Cambridge International AS & A Level Biology 9700: Proteins – Revision Notes

These revision notes cover 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: learning outcomes 1 to 8. It is AS Level content, examined on Papers 1 and 2, and Paper 4 can draw on it. For full explanations and worked examples, use the Proteins study guide.

Course hub: Cambridge A Level Biology · Checklist: 9700 checklist · Exam-style questions: Proteins practice · Check your AS topics: 9700 AS diagnostic · Whole topic: Biological molecules revision notes

Amino acids and peptide bonds (2.3.1)

General structure: a central carbon atom bonded to an amine group (–NH₂), a carboxyl group (–COOH), a hydrogen atom and an R group. About 20 amino acids are used in proteins; only the R group differs. Glycine’s R group is –H; cysteine’s contains sulfur.

      H   R   O
       \  |  //
        N–C–C
       /  |  \
      H   H   OH

Method in steps: drawing a peptide bond forming

1. Draw two amino acids side by side, carboxyl group of the first facing the amine group of the second.
2. Ring the –OH of the carboxyl group and one –H of the amine group.
3. Show these leaving as H₂O.
4. Draw the product with –CO–NH– linking the two, and label it peptide bond.
5. Label the reaction condensation. For the reverse, add H₂O and label it hydrolysis.

Counting rule: a chain of n amino acids has n − 1 peptide bonds and releases n − 1 water molecules when it forms. Count separate chains separately.

Mass rule: Mr of a polypeptide = sum of the amino acid Mr values − 18 × (number of peptide bonds).

Worked reminders

• Mass: alanine (Mr 89) + serine (Mr 105) → Ala–Ser = 89 + 105 − 18 = 176.
• Bonds in a multi-chain protein: chains of 50 and 30 amino acids give (50 − 1) + (30 − 1) = 78 peptide bonds, not 79.
• Direction: in Ala–Ser, alanine keeps its free amine group and serine keeps its free carboxyl group.

The four levels of structure (2.3.2)

Level	What it is	Held by
Primary	Sequence of amino acids in a polypeptide	Peptide bonds (covalent)
Secondary	Regular coiling or folding of the backbone: α-helix or β-pleated sheet	Hydrogen bonds between backbone C=O and N–H
Tertiary	Further folding of the whole chain into a precise 3D shape	Interactions between R groups
Quaternary	Two or more polypeptide chains joined into one functional protein	The same R group interactions, between chains

• α-helix: N–H of one amino acid bonds to C=O of the amino acid four places earlier; R groups point outwards.
• β-pleated sheet: neighbouring lengths of chain lie side by side, hydrogen bonded backbone to backbone.
• Primary structure decides everything else, because the R groups it places along the chain decide how the chain folds.

Interactions that hold proteins in shape (2.3.3)

Interaction	Formed between	Key fact
Hydrophobic interactions	Non-polar R groups	Cluster away from water, inside globular proteins
Hydrogen bonds	Polar R groups; backbone C=O and N–H	Weak individually, many in total
Ionic bonds	Oppositely charged R groups (–NH₃⁺ and –COO⁻)	Disrupted by pH changes
Covalent: disulfide bonds	Sulfur atoms of two cysteine R groups (–S–S–)	Strongest R group link
Covalent: peptide bonds	Amine and carboxyl groups of neighbouring amino acids	Primary structure

Must-know distinctions

• Secondary vs tertiary: secondary uses backbone hydrogen bonds only; tertiary uses R group interactions.
• Tertiary vs quaternary: tertiary is one chain folding; quaternary is more than one chain fitting together.
• Disulfide vs hydrogen bond: disulfide is covalent and only between cysteines; hydrogen bonds are weak and form between many polar groups.
• Condensation vs hydrolysis: condensation removes water and makes the bond; hydrolysis adds water and breaks it.
• Globular vs fibrous (2.3.4):

Globular	Fibrous
Compact, roughly spherical	Long strands or fibres
Generally soluble	Generally insoluble
Physiological roles	Structural roles
Haemoglobin, enzymes	Collagen, keratin

Why globular proteins dissolve: hydrophobic R groups point inwards, hydrophilic R groups face outwards and interact with water.

Haemoglobin (2.3.5 and 2.3.6)

Structure

• Globular protein with quaternary structure.
• Four polypeptide chains: two α-globin (141 amino acids each) and two β-globin (146 each).
• One haem group per chain (four in total). Haem is a prosthetic group with Fe²⁺ at its centre, held in a pocket in the folded chain.
• Chains held together by hydrophobic interactions, hydrogen bonds and ionic bonds.

Structure → function

Feature	Why it matters
Fe²⁺ in each haem	Binds one O₂ reversibly; up to 4 O₂ per haemoglobin
Hydrophilic R groups on the outside	Soluble, so packed densely in red blood cells
Four chains (quaternary structure)	Binding of one O₂ changes the shape, so the next binds more easily: S-shaped dissociation curve (Topic 8)
Reversible binding	Loads O₂ in the lungs, unloads it in respiring tissues
Iron needed to make haem	Too little iron means less haemoglobin and less oxygen carried

The rule of four: 4 chains → 4 haem groups → 4 Fe²⁺ → up to 4 O₂ per haemoglobin molecule. Learn it as one chain of reasoning, because questions often test the counts.

Collagen (2.3.7 and 2.3.8)

Molecule

• Three polypeptide chains, each a helix, wound into a triple helix.
• Hydrogen bonds between the three chains.
• Glycine at almost every third position (Gly–X–Y). Its small R group (–H) fits in the centre of the triple helix, so the chains pack tightly.

Method in steps: molecule to fibre

1. Collagen molecules lie side by side, parallel.
2. Their ends are staggered, so there is no line of weakness.
3. Covalent cross-links form between lysine R groups of neighbouring molecules.
4. Cross-linked molecules form fibrils; fibrils bundle into fibres.

Structure → function: high tensile strength, does not stretch, insoluble. Found in tendons, ligaments, skin, bone, cartilage and artery walls.

Method in steps: a “relate structure to function” answer

1. Pick one structural feature and name it precisely (for example “covalent cross-links between neighbouring collagen molecules”).
2. Say what that feature does physically (molecules cannot slide past each other).
3. Link it to the job the protein does (high tensile strength, so tendons do not tear under tension).
4. Repeat for a second and third feature. Each linked feature is usually worth a mark; a list of features with no links often earns little.

Quick self-test

1. Name the two functional groups present in every amino acid.
2. How many peptide bonds are in a tetrapeptide, and how many water molecules are released when it forms?
3. Cysteine has Mr 121. Calculate the Mr of the dipeptide Cys–Cys. (Mr of water = 18.)
4. Which type of bond holds an α-helix in shape, and between which groups?
5. State the difference between tertiary and quaternary structure.
6. Which interaction is most sensitive to a change in pH? Give the reason.
7. A single polypeptide of 300 amino acids is fully hydrolysed. How many water molecules are used?
8. State two differences between globular and fibrous proteins.
9. How many oxygen molecules can five haemoglobin molecules carry at full saturation?
10. Which ion in haem binds oxygen?
11. Why is glycine found at almost every third position in a collagen chain?
12. Give two features of collagen fibres that stop them breaking under tension.

Answers

1. Amine group (–NH₂) and carboxyl group (–COOH).
2. Three peptide bonds; three water molecules.
3. 121 + 121 − 18 = 224.
4. Hydrogen bonds between the C=O of one amino acid and the N–H of another in the backbone.
5. Tertiary is the 3D folding of one polypeptide chain; quaternary is two or more chains joined into one protein.
6. Ionic bonds: a change in pH changes the charge on R groups such as –NH₃⁺ and –COO⁻.
7. 299.
8. Any two: globular are generally soluble, fibrous insoluble; globular have physiological roles, fibrous structural roles; globular are compact and spherical, fibrous are long strands.
9. 5 × 4 = 20.
10. Iron, Fe²⁺.
11. Its R group is a single hydrogen atom, small enough to fit in the centre of the triple helix, so the three chains can pack closely.
12. Any two: covalent cross-links between neighbouring molecules; staggered ends; hydrogen bonds within the triple helix; many molecules bundled into fibrils and fibres.

Where marks are usually lost

• Missing the –OH on the carboxyl group or the second H on the amine group in a drawn amino acid.
• Showing the water molecule coming from two R groups, or not showing it at all.
• Calling hydrolysis “breaking down” without saying water is added.
• Saying secondary structure is held by R group interactions.
• Writing “bonds between amino acids” instead of naming hydrogen, ionic, disulfide or hydrophobic interactions.
• Putting disulfide bonds between any amino acids, rather than between two cysteines.
• Saying haemoglobin has one haem group, or that the protein part (globin) binds oxygen.
• Describing collagen as one helix, or forgetting the cross-links and staggered ends when explaining strength.
• Stating a structural feature without the function it serves: the mark is usually for the link.

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).