JEE Advanced 2026 Paper 2 — Full Mock Test (54 Questions, 180 Marks)
Mathematics · Physics · Chemistry
This MCQ module is based on: Protein Structure Enzymes
TOPIC 23 OF 25
Protein Structure Enzymes
🎓 Class 12
Chemistry
CBSE
Theory
Ch 10 – Biomolecules
⏱ ~14 min
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Protein Structure, Denaturation and Enzymes
Part 3 built the polypeptide chain. A chain of amino acids is not yet a working protein — it becomes one only when it folds into a precise three-dimensional shape. Structure and shape of proteins can be studied at four different levels: primary, secondary, tertiary and quaternary, each level being more complex than the previous one.
10.2.3 Structure of Proteins (continued)
(i) Primary structure
Proteins may have one or more polypeptide chains. Each polypeptide in a protein has amino acids linked with each other in a specific sequence, and it is this sequence of amino acids that is said to be the primary structure of that protein.
Any change in this primary structure — that is, in the sequence of amino acids — creates a different protein. A single substitution anywhere along the chain produces a new molecule with, potentially, entirely different biological behaviour.
(ii) Secondary structure
The secondary structure refers to the shape in which a long polypeptide chain can exist. Such chains are found to exist in two different types of structure: the α-helix and the β-pleated sheet. These structures arise due to the regular folding of the backbone of the polypeptide chain due to hydrogen bonding between the >C=O and –NH– groups of the peptide bond.
α-Helix
The α-helix 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), with the –NH group of each amino acid residue hydrogen bonded to the >C=O of an adjacent turn of the helix.
β-Pleated sheet
In the β-pleated sheet structure, all peptide chains are stretched out to nearly maximum extension and then laid side by side, held together by intermolecular hydrogen bonds. The structure resembles the pleated folds of drapery, and therefore is known as the β-pleated sheet.
(iii) Tertiary structure
The tertiary structure represents the overall folding of the polypeptide chains, that is, further folding of the secondary structure. It gives rise to two major molecular shapes, fibrous and globular.
The forces that hold 2° and 3° structure together. The main forces which stabilise the secondary and tertiary structures of proteins are hydrogen bonds, disulphide linkages, van der Waals forces and electrostatic forces of attraction.
(iv) Quaternary structure
Some proteins are composed of two or more polypeptide chains referred to as sub-units. The spatial arrangement of these subunits with respect to each other is known as the quaternary structure. Haemoglobin is the standard example, its primary, secondary, tertiary and quaternary structures together producing the oxygen-carrying molecule.
10.2.4 Denaturation of Proteins
Native protein. A protein found in a biological system with a unique three-dimensional structure and biological activity is called a native protein.
When a protein in its native form is subjected to a physical change such as a change in temperature, or a chemical change such as a change in pH, the hydrogen bonds are disturbed. Due to this, globules unfold and the helix gets uncoiled, and the protein loses its biological activity. This is called denaturation of protein.
The single most examined fact about denaturation. During denaturation the secondary and tertiary structures are destroyed, but the primary structure remains intact. The peptide bonds are not broken — only the weaker hydrogen bonds and other stabilising interactions that hold the folded shape.
Everyday examples
The coagulation of egg white on boiling is a common example of denaturation. Another example is the curdling of milk, which is caused by the formation of lactic acid by the bacteria present in milk — here the agent is a change of pH rather than temperature.
10.3 Enzymes
Life is possible due to the coordination of various chemical reactions in living organisms — the digestion of food, absorption of appropriate molecules, and ultimately production of energy. This process involves a sequence of reactions, and all of them occur in the body under very mild conditions. This occurs with the help of certain biocatalysts called enzymes.
Almost all the enzymes are globular proteins. Enzymes are very specific for a particular reaction and for a particular substrate.
Naming of enzymes
Enzymes are generally named after the compound or class of compounds upon which they work. For example, the enzyme that catalyses the hydrolysis of maltose into glucose is named maltase.
C₁₂H₂₂O₁₁ —[maltase]→ 2 C₆H₁₂O₆
maltose glucose
maltose glucose
Sometimes enzymes are named after the reaction in which they are used. For example, enzymes which catalyse the oxidation of one substrate with simultaneous reduction of another are named oxidoreductase enzymes. The ending of the name of an enzyme is -ase.
10.3.1 Mechanism of enzyme action
Enzymes are needed only in small quantities for the progress of a reaction. Similar to the action of chemical catalysts, enzymes are said to reduce the magnitude of the activation energy.
The NCERT figures to quote. The activation energy for the acid hydrolysis of sucrose is 6.22 kJ mol⁻¹, while the activation energy is only 2.15 kJ mol⁻¹ when it is hydrolysed by the enzyme sucrase. The enzyme does not change the products — it lowers the barrier to reaching them.
🧪 Activity 10.4 — What exactly does boiling do to an egg?L4 Analyse
Everyone has boiled an egg. This activity converts that familiar observation into a precise statement about which bonds break and which do not.
Predict: Egg white is a solution of the globular protein albumin. On boiling it turns into an opaque white solid that never becomes liquid again on cooling. Which bonds have been broken? Write your answer before proceeding.
- List the forces that stabilise the secondary and tertiary structure of a protein.
- List the bond that holds the primary structure together.
- Compare their strengths and decide which will be disrupted by boiling water at 373 K.
- Explain why the change is not reversed on cooling.
- Now explain the curdling of milk on the same principles, identifying the agent involved.
Only the weak interactions break. The peptide bonds survive, so the primary structure is unchanged.
Steps 1–3. The 2° and 3° structures are held by hydrogen bonds, disulphide linkages, van der Waals forces and electrostatic attractions — all comparatively weak. The 1° structure is held by covalent peptide bonds, which are far stronger. Boiling supplies enough energy to disturb the hydrogen bonds but not to break peptide bonds. Hence the helix gets uncoiled and the globules unfold, while the amino acid sequence stays exactly as it was. This is denaturation.
Step 4 — why it is irreversible in practice. Once unfolded, the exposed chains of neighbouring molecules become entangled and form new interactions with one another rather than refolding into their original unique shape. The protein coagulates into an insoluble mass, and the precise native conformation on which biological activity depended cannot reassemble on cooling.
Step 5 — curdling of milk. The principle is identical but the agent differs. Bacteria present in milk produce lactic acid, which lowers the pH. The change in pH alters the charges on the acidic and basic side chains, disrupting the electrostatic and hydrogen-bonding pattern that held the protein folded. The milk protein therefore denatures and coagulates. So denaturation can be brought about by a physical change such as temperature or a chemical change such as pH — and in both cases the answer to "which bonds broke?" is the same: not the peptide bonds.
Intext question
Intext 10.5 — Where does the water present in the egg go after boiling the egg?
Egg white is a colloidal solution of the globular protein albumin in water. On boiling, the protein is denatured — the hydrogen bonds are disturbed, the globules unfold and the helix uncoils. The unfolded chains then become entangled with one another and coagulate, and in doing so they trap the water molecules within the network of the coagulated protein mass. The water is not driven off or chemically consumed; it is simply absorbed and held inside the solidified protein, which is why boiled egg white is a firm solid rather than a dry one.
Competency-Based Questions
A biotechnology laboratory is troubleshooting a batch of a therapeutic enzyme. The purified enzyme worked perfectly at 310 K and pH 7.4, but a batch accidentally held at 353 K for twenty minutes now shows no catalytic activity, although chemical analysis confirms the amino acid composition and sequence are unchanged. A second batch stored at pH 2 is likewise inactive.
1. Name the process that has occurred and explain why the sequence analysis still comes back normal. L2 Understand
The enzyme has undergone denaturation. Heating disturbed the hydrogen bonds, so the globules unfolded and the helix uncoiled, and the protein lost its biological activity. Sequence analysis is unaffected because during denaturation the secondary and tertiary structures are destroyed but the primary structure remains intact — the covalent peptide bonds are not broken, so the order of amino acids is exactly as before.
2. Why does the batch stored at pH 2 behave the same way as the heated batch? L4 Analyse
Denaturation can be brought about by a physical change like temperature or a chemical change like a change in pH. At pH 2 the acidic and basic side chains are protonated differently from their state at pH 7.4, which destroys the pattern of electrostatic attractions and hydrogen bonds holding the folded shape. The outcome is the same: the tertiary and secondary structures collapse and the enzyme loses activity. The everyday parallel is the curdling of milk, caused by lactic acid produced by bacteria.
3. Using the sucrose data in Section 10.3.1, calculate how much lower the activation energy is with the enzyme, and state what the enzyme does not change. L3 Apply
Activation energy for acid hydrolysis is 6.22 kJ mol⁻¹; with the enzyme sucrase it is 2.15 kJ mol⁻¹. The reduction is 6.22 − 2.15 = 4.07 kJ mol⁻¹. What the enzyme does not change is the identity of the products — glucose and fructose are obtained either way — nor the position of equilibrium. Like any catalyst it only lowers the energy barrier, and it is needed in small quantities only.
4. Fill in the blanks: The secondary structures of proteins are the ______ and the ______, and both arise from hydrogen bonding between the ______ and ______ groups of the peptide bond. L1 Remember
α-helix; β-pleated sheet; >C=O; –NH–. In the α-helix the –NH group of each residue is hydrogen bonded to the >C=O of an adjacent turn of the same chain; in the β-pleated sheet the chains are stretched out and held side by side by intermolecular hydrogen bonds.
5. A colleague suggests that since the primary structure is intact, the denatured enzyme should simply be cooled back to 310 K to restore activity. Evaluate this suggestion. L5 Evaluate
The suggestion rests on a correct premise but an unsound conclusion. It is true that the primary structure survives denaturation, and the sequence does carry the information that specifies the fold. But biological activity depends on the protein occupying one unique three-dimensional structure — the native form — and simply removing the stress does not reliably restore it. Once unfolded, the exposed chains of different molecules interact with each other and become entangled, so the protein coagulates into an insoluble aggregate rather than refolding individually. That is exactly what is seen when boiled egg white does not liquefy again on cooling. Since an enzyme is very specific for a particular reaction and a particular substrate, and that specificity comes from the precise shape of its active site, an aggregated protein with the correct sequence but the wrong conformation has no catalytic activity. The practical answer is that the batch must be discarded and the process controlled so the enzyme is never taken outside its narrow window of temperature and pH.
Assertion–Reason Questions
For each pair choose: (A) Both A and R are true and R is the correct explanation of A. (B) Both A and R are true but R is not the correct explanation of A. (C) A is true but R is false. (D) A is false but R is true.
Assertion (A): On boiling an egg, the egg white coagulates and does not liquefy again on cooling.
Reason (R): Heating disturbs the hydrogen bonds, so the globules unfold and the helix uncoils, and the protein loses its native three-dimensional structure.
Answer: A. This is denaturation. The unfolded chains then entangle and coagulate, so the unique native conformation cannot reassemble on cooling.
Assertion (A): Denaturation of a protein destroys its primary structure.
Reason (R): Denaturation is caused by disturbance of hydrogen bonds on heating or on change of pH.
Answer: D. The assertion is false — during denaturation the secondary and tertiary structures are destroyed but the primary structure remains intact, because the covalent peptide bonds are not broken. The reason is a correct description of how denaturation is brought about.
Assertion (A): Enzymes increase the rate of biochemical reactions under mild conditions.
Reason (R): Enzymes reduce the magnitude of the activation energy of the reaction.
Answer: A. Lowering the activation energy is precisely how enzymes accelerate reactions — for sucrose hydrolysis, from 6.22 kJ mol⁻¹ with acid to 2.15 kJ mol⁻¹ with sucrase.
Coming next. Part 5 completes the chapter's content with Sections 10.4 to 10.6 — vitamins and their deficiency diseases, nucleic acids including the structure of DNA and RNA, and hormones.
Frequently Asked Questions
What are the four levels of protein structure?
Primary structure is the specific sequence of amino acids in each polypeptide chain. Secondary structure is the shape the chain adopts, either an α-helix or a β-pleated sheet, arising from hydrogen bonding between the >C=O and –NH– groups of peptide bonds. Tertiary structure is the overall further folding of the secondary structure, giving fibrous or globular shapes. Quaternary structure is the spatial arrangement of two or more polypeptide sub-units with respect to each other.
What is the difference between the alpha helix and the beta pleated sheet?
In the α-helix a single polypeptide chain twists into a right-handed screw, with the –NH group of each amino acid residue hydrogen bonded to the >C=O group of an adjacent turn of the same helix. In the β-pleated sheet the chains are stretched out to nearly maximum extension and laid side by side, held together by intermolecular hydrogen bonds, giving a structure that resembles the pleated folds of drapery.
What is denaturation of proteins and which structures are affected?
Denaturation occurs when a native protein is subjected to a physical change such as a change in temperature or a chemical change such as a change in pH. The hydrogen bonds are disturbed, the globules unfold, the helix uncoils and the protein loses its biological activity. During denaturation the secondary and tertiary structures are destroyed but the primary structure remains intact, because the covalent peptide bonds are not broken.
What are common everyday examples of denaturation?
The coagulation of egg white on boiling is the standard example, caused by heat. The curdling of milk is another, caused by the formation of lactic acid by the bacteria present in milk, so here the agent is a change of pH rather than temperature.
What forces stabilise the secondary and tertiary structures of proteins?
The main forces are hydrogen bonds, disulphide linkages, van der Waals forces and electrostatic forces of attraction. These are all comparatively weak, which is why heating or a change in pH can disrupt them and denature the protein while leaving the much stronger covalent peptide bonds of the primary structure untouched.
How do enzymes work and how are they named?
Enzymes are biocatalysts, and almost all of them are globular proteins. They are very specific for a particular reaction and a particular substrate, are needed only in small quantities, and work by reducing the magnitude of the activation energy — for sucrose hydrolysis the activation energy falls from 6.22 kJ per mole with acid to 2.15 kJ per mole with sucrase. They are generally named after the compound they act on, such as maltase for maltose, or after the reaction, such as oxidoreductase, and the name always ends in -ase.
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