13.4 Biological Molecules: DNA Structure, Replication & Repair

DNA: Structure, Replication, and Repair

The PA-CAT Bulletin of Information, rev. 20240815 places Biological Molecules and DNA structure/replication within General Biology (Table 6). DNA is the molecule of heredity; its structure dictates how it is copied and repaired, and misrepair underlies mutation and disease.

DNA Structure: The Double Helix

DNA is a double-stranded helix (Watson-Crick, 1953). Each strand is a polymer of nucleotides, and each nucleotide has three parts:

1. A five-carbon sugar — deoxyribose (lacks a 2' -OH).
2. A phosphate group — links the 5' carbon of one sugar to the 3' carbon of the next via a phosphodiester bond, giving the backbone a directionality (5' to 3').
3. A nitrogenous base — adenine (A), guanine (G) [purines, two rings]; thymine (T), cytosine (C) [pyrimidines, one ring].

The two strands run antiparallel (one 5' to 3', the other 3' to 5') and are held by complementary base pairing: A pairs with T via two hydrogen bonds; G pairs with C via three hydrogen bonds. G-C pairs are therefore more stable (higher melting temperature), so G-C-rich DNA requires more heat to denature. The outer backbone is hydrophilic; the inward bases are hydrophobic and stack via van der Waals forces. The helix completes one turn every ~10 base pairs (~3.4 nm) in the B-form most common in cells. The major and minor grooves wind around the helix, providing sites where proteins bind specific base sequences.

RNA vs. DNA

The 2' -OH on ribose makes RNA chemically reactive and able to act as a catalyst (ribozymes); it also makes RNA more labile, which is why DNA is the archive and RNA the working copy. Uracil replaces thymine in RNA because uracil is energetically cheaper to synthesize, and DNA uses thymine (a methylated uracil) to help distinguish damaged cytosine from genuine uracil.

Replication: Semi-Conservative

Meselson and Stahl (1958) proved DNA replication is semi-conservative: each daughter molecule has one parental and one newly synthesized strand. Key enzymes:

• Helicase unwinds the double helix at the replication fork, breaking hydrogen bonds.
• Topoisomerase relieves supercoiling ahead of the fork by cutting and rejoining DNA; topoisomerase II (gyrase) introduces negative supercoils in bacteria.
• Primase lays down a short RNA primer (5' to 3') so DNA polymerase can start, because DNA polymerase requires a free 3' -OH.
• DNA polymerase III (prokaryotes) / polymerases delta and epsilon (eukaryotes) extends the primer 5' to 3', adding nucleotides complementary to the template. Error rate about 1 in 10^7 before proofreading.
• Leading strand is synthesized continuously toward the fork; the lagging strand is synthesized discontinuously as Okazaki fragments (because synthesis must run 5' to 3' away from the fork).
• DNA polymerase I removes RNA primers (5' to 3' exonuclease) and fills gaps.
• DNA ligase seals the final nick, joining Okazaki fragments.
• Single-strand binding proteins (SSBs) keep strands apart and protected from nuclease attack.

Replication initiates at origins of replication (oriC in E. coli, one; eukaryotes have thousands) and is bidirectional. In eukaryotes, telomeres (repeated TTAGGG sequences) cap chromosome ends; because lagging-strand synthesis cannot complete the very tip (the end-replication problem), telomeres shorten each division. Telomerase extends telomeres in germ cells and stem cells and is reactivated in most cancers, making it a therapeutic target.

DNA Repair

Errors and damage are inevitable; repair pathways preserve sequence integrity:

• Proofreading — DNA polymerase checks each just-added base; a mismatch triggers 3' to 5' exonuclease removal and re-extension. Catches about 99% of errors.
• Mismatch repair (MMR) — post-replication proteins (MutS/MutL in E. coli; MSH/MLH in humans) recognize distortions from mispaired bases, excise the new strand segment, and resynthesize. Defects cause Lynch syndrome (hereditary non-polyposis colon cancer).
• Base excision repair (BER) — removes damaged bases (deamination, oxidation) via DNA glycosylases; AP endonuclease cuts the backbone; polymerase and ligase fill. Handles small, non-bulky lesions. Oxidative damage produces 8-oxoguanine, which pairs with adenine instead of cytosine if not repaired.
• Nucleotide excision repair (NER) — removes bulky adducts such as thymine dimers from UV light. A multi-enzyme complex cuts 12-24 nucleotides around the lesion. Xeroderma pigmentosum results from NER defects, causing severe UV-induced skin cancers.
• Direct repair — photolyase (in some organisms) reverses thymine dimers directly; O6-methylguanine methyltransferase reverses alkylation.

Why This Matters for the PA-CAT

Expect items testing: which enzyme unwinds DNA (helicase), which joins Okazaki fragments (ligase), why replication is semi-conservative, the A-T / G-C pairing rules, and the consequence of a repair defect (e.g., UV to thymine dimers to NER; mismatch repair defects to Lynch syndrome). Remember the 5' to 3' directionality rule: polymerases synthesize only in the 5' to 3' direction, which is why the lagging strand is fragmented. Telomere shortening and telomerase are a common clinical application item, especially in cancer biology.