AQA A-Level Chemistry Paper 2, 2019: Question 12

✅ Exact Scheme Requirements

• M1 (1 mark): Exactly 2 linear, dashed lines between Thymine (top left) and Adenine (top right):
  1. Top C=O of Thymine – – – H–N of Adenine's exocyclic –NH₂
  2. Ring N–H of Thymine – – – Ring N acceptor on Adenine
• M2 (1 mark): Exactly 3 linear, dashed lines between Cytosine (bottom left) and Guanine (bottom right):
  1. H–N of Cytosine's –NH₂ – – – C=O of Guanine
  2. Ring N of Cytosine – – – Ring H–N of Guanine
  3. Bottom C=O of Cytosine – – – H–N of Guanine's exocyclic –NH₂

💡 Key Knowledge: Base Pairing Rules

• A to T: Forms 2 hydrogen bonds. Thymine has two C=O groups and one N–H; Adenine has one –NH₂ donor and a ring nitrogen acceptor.
• C to G: Forms 3 hydrogen bonds. Cytosine provides one donor and two acceptors; Guanine provides two donors and one acceptor.
• A hydrogen bond forms between an electronegative atom with a lone pair (O or N) and a hydrogen atom covalently bonded to another electronegative atom (N–H).

🧠 Exam Technique: Drawing H-Bonds

• Use dashed lines only: Solid lines represent covalent bonds. If you draw solid lines, you lose marks immediately.
• Keep them linear: Aim your dashed line directly from the H atom to the relevant O or N atom opposite it.
• Do not overcrowd: The question states you do not need lone pairs or partial charges (δ⁺/δ⁻). Drawing them risks losing marks if placed incorrectly.

❌ Common Student Pitfalls

• Drawing too many bonds: The scheme applies a Lose 1 mark for each extra bond penalty. Do not connect every hydrogen you see.
• Bonding H to H: Never draw a dashed line between two H atoms; it must always connect an H to an electronegative atom (O or N).
• Targeting the wrong C=O on Thymine: The hydrogen bond forms with the top C=O, not the lower carbonyl between the two ring nitrogens.

✅ Correct Answer Breakdown

A nucleotide consists of three component parts. You must circle:

1. The Cytosine Base: The bottom-left pyrimidine ring (containing one =O and one –NH₂).
2. The Deoxyribose Ring: The 5-membered sugar ring attached directly to this Cytosine base.
3. The UPPER Phosphate Group: The phosphate group directly above this sugar ring (attached via the –CH₂–O– group at carbon-5').

Note: You can circle all three separately, or circle the entire nucleotide unit together in one large continuous loop.

💡 Biochemistry: Which Phosphate Belongs to Which Nucleotide?

• A nucleotide monomer is a nucleoside 5'-monophosphate before polymerisation.
• The phosphate group attached to the 5'-CH₂ carbon of the 2-deoxyribose ring is part of that original nucleotide unit.
• During condensation polymerisation to form DNA, the 5'-phosphate forms a phosphodiester bond with the 3'-OH group of the preceding sugar.
• Therefore, in a strand running top-to-bottom 5'→3', each nucleotide owns the phosphate directly above its deoxyribose ring!

❌ The Classic "Wrong Phosphate" Trap

• Choosing the bottom phosphate: Many students intuitively circle the phosphate below the cytosine sugar. That lower phosphate is attached to the 3'-oxygen and actually belonged to the next incoming nucleotide.
• Confusing Cytosine with Thymine: The top-left base has a methyl (–CH₃) group and two C=O groups – that is Thymine. Cytosine is the bottom-left base.

🧠 Exam Technique

• Double-check strand directionality. If the strand is oriented 5' to 3' downwards (the –CH₂– extends upwards from the sugar ring), the nucleotide's original phosphate is the upper one.
• The mark scheme permits splitting the ring either side of the bridging oxygen atom, but make sure you encompass the central phosphorus and its surrounding oxygen atoms cleanly.

✅ Acceptable Answers

• Base sequences on one strand pair/match specifically with the other: A matches to T and C matches to G.
• (The strands have base sequences that) match all A to T and C to G.

❌ What Fails to Score

• Only stating "they hydrogen bond": The mark scheme explicitly notes: Ignore reference to (hydrogen) bonding . Merely saying strands are held together by hydrogen bonds does not explain what complementary means.
• Saying "opposite bases attract": Too vague. You must explicitly name the complementary pairs: Adenine pairs with Thymine, and Cytosine pairs with Guanine.
• Saying A=U: This question specifically asks about DNA, where Thymine (T) is present, not Uracil (U).