ChemistryISC Class 12 · Biomolecules

Proteins: Amino Acids, Peptide Bond and Structure (ISC Class 12)

Updated 15 October 2026 · Fact-checked

Proteins are polymers of α-amino acids joined by peptide bonds (–CO–NH–). In water an amino acid exists as a zwitter ion, H₃N⁺–CHR–COO⁻, and is amphoteric. A protein's primary structure is its amino acid sequence; hydrogen bonds give secondary structures (α-helix, β-pleated sheet); further folding gives tertiary and quaternary structures, which denaturation destroys.

Notice that the COOH of one amino acid and the H₂N of the next lose H₂O, leaving the CO–NH peptide bond.

Illustration drawn for QuestionBuddy.

Understand Proteins: Amino Acids, Peptide Bond and Structure

α-Amino acids. Proteins are built from α-amino acids, $H_{2} N - C H (R) - C O O H$ , in which the amino group is on the carbon next to the carboxyl group. About 20 occur in proteins; they differ only in the side chain R. Glycine (R = H) is the only one without a chiral carbon; the rest are optically active and occur as the L-form. Classification: by the relative number of amino and carboxyl groups, amino acids are neutral (one of each, e.g. glycine, alanine), acidic (more –COOH, e.g. aspartic and glutamic acid) or basic (more –NH₂, e.g. lysine). Amino acids that the body can make are non-essential; the ten that must be obtained from the diet (for example valine, leucine, lysine) are essential amino acids.

Zwitter ion and isoelectric point. In an amino acid the acidic –COOH group donates a proton to the basic –NH₂ group of the same molecule, giving a dipolar ion or zwitter ion: $H_{2} N - C H R - C O O H ⇌ H_{3} N^{+} - C H R - C O O^{-}$ . This explains why amino acids are crystalline solids with high melting points and are soluble in water but not in non-polar solvents. The zwitter ion is amphoteric: in acid, –COO⁻ takes a proton and the molecule becomes a cation, $H_{3} N^{+} C H R C O O H$ ; in alkali, –NH₃⁺ loses a proton and it becomes an anion, $H_{2} N C H R C O O^{-}$ . The pH at which the amino acid exists mainly as the neutral zwitter ion and does not move in an electric field is its isoelectric point.

Peptide bond. The –COOH group of one amino acid condenses with the –NH₂ group of another, with loss of water, to give an amide link –CO–NH–, called a peptide bond: $H_{2} N C H_{2} C O O H + H_{2} N C H (C H_{3}) C O O H \to H_{2} N C H_{2} C O N H C H (C H_{3}) C O O H + H_{2} O$ (glycylalanine, Gly-Ala). Two amino acids give a dipeptide, three a tripeptide; more than ten give a polypeptide, and a polypeptide with more than about a hundred amino acid residues (molar mass above 10 000 u) is a protein. A chain of $n$ amino acids has $n - 1$ peptide bonds. The end with the free –NH₂ is the N-terminal; the end with free –COOH is the C-terminal. The order matters: Gly-Ala and Ala-Gly are different dipeptides.

Classification by molecular shape. Fibrous proteins: chains run parallel, held together by hydrogen and disulphide bonds; fibre-like and insoluble in water, e.g. keratin (hair, wool, silk) and myosin (muscles). Globular proteins: chains coil into a spherical shape; usually water soluble, e.g. insulin and albumins.

Levels of structure (definitions only for ISC). Primary: the sequence of amino acids in each chain; changing even one amino acid gives a different protein. Secondary: the regular shape of the chain due to hydrogen bonds between –C=O and –NH– groups of peptide bonds: the α-helix (a right-handed coil held by H-bonds within the same chain) and the β-pleated sheet (chains side by side, nearly fully extended, held by H-bonds between neighbouring chains). Tertiary: the overall folding of the chain, held by hydrogen bonds, disulphide (–S–S–) linkages, van der Waals and electrostatic forces; it gives fibrous or globular shapes. Quaternary: the spatial arrangement of two or more polypeptide subunits in a protein.

Denaturation. A protein in its natural form, with biological activity, is a native protein. Physical change (heat) or chemical change (pH change, acids) disrupts the hydrogen bonds; globules unfold and helices uncoil, and the protein loses its biological activity. This is denaturation. The secondary and tertiary structures are destroyed, but the primary structure stays intact. Examples: coagulation of egg white on boiling and curdling of milk by lactic acid formed by bacteria (or by added vinegar).

Enzymes and hormones (elementary). Almost all enzymes are globular proteins that catalyse biochemical reactions with great specificity. Some hormones, such as insulin, are proteins.

Proteins: Amino Acids, Peptide Bond and Structure: formulas and key facts

Zwitter ion: $H_{2} N - C H R - C O O H ⇌ H_{3} N^{+} - C H R - C O O^{-}$; Amphoteric; cation in acid, anion in alkali.
Peptide bond formation: $H_{2} N C H_{2} C O O H + H_{2} N C H (C H_{3}) C O O H \to H_{2} N C H_{2} C O N H C H (C H_{3}) C O O H + H_{2} O$; Glycine + alanine → Gly-Ala; –CO–NH– link.
Counting in peptides: $n amino acids \Rightarrow (n - 1) peptide bonds and (n - 1) H_{2} O lost$; Molar mass of peptide = sum of amino acids − 18(n − 1).
Levels of structure: $1^{\circ} sequence; 2^{\circ} α -helix, β -sheet; 3^{\circ} folding; 4^{\circ} subunits$; Denaturation destroys 2° and 3°, not 1°.
Shapes: $Fibrous: keratin, myosin; Globular: insulin, albumins$; Fibrous insoluble; globular usually soluble.

How to solve Proteins: Amino Acids, Peptide Bond and Structure questions

ISC asks protein questions as definitions, structure drawings (dipeptides, zwitter ions), counting peptide bonds, and case items on denaturation. Keep the amide link and the four levels of structure at the centre.

1For a dipeptide, join the –COOH of the first-named amino acid to the –NH₂ of the second and remove H₂O; mark the –CO–NH– bond.
2For counts: n residues → n − 1 peptide bonds and n − 1 water molecules (removed on formation, added on hydrolysis).
3For a peptide's molar mass, add the amino acids' molar masses and subtract 18 for each peptide bond.
4For zwitter-ion questions, show H₃N⁺ and COO⁻ and the changes in acid (cation) and alkali (anion).
5For denaturation cases, name the cause (heat or pH), say which structures are lost (2° and 3°) and that the sequence is unchanged.
6Use the exact examples: keratin and myosin (fibrous), insulin and albumins (globular).

Proteins: Amino Acids, Peptide Bond and Structure in real life

Each concept, met in an everyday situation. Read the situation, try the problem, then check the solution. The one-line hook is what to remember.

An enzyme breaks peptide bonds, and heat denatures it

Suppose a cook marinates tough meat in fresh pineapple juice, which contains a protein-digesting enzyme, and finds the meat becomes softer. When she uses canned pineapple juice that has been heated during canning, the meat stays tough.

Which bonds in the meat's proteins does the enzyme break, and what are the products? Why does the heated juice not work?

Try it first, then show the solutionSolution

The enzyme catalyses hydrolysis of peptide bonds: –CO–NH– + H₂O → –COOH + H₂N–.
Breaking peptide bonds in the meat's proteins gives smaller peptides and amino acids, so the tissue softens.
The enzyme is itself a globular protein; heating during canning denatures it by destroying its secondary and tertiary structure.
A denatured enzyme loses its biological (catalytic) activity, although its amino acid sequence is unchanged.

Answer: Peptide bonds are hydrolysed to smaller peptides and amino acids. Heat denatures the enzyme (2° and 3° structure lost), so it no longer catalyses the reaction.

Memory hook: Enzymes are proteins too: heat unfolds them and they stop working.

Tricks to remember Proteins: Amino Acids, Peptide Bond and Structure

Short memory aids. Say each one aloud once, then use it on a question the same day.

Zwitter = hybrid
'Zwitter' means hybrid: one molecule carrying both + (NH₃⁺) and − (COO⁻) charges.
Use it when: Defining and drawing zwitter ions.
1-2-3-4: Sequence, Shape, Shrink-fold, Subunits
Primary = Sequence; Secondary = Shape of the chain (helix or sheet); Tertiary = whole chain folded; Quaternary = Subunits together.
Use it when: Levels of protein structure.
Fibrous for fibres, globular for globes
Keratin (hair) and myosin (muscle) are long fibres; insulin and albumins are compact globes.
Use it when: Classification examples.

Proteins: Amino Acids, Peptide Bond and Structure: solved examples

Ordered from board level to HOTS. Try each one before you open the solution.

Example 1: The peptide link · 1 mark · MCQBoard level

A peptide bond is:
(a) –CO–O–
(b) –CO–NH–
(c) –C–O–C–
(d) –NH–NH–

Try it first, then show the solutionSolution

It forms when –COOH of one amino acid condenses with –NH₂ of another.
The result is an amide link.

Answer: (b) –CO–NH–.

Example 2: Forming Gly-Ala · 2 marks · Short answerBoard level

Write the equation for the formation of the dipeptide glycylalanine (Gly-Ala) from glycine and alanine, and mark the peptide bond.

Try it first, then show the solutionSolution

–COOH of glycine reacts with –NH₂ of alanine, eliminating water (1 mark).
$H_{2} N C H_{2} C O O H + H_{2} N C H (C H_{3}) C O O H \to H_{2} N C H_{2} C O - N H C H (C H_{3}) C O O H + H_{2} O$ ; the bond –CO–NH– is the peptide bond (1 mark).

Answer: H₂NCH₂CO–NHCH(CH₃)COOH + H₂O; –CO–NH– is the peptide bond.

Example 3: Amino acids in acid and alkali · 3 marks · Short answerHarder board level

Write the zwitter ion of alanine, CH₃CH(NH₂)COOH, and the forms it takes (a) in strongly acidic solution and (b) in strongly basic solution. Define isoelectric point.

Try it first, then show the solutionSolution

Zwitter ion: CH₃CH(NH₃⁺)COO⁻ (1 mark).
(a) In acid, COO⁻ accepts H⁺: CH₃CH(NH₃⁺)COOH, a cation. (b) In alkali, NH₃⁺ loses H⁺: CH₃CH(NH₂)COO⁻, an anion (1 mark).
Isoelectric point: the pH at which the amino acid exists mainly as the neutral zwitter ion and does not migrate in an electric field (1 mark).

Answer: CH₃CH(NH₃⁺)COO⁻; cation in acid, anion in alkali; isoelectric point as defined.

Example 4: Classifying amino acids · 3 marks · Short answerHarder board level

(a) Distinguish between essential and non-essential amino acids, with one example of an essential amino acid. (b) Classify glycine, glutamic acid and lysine as neutral, acidic or basic, giving the basis of classification.

Try it first, then show the solutionSolution

(a) Non-essential amino acids are synthesised in the body; essential amino acids are not and must come from the diet, e.g. valine (or leucine, lysine) (1 mark).
(b) The basis is the relative number of –NH₂ and –COOH groups (1 mark).
Glycine: one of each, neutral. Glutamic acid: two –COOH, one –NH₂, acidic. Lysine: two –NH₂, one –COOH, basic (1 mark).

Answer: (a) Diet-dependent versus body-made; valine. (b) Glycine neutral, glutamic acid acidic, lysine basic.

Example 5: A tripeptide in numbers · 5 marks · Long answerHOTS / competency

A tripeptide is made from glycine (M = 75), alanine (M = 89) and valine (M = 117) in the order Gly-Ala-Val.
(a) How many peptide bonds does it contain, and what is its molar mass? [2]
(b) What mass of water is needed to hydrolyse 2.45 g of it completely? [2]
(c) Name the N-terminal and C-terminal residues. [1]

Try it first, then show the solutionSolution

(a) Three residues give 2 peptide bonds; 2 molecules of water are lost (1 mark).
Molar mass $= 75 + 89 + 117 - 2 \times 18 = 245$ g mol⁻¹ (1 mark).
(b) Moles of tripeptide $= \frac{2.45}{245} = 0.010$ mol; each needs 2 mol H₂O (1 mark).
Water $= 0.020 \times 18 = 0.36$ g (1 mark).
(c) N-terminal: glycine (free –NH₂); C-terminal: valine (free –COOH) (1 mark).

Answer: (a) 2 peptide bonds; 245 g mol⁻¹. (b) 0.36 g of water. (c) Glycine (N-terminal), valine (C-terminal).

Where students lose marks in Proteins: Amino Acids, Peptide Bond and Structure

The slips examiners see most often, and what to write instead.

Mistake: Writing 'amino acid' instead of 'zwitter ion'
ISC examiners reported this in a 2025 fill-in on the dipolar form of amino acids.
Do this: The dipolar form H₃N⁺–CHR–COO⁻ is a zwitter ion; with R = H the amino acid is glycine.
Usually costs: 1 mark.
Mistake: Vague words for denaturation
Examiners noted 'milk bursts' or 'cracks' instead of curdling, and the process not named as denaturation (2024).
Do this: Say: the milk curdles; the proteins are denatured (coagulated).
Usually costs: 1 mark.
Mistake: Saying denaturation breaks peptide bonds
Students think denaturation changes the sequence.
Do this: Denaturation destroys secondary and tertiary structure; peptide bonds (primary structure) stay intact. Hydrolysis breaks peptide bonds.
Usually costs: 1 mark.
Mistake: Wrong linkage named
Students confuse peptide and glycosidic linkages, or write 'hydrogen bond' for the link between residues.
Do this: Amino acids: peptide bond (–CO–NH–). Sugars: glycosidic linkage (C–O–C).
Usually costs: 1 mark.

Exam tips

Draw zwitter ions with clear charges on N and O.
When writing a dipeptide, the first-named amino acid provides the –CO– and keeps the free –NH₂ (N-terminal).
For structure questions CISCE needs definitions only; give one stabilising force for each level.
Use NCERT examples exactly: keratin and myosin (fibrous), insulin and albumins (globular); egg white and curdling of milk (denaturation).
In counting questions, show the n − 1 rule.

Practice questions on Proteins: Amino Acids, Peptide Bond and Structure

Write each answer on paper first. Open the hint only if you are stuck, and the answer only when you have finished.

Q1 · 1 mark · MCQBoard level
Which of the following is a fibrous protein?
(a) insulin
(b) albumin
(c) keratin
(d) haemoglobin
Hint
It is found in hair and wool.
Answer
(c) keratin.
Q2 · 2 marks · Short answerBoard level
Define the tertiary and quaternary structures of proteins, and name two forces that stabilise the tertiary structure.
Hint
Folding of one chain versus arrangement of several chains.
Answer
Tertiary: the overall folding of a polypeptide chain, giving fibrous or globular shapes. Quaternary: the spatial arrangement of two or more polypeptide subunits. Forces: hydrogen bonds, disulphide linkages, van der Waals and electrostatic forces (any two).
Q3 · 2 marks · Short answerHarder board level
Distinguish between the α-helix and the β-pleated sheet.
Hint
Where are the hydrogen bonds?
Answer
α-Helix: a single chain twisted into a right-handed coil, held by hydrogen bonds between –C=O and –NH– groups of the same chain. β-Pleated sheet: nearly fully extended chains lying side by side, held by hydrogen bonds between neighbouring chains, giving a pleated (folded) sheet.
Q4 · 3 marks · Short answerHarder board level
A few drops of vinegar are added to warm milk, and the milk curdles. (a) Name the process. (b) Which levels of protein structure are affected and which is not? (c) Give one other example of the same process.
Hint
A change of pH.
Answer
(a) Denaturation (coagulation) of the milk proteins. (b) Hydrogen bonds are disrupted, so the secondary and tertiary structures are lost; the primary structure (sequence) is unchanged. (c) Coagulation of egg white on boiling.
Q5 · 1 mark · Assertion-reasonHarder board level
Assertion (A): Amino acids are amphoteric in nature.
Reason (R): In the zwitter-ion form, an amino acid has both an acidic group (–NH₃⁺) and a basic group (–COO⁻).
(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.
Hint
–NH₃⁺ can give a proton; –COO⁻ can take one.
Answer
(a).
Q6 · 3 marks · Short answerHarder board level
A polypeptide chain contains 50 amino acid residues. How many peptide bonds does it have, and how many water molecules were eliminated in forming it? Would you call it a protein? Explain.
Hint
n − 1 rule; proteins usually have more than about 100 residues.
Answer
49 peptide bonds; 49 water molecules eliminated. It is a polypeptide rather than a protein: proteins usually contain more than about a hundred amino acid residues (molar mass above 10 000 u).
Q7 · 3 marks · Short answerHOTS / competency
A solution of an amino acid is placed in an electric field. Explain what happens at (a) pH 1, (b) pH 13 and (c) the isoelectric point.
Hint
Which form exists at each pH?
Answer
(a) At pH 1 the amino acid is protonated, H₃N⁺CHRCOOH (a cation), so it moves towards the cathode. (b) At pH 13 it is H₂NCHRCOO⁻ (an anion) and moves towards the anode. (c) At the isoelectric point it exists mainly as the neutral zwitter ion and does not move.
Q8 · 3 marks · Case-basedHOTS / competency
Read and answer.
Suppose a hair stylist explains that a 'perm' first uses a chemical that breaks some bonds in the hair protein, the hair is then set on rollers, and a second chemical re-forms the bonds in new positions so the curls stay.
(i) Is hair keratin a fibrous or a globular protein? [1]
(ii) Which type of covalent bond between chains, mentioned in the tertiary structure, is being broken and re-formed? [1]
(iii) Is the primary structure of keratin changed by a perm? Explain. [1]
Hint
Sulphur atoms of cysteine residues form –S–S– links.
Answer
(i) Fibrous. (ii) Disulphide (–S–S–) linkages, which hold the chains in shape. (iii) No. Only the linkages between chains (part of the tertiary structure) are broken and re-formed; the amino acid sequence (peptide bonds) is unchanged.

Test your recall

Answer in your head or on paper first, then open the card. Pulling an answer out of memory makes it stick far better than re-reading.

1.What is a peptide bond?Show answer
The amide link –CO–NH– between the –COOH of one amino acid and the –NH₂ of another.
2.Which amino acid is not optically active?Show answer
Glycine.
3.Which bonds hold the α-helix?Show answer
Hydrogen bonds between –C=O and –NH– groups of the same chain.
4.Which structure survives denaturation?Show answer
The primary structure.
5.Give two globular proteins.Show answer
Insulin and albumins.
6.What is the isoelectric point?Show answer
The pH at which an amino acid exists mainly as the zwitter ion and does not move in an electric field.

Proteins: Amino Acids, Peptide Bond and Structure: frequently asked questions

What is a zwitter ion?

A dipolar ion, H₃N⁺–CHR–COO⁻, formed when the –COOH group of an amino acid transfers a proton to its own –NH₂ group.

What is the difference between fibrous and globular proteins?

Fibrous proteins have parallel chains held by hydrogen and disulphide bonds, are fibre-like and insoluble in water (keratin, myosin). Globular proteins are coiled into spherical shapes and are usually water soluble (insulin, albumins).

What is denaturation of proteins?

Loss of biological activity when heat or a change of pH disrupts hydrogen bonds, destroying the secondary and tertiary structures while the primary structure remains.

What are essential amino acids?

Amino acids that the body cannot synthesise and must obtain from food, such as valine, leucine and lysine.

How many peptide bonds are there in a tetrapeptide?

Three (one fewer than the number of amino acid residues).