Explain how the 5' to 3' directionality of nucleic acid strands arises from the chemistry of nucleotide polymerisation.

IB DP Biology Higher Level (2023 syllabus) — A1.2 Nucleic acids · Explain · 4 marks · View as Markdown

Written & reviewed by James Millett — Biology (Imperial College London), PGCE Science (University of Cambridge).

Model answer (4 marks)

Nucleotides are joined by phosphodiester bonds formed between the 3′‑hydroxyl group of the terminal nucleotide on the growing chain and the 5′‑phosphate of the incoming nucleotide. The incoming nucleotide always carries a triphosphate at its 5′ carbon, and the 5′‑phosphate attacks the 3′‑OH of the chain, forming the bond. Because new nucleotides are added only to the 3′ end, the new strand ends with a free 5′‑phosphate and a free 3′‑hydroxyl, giving the strand a 5′→3′ directionality. The two strands of a DNA double helix therefore run antiparallel: one strand is 5′→3′ in one direction, the complementary strand is 5′→3′ in the opposite direction.

Examiner tips

  • Use the phrase ‘phosphodiester bond between the 3′‑OH and 5′‑phosphate’ to hit the first point.
  • Show that the incoming nucleotide has a 5′‑triphosphate to justify the direction of addition.
  • Explain that the free 5′‑phosphate and 3′‑hydroxyl give inherent directionality.
  • Mention antiparallel strands to cover the final point.

Mark scheme (4 marks)

  1. Nucleotides are joined by phosphodiester bonds formed between the 3'-hydroxyl group of one nucleotide and the 5'-phosphate group of the next nucleotide being added.
  2. The incoming nucleotide always carries a triphosphate group at its 5' carbon, and it is this 5'-phosphate that attacks / bonds to the 3'-OH of the growing chain.
  3. Because new nucleotides are always added to the 3' end, the newly synthesised strand has a free 5'-phosphate at one end and a free 3'-hydroxyl at the other, creating an inherent directionality.
  4. The two strands of a DNA double helix run antiparallel because each strand has inherent 5'→3' directionality; one strand runs 5'→3' in one direction whilst the complementary strand runs 5'→3' in the opposite direction.

Key terms in this question

5' to 3' directionality · nucleotide polymerisation

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