AP Syllabus focus:
‘In S phase, chromatin is replicated to form pairs of sister chromatids joined together at a centromere.’
S phase is the part of interphase when a cell accurately duplicates its DNA so each daughter cell can inherit a complete genome. Replication is tightly coordinated with chromatin structure and chromosome architecture.
What happens in S phase
During S phase (synthesis phase), the cell copies its nuclear DNA and converts each chromosome from one DNA molecule into two identical DNA molecules.
S phase (Synthesis phase): The interphase period when the cell replicates its DNA, producing duplicated chromosomes.
The DNA is replicated as chromatin (DNA plus associated proteins), not as “naked” DNA, so replication must proceed while DNA is packaged and protected.
The chromosome-level outcome: sister chromatids
After replication, each chromosome consists of two identical DNA molecules.
Sister chromatids: Two identical DNA copies of a chromosome produced during S phase and held together as one duplicated chromosome.
These sister chromatids remain physically connected at a specialized chromosomal region.
Centromere: The chromosomal region where sister chromatids are most tightly associated and where kinetochore proteins later assemble for chromosome movement.
This duplication (two chromatids joined at a centromere) is the structural basis for accurate chromosome distribution when the cell eventually divides.
This diagram contrasts chromosomes before and after DNA replication, emphasizing that replication produces duplicated chromosomes composed of two sister chromatids. The sister chromatids are shown joined at the centromere, which is the key physical connection maintained until chromosome segregation. Source
Core principles of DNA replication in S phase
DNA replication is semiconservative: each new DNA double helix contains one parental strand and one newly synthesised strand.
This figure compares three proposed models of DNA replication, highlighting why the semiconservative model is correct: each daughter double helix contains one parental strand paired with one newly synthesized strand. The side-by-side comparison makes it easy to see how semiconservative replication differs from conservative and dispersive alternatives. Source
Semiconservative replication: A replication mechanism in which each daughter DNA molecule contains one original (template) strand and one newly made strand.
Replication is also:
Bidirectional: it proceeds in two directions from each start site.
Template-directed: base pairing (A–T, G–C) guides accuracy.
Limited by chemistry: DNA polymerases add nucleotides only to a 3′ end, so synthesis proceeds 5′ → 3′.
Initiation: starting replication at origins
Eukaryotic chromosomes have many origins of replication, allowing the genome to be copied efficiently within S phase.
Origin of replication: A DNA sequence where replication begins, creating a replication bubble with two replication forks.
From each origin:
A replication bubble forms as DNA is opened.
Two replication forks move away from the origin.
Replication fork: The Y-shaped region where parental DNA strands are separated and new DNA strands are synthesised.
Elongation: building new DNA strands
At each replication fork, multiple proteins coordinate to unwind DNA, stabilise single strands, and synthesise new strands.
Replication at a fork requires coordinated enzyme activity: helicase unwinds the parental duplex, single-strand binding proteins stabilise exposed templates, and DNA polymerase synthesises new DNA only in the 5′ → 3′ direction. The figure highlights continuous leading-strand synthesis versus discontinuous lagging-strand synthesis through Okazaki fragments that are later sealed by DNA ligase. Source
Unwinding and stabilising the template
Key functions at the fork include:
Helicase unwinds the parental double helix by breaking hydrogen bonds.
Single-strand binding proteins bind exposed DNA strands to prevent re-annealing and protect them.
Topoisomerase relieves twisting strain ahead of the fork to prevent excessive supercoiling and breakage.
Priming and DNA polymerase activity
DNA polymerases cannot start synthesis de novo; they require a pre-existing 3′-OH.
Primase synthesises a short RNA primer complementary to the template.
DNA polymerase extends from the primer, adding DNA nucleotides to the 3′ end (therefore synthesising 5′ → 3′).
Leading vs. lagging strand synthesis
Because the two template strands run antiparallel, replication differs on each side of the fork:
Leading strand: synthesised continuously toward the fork as the template is read 3′ → 5′.
Lagging strand: synthesised discontinuously away from the fork as short Okazaki fragments, each requiring a new primer.
Lagging-strand completion requires additional processing:
RNA primers are removed and replaced with DNA.
DNA ligase seals remaining nicks in the sugar-phosphate backbone, joining fragments into one continuous strand.
Fidelity and completion of replication
High fidelity is essential because S phase permanently copies genetic information.
Many DNA polymerases proofread by removing mispaired nucleotides before continuing.
Additional repair systems can correct remaining mismatches shortly after synthesis.
Replication ends when forks meet or reach chromosome ends, producing two identical DNA molecules per chromosome. These DNA molecules are packaged back into chromatin and maintained as sister chromatids joined at the centromere, preserving genome integrity and chromosome organisation through the rest of interphase.
FAQ
Eukaryotic genomes are large and DNA polymerases have finite speeds. Multiple origins create many replication bubbles, allowing parallel copying and timely completion of S phase.
Origin usage can also vary by cell type, helping coordinate replication with chromatin state and gene activity.
As the fork progresses, nucleosomes are temporarily disassembled ahead of it and reassembled behind it.
Parental histones can be recycled onto daughter DNA
New histones are added to fill gaps
Chaperone proteins help restore chromatin structure without tangling DNA
After the last RNA primer on the lagging strand is removed, DNA polymerase cannot fill the extreme 5′ end, causing progressive shortening.
Telomerase extends telomeres by using an internal RNA template to add repetitive DNA, enabling completion of the lagging strand at chromosome ends.
Proofreading occurs during synthesis: the polymerase detects a mispair and removes the incorrect nucleotide immediately.
Mismatch repair acts after replication: it identifies remaining mismatches, distinguishes the newly synthesised strand from the template, excises a segment, and resynthesises it correctly.
Replication timing reflects chromosome organisation.
Open, gene-rich euchromatin often replicates earlier
Dense heterochromatin often replicates later
Timing can support accurate copying of difficult regions and help maintain epigenetic patterns
Practice Questions
State what sister chromatids are and identify the chromosome region that joins them after DNA replication in S phase. (2 marks)
Two identical copies of a chromosome/DNA molecule produced during S phase (1)
Joined together at the centromere (1)
Describe how DNA is replicated at a replication fork during S phase. Include the roles of at least four named enzymes/proteins and explain why one strand is synthesised discontinuously. (6 marks)
Helicase unwinds/separates the parental DNA strands (1)
Single-strand binding proteins stabilise separated strands/prevent re-annealing (1)
Primase makes RNA primers to provide a 3′-OH start point (1)
DNA polymerase extends new DNA 5′ → 3′ from the primer (1)
Antiparallel templates mean one strand is made continuously (leading) and the other discontinuously (lagging) as Okazaki fragments (1)
DNA ligase joins fragments/seals sugar-phosphate backbone after primer removal and replacement (1)
