Biomolecules — Proteins & Nucleic Acids

Question 1 (10 marks)

(a) Sulphur is found in the R-groups of the amino acids cysteine (and methionine) (1). Cysteine's –SH groups form disulphide bonds/bridges (1) which stabilise tertiary structure (1). Why: only certain amino acid side chains carry S, and cross-linking of two cysteines fixes the 3-D fold.

(b) "4 polypeptide chains" refers to quaternary structure (1) — quaternary structure exists only when two or more separate polypeptide subunits assemble into one functional protein (1). (This description matches haemoglobin.)

(c) Denaturation (1). Heat disrupts the weak bonds (hydrogen bonds, ionic bonds, hydrophobic interactions) holding the tertiary/quaternary shape (1), so the protein unfolds/loses its specific 3-D shape and active site, but the sequence of amino acids (primary structure) and peptide bonds remain intact (1). Why: peptide bonds are strong covalent bonds not broken by mild heat.

(d) Generally no — for most proteins denaturation is irreversible because the exact folding pathway/native shape cannot be spontaneously recovered once disrupted (1). The primary structure is unchanged but refolding to the precise functional conformation does not occur (1). (Accept: some small proteins can renature, but a large multi-subunit oxygen-carrier typically does not.)

Question 2 (11 marks)

(a) Central (alpha) carbon bonded to: amino group –NH₂ (1), carboxyl group –COOH (1), hydrogen atom –H and variable R-group / side chain (1 for both correctly shown/labelled).

        H
        |
 H2N — C — COOH
        |
        R

(b) Dipeptide with peptide bond (–CO–NH–) between glycine's carboxyl C and alanine's amino N:

$\text{H}_2\text{N–CH}_2\text{–}\underbrace{\text{CO–NH}}_{\text{peptide bond}}\text{–CH(CH}_3\text{)–COOH}$

Correct backbone (1); correct peptide linkage formed at right groups (1); peptide bond circled/identified (1).

(c) Condensation (dehydration synthesis) reaction (1); water (H₂O) released (1).

(d) Tripeptide: 2 peptide bonds (1), 2 water molecules released (1). General: for $n$ amino acids in one chain, water released $= n - 1$ (1).

Question 3 (10 marks)

(a) Template read $5'$→$3'$: A T G C C A T G. Complement is antiparallel:

Original: $5'$–A T G C C A T G–$3'$ Complement: $3'$–T A C G G T A C–$5'$

Written conventionally $5'$→$3'$: $5'$–C A T G G C A T–$3'$

Correct base pairing (A–T, G–C) (1); antiparallel/correct end labelling (1); correct final sequence (1).

(b) Given strand A T G C C A T G:

• Purines (A, G): A, G, A, G = 4 purines (1)
• Pyrimidines (C, T): T, C, C, T = 4 pyrimidines (1)

Chargaff for whole duplex: %G = %C = 30%, so G + C = 60% (1). Remaining 40% is A + T, and %A = %T, so %A = 20% (1).

(c) Any two (1 each, +1 for correctness): sugar changes from deoxyribose → ribose; base thymine (T) replaced by uracil (U); RNA is typically single-stranded (shorter/no complementary strand needed). (max 3)

Question 4 (10 marks)

(a) (1 each)

• Glucose (reducing sugar): Benedict's reagent, heat → brick-red/orange precipitate
• Starch: Iodine solution → blue-black
• Protein: Biuret reagent → violet/purple
• Lipid: Sudan III/ethanol emulsion test → red-stained layer / white emulsion

(b) Benedict's positive → contains a reducing sugar (1). Biuret positive → contains protein (1). Iodine negative → no starch present (1).

(c) No — the Benedict's test only shows a reducing sugar is present; it does not distinguish a monosaccharide (e.g. glucose) from a reducing disaccharide (e.g. maltose) (1). "Sweetness" is not a valid chemical criterion (1). To confirm a disaccharide you would need e.g. a further test (boil with acid then re-test) — so the claim is not justified by Benedict's alone (1).

Question 5 (9 marks)

(a) Adenine (nitrogenous base) (1), ribose (5-carbon sugar) (1), three phosphate groups (1).

(b) Energy is stored in the bonds between phosphate groups (1). Hydrolysis removes the terminal phosphate, breaking the bond and releasing energy (1), converting ATP → ADP + inorganic phosphate (Pi) (1).

(c) ATP is continuously regenerated — ADP + Pi are recombined using energy from respiration (1), so ATP is recycled rapidly (turned over) rather than stored in bulk (1); the rate of synthesis matches the rate of use, keeping concentration steady (1).

[
  {"claim": "n amino acids joined in one chain release n-1 water molecules; for n=3 this is 2",
   "code": "n=3; water=n-1; result = (water==2)"},
  {"claim": "Given strand ATGCCATG has 4 purines and 4 pyrimidines",
   "code": "s='ATGCCATG'; pur=sum(1 for b in s if b in 'AG'); pyr=sum(1 for b in s if b in 'CT'); result=(pur==4 and pyr==4)"},
  {"claim": "If duplex is 30% G then %A = 20%",
   "code": "G=30; C=G; A=(100-(G+C))/2; result=(A==20)"},
  {"claim": "ATP hydrolysis yields ADP + Pi (3 phosphates -> 2 phosphates + 1 free)",
   "code": "atp_p=3; adp_p=2; pi=1; result=(adp_p+pi==atp_p)"}
]