DNA: Genetic Material & Replication – Concise Exam Notes

1928 Griffith: transformation in Streptococcus indicates a heritable “transforming principle”.
1944 Avery, MacLeod & McCarty: biochemical tests show the transforming principle is DNA (protein/RNA removal no effect; DNase abolishes activity).
1952 Hershey–Chase: only phage DNA, not protein, enters bacteria → DNA is viral genetic material.

Components: 5-C deoxyribose, phosphate, nitrogenous base (purines A & G; pyrimidines T & C; RNA uses U).
Chargaff’s rules: A=T, G=C; \frac{G{+}C}{A{+}T} ratio differs among species.
X-ray diffraction (Wilkins & Gosling, 1950) → helix, diameter ≈ 2\,\text{nm}, pitch 3.4\,\text{nm} (≈10 bp/turn).
Double helix: antiparallel strands (5′→3′ / 3′→5′), phosphodiester backbone outside, bases inside.
• Base pairing: A–T (2 H-bonds), G–C (3 H-bonds) → complementarity.

Meselson–Stahl (1958): replication is semiconservative.
Needs: template strand, DNA polymerase(s), dNTPs.
Phases: initiation → elongation → termination.
DNA polymerases add nucleotides to the free 3′-OH; synthesis proceeds 5′→3′.
Leading strand: continuous; Lagging strand: discontinuous Okazaki fragments, each primed by RNA primer.

Helicase: unwinds helix.
Primase: synthesises short RNA primer.
DNA polymerase(s): extend primer; Pol III (prokaryotic main), Pol ε/Pol δ (eukaryotic complex).
Sliding clamp: β (prokaryotes) / PCNA (eukaryotes) ↑ processivity; loaded by clamp loader.
Topoisomerase / DNA gyrase: relieves torsional strain.
SSB proteins: stabilise single strands.
DNA Pol I (prokaryotes): replaces RNA primers; also 5′→3′ & 3′→5′ exonuclease.
DNA ligase: seals nicks between fragments.

Single circular chromosome, one origin (oriC) → bidirectional forks to terminus.
Replisome = primosome (helicase + primase + helpers) + two DNA Pol III complexes.
Leading strand: one primer; Lagging: multiple primers → Okazaki fragments joined by Pol I & ligase.

Multiple, larger, linear chromosomes → many origins; each origin defines a replicon.
Primase complex makes RNA primer then extends it with short DNA.
Main polymerase complex: Pol ε (leading) + Pol δ (lagging) with PCNA clamp.
Nucleosome/displacement handled by additional chromatin factors (not detailed here).

Telomeres = short tandem repeats at chromosome ends; protect against exonucleases and loss of genes.
End-replication problem: final RNA primer on lagging strand cannot be replaced → 3′ overhang shortening.
Telomerase (ribonucleoprotein) extends 3′ end using internal RNA template, allowing standard replication to fill in.
Low telomerase → gradual telomere shortening (cell senescence); reactivation common in cancer cells.

Specific repair:
• Photorepair: photolyase + visible light splits UV-induced thymine dimers.
• Mismatch repair: excises mispaired bases post-replication.
Nonspecific repair:
• Excision repair (NER/BER): damage recognition → removal of short ssDNA segment → gap filled by DNA polymerase, sealed by ligase.
Effective repair prevents mutation accumulation from UV, ionising radiation, chemicals, metabolic by-products.