DNA Replication

Core Concept

DNA replication copies the entire genome once per cell cycle, producing two identical double helices. It is semiconservative: each new molecule contains one original ("parent") strand and one newly synthesized strand. This follows directly from complementary base pairing — each original strand serves as a template for a new partner.

Key Concepts

Semiconservative replication

In the Meselson–Stahl experiment (1958), bacteria were grown in heavy ¹⁵N medium, then switched to light ¹⁴N. After one round of replication, DNA was of intermediate density (one heavy + one light strand); after two rounds, equal amounts of intermediate and light DNA appeared. This pattern rules out conservative and dispersive models and proves semiconservative replication.

Origins and the replication fork

Replication begins at specific sequences called origins of replication, where the two strands separate to form a replication bubble with a replication fork at each end. Prokaryotes have a single origin; eukaryotes have many origins per chromosome, allowing fast replication of large genomes. Replication proceeds bidirectionally from each origin.

The replication enzymes

• Helicase unwinds the double helix by breaking hydrogen bonds between base pairs.
• Topoisomerase relieves the torsional strain (supercoiling) ahead of the fork by cutting and resealing DNA strands.
• Single-strand binding proteins (SSBs) coat the separated strands and keep them from re-annealing.
• Primase synthesizes a short RNA primer, giving DNA polymerase a free 3′—OH to extend from.
• DNA polymerase adds nucleotides to the 3′ end of a growing strand, synthesizing in the 5′→3′ direction; the main replicative polymerases also proofread (3′→5′ exonuclease) to correct mistakes.
• DNA ligase seals the nicks between fragments by forming phosphodiester bonds.

Leading vs. lagging strand

Because DNA polymerase can only add to a 3′—OH (synthesis is always 5′→3′) and the strands are antiparallel, the two template strands are copied differently. The leading strand is synthesized continuously toward the fork in the 5′→3′ direction from a single primer. The lagging strand is synthesized discontinuously, away from the fork, in short Okazaki fragments, each requiring its own RNA primer. Primers are later replaced with DNA, and ligase joins the fragments.

Telomeres and telomerase

Linear eukaryotic chromosomes have a problem: the lagging strand cannot be fully replicated at the very ends, so chromosomes would shorten every round. Telomeres are repetitive, noncoding sequences (TTAGGG in humans) that buffer this loss. Telomerase, active in germ cells, stem cells, and most cancer cells, extends telomeres using an internal RNA template, allowing continued division. Most somatic cells lack telomerase, so their telomeres shorten with age — a contributor to cellular aging.

How It Works

At an origin, helicase unwinds the DNA and topoisomerase relieves strain. Primase lays down RNA primers. DNA polymerase III (in prokaryotes) extends each primer with complementary nucleotides, moving 5′→3′: one strand (leading) is made in one long piece, the other (lagging) in Okazaki fragments. DNA polymerase I removes the RNA primers and fills the gaps with DNA; ligase seals the remaining nicks. Proofreading by the polymerase catches most mispaired bases, giving an error rate of roughly one mistake per 10⁹–10¹⁰ bases.

How it works

At an origin, helicase unwinds the DNA and topoisomerase relieves strain. Primase lays down RNA primers. DNA polymerase III (in prokaryotes) extends each primer with complementary nucleotides, moving 5′→3′: one strand (leading) is made in one long piece, the other (lagging) in Okazaki fragments. DNA polymerase I removes the RNA primers and fills the gaps with DNA; ligase seals the remaining nicks. Proofreading by the polymerase catches most mispaired bases, giving an error rate of roughly one mistake per 10⁹–10¹⁰ bases.

Common confusions

• "DNA polymerase adds nucleotides to the 5′ end." Wrong — it adds to the free 3′—OH, so new DNA grows 5′→3′.
• "The lagging strand is synthesized 3′→5′." Wrong — all synthesis is 5′→3′; the lagging strand is just made in short pieces, and the strand overall grows in the 3′→5′ direction of the template.
• "Helicase seals the DNA." Wrong — helicase unwinds; ligase seals nicks.
• "Primers are made of DNA." Wrong — primers are RNA.
• "Telomerase is active in all cells." Wrong — it is largely inactive in most adult somatic cells, which is why they age; it's active in germ, stem, and most cancer cells.

Quick review

• Semiconservative: one old + one new strand per daughter molecule.
• Origins → replication bubble → forks (bidirectional).
• Helicase unwinds; topoisomerase relieves supercoiling; SSBs stabilize.
• Primase makes RNA primers; polymerase extends 5′→3′ and proofreads.
• Leading strand continuous; lagging strand = Okazaki fragments + ligase.
• Telomeres/telomerase protect chromosome ends.
• Errors = mutations; replication enzymes are drug targets.