describe the structure of a DNA molecule as a double helix, including: the importance of complementary base pairing between the 5′ to 3′ strand and the 3′ to 5′ strand (antiparallel strands), differences in hydrogen bonding between C–G and A–T base p

6.1 Structure of Nucleic Acids & DNA Replication (Cambridge IGCSE/A‑Level 9700)

6.1.1 Nucleotide – the Building Block

• Three components:

  • Phosphate group – attached to the 5′ carbon of the sugar.
  • Five‑carbon sugar:

    • DNA – deoxyribose (no –OH on C‑2′).
    • RNA – ribose (has –OH on C‑2′).

  • Nitrogenous base – attached to C‑1′ of the sugar.

    • Purines (double‑ring): Adenine (A), Guanine (G).
    • Pyrimidines (single‑ring): Cytosine (C), Thymine (T) in DNA; Uracil (U) replaces T in RNA.

• When nucleotides join, the 3′‑hydroxyl of one sugar forms a phosphodiester bond with the 5′‑phosphate of the next, producing a sugar‑phosphate backbone.

6.1.2 DNA Double‑Helix & Antiparallel Orientation

Overall Shape

DNA is a right‑handed double helix – two long polymer strands wind around a common axis, resembling a twisted ladder.

Antiparallel Strands

• Each strand has a direction defined by the carbon numbers of its sugar:

  • 5′ end – phosphate attached to the 5′ carbon.
  • 3′ end – free –OH on the 3′ carbon.

• In the helix the strands run in opposite directions:

  • Strand A: 5′ → 3′ (often called the “sense” strand).
  • Strand B: 3′ ← 5′ (the “antisense” strand).

• Antiparallel orientation is essential because DNA polymerases can only add nucleotides to a 3′‑OH, and the hydrogen‑bonding pattern of the bases matches only when the strands run opposite to each other.

Complementary Base Pairing

• Base pairing occurs between exposed nitrogenous bases on opposite strands.
• Watson‑Crick rules:

  • A ↔ T – 2 hydrogen bonds
  • C ↔ G – 3 hydrogen bonds

• The donor‑acceptor pattern on each base fits only its partner, giving the pairing its complementary nature.

Hydrogen‑Bonding Differences

Contextual Note – DNA Packaging

In eukaryotes the double helix is wrapped around histone proteins to form nucleosomes, which further coil into chromatin fibres. This packaging is not required for the syllabus but provides useful context for how DNA is organised in the nucleus.

6.1.3 Phosphodiester Bond Formation (Backbone Construction)

Within each strand a phosphodiester bond is created by a condensation (dehydration) reaction:

\$\text{(deoxyribose)}n\text{-OH}{3'} + \text{PO}4^{2-}{5'} \;\longrightarrow\; \text{(deoxyribose)}n\text{-O‑P‑O‑(deoxyribose)}{n+1} + \text{H}_2\text{O}\$

• The 3′‑OH of one nucleotide joins to the 5′‑phosphate of the next, releasing water.
• These covalent bonds give the DNA backbone its great chemical stability, whereas the hydrogen bonds between bases are relatively weak and can be broken during replication or transcription.

6.1.4 Semi‑Conservative DNA Replication

Each daughter DNA molecule contains one original (parental) strand and one newly synthesised strand.

Key Steps & Enzymes (conceptual flow)

1. Origin of replication – specific DNA sequences where unwinding begins.
2. Helicase – breaks the hydrogen bonds, separating the two strands and creating a replication fork.
3. Single‑strand binding proteins (SSBs) – stabilise the separated strands and prevent re‑annealing.
4. Topoisomerase (gyrase) – relieves super‑coiling ahead of the fork by cutting and resealing DNA.
5. Primase – synthesises a short RNA primer (5′‑RNA‑3′) providing a free 3′‑OH for DNA polymerase.
6. DNA polymerase III (or equivalent) – adds deoxyribonucleotides to the 3′‑OH, synthesising DNA in the 5′→3′ direction.

   • Leading strand – synthesis is continuous in the direction of fork movement.
   • Lagging strand – synthesis is discontinuous; short fragments (Okazaki fragments) are made away from the fork.

7. DNA ligase – joins adjacent Okazaki fragments by forming phosphodiester bonds, creating an uninterrupted backbone.
8. Proofreading – many DNA polymerases possess 3′→5′ exonuclease activity to remove mis‑incorporated nucleotides.

Result

Two identical double‑helical DNA molecules, each composed of one parental strand and one newly synthesised strand.

6.1.5 RNA – Key Differences from DNA

• Sugar: ribose (contains a 2′‑OH).
• Base: uracil (U) replaces thymine (T).
• Structure: normally single‑stranded, but can fold into secondary structures (hairpins, loops).

6.2 Protein Synthesis (Transcription, RNA Processing & Translation)

6.2.1 Transcription – DNA → mRNA

Core Enzyme

RNA polymerase binds to the promoter region of a gene and synthesises a complementary RNA strand.

Steps

1. Initiation

   • RNA polymerase recognises the promoter (e.g., TATA box in eukaryotes, –35 and –10 regions in prokaryotes).
   • The enzyme unwinds a short stretch of DNA, exposing the template strand.

2. Elongation

   • Ribonucleotides are added complementary to the DNA template (A↔U, T↔A, C↔G) in the 5′→3′ direction.
   • The growing RNA chain remains attached to the DNA template until the polymerase moves forward.

3. Termination

   • In prokaryotes, a terminator sequence causes the polymerase to dissociate.
   • In eukaryotes, specific termination factors and poly‑adenylation signals (AAUAAA) signal the end of transcription.

6.2.2 RNA Processing (Eukaryotic Pre‑mRNA)

• 5′ Capping – a modified guanine nucleotide (7‑methyl‑guanosine) is added to the first transcribed nucleotide; protects mRNA from degradation and assists ribosome binding.
• Poly‑A Tail – ~200 adenine residues are added to the 3′ end after cleavage at a poly‑adenylation signal; enhances stability and export from the nucleus.
• Splicing – introns (non‑coding regions) are removed by the spliceosome; exons are ligated to produce a continuous coding sequence.

6.2.3 Translation – mRNA → Polypeptide

Ribosome Structure

• Two subunits (large & small) composed of ribosomal RNA (rRNA) and proteins.

  • Prokaryotes: 70 S (30 S + 50 S).
  • Eukaryotes: 80 S (40 S + 60 S).

• Three functional sites on the large subunit:

  • A site – entry point for aminoacyl‑tRNA.
  • P site – holds the tRNA with the growing peptide chain.
  • E site – exit point for de‑acylated tRNA.

Steps of Translation

1. Initiation

   • Small subunit binds the 5′‑cap (eukaryotes) or Shine‑Dalgarno sequence (prokaryotes).
   • Initiator tRNA (formyl‑Met in prokaryotes, Met in eukaryotes) pairs with the start codon (AUG) in the P site.
   • Large subunit joins, forming a complete ribosome.

2. Elongation

   • An aminoacyl‑tRNA matching the next mRNA codon enters the A site.
   • A peptide bond forms between the peptide on the P‑site tRNA and the amino acid on the A‑site tRNA.
   • The ribosome translocates 3′ along the mRNA, shifting tRNAs to the P and E sites.

3. Termination

   • When a stop codon (UAA, UAG, or UGA) enters the A site, release factors bind.
   • The completed polypeptide is released, and the ribosomal subunits dissociate.

6.2.4 Gene Mutations – Types & Effects

Summary of Key Points

• DNA is a double‑helix of two antiparallel strands linked by phosphodiester bonds; the backbone is chemically stable, while base‑pair hydrogen bonds are reversible.
• Complementary base pairing (A–T, C–G) holds the strands together; C–G is stronger because it forms three hydrogen bonds.
• RNA differs from DNA in sugar (ribose), base (uracil) and is normally single‑stranded.
• Semi‑conservative replication copies each parental strand once, using a coordinated set of enzymes (helicase, primase, DNA polymerase, ligase, topoisomerase).
• Transcription produces a complementary RNA copy; eukaryotic pre‑mRNA undergoes capping, poly‑adenylation and splicing before becoming mature mRNA.
• Translation reads mRNA codons in triplets, with tRNA anticodons delivering the correct amino acids at the ribosomal A, P and E sites.
• Mutations (substitution, insertion, deletion) can alter the amino‑acid sequence and therefore protein function.