# DNA Replication and Repair

> DNA replication enzymes, semi-conservative proof, Okazaki fragments and repair pathways with disease links for MBBS Biochemistry exams.

- Canonical URL: https://prepelephant.com/topics/mbbs/biochemistry/dna-replication-and-repair
- Exam / course: MBBS · Subject: Biochemistry
- Publisher: PrepElephant (https://prepelephant.com) — Prepared and reviewed by the PrepElephant Academic Review Team
- First published: 2026-10-02
- Last updated: 2026-10-02
- How to cite: "DNA Replication and Repair", PrepElephant, https://prepelephant.com/topics/mbbs/biochemistry/dna-replication-and-repair

## Direct answer

Meselson and Stahl proved in 1958, using heavy nitrogen and caesium chloride density gradients, that DNA replicates semi-conservatively — each daughter duplex keeps one parental strand. Replication is bidirectional from origins: helicase unwinds, primase lays RNA primers, polymerase III builds the leading strand continuously and the lagging in Okazaki fragments, polymerase I excises primers, and ligase seals the nicks. Repair pathways then police the genome, and their failures name the exam's famous diseases: xeroderma pigmentosum (nucleotide excision repair), Lynch syndrome (mismatch repair) and ataxia telangiectasia (double-strand break sensing).

## What you must remember

- Replication is semi-conservative, bidirectional and 5-prime-to-3-prime; E. coli has one origin (oriC), human chromosomes have thousands, licensed once per cell cycle.
- Prokaryotic cast: DnaA recognises the origin; DnaB helicase unwinds; single-strand binding proteins protect; DNA gyrase (topoisomerase II) relieves supercoils — the target of fluoroquinolones.
- Primase (DnaG) makes the RNA primer; polymerase III holoenzyme is the main replicative enzyme with 3-prime-to-5-prime proofreading and a sliding beta clamp; polymerase I removes primers and fills gaps; ligase seals phosphodiester bonds.
- Okazaki fragments: roughly 1,000–2,000 nucleotides in bacteria, 100–200 in eukaryotes.
- Eukaryotic polymerases: alpha (primase-associated), delta (lagging strand), epsilon (leading strand) and gamma — the sole mitochondrial replicase, a favourite one-liner.
- Telomerase, a reverse transcriptase carrying its own RNA template, lengthens chromosome ends in germline, stem and cancer cells, solving the end-replication problem.
- Repair roster: base excision repair (glycosylase initiates; handles deamination, oxidation) — ties to uracil-DNA glycosylase and 5-methylcytosine hotspots; nucleotide excision repair removes bulky lesions such as UV pyrimidine dimers — defective in xeroderma pigmentosum.
- Mismatch repair (MutS/MutL in bacteria; MSH2/MLH1 in humans) corrects replication slips; germline defects cause Lynch syndrome (hereditary non-polyposis colorectal cancer) with microsatellite instability.
- Double-strand breaks: homologous recombination repair needs BRCA1/BRCA2 (breast–ovarian cancer predisposition); non-homologous end joining (Ku, DNA-PK, ligase IV) is error-prone; ATM kinase senses breaks — mutated in ataxia telangiectasia with radiosensitivity.
- Direct reversal: O6-methylguanine-DNA methyltransferase removes alkyl groups; photolyase (absent in humans) would undo pyrimidine dimers.
- Combined proofreading and repair push the final error rate to about one in a billion to ten billion bases.

## Walking the fork and then repairing it

Visualise the growing fork: gyrase relieves positive supercoils ahead, helicase opens the duplex, single-strand binding protein coats the template, and primase drops an RNA primer. On the leading template, polymerase III (epsilon in humans) runs continuously toward the fork; on the lagging side the polymerase keeps hopping back, building each Okazaki fragment from a fresh primer until polymerase I chews out the RNA (its unique 5-prime-to-3-prime exonuclease) and ligase glues the nicks. At chromosome ends, the lagging strand cannot be finished — hence telomeric shortening in somatic cells, the mitotic clock, countered by reactivated telomerase in over 85 per cent of cancers. Then imagine ultraviolet light fusing adjacent thymine bases into a cyclobutane dimer. In a normal person, the nucleotide excision repair complex recognises the helical distortion, excises a 25–30 nucleotide patch, and polymerase refills. In xeroderma pigmentosum, seven complementation-group genes fail: the child freckles by age two, burns after minutes of sun and develops skin cancers at thousands-fold increased rates — strict photoprotection is the only defence. If instead a single mispaired base escapes polymerase proofreading, mismatch repair fixes it within minutes; when MSH2 or MLH1 is defective, microsatellites lengthen and shorten unchecked, and colon and endometrial cancers follow through the Vogelstein multistep sequence.

## Where students slip

Three confusions dominate. Students swap the exonuclease directions: only polymerase I has the 5-prime-to-3-prime exonuclease that removes primers, while both I and III proofread 3-prime-to-5-prime — the exam asks exactly this. Second, they attribute xeroderma pigmentosum to mismatch repair; it is nucleotide excision repair, whereas mismatch repair defects give Lynch syndrome — no photosensitivity, but tumours. Third, remember eukaryotic polymerase gamma is mitochondrial: mutations cause mitochondrial DNA depletion syndromes and are the reason some mitochondrial diseases show maternal plus Mendelian patterns.

## Frequently asked questions

### What did the Meselson–Stahl experiment demonstrate?
Semi-conservative replication. E. coli grown in 15N then switched to 14N showed, after one generation, hybrid-density DNA and, after two, a 1:1 mix of hybrid and light DNA — exactly the semi-conservative prediction.

### Which enzyme removes RNA primers and which seals the nick?
DNA polymerase I digests the primer with its 5-prime-to-3-prime exonuclease while filling in with DNA; ligase then seals the final phosphodiester bond, consuming ATP in eukaryotes (NAD+ in bacteria).

### Which repair pathway is defective in xeroderma pigmentosum?
Nucleotide excision repair, which removes bulky adducts such as ultraviolet-induced pyrimidine dimers; patients suffer extreme photosensitivity and early skin and mucosal cancers.

### Why do BRCA1 and BRCA2 mutations predispose to cancer?
They are needed for homologous recombination repair of DNA double-strand breaks; without them, breaks are mis-repaired by error-prone pathways, accelerating genomic instability in breast and ovarian epithelium.

### What is the end-replication problem and how do cancer cells solve it?
The lagging strand cannot copy the extreme chromosome tip, so telomeres shorten each division; cancer cells reactivate telomerase, a reverse transcriptase with a built-in RNA template, achieving replicative immortality.