number of weak interactions
and bonds results in a decrease in the activation energy.
• The substrate bound to the enzyme is a transition state structure. Although it is short-lived,
it is essential for catalysis.
• The active site of the enzyme, which is now in a close proximity of the substrate, breaks the
chemical bonds of the substrate, and a new enzyme-product complex is formed.

Substrate + Enzyme E - S Complex E - P Complex

• Enzymes are highly specific (They have a high degree of specificity for their substrates).
• An enzyme can bind to only one kind of a substrate. Therefore, as soon as the product is
formed due to the bond breaking/bond making, the product is released from the active site.
• The free enzyme is now ready to bind to another molecule of the substrate and run through
the catalytic cycle again.

Without enzyme

Activation energy
without enzyme
With Activation energy
Energy

enzyme with enzyme

Reactants Overall energy released

(e.g. CO2 + H2O) during rection

Products (H2CO2)

Reaction coordinate

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Summary Sheet

Based on composition

Simple: Long chains of amino acids

Conjugated: Protein part + Non-protein part
(Prosthetic group)

Types of proteins Based on shape and structure

Fibrous: Form long and narrow fibres and

provide structural support
Globular: Round or spherical in shape and
have multi-functional roles

Based on function

Play a role in structural, defence, contractile,

nutrient, regulatory, transport, and catalytic
activities in the body.

Enzyme

Composition Mechanism of action

Simple enzymes Conjugated enzymes Endothermic reaction Exothermic reaction

Substrate + Enzyme (E) E-S complex E-P complex

Apoenzyme Cofactors
Protein part Non-protein part
(Biologically inactive)

Prosthetic group Coenzymes Metal ions

• Organic compounds • Organic compounds • Inorganic compounds
• Tightly bound to the • Transient association • Required for the activity
apoenzyme with apoenzyme of the active site

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