describe the semi-conservative replication of DNA during the S phase of the cell cycle, including: the roles of DNA polymerase and DNA ligase (knowledge of other enzymes in DNA replication in cells and different types of DNA polymerase is not expecte

Cambridge International AS & A Level Biology – Nucleic Acids & DNA Replication

Learning Objectives

  • Describe the structure of nucleotides, DNA and RNA.

  • Explain the semi‑conservative replication of DNA during the S‑phase, with particular emphasis on the roles of DNA polymerase and DNA ligase.

  • Compare leading‑strand and lagging‑strand synthesis.

  • Outline the flow of genetic information (DNA → RNA → protein) and list the main types of gene mutation covered in the syllabus.

1. Nucleotides – the building blocks of nucleic acids

  • Components of a nucleotide

    • 5‑carbon sugar – deoxyribose (DNA) or ribose (RNA)

    • One phosphate group (attached to the 5′‑carbon of the sugar)

    • A nitrogenous base – purine (A, G) or pyrimidine (C, T in DNA; U in RNA)

  • Neighbouring nucleotides are linked by phosphodiester bonds (3′‑OH of one sugar to 5′‑phosphate of the next), giving each strand a directionality: 5′ → 3′.

2. DNA – double‑helix architecture

  • Two antiparallel strands (one runs 5′→3′, the other 3′→5′).

  • Base‑pairing (hydrogen bonds):

    \$\$\text{A}\;\leftrightarrow\;\text{T}\;(2\;\text{H‑bonds}),\qquad

    \text{G}\;\leftrightarrow\;\text{C}\;(3\;\text{H‑bonds})\$\$

  • Right‑handed double helix, uniform diameter ≈ 2 nm.

3. RNA – the single‑stranded counterpart

  • Contains ribose instead of deoxyribose and uracil (U) instead of thymine (T).

  • Usually single‑stranded but can fold into secondary structures (e.g., hairpins).

  • Messenger RNA (mRNA) carries the genetic code from the nucleus to the ribosome for protein synthesis.

4. Semi‑conservative DNA replication (S‑phase)

4.1 What “semi‑conservative” means

Each of the two parental DNA strands serves as a template for a new complementary strand. After replication each daughter molecule consists of one old (parental) strand and one newly synthesised strand.

4.2 Key enzymes (focus on DNA polymerase & DNA ligase)

EnzymeMain function in replication
DNA polymeraseAdds deoxyribonucleotides to the 3′‑OH of a growing strand, using the template strand to select the correct base. Synthesis proceeds only in the 5′→3′ direction.
DNA ligaseForms phosphodiester bonds between adjacent nucleotides, sealing the nicks left after RNA‑primer removal and joining Okazaki fragments on the lagging strand.
HelicaseUnwinds the double helix, creating two replication forks.
Single‑strand‑binding (SSB) proteinsStabilise the separated template strands and prevent re‑annealing.
RNA primaseSynthesises a short RNA primer (provides the 3′‑OH required for DNA polymerase).
Topoisomerase (DNA gyrase)Relieves super‑coiling ahead of the replication fork by transiently cutting and resealing DNA.

4.3 Leading‑strand vs. lagging‑strand synthesis

FeatureLeading strandLagging strand
Direction of synthesis relative to fork movementSame direction as fork; continuous synthesis.Opposite direction to fork; discontinuous synthesis.
Mode of synthesisOne DNA polymerase adds nucleotides continuously toward the fork.Series of short fragments (Okazaki fragments) each started by a new RNA primer.
Primer requirementSingle RNA primer at the origin.New RNA primer for every Okazaki fragment.
Enzyme that joins fragmentsNot required (continuous strand).DNA ligase seals the nicks between fragments.
Resulting strand after processingIntact phosphodiester backbone from the start.Continuous strand formed after primer removal, gap‑filling and ligation.

4.4 Step‑by‑step replication (simplified)

  1. Unwinding: Helicase breaks the hydrogen bonds, producing a replication fork.

  2. Stabilisation: SSB proteins bind to the exposed single strands.

  3. Primer synthesis: RNA primase lays down a short RNA primer on each template.

  4. Chain elongation – DNA polymerase

    • Leading strand: Polymerase adds nucleotides continuously 5′→3′ toward the fork.

    • Lagging strand: Polymerase adds nucleotides 5′→3′ away from the fork, forming Okazaki fragments.

  5. Primer removal & gap filling: DNA polymerase (or a specialised exonuclease activity) removes the RNA primers and replaces them with DNA.

  6. Fragment joining: DNA ligase creates phosphodiester bonds between adjacent Okazaki fragments, producing a continuous lagging strand.

  7. Super‑coil relief: Topoisomerase cuts, swivels and reseals DNA ahead of the fork to prevent torsional stress.

4.5 Diagram suggestion

Insert a schematic of a replication fork showing:

  • Helicase at the fork apex

  • Leading‑strand polymerase moving continuously toward the fork

  • Lagging‑strand polymerase synthesising Okazaki fragments away from the fork

  • RNA primers (short lines) on both strands

  • DNA ligase sealing the gaps between fragments

  • Direction arrows indicating 5′→3′ synthesis

5. The central dogma – flow of genetic information

  1. Transcription: RNA polymerase synthesises a complementary mRNA strand from the DNA template (5′→3′).

  2. RNA processing (eukaryotes): 5′‑cap addition, poly‑A tail, and intron removal (splicing).

  3. Translation: Ribosomes read mRNA codons; transfer RNAs (tRNAs) bring the appropriate amino‑acids, forming a polypeptide chain.

6. Gene mutations – types relevant to the syllabus

Mutation typeDefinition (example)Typical effect on protein
Point (substitution) mutationSingle base change, e.g., A → GMay be silent, missense (different amino‑acid) or nonsense (premature stop).
InsertionOne or more bases added, e.g., …ATG|C… → …ATGC|C…If not in multiples of three, causes a frameshift → altered downstream amino‑acid sequence.
DeletionOne or more bases removed, e.g., …ATGC|A… → …ATG|A…Can also cause a frameshift; may truncate the protein.
Frameshift mutationInsertion or deletion that changes the reading frame.Usually produces a non‑functional protein.
Chromosomal mutation (brief)Large‑scale changes – duplication, inversion, translocation.May affect many genes; often lethal or disease‑causing.

7. Summary

DNA is composed of nucleotides that pair (A‑T, G‑C) to form an antiparallel double helix. During the S‑phase each parental strand acts as a template, giving rise to two daughter molecules each containing one old and one new strand – the semi‑conservative pattern. Because DNA polymerase can only add nucleotides in the 5′→3′ direction, the leading strand is synthesised continuously, whereas the lagging strand is built in short Okazaki fragments that are later joined by DNA ligase. Accurate replication is essential for the faithful transmission of genetic information, which subsequently flows to RNA (transcription) and protein (translation). Mutations that alter the DNA sequence can modify the resulting protein, with consequences ranging from neutral to severe.