AQA A-Level Chemistry Paper 2, 2017: Question 9

4 marks · Medium difficulty · State/Explain/Describe

Identify the groups attached to 2-deoxyribose and draw the complementary base thymine forming hydrogen bonds with adenine in a DNA strand.

Practise this question

Question

Question 09 consists of two parts. In 09.1, a skeletal structure of a 2-deoxyribose ring within a DNA strand is shown, labeled with substituent X at C1 and Y at C3, with the C5 CH2 group connected to '[DNA strand]'. Students are asked to name the groups attached at positions X and Y (2 marks). In 09.2, the chemical structure of adenine attached to '[DNA strand]' is shown, and students are asked to complete the diagram by drawing the complementary molecule and the hydrogen bonds between it and adenine (2 marks).
Question text

09 Use the Data Booklet to help you answer these questions.

DNA exists as two strands of nucleotides in the form of a double helix with

hydrogen bonding between the two strands.

09.1 A deoxyribose molecule in a strand of DNA is shown.

Name the types of group attached to 2-deoxyribose at positions X and Y.

[2 marks]

X

Y

09.2 In the DNA double helix, adenine is linked by hydrogen bonds to a molecule in

the other strand of DNA.

Complete the diagram below to show the other molecule and the

hydrogen bonds between it and adenine.

[2 marks]

Mark scheme

Show the mark scheme The mark scheme for 09.1 awards 1 mark for X = base and 1 mark for Y = phosphate (group). For 09.2, 2 marks are awarded for drawing the correct structure of thymine properly oriented opposite adenine, showing two dashed hydrogen bonds between the amino H of adenine and carbonyl O of thymine, and between the ring N of adenine and ring N-H of thymine.

Question Answers Mark Additional Comments/Guidance

X – base 1 Ignore organic

09.1 Any mention of sugar in either loses that mark

Y – phosphate (group) 1

If not Thymine CE=0

H Ignore lp on N and O

N N H O CH3 Don’t penalise non-linear H bonds

on RHS of thymine – allow with or without H or [DNA

N N H N strand]

[DNA strand]

09.2 N N

O (H) 2

Correct structure scores 2, penalise by 1 each error in

structure of thymine

orientation of thymine

hydrogen bonding

Total 4

How to answer it

DNA Structure & Complementary Base Pairing

📋 Revision Overview

What this question tests

This question assesses your understanding of the structure of DNA nucleotides and the molecular basis of the double helix:

  • Identifying the covalent attachment points on 2-deoxyribose in a polynucleotide chain (phosphate vs. nitrogenous base).
  • Knowing the specific complementary base pairing partner for adenine (thymine in DNA).
  • Drawing the structure of thymine in its correct spatial orientation relative to adenine using the Data Booklet.
  • Representing hydrogen bonding accurately between complementary functional groups (N–H···O=C and N–H···N).
Question 09.1 • 2 Marks

Identifying Groups on 2-Deoxyribose

Positions X and Y on the sugar ring

✅ Correct Answers

  • X: base (allow "nitrogenous base" or "organic base")
  • Y: phosphate or phosphate group

💡 Key Knowledge

  • A nucleotide consists of three components: phosphate group, 2-deoxyribose, and a nitrogenous base.
  • The 5-carbon sugar (2-deoxyribose) links to:
    • C1 (position X): forms a bond to the nitrogen atom of the organic base.
    • C3 (position Y): forms a phosphodiester bond to the phosphate group of the adjacent nucleotide.
    • C5 (via –CH₂–): links to the phosphate group of its own nucleotide.

🧠 Exam Technique

  • Notice the question asks for "types of group", not specific molecules. Giving broad functional components is required.
  • Use the structural diagram: C1 is attached to X (where bases always attach in nucleosides). C3 has the –OH in free deoxyribose, which condenses to give the phosphate backbone link Y.

❌ Common Errors

  • Naming sugar: Any mention of "sugar" or "ribose" for either X or Y loses the mark entirely.
  • Confusing X and Y: Swapping phosphate and base.
  • Giving a specific base: Writing "adenine" instead of the general type of group "base" (examiners look for the category).
Mark Scheme Breakdown:
• [1 mark] X = base (ignore 'organic')
• [1 mark] Y = phosphate (group)
Note: Any mention of "sugar" in either response forfeits that mark.
Question 09.2 • 2 Marks

Complementary Base Pairing: Adenine & Thymine

Completing the diagram with thymine and hydrogen bonds

✅ Required Structural Details

  • Identify Base: Must be thymine (complementary partner to adenine in DNA). Identifying any other base triggers a Chemical Error ( CE = 0 ).
  • 2 Hydrogen Bonds:
    • From the top N–H of adenine to the C=O of thymine: N–H ··· O=C
    • From the ring N of adenine to the ring N–H of thymine: N ··· H–N
  • Correct Orientation: Thymine's C=O and ring N–H must point directly toward Adenine's complementary donors/acceptors. The –CH₃ group points up-right, and the sugar-attaching ring N points down-right.

💡 Hydrogen Bonding Rules in DNA

  • A–T pairs have 2 hydrogen bonds; G–C pairs have 3.
  • Each hydrogen bond forms between an electronegative atom (N or O) with a lone pair and a hydrogen atom attached to an electronegative atom (N–H).
  • Represent H-bonds using dashed or dotted lines ( ···· ), never solid covalent lines.

🧠 How to Draw the Molecule Step-by-Step

1. Position Thymine: Draw a 6-membered ring opposite Adenine.
2. Align functional groups facing Adenine:
  • Top-left of ring: Carbonyl group ( C=O ) directly opposite adenine's top –NH₂ group.
  • Middle-left of ring: N–H group directly opposite adenine's ring nitrogen.
3. Complete Thymine's ring:
  • Bottom of ring: Second carbonyl ( C=O ).
  • Bottom-right: Ring N–H (or attached to DNA strand).
  • Top-right: Carbon with a methyl group ( –CH₃ ).
4. Add Hydrogen Bonds: Draw dashed lines between:
  • Adenine N–H ···· O=C Thymine
  • Adenine N ···· H–N Thymine

❌ Common Errors & Penalties

  • Drawing Uracil: Thymine is in DNA; uracil is only in RNA! Drawing uracil or cytosine gives 0/2 .
  • Flipping the ring: Drawing thymine upside down or backwards so non-bonding groups face adenine.
  • Wrong number of H-bonds: Drawing 3 hydrogen bonds (confusing A–T with G–C).
  • Line style: Drawing solid lines for hydrogen bonds (may be penalised as covalent bonds).
Mark Scheme Breakdown:
• If not Thymine: CE = 0/2
• Correct structure scores [2 marks].
• Penalise by 1 mark for each error in:
  1. Structure of thymine (e.g. missing –CH₃ group or wrong double bonds)
  2. Orientation of thymine (incorrect groups facing adenine)
  3. Hydrogen bonding (wrong atoms connected or incorrect number of bonds)
Examiner notes: Lone pairs on N and O are not required (ignore lp). Non-linear H-bonds are not penalised. On the RHS of thymine, allow with or without H or [DNA strand].

Topics

Organic Chemistry · Physical Chemistry · 3.3.13 Amino Acids, Proteins and DNA · 3.1.3 Bonding

Question and mark scheme from the AQA A-Level Chemistry examination, Paper 2, 2017. QuestionVault is an independent revision resource; questions remain the copyright of the awarding body.