Exhaustive Guide: Proteins, Enzymes & Vitamins | Biomolecules | ChemCA

Proteins, Enzymes & Vitamins

Module 2 | CBSE Class 12 Chemistry | Biomolecules

1. Amino Acids: The Building Blocks

Proteins are the most abundant biomolecules of the living system. Chief sources of proteins are milk, cheese, pulses, peanuts, fish, meat, etc. All proteins are polymers of α-amino acids.

Amino acids contain both an amino (-NH₂) and a carboxyl (-COOH) functional group. In α-amino acids, the -NH₂ group is attached to the α-carbon (the carbon atom directly adjacent to the carboxyl group).

1.1 Essential vs. Non-Essential Amino Acids

Non-Essential Amino Acids: The amino acids which can be synthesized in our body are known as non-essential amino acids. Examples: Glycine, Alanine, Glutamic acid.
Essential Amino Acids: The amino acids which cannot be synthesized in our body and must be obtained through our diet are known as essential amino acids. Examples: Valine, Leucine, Isoleucine, Lysine.

1.2 Zwitterion & Isoelectric Point (Highly Tested)

Amino acids are usually colourless, crystalline solids. These are water-soluble, high melting solids and behave like salts rather than simple amines or carboxylic acids.

Why do they behave like salts? (Zwitterion Formation)
In aqueous solution, the carboxyl group (-COOH) can lose a proton (H⁺) and the amino group (-NH₂) can accept a proton. This internal acid-base reaction forms a dipolar ion known as a Zwitterion.
H₂N-CH(R)-COOH ⇔ ⁺H₃N-CH(R)-COO^- (Zwitterion)

In zwitterionic form, amino acids show amphoteric behavior as they react both with acids and bases.

In acidic medium, the -COO^- group accepts a proton, and the molecule becomes positively charged (moves to the cathode).
In basic medium, the -NH₃⁺ group loses a proton, and the molecule becomes negatively charged (moves to the anode).

Isoelectric Point: The specific pH at which the amino acid molecule carries no net electric charge (exists purely as a zwitterion) and does not migrate in an electric field is called its isoelectric point. At this point, the amino acid has minimum solubility in water.

2. Peptides and Proteins

2.1 The Peptide Bond

Proteins are formed by joining the carboxyl group of one amino acid to the α-amino group of another amino acid. This linkage is an amide formed by the elimination of a water molecule.

Peptide Linkage: -CO-NH- bond formed between two amino acids.
H₂N-CH₂-COOH (Glycine) + H₂N-CH(CH₃)-COOH (Alanine)
→ H₂N-CH₂-CO-NH-CH(CH₃)-COOH (Glycylalanine, a dipeptide) + H₂O

When the number of such amino acids is more than ten, the products are called polypeptides. A polypeptide with more than hundred amino acid residues, having molecular mass higher than 10,000 u, is called a protein.

2.2 Classification: Fibrous vs. Globular Proteins

Fibrous Proteins	Globular Proteins
Polypeptide chains run parallel and are held together by hydrogen and disulphide bonds.	Chains of polypeptides coil around to give a spherical (globe-like) shape.
They possess a fibre-like structure.	They are highly folded and compact.
They are generally insoluble in water.	They are generally soluble in water.
Examples: Keratin (in hair, wool, silk), Myosin (in muscles).	Examples: Insulin, Albumin (egg white), Hemoglobin.

3. Structure of Proteins (1°, 2°, 3°, 4°)

The structure and shape of proteins can be studied at four different levels.

Primary Structure (1°): Proteins may have one or more polypeptide chains. The specific sequence in which amino acids are linked with each other constitutes the primary structure. Note: Any change in this primary sequence (even a single amino acid) creates a different protein and can lead to diseases like sickle cell anemia.
Secondary Structure (2°): It refers to the shape in which a long polypeptide chain can exist. They are found to exist in two different types of structures: α-helix and β-pleated sheet.
Tertiary Structure (3°): Represents overall folding of the polypeptide chains (further folding of the secondary structure). It gives rise to two major molecular shapes: fibrous and globular. The main forces stabilizing the 2° and 3° structures are hydrogen bonds, disulphide linkages, van der Waals, and electrostatic forces of attraction.
Quaternary Structure (4°): Some proteins are composed of two or more polypeptide chains referred to as sub-units. The spatial arrangement of these sub-units with respect to each other is known as quaternary structure.

3.1 Deep Dive: Secondary Structure (α-helix & β-pleated sheet)

A. α-Helix Structure: It is one of the most common ways in which a polypeptide chain forms all possible hydrogen bonds by twisting into a right-handed screw (helix). The -NH group of each amino acid residue is hydrogen bonded to the >C=O of an adjacent turn of the helix.

B. β-Pleated Sheet Structure: All polypeptide chains are stretched out to nearly maximum extension and then laid side by side. They are held together by intermolecular hydrogen bonds. The structure resembles the pleated folds of drapery.

4. Denaturation of Proteins (Board Favorite)

A protein found in a biological system with a unique 3-dimensional structure and biological activity is called a native protein.

Denaturation: When a protein in its native form is subjected to physical change like change in temperature or chemical change like change in pH, the hydrogen bonds are disturbed. Due to this, globules unfold and helix gets uncoiled, and protein loses its biological activity. This is called denaturation of protein.

What happens structurally during Denaturation?
During denaturation, the secondary (2°) and tertiary (3°) structures are destroyed, but the primary (1°) structure remains intact (the peptide bonds do not break).

Common Examples:
- Coagulation of egg white on boiling.
- Curdling of milk (caused due to the formation of lactic acid by bacteria present in milk).

5. Enzymes

Enzymes are biocatalysts that catalyze the numerous reactions occurring in the body. Almost all enzymes are globular proteins.

They are highly specific for a particular reaction and a particular substrate. (e.g., Maltase only hydrolyzes maltose).
They are needed in very small quantities and operate at optimum temperature (37°C) and optimum pH in the body.
Mechanism: Enzymes lower the activation energy of the reaction. For example, the activation energy of acid hydrolysis of sucrose is 6.22 kJ/mol, while the activation energy is only 2.15 kJ/mol when hydrolyzed by the enzyme sucrase.

6. Vitamins & Deficiency Diseases

Vitamins are organic compounds required in the diet in small amounts to perform specific biological functions for normal maintenance of optimum growth and health of the organism.

Classification of Vitamins

Fat Soluble Vitamins: Vitamins which are soluble in fat and oils but insoluble in water. They are stored in liver and adipose (fat storing) tissues. Examples: Vitamins A, D, E, and K.
Water Soluble Vitamins: B group vitamins and vitamin C are soluble in water. They must be supplied regularly in diet because they are readily excreted in urine and cannot be stored in our body (Except Vitamin B₁₂, which can be stored in the liver).

High-Yield Table: Vitamins & Deficiency Diseases

Vitamin	Chemical Name	Deficiency Disease
Vitamin A	Retinol	Xerophthalmia (hardening of cornea), Night blindness.
Vitamin B₁	Thiamine	Beri-beri (loss of appetite, retarded growth).
Vitamin B₂	Riboflavin	Cheilosis (fissuring at corners of mouth and lips).
Vitamin B₁₂	Cyanocobalamin	Pernicious anemia (RBC deficient in hemoglobin).
Vitamin C	Ascorbic Acid	Scurvy (bleeding gums).
Vitamin D	Calciferol	Rickets (bone deformities in children), Osteomalacia in adults.
Vitamin K	Phylloquinone	Increased blood clotting time.

7. NCERT Solved Examples (Step-by-Step)

NCERT Example 14.3: Why are amino acids usually solid at room temperature and have high melting points, unlike simple amines or carboxylic acids?

Solution:
In an aqueous solution or in solid state, the carboxyl group (-COOH) of an amino acid loses a proton and the amino group (-NH₂) accepts that proton to form a dipolar ion called a Zwitterion (⁺H₃N-CH(R)-COO^-).
Because of this zwitterionic nature, strong electrostatic forces of attraction (ionic interactions) exist between the molecules, causing them to behave like salts. Consequently, they are crystalline solids with high melting points.

NCERT Example 14.4: What is the difference between a nucleoside and a nucleotide? *(Note: This connects to nucleic acids, but often appears alongside protein basics)*

Solution:
A Nucleoside consists of two components: a nitrogenous base and a pentose sugar.
A Nucleotide consists of three components: a nitrogenous base, a pentose sugar, and a phosphoric acid (phosphate) group. Phosphorylation of a nucleoside yields a nucleotide.

8. Previous Year Questions (PYQs) & Exhaustive Question Bank

Part A: Conceptual (1-2 Marks)

[CBSE 2018, 2021]

Q1. What type of bonding helps in stabilizing the $\alpha$-helix structure of proteins?

Answer: The $\alpha$-helix structure is primarily stabilized by hydrogen bonds. These hydrogen bonds are formed between the -NH group of one amino acid residue and the >C=O group of an adjacent turn of the helix (typically 3.6 amino acids away).

[CBSE 2017, 2020]

Q2. Define Denaturation of proteins. Does it affect the primary structure of proteins?

Answer: Denaturation is the process where a native protein loses its biological activity due to physical (heat) or chemical (pH) changes that disrupt its hydrogen bonds, causing globules to unfold and helices to uncoil.
No, denaturation does not affect the primary structure. The sequence of amino acids linked by peptide bonds remains entirely intact. Only the secondary and tertiary structures are destroyed.

Part B: Assertion-Reason Type (1 Mark)

[CBSE Sample Paper 2024]

Q3. Assertion (A): Vitamin C cannot be stored in our body.
Reason (R): Vitamin C is a water-soluble vitamin and is readily excreted in urine.

Answer: Both Assertion and Reason are correct, and Reason is the correct explanation for Assertion. Because it dissolves in water, the body cannot store it in fatty tissues or the liver. It passes through the bloodstream and the excess is excreted via urine, necessitating regular dietary intake.

Part C: Differences & Classifications (3 Marks)

[CBSE 2016, 2019]

Q4. Differentiate between:
(a) Globular and Fibrous proteins.
(b) Essential and Non-essential amino acids.

Answer:
(a) Fibrous proteins have polypeptide chains running parallel to form fiber-like structures, are insoluble in water, and are stabilized by strong hydrogen/disulphide bonds (e.g., Keratin). Globular proteins have polypeptide chains folded into a spherical shape, are generally soluble in water, and are biologically highly active (e.g., Insulin).

(b) Essential amino acids cannot be synthesized by the human body and must be supplied through the diet (e.g., Valine, Leucine). Non-essential amino acids can be synthesized within the body (e.g., Glycine, Alanine).

[CBSE 2015]

Q5. Name the diseases caused by the deficiency of Vitamin A, Vitamin B₁₂, and Vitamin D.

Answer:
- Deficiency of Vitamin A (Retinol) causes Night Blindness and Xerophthalmia.
- Deficiency of Vitamin B₁₂ (Cyanocobalamin) causes Pernicious Anemia.
- Deficiency of Vitamin D (Calciferol) causes Rickets in children and Osteomalacia in adults.

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Exhaustive Guide: Proteins, Enzymes & Vitamins | Biomolecules