← Unit 4: Heredity and continuity of life
Topic 1: DNA, genes and the continuity of life
Describe the structure of DNA, the process of semi-conservative replication and the role of key enzymes including helicase, DNA polymerase, primase and ligase
A focused answer to the QCE Biology Unit 4 dot point on DNA. Walks through the double-helix structure (sugar, phosphate, four bases, complementary pairing, antiparallel strands), the semi-conservative model demonstrated by Meselson and Stahl, and the roles of helicase, primase, DNA polymerase III, DNA polymerase I and ligase on the leading and lagging strands.
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What this dot point is asking
QCAA wants you to describe the molecular structure of DNA, explain why replication is described as semi-conservative, and name the enzymes that do each job at the replication fork. Diagrams of the double helix and the replication fork are common stimulus material.
The answer
DNA is the molecule that stores hereditary information in all cellular life. Its structure is elegantly suited to two jobs: storing information stably, and being copied accurately every time a cell divides.
The structure of DNA
DNA is a polymer of nucleotides. Each nucleotide has three parts:
- A deoxyribose sugar (five-carbon sugar with a hydroxyl group on carbon 3 and a hydrogen on carbon 2).
- A phosphate group attached to carbon 5 of the sugar.
- A nitrogenous base attached to carbon 1.
There are four bases, in two chemical classes:
- Purines (double-ring): adenine (A) and guanine (G).
- Pyrimidines (single-ring): thymine (T) and cytosine (C).
Nucleotides join into a single strand through phosphodiester bonds between the phosphate of one nucleotide and the 3 prime hydroxyl of the next. This gives every strand a direction, called 5 prime to 3 prime.
Two strands then pair to form the double helix, held together by hydrogen bonds between complementary bases:
- A pairs with T using two hydrogen bonds.
- C pairs with G using three hydrogen bonds.
The two strands are antiparallel: one runs 5 prime to 3 prime, the other 3 prime to 5 prime. The whole structure twists into a right-handed helix, about 10 base pairs per turn, with the sugar to phosphate backbone on the outside and the bases stacked on the inside.
Why the structure works for storage and copying.
- Hydrogen bonds are strong enough collectively to hold the helix together at body temperature, but individually weak enough to be broken by enzymes when the molecule is read or copied.
- Complementary base pairing means each strand carries the full information needed to rebuild the other.
- The sugar to phosphate backbone is chemically uniform, so any sequence of bases can be stored without changing the physical shape of the helix.
Semi-conservative replication
When a cell divides, every DNA molecule must be copied. The copy mechanism is semi-conservative: each daughter double helix contains one parental (original) strand and one newly synthesised strand.
Two alternative models existed historically:
- Conservative. The parental helix stays intact and the daughter helix is entirely new.
- Dispersive. Strands are broken into fragments that mix old and new DNA.
The famous Meselson and Stahl (1958) experiment used the heavy nitrogen isotope 15N. E. coli grown in 15N medium had heavy DNA; transferred to 14N medium and allowed to replicate, the DNA was sampled at each generation and separated by density gradient centrifugation:
- After one generation: a single band of intermediate density. (Rules out conservative.)
- After two generations: two bands, one intermediate and one light. (Rules out dispersive.)
Only the semi-conservative model predicted this exact pattern.
The replication fork
Replication begins at a specific sequence called the origin of replication. Several enzymes act at the replication fork where the helix opens.
Helicase. Breaks hydrogen bonds between paired bases and unwinds the helix. Single-strand binding proteins keep the separated strands from re-annealing. Topoisomerase relieves the supercoiling tension ahead of the fork.
Primase. Synthesises a short RNA primer (about 5 to 10 ribonucleotides) complementary to the template. The primer provides a free 3 prime hydroxyl group, which is what DNA polymerase needs to extend from.
DNA polymerase III. The main copying enzyme in prokaryotes (eukaryotes use a family of polymerases). It adds DNA nucleotides to the 3 prime end of the growing strand, reading the template 3 prime to 5 prime and synthesising the new strand 5 prime to 3 prime. Each new nucleotide arrives as a deoxynucleoside triphosphate (dATP, dTTP, dCTP, dGTP); two phosphates are cleaved off, releasing energy for the bond. DNA polymerase also proofreads, removing mismatched bases as it goes.
Leading and lagging strands. Because the two template strands are antiparallel, only one of them can be copied continuously toward the fork. This is the leading strand. The other, the lagging strand, is copied in short pieces called Okazaki fragments, each starting from a new primer. The lagging strand needs many primers.
DNA polymerase I. Removes the RNA primers and fills the gaps with DNA.
Ligase. Seals the nicks between Okazaki fragments by forming the final phosphodiester bond, producing one continuous strand.
Accuracy
DNA polymerase has a built-in proofreading function: it checks each newly added nucleotide and excises mistakes (3 prime to 5 prime exonuclease activity). Combined with mismatch repair after replication, the overall error rate is about one mistake in a billion bases.
Common traps
Saying DNA is "made of genes". Genes are sections of DNA. The molecule itself is a polymer of nucleotides.
Confusing the 5 prime to 3 prime direction. Synthesis is always 5 prime to 3 prime, never the reverse. The template is therefore read 3 prime to 5 prime.
Forgetting the primer. DNA polymerase cannot start a new strand from scratch. Primase makes an RNA primer first.
Mixing up leading and lagging strands. Leading strand is continuous and runs toward the fork. Lagging strand is in Okazaki fragments and runs away from the fork.
Calling Meselson and Stahl's experiment evidence for the double helix. It is evidence for semi-conservative replication, not for the structure itself (that was Watson, Crick, Wilkins and Franklin).
In one sentence
DNA is an antiparallel double helix of sugar to phosphate strands held together by complementary base pairing (A to T, C to G), and it is copied semi-conservatively by helicase unwinding the helix, primase laying down RNA primers, DNA polymerase III extending new strands 5 prime to 3 prime continuously on the leading strand and in Okazaki fragments on the lagging strand, DNA polymerase I replacing primers and ligase sealing the nicks.
Past exam questions, worked
Real questions from past QCAA papers on this dot point, with our answer explainer.
2023 QCAA6 marksDescribe the structure of a DNA molecule and explain how the structure supports accurate semi-conservative replication. Name the enzymes responsible for unwinding, priming, synthesising and sealing the new strands.Show worked answer →
A 6-mark answer needs structure, the semi-conservative model and the four enzymes with their roles.
Structure. DNA is a double helix of two antiparallel polynucleotide strands. Each nucleotide has a deoxyribose sugar, a phosphate group and one of four nitrogenous bases: adenine (A), thymine (T), cytosine (C) and guanine (G). The sugar of one nucleotide bonds to the phosphate of the next via a phosphodiester bond, forming a sugar to phosphate backbone with a 5 prime to 3 prime direction. The two strands run in opposite directions (one 5 prime to 3 prime, the other 3 prime to 5 prime) and are held together by hydrogen bonds between complementary bases: A with T (two bonds) and C with G (three bonds).
Why the structure supports replication. Complementary base pairing means each strand carries the template for the other, so an exact copy can be built from each.
Semi-conservative replication. Each new DNA molecule contains one original (parental) strand and one newly synthesised strand. Demonstrated by Meselson and Stahl using nitrogen isotopes (15N and 14N) and density gradient centrifugation.
Enzymes.
- Helicase unwinds the double helix by breaking hydrogen bonds, creating the replication fork.
- Primase synthesises a short RNA primer that gives DNA polymerase a 3 prime hydroxyl to extend from.
- DNA polymerase III adds new nucleotides 5 prime to 3 prime, reading the template 3 prime to 5 prime. On the leading strand it works continuously toward the fork. On the lagging strand it works away from the fork in short Okazaki fragments.
- DNA polymerase I removes RNA primers and replaces them with DNA.
- Ligase seals nicks between Okazaki fragments by forming phosphodiester bonds.
Markers reward antiparallel orientation, correct base pairing, the leading versus lagging distinction and at least four named enzymes.
2021 QCAA3 marksMeselson and Stahl grew E. coli in medium containing the heavy isotope 15N for many generations, then transferred them to 14N medium and sampled DNA after one and two rounds of replication. Explain how the banding patterns observed support the semi-conservative model.Show worked answer →
A 3-mark answer needs the predictions of each model and the observed result.
Three competing models.
- Conservative. Original double helix kept intact, new molecule entirely new. After one round, two bands (one heavy, one light).
- Semi-conservative. Each daughter molecule has one old and one new strand. After one round, a single intermediate band.
- Dispersive. Each strand is a patchwork of old and new. After one round, a single intermediate band, but the pattern persists in later generations.
Observed results.
- After one round in 14N: a single band of intermediate density. This rules out the conservative model.
- After two rounds in 14N: two bands, one intermediate and one light. The intermediate band contains molecules with one 15N (old) strand and one 14N (new) strand. The light band contains molecules where both strands are new. This rules out the dispersive model.
Conclusion. Only the semi-conservative model predicts this exact pattern, so DNA replication is semi-conservative.
Markers reward stating the prediction of each model, naming the two-band result at generation two, and the elimination logic.
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