AQA A-Level Chemistry Paper 2, 2018: Question 9

✅ Correct Answer

💡 Key Knowledge

• Adenine (A) pairs exclusively with Thymine (T).
• Cytosine (C) pairs exclusively with Guanine (G).
• The given strand template is:
  A – C – G – T – C
• Complementary strand reads:
  T – G – C – A – G

❌ Common Errors

• Writing U (Uracil) instead of T (Thymine) — Uracil is only found in RNA, whereas the question explicitly specifies DNA.
• Inverting the pairing rules (e.g. accidentally matching A with C).

🧠 Exam Technique

Always write capital letters clearly. When filling in table cells, ensure there is no ambiguity between 'C' and 'G'.

✅ Correct Answer

Tick box: 13

📐 Step-by-Step Calculation

Count the hydrogen bonds formed across each individual base pair:

1. A = T pair forms 2 hydrogen bonds.
2. C ≡ G pair forms 3 hydrogen bonds.
3. G ≡ C pair forms 3 hydrogen bonds.
4. T = A pair forms 2 hydrogen bonds.
5. C ≡ G pair forms 3 hydrogen bonds.

Total H-bonds = 2 + 3 + 3 + 2 + 3 = 13

💡 Why A–T has 2 and C–G has 3 H-Bonds

• A–T base pair: Stabilised by 2 hydrogen bonds: one between the carbonyl oxygen of T and an amino group of A, and another between ring N–H and ring N.
• C–G base pair: Stabilised by 3 hydrogen bonds due to complementary arrangement of three dipole donor/acceptor sites.
• This information can be confirmed directly from the structures supplied in the AQA Data Booklet!

❌ Common Distractor Traps

• 10: Assuming every base pair forms only 2 H-bonds (5 × 2 = 10).
• 15: Assuming every base pair forms 3 H-bonds (5 × 3 = 15).
• 12: Making a simple addition slip (e.g. counting C–G as 2 or missing one pair).

✅ Mark Scheme Requirements

• Mark 1: Completed 2-deoxyribose ring with base A attached:
  • Letter A attached to the top-right carbon (C1).
  • An –OH group (or trailing bond –O– ) attached to C3 (bottom left).
  • Correct hydrogens on the furanose ring carbons (C1 has H, C2 has two H atoms / sticks, C3 has H, C4 has H).
• Mark 2: Correct phosphate group attached via a –CH₂– group to C4 (top-left ring position):
  • Must show –CH₂–O–P(=O)(O⁻)₂ or protonated/ester equivalents.

🧠 Examiner Instructions: How to Draw the Structure

Starting from the incomplete pentose ring shown in the question paper:

• At Carbon 1 (far right): Draw base A pointing upwards and an H pointing downwards.
• At Carbon 2 (bottom right): Draw two H atoms (one pointing up, one pointing down) to reflect 2-deoxyribose (no –OH here!).
• At Carbon 3 (bottom left): Ensure an –OH (or trailing bond –O– ) is pointing down, with an H pointing up.
• At Carbon 4 / 5 (top left): Add a –CH₂– group pointing upwards from the ring, connected to an oxygen atom of the phosphate unit:
  –CH₂–O–P(=O)(O⁻)₂ (or with –OH groups).

💡 Carbon Numbering & Attachments in 2-Deoxyribose

• C1' (rightmost): Carries the nitrogenous base (Adenine, A) via a glycosidic bond.
• C2' (bottom right): Has only hydrogen atoms ( –CH₂– ) — this distinguishes 2-deoxyribose from ribose.
• C3' (bottom left): Possesses an –OH group that forms the phosphodiester link in the DNA backbone.
• C5' (top left branch): Is an exocyclic –CH₂– carbon that bonds to the phosphate ester group.

❌ Key Guidance & Penalties from the Mark Scheme

• Missing CH₂ group: Attaching the phosphate directly to the ring carbon (C4) loses Mark 2. However, if there are no further errors, Mark 1 can still be awarded.
• Two phosphates drawn: A single nucleotide has only one phosphate group. If two phosphates are shown, a Consequential Error rule applies: CE = 0/2.
• Phosphate on C3: If the phosphate is attached to C3 instead of C5, Mark 2 is lost (award 1 mark if no other errors).
• 'Sticks' allowed: Bare bonds ("sticks") representing C–H bonds on the ring are not penalised. Trailing bonds (indicating polymer continuation) or free –OH groups are both acceptable.