Cambridge International AS & A Level Biology 9700: Proteins – Study Guide

This study guide teaches section 2.3 Proteins, part of Topic 2 Biological molecules, in the Cambridge International AS & A Level Biology 9700 syllabus for examination in 2025, 2026 and 2027. It covers all eight learning outcomes in 2.3. This is AS Level content: it is examined on Paper 1 (Multiple Choice) and Paper 2 (AS Level Structured Questions), and Paper 4 can draw on it because A Level questions require knowledge of the AS content.

Course hub: Cambridge A Level Biology · Printable checklist: 9700 checklist · Condensed version: proteins revision notes · Test yourself: proteins practice questions · Whole topic: Biological molecules overview

What this section covers

Outcome	What you must be able to do
2.3.1	Describe and draw the general structure of an amino acid, and the formation and breakage of a peptide bond
2.3.2	Explain primary, secondary, tertiary and quaternary structure
2.3.3	Describe hydrophobic interactions, hydrogen bonding, ionic bonding and covalent bonding (including disulfide bonds)
2.3.4	State that globular proteins are generally soluble with physiological roles, and fibrous proteins generally insoluble with structural roles
2.3.5	Describe the structure of haemoglobin: two α-globin chains, two β-globin chains and haem
2.3.6	Relate the structure of haemoglobin to its function, including the importance of iron
2.3.7	Describe the structure of a collagen molecule and how molecules form collagen fibres
2.3.8	Relate the structure of collagen molecules and fibres to their function

2.3.1 Amino acids and the peptide bond

The general structure

Every amino acid has the same core. A central carbon atom carries four different groups:

• an amine group, –NH₂
• a carboxyl group, –COOH
• a hydrogen atom, –H
• an R group (side chain), which differs between amino acids.

        H     R     O
         \    |    //
          N — C — C
         /    |    \
        H     H     O — H
   amine group       carboxyl group

About 20 different amino acids are used to build proteins, differing only in their R group. Glycine’s R group is a single hydrogen atom. R groups may be non-polar, polar or charged, and cysteine’s contains sulfur. These differences decide how a chain folds.

When you draw an amino acid, show the –OH of the carboxyl group and both hydrogens of the amine group.

Forming a peptide bond: condensation

Two amino acids join by a condensation reaction. The –OH from the carboxyl group of one amino acid and an –H from the amine group of the other are removed as one molecule of water. A covalent peptide bond, –CO–NH–, forms between the carbon of the first and the nitrogen of the second.

H₂N–CH(R₁)–COOH + H₂N–CH(R₂)–COOH  →  H₂N–CH(R₁)–CO–NH–CH(R₂)–COOH + H₂O
                                                     peptide bond

Two amino acids make a dipeptide; many make a polypeptide, with a free amine group at one end and a free carboxyl group at the other. A protein is one or more polypeptides folded into a specific shape.

Breaking a peptide bond: hydrolysis

Hydrolysis is the reverse. A molecule of water is added across the peptide bond, which breaks and re-forms the –COOH and –NH₂ groups. In cells, protease enzymes catalyse this. In the laboratory, boiling with acid also hydrolyses peptide bonds.

Worked example 1. Glycine has Mr 75 and alanine has Mr 89. (Mr of water = 18.)

(a) Calculate the Mr of the dipeptide Gly–Ala. (b) How many water molecules are released when a single polypeptide of 120 amino acids is made? (c) A protein has two polypeptide chains of 60 and 45 amino acids. How many peptide bonds does it contain?

Solution. (a) One condensation removes one water: 75 + 89 − 18 = 146. (b) A chain of n amino acids has n − 1 peptide bonds, so 120 − 1 = 119 water molecules. (c) Count each chain separately, because the chains are not joined by peptide bonds: (60 − 1) + (45 − 1) = 103 peptide bonds.

2.3.2 The four levels of protein structure

Primary structure is the sequence of amino acids in a polypeptide chain, held by peptide bonds. Changing one amino acid can change how the whole chain folds, because every later level depends on the R groups the sequence sets.

Secondary structure is the regular coiling or folding of the polypeptide backbone, held by hydrogen bonds between the –C=O of one amino acid and the –N–H of another. The R groups are not involved. Two forms:

• α-helix: the chain coils into a spiral. Each –N–H forms a hydrogen bond with the –C=O of the amino acid four places earlier in the chain. The R groups point outwards from the helix.
• β-pleated sheet: lengths of chain lie side by side, and hydrogen bonds form between the backbones of neighbouring lengths, giving a flat, folded sheet.

Tertiary structure is the further folding of the whole chain, helices and sheets included, into a precise three-dimensional shape. It is held by interactions between R groups that may be far apart in the sequence.

Quaternary structure is the association of two or more polypeptide chains into one functional protein. The same interactions as in tertiary structure hold the chains together. A protein made of a single chain has no quaternary structure.

2.3.3 The interactions that hold proteins in shape

Interaction	Between	Notes
Hydrophobic interactions	Non-polar R groups	They cluster together away from water, usually in the middle of a globular protein
Hydrogen bonds	Polar R groups (for example –OH, –NH₂); also backbone C=O and N–H in secondary structure	Individually weak, but there are many
Ionic bonds	R groups carrying opposite charges, such as –NH₃⁺ and –COO⁻	Broken by changes in pH, which alter the charges
Covalent bonds, including disulfide bonds	Peptide bonds join amino acids; disulfide bonds (–S–S–) form between the sulfur atoms of two cysteine R groups	Disulfide bonds are the strongest of the R group interactions

Name the actual interaction and the groups involved: “an ionic bond between oppositely charged R groups” scores, “a bond between amino acids” does not. Covalent bonding covers both the peptide bonds of the primary structure and the disulfide bonds of tertiary and quaternary structure.

Worked example 2. In a folded protein, a cysteine at position 23 lies next to a cysteine at position 88, a lysine R group (–NH₃⁺) lies next to an aspartate R group (–COO⁻), and several leucine R groups (non-polar) sit in the centre. Name the interaction in each case and state which is most likely to survive heating to 60 °C.

Solution. Cysteine–cysteine: a disulfide bond. Lysine–aspartate: an ionic bond. Leucines: hydrophobic interactions. The disulfide bond is covalent, so it is the strongest and most likely to survive heating; hydrogen bonds, ionic bonds and hydrophobic interactions are weaker and are disrupted first.

2.3.4 Globular and fibrous proteins

	Globular proteins	Fibrous proteins
Shape	Chains folded into a compact, roughly spherical shape	Long strands or fibres
Solubility	Generally soluble in water	Generally insoluble
Role	Physiological (metabolic): transport, catalysis, signalling	Structural: strength and support
Examples	Haemoglobin, enzymes, antibodies	Collagen, keratin

Globular proteins are soluble because hydrophobic R groups fold inside and hydrophilic (polar or charged) R groups face outwards, interacting with water.

2.3.5 The structure of haemoglobin

Haemoglobin is the globular protein that carries oxygen in red blood cells. One molecule has:

• four polypeptide chains: two α-globin chains and two β-globin chains. In adult haemoglobin each α chain has 141 amino acids and each β chain has 146.
• one haem group attached to each chain, so four haem groups per molecule. Haem is a non-protein (prosthetic) group with an iron ion (Fe²⁺) at its centre.

Each chain has its own primary, secondary (mostly α-helix) and tertiary structure, folding to leave a pocket that holds its haem group. The four chains fit together into the quaternary structure, held by hydrophobic interactions, hydrogen bonds and ionic bonds.

2.3.6 Relating haemoglobin’s structure to its function

• Iron in haem binds oxygen. Each Fe²⁺ binds one oxygen molecule reversibly, so one haemoglobin molecule carries up to four O₂ molecules. Without enough iron, less haemoglobin is made and the blood carries less oxygen.
• Solubility. Hydrophilic R groups face outwards, so haemoglobin stays dissolved at a very high concentration inside red blood cells.
• Quaternary structure allows cooperative binding. When one oxygen molecule binds, the molecule changes shape slightly, making it easier for the next oxygen to bind. This is why the oxygen dissociation curve in Topic 8 is S-shaped.
• Reversible binding. Oxygen loads in the lungs and unloads in respiring tissues.

Worked example 3. A red blood cell contains about 2.8 × 10⁸ haemoglobin molecules. Calculate the maximum number of oxygen molecules it can carry.

Solution. Four haem groups per molecule, one O₂ per haem: 4 × 2.8 × 10⁸ = 1.12 × 10⁹ oxygen molecules.

For transport of oxygen and carbon dioxide, and the dissociation curve, see the Transport in mammals study guide.

2.3.7 The structure of collagen

One collagen molecule is made of three polypeptide chains. Each chain is a long, tightly wound helix (not an α-helix). The three chains wind round each other to form a triple helix, rather like a rope. Hydrogen bonds between the chains hold the triple helix together.

The primary structure is a repeating pattern: almost every third amino acid is glycine, often written Gly–X–Y. Proline and hydroxyproline are common in the other positions. Glycine has the smallest R group (a hydrogen atom). Every third amino acid sits in the centre of the triple helix, where there is only room for this small R group, so the three chains can pack very closely.

From molecules to fibres.

1. Collagen molecules lie side by side in parallel rows.
2. Neighbouring molecules are staggered, so their ends do not line up. This avoids a line of weakness running across the bundle.
3. Covalent cross-links form between R groups (lysine residues) of neighbouring molecules.
4. The cross-linked molecules form fibrils; many fibrils bundle together into collagen fibres.

Worked example 4. The triple-helical part of one collagen chain has 1011 amino acids in a Gly–X–Y repeat. How many glycine residues are in this region of one chain, and in one collagen molecule?

Solution. One in every three: 1011 ÷ 3 = 337 per chain. Three chains: 3 × 337 = 1011 per molecule.

2.3.8 Relating collagen’s structure to its function

Collagen is a structural protein in skin, tendons, ligaments, bone, cartilage and blood vessel walls. It must resist pulling forces.

• Triple helix with many hydrogen bonds → each molecule is strong and resists stretching.
• Glycine every third position → tight packing of the three chains, adding strength.
• Staggered ends → no weak line across the fibre.
• Covalent cross-links → molecules cannot slide past each other, giving very high tensile strength.
• Many molecules in fibrils and fibres → strength over large distances, for example along a tendon.
• Insoluble → it stays in place in tissues and is not dissolved by body fluids.

Common errors

• Saying the peptide bond forms between two R groups. It forms between the carboxyl group of one amino acid and the amine group of the next.
• Saying secondary structure is held by bonds between R groups. It is held by hydrogen bonds in the backbone.
• Giving “disulfide bonds” as an interaction between any two amino acids. They form only between cysteines.
• Writing that haemoglobin has “one haem group”. There are four: one per chain.
• Describing collagen as a single helix, or calling its chains α-helices.
• Forgetting the cross-links and the staggered arrangement when asked how fibres resist tension.

Where to go next

• Condensed recall: Proteins revision notes
• Exam-style questions with mark-by-mark answers: Proteins practice questions
• Whole of Topic 2: revision notes and practice questions
• How protein shape controls enzyme action: Enzymes study guide
• Check your AS topics: 9700 AS diagnostic

Official syllabus

Cambridge International AS & A Level Biology 9700 syllabus for examination in 2025, 2026 and 2027, Cambridge University Press & Assessment – Topic 2, Biological molecules (section 2.3 Proteins).