10.2 Proteins and Enzymes
Twenty α-amino acids, joined by peptide bonds and folded into precise shapes, make the proteins that build, move and run every living cell, including the enzymes that catalyse its reactions.
Your hair, your muscles, the haemoglobin that carries oxygen in your blood, the insulin that controls your blood sugar and the antibodies that fight an infection are all proteins. So are the enzymes that digest your food, copy your DNA and make almost every reaction in your body run millions of times faster than it would on its own. A typical human cell contains about ten thousand different kinds of protein, and each one is a chain built from just twenty building blocks, the α-amino acids.
How can twenty small molecules make so many different machines? The answer lies in the order in which they are joined and in the shapes the chains fold into. In this section you will meet the amino acids and their dipolar-ion form, see how peptide bonds join them, describe the four levels of protein structure, learn why boiling an egg changes it for ever, and see how enzymes act as the cell's catalysts.
Amino Acids: the Building Blocks
Amino acids contain an amino group, $\mathrm{{-}NH_{2}}$, and a carboxyl group, $\mathrm{{-}COOH}$. Depending on the position of the amino group relative to the carboxyl group they are called α, β, γ, … amino acids. Only α-amino acids, $\mathrm{H_{2}N{-}CH(R){-}COOH}$, with both groups on the same carbon, are obtained by hydrolysis of proteins; they differ only in the side chain $\mathrm{R}$.
- By the numbers of amino and carboxyl groups: neutral (equal numbers, e.g. glycine, alanine), acidic (more carboxyl groups, e.g. aspartic acid, glutamic acid) and basic (more amino groups, e.g. lysine, arginine).
- By nutrition: non-essential amino acids can be made in the body (glycine, alanine, glutamic acid, …); essential amino acids cannot and must come from the diet. The ten usually listed are valine, leucine, isoleucine, arginine, lysine, threonine, methionine, phenylalanine, tryptophan and histidine.
Except glycine ($\mathrm{R=H}$), all natural α-amino acids have a stereocentre at the α-carbon and are optically active; almost all have the L configuration (the $\mathrm{{-}NH_{2}}$ on the left in a Fischer projection with $\mathrm{COOH}$ at the top). Amino acids are named by three-letter and one-letter codes.
| Amino acid | Codes | Side chain R | Type |
|---|---|---|---|
| glycine | Gly, G | $\mathrm{{-}H}$ | neutral |
| alanine | Ala, A | $\mathrm{{-}CH_{3}}$ | neutral |
| valine* | Val, V | $\mathrm{{-}CH(CH_{3})_{2}}$ | neutral |
| leucine* | Leu, L | $\mathrm{{-}CH_{2}CH(CH_{3})_{2}}$ | neutral |
| serine | Ser, S | $\mathrm{{-}CH_{2}OH}$ | neutral |
| cysteine | Cys, C | $\mathrm{{-}CH_{2}SH}$ | neutral |
| phenylalanine* | Phe, F | $\mathrm{{-}CH_{2}C_{6}H_{5}}$ | neutral |
| Amino acid | Codes | Side chain R | Type |
|---|---|---|---|
| tyrosine | Tyr, Y | $\mathrm{{-}CH_{2}C_{6}H_{4}OH}$ | neutral |
| aspartic acid | Asp, D | $\mathrm{{-}CH_{2}COOH}$ | acidic |
| glutamic acid | Glu, E | $\mathrm{{-}CH_{2}CH_{2}COOH}$ | acidic |
| lysine* | Lys, K | $\mathrm{{-}(CH_{2})_{4}NH_{2}}$ | basic |
| arginine* | Arg, R | $\mathrm{{-}(CH_{2})_{3}NHC({=}NH)NH_{2}}$ | basic |
A selection of the twenty amino acids found in proteins; * marks essential amino acids.
Amino acids are colourless, crystalline solids that melt (usually with decomposition) at high temperatures and dissolve in water, but hardly at all in organic solvents. These are the properties of salts, not of ordinary organic acids or amines, and they come from the fact that an amino acid is a base and an acid in the same molecule.
In an α-amino acid the acidic $\mathrm{{-}COOH}$ group transfers a proton to the basic $\mathrm{{-}NH_{2}}$ group of the same molecule, giving a dipolar ion called a zwitterion (German zwitter, hybrid): $\mathrm{H_{3}\overset{+}{N}{-}CH(R){-}COO^{-}}$. It carries both charges but is electrically neutral overall. In aqueous solution and in the crystal, amino acids exist mainly as zwitterions; the strong attractions between them explain the high melting points and water solubility.
A zwitterion is amphoteric: it accepts a proton from acid (the $\mathrm{{-}COO^{-}}$ becomes $\mathrm{{-}COOH}$, giving a cation) and gives a proton to base (the $\mathrm{{-}NH_{3}^{+}}$ becomes $\mathrm{{-}NH_{2}}$, giving an anion). The pH at which an amino acid is present almost entirely as the neutral zwitterion, and so does not move in an electric field, is its isoelectric point (about 6 for glycine).
Peptides and Proteins
When the $\mathrm{{-}COOH}$ group of one amino acid and the $\mathrm{{-}NH_{2}}$ group of another combine with the loss of a molecule of water, the amide link formed, $\mathrm{{-}CO{-}NH{-}}$, is called a peptide bond (or peptide linkage). The product of two amino acids is a dipeptide; of three, a tripeptide; and so on.
A chain of more than ten amino acid units is a polypeptide. A polypeptide with more than about a hundred amino acid residues, with molar mass above about $10\,000\ \mathrm{g\,mol^{-1}}$ ($10\,000\ \mathrm{u}$), is called a protein. (The dividing line is not sharp: insulin, with 51 amino acids, is also called a protein.) A chain of $n$ amino acids contains $n-1$ peptide bonds and is formed with the loss of $n-1$ water molecules.
Naming peptides. A peptide is written and named from the N-terminal residue (free $\mathrm{{-}NH_{2}}$, on the left) to the C-terminal residue (free $\mathrm{{-}COOH}$, on the right). Gly-Ala and Ala-Gly are different compounds: in Gly-Ala glycine provides the $\mathrm{C{=}O}$ of the peptide bond and alanine the $\mathrm{NH}$. Because the order matters, a few amino acids can make an enormous number of different peptides: $20^{n}$ possible sequences for a chain of $n$ residues.
Fibrous and globular proteins. In fibrous proteins the polypeptide chains run parallel and are held together by hydrogen and disulphide bonds into fibres; they are generally insoluble in water. Examples are keratin (in hair, wool and silk) and myosin (in muscles). In globular proteins the chains coil round to give a roughly spherical shape; they are usually soluble in water. Examples are insulin and the albumins.
The Structure of Proteins and Denaturation
A protein works only if its chain is folded into exactly the right shape. Chemists describe that shape at four levels, from the order of the amino acids up to the packing of several chains together.
- Primary structure: the sequence (order) of amino acids in each polypeptide chain. Any change in it, even of one amino acid, gives a different protein.
- Secondary structure: the shape in which a stretch of the chain exists, held by hydrogen bonds between the $\mathrm{{>}C{=}O}$ and $\mathrm{{-}NH{-}}$ groups of peptide bonds. The two common types are the α-helix, in which the chain twists into a right-handed screw with the $\mathrm{{-}NH}$ of each residue hydrogen-bonded to a $\mathrm{{>}C{=}O}$ of the next turn, and the β-pleated sheet, in which chains stretched out almost to full length lie side by side, held together by hydrogen bonds between neighbouring chains.
- Tertiary structure: the overall folding of the whole polypeptide chain, which gives the fibrous or globular shape.
- Quaternary structure: the arrangement of two or more polypeptide chains (subunits) with respect to one another, in proteins that have more than one chain. Haemoglobin has four subunits, two α and two β chains.
The primary structure is held by covalent peptide bonds. The higher levels are held mainly by weaker interactions between groups along the chain or between chains:
- hydrogen bonds (between $\mathrm{{>}C{=}O}$ and $\mathrm{{-}NH{-}}$ of peptide bonds, and between polar side chains);
- disulphide linkages $\mathrm{{-}S{-}S{-}}$ (covalent bridges formed by oxidation of two cysteine $\mathrm{{-}SH}$ groups);
- electrostatic (ionic) attractions between charged side chains such as $\mathrm{{-}NH_{3}^{+}}$ and $\mathrm{{-}COO^{-}}$;
- van der Waals forces between non-polar side chains.
Tertiary structure is stabilised by all four; secondary structure mainly by hydrogen bonds.
A protein in its natural shape, with its biological activity, is a native protein. A physical change such as heating, or a chemical change such as a change of pH, disrupts the hydrogen bonds and other weak interactions: the 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 remains intact, because peptide bonds are not broken. Examples: the white of an egg (soluble globular albumin) coagulates on boiling; milk curdles when bacteria in it produce lactic acid, which lowers the pH.
Enzymes: Nature's Catalysts
Life depends on thousands of reactions that must run quickly at body temperature and near-neutral pH. Each is speeded up by its own catalyst. (Catalysts and activation energy are explained in Section 3.3.)
Enzymes are biological catalysts; almost all of them are globular proteins. They are
- very efficient: they lower the activation energy of a reaction, often making it millions of times faster;
- highly specific: each enzyme catalyses one reaction, or one type of reaction, of a particular substance, its substrate;
- active under mild conditions of temperature and pH, and inactivated (denatured) by heat or by extremes of pH.
Enzymes are usually named after the compound or the class of reaction they act on, with the ending -ase: maltase hydrolyses maltose to glucose, invertase (sucrase) hydrolyses sucrose, and an oxidoreductase catalyses the oxidation of one substrate together with the reduction of another.
In the simplest picture, the substrate fits into a pocket on the enzyme's surface, the active site, like a key into a lock, forming an enzyme–substrate complex; the reaction happens there, the products leave, and the enzyme is free to act again. Because the fit depends on the exact folding of the chain, any change that denatures the enzyme, such as heating, destroys its activity, and a substance with a similar shape can block the active site. Many medicines work in exactly this way, by blocking an enzyme.
- Bonds and water. $n$ residues in one chain: $n-1$ peptide bonds, $n-1$ water molecules lost on formation and taken up on complete hydrolysis. Several chains: count each chain separately.
- Formula and mass. Add the formulas of the amino acids and subtract $(n-1)\,\mathrm{H_{2}O}$; $M=\sum M_{i}-18.02(n-1)$.
- Counting sequences. $k$ amino acids, each usable any number of times: $k^{n}$ peptides of length $n$. $n$ different residues used once each: $n!$. Repeats: divide by the factorials of the repeat counts.
- Names run from the N-terminus (free $\mathrm{NH_{2}}$) to the C-terminus (free $\mathrm{COOH}$).
1. "Neutral" amino acid does not mean uncharged. In water it is a zwitterion with $+$ and $-$ charges; only its net charge is zero at the isoelectric point.
2. Gly-Ala ≠ Ala-Gly. The order is read from the N-terminus; the two are structural isomers.
3. Denaturation is not hydrolysis. It unfolds the chain (secondary and tertiary structure) but breaks no peptide bonds.
4. Glycine is not chiral. Its α-carbon carries two H atoms.
5. Water count. Forming a pentapeptide releases four water molecules, not five.
In JEE Advanced 2026 (amino acids, with acid–base equilibria); not in the CBSE syllabus, and JEE Main and NEET list only an elementary idea of amino acids.
For an amino acid with no ionisable side chain, the isoelectric point lies midway between the $\mathrm{p}K_{a}$ of the $\mathrm{{-}COOH}$ group and that of the $\mathrm{{-}NH_{3}^{+}}$ group: $\mathrm{pI}=\tfrac{1}{2}(\mathrm{p}K_{a1}+\mathrm{p}K_{a2})$. For glycine ($\mathrm{p}K_{a}\approx2.34$ and $9.60$), $\mathrm{pI}\approx5.97$. For an acidic amino acid take the two lowest $\mathrm{p}K_{a}$ values (aspartic acid: $\tfrac{1}{2}(1.88+3.65)\approx2.76$); for a basic one the two highest (lysine: $\tfrac{1}{2}(8.95+10.53)\approx9.74$). Interactive 1 finds the same values by locating where the net charge is zero.
Exercises
- 1 What are α-amino acids? Write their general formula.
- 2 Classify as neutral, acidic or basic: alanine, aspartic acid, lysine, serine, glutamic acid, arginine.
- 3 What are essential amino acids? Give two examples each of essential and non-essential amino acids.
- 4 What is a zwitterion? Write the zwitterion of alanine.
- 5 Show, with equations, that the glycine zwitterion is amphoteric.
- 6 Why do amino acids have high melting points and dissolve in water but not in benzene?
- 7 Which of the common amino acids is not optically active? Why?
- 8 Towards which electrode does alanine move during electrophoresis at pH 1, at its isoelectric point, and at pH 12?
- 1 What is a peptide bond? Write the equation for the formation of Ala-Gly and mark the peptide bond.
- 2 How do Gly-Ala and Ala-Gly differ?
- 3 How many peptide bonds does a decapeptide (one chain) contain, and how many water molecules does its complete hydrolysis need?
- 4 How many tripeptides can be made from glycine and alanine if each can be used any number of times?
- 5 Find the molar masses of Gly-Gly and of Ala-Ala-Ala.
- 6 Distinguish between a polypeptide and a protein.
- 7 Distinguish fibrous and globular proteins, with one example of each.
- 8 What mass of water is taken up in the complete hydrolysis of $0.0100\ \mathrm{mol}$ of a pentapeptide?
- 1 What is meant by the primary structure of a protein? Why can a change of a single amino acid alter a protein's function?
- 2 Compare the α-helix and the β-pleated sheet.
- 3 Name the forces that stabilise the tertiary structure of a protein.
- 4 What is quaternary structure? Give an example.
- 5 What is denaturation? Which levels of structure are affected?
- 6 Explain what happens to egg white when an egg is boiled.
- 7 Why does milk curdle when it turns sour?
- 8 Is denaturation the same as hydrolysis of a protein? Explain.
- 1 What are enzymes? Give two ways in which they differ from ordinary chemical catalysts.
- 2 Name the enzymes that hydrolyse maltose and sucrose, and give the products.
- 3 Explain, using the idea of an active site, why an enzyme acts only on its own substrate.
- 4 Why does an enzyme stop working when it is heated to $90\ ^{\circ}\mathrm{C}$?
- 5 (Illustrative.) An enzyme lowers $E_{a}$ of a reaction from $75$ to $45\ \mathrm{kJ\,mol^{-1}}$ at $310\ \mathrm{K}$. Assuming $A$ is unchanged, by what factor does the rate increase?
- 6 Insulin has two chains, of 21 and 30 amino acid residues. How many peptide bonds does it have, and how many water molecules are needed to hydrolyse it completely to amino acids?
- 7 (Illustrative.) A single-chain protein has a molar mass of $55\,000\ \mathrm{g\,mol^{-1}}$. Taking $110\ \mathrm{g\,mol^{-1}}$ as the average mass of a residue in a chain, estimate the number of amino acid residues.
E1. Board · 2 marks What is meant by the denaturation of a protein? Give one example, and state which level of structure is not affected.
E2. NEET Which of the following is not an essential amino acid? (A) valine (B) lysine (C) glycine (D) leucine
E3. JEE Main Numerical value. A tripeptide is made from glycine ($75.07$), alanine ($89.09$) and valine ($117.15\ \mathrm{g\,mol^{-1}}$), one residue of each. If $N$ is the number of such tripeptides possible and $M$ is the molar mass of any one of them in $\mathrm{g\,mol^{-1}}$ (water $18.02$), find $N+M$ to the nearest integer.
E4. JEE Main Which statement about protein structure is correct? (A) The α-helix is held mainly by disulphide bonds. (B) In a β-pleated sheet, hydrogen bonds link neighbouring chains lying side by side. (C) Denaturation breaks the peptide bonds. (D) The primary structure is the overall three-dimensional folding of a chain.
E5. Board · 3 marks Distinguish between the primary, secondary and tertiary structures of proteins, naming the bonds or forces involved in each.
E6. Board · Case study Haemoglobin is made of four polypeptide chains, two α and two β, each carrying an iron-containing haem group. In sickle-cell anaemia, one glutamic acid near the start of each β chain is replaced by valine. The altered molecules stick together when they give up oxygen, and the red cells become stiff and sickle-shaped. (a) Which level of structure is changed directly by the mutation, and which level describes the four chains? (2 marks) (b) Classify glutamic acid and valine as acidic, basic or neutral. (1 mark) (c) Suggest why replacing glutamic acid by valine makes the molecules stick together. (1 mark)
Research question. How do "cold-wash" laundry detergents use enzymes to remove stains at $30\ ^{\circ}\mathrm{C}$, and how much energy does washing cooler save?
Why it matters. Heating water uses most of the energy of a washing machine. Detergent makers in Europe, India and elsewhere add proteases (which hydrolyse protein stains such as egg, blood and grass), amylases and lipases, engineered to work at low temperature. Lower wash temperatures cut electricity use and carbon dioxide emissions worldwide.
What to do.
- Explain which bonds a protease breaks in a protein stain, and why the products wash away more easily.
- (Illustrative, constructed for this exercise.) A wash heats $15\ \mathrm{kg}$ of water from $15\ ^{\circ}\mathrm{C}$. Using $c=4.18\ \mathrm{J\,g^{-1}\,K^{-1}}$, find the heat needed to reach $30\ ^{\circ}\mathrm{C}$ and $60\ ^{\circ}\mathrm{C}$, and the saving in kWh ($1\ \mathrm{kWh}=3600\ \mathrm{kJ}$).
- Without an enzyme, stain removal is a chemical reaction with (say) $E_{a}=50\ \mathrm{kJ\,mol^{-1}}$. By what factor is it slower at $303\ \mathrm{K}$ than at $333\ \mathrm{K}$? Use the Arrhenius equation from Section 3.3.
- Explain why simply heating an enzyme detergent to $90\ ^{\circ}\mathrm{C}$ would make it work worse, not better.
Tools: A calculator; detergent packaging (ingredients and recommended temperature); the Arrhenius equation.
Hand in: Your calculations, a short explanation of the enzyme's role, and a recommendation for your household.
Going further. Find out how protein engineers change a few amino acids in a protease to make it work better in the cold, and why that is a change to the primary structure.
🧪 Self-check quiz
Q1. The zwitterion of glycine is
Q2. How many peptide bonds are there in a pentapeptide?
Q3. Denaturation of a protein does not destroy its
Q4. The α-helix is an example of
Q5. Which of these is an essential amino acid?