DNA Replication and Repair Mechanisms

DNA Replication Essentials - The Blueprint Copiers

• Semiconservative: Each new DNA: one parental, one new strand. Ensures faithful copying.
• Bidirectional: From origin (Ori), two replication forks proceed in opposite directions.
• Direction: Synthesis strictly $5' \to 3'$. Leading strand continuous; lagging discontinuous (Okazaki fragments).
• Core Sequence:

• Key Enzymes:
  • Helicase: Unwinds DNA (ATP-dependent). 📌 "Heli-case cuts helix."
  • Topoisomerases: Relieve supercoils (e.g., DNA gyrase).
  • Primase: Synthesizes RNA primers for DNA Pol.
  • DNA Polymerase: Synthesizes DNA; proofreads ($3' \to 5'$ exonuclease). (Prok: Pol III; Euk: Pol $\delta, \epsilon$).
  • Ligase: Joins DNA fragments.

⭐ DNA replication in eukaryotes initiates at multiple origins of replication (ARS - autonomously replicating sequences) per chromosome, unlike prokaryotes with a single origin (OriC).

Prokaryotic vs. Eukaryotic Replication - Cellular Copying Quirks

• Core Contrast: Prokaryotic replication is simpler, faster, with a single origin; Eukaryotic is complex, slower, featuring multiple origins and telomere maintenance.

⭐ Eukaryotic replication is tightly coupled to the cell cycle, primarily occurring during the S phase, unlike prokaryotes where it can occur continuously.

DNA Damage & Repair Pathways - Code Correction Crew

• Damage Sources:
  • Endogenous: Depurination, Deamination (C→U), Oxidation (8-oxoG).
  • Exogenous: UV (pyrimidine dimers), Alkylating agents, X-rays (DSBs).
• Key Repair Systems:
  • Direct Reversal: MGMT (O6-methylguanine).
  • Base Excision Repair (BER): For single base damage (uracil, 8-oxoG).
    • Key Enzymes: Glycosylase, AP Endo, Pol, Ligase. 📌 Go Eat Pizza Later.
  • Nucleotide Excision Repair (NER): For bulky lesions (pyrimidine dimers).
    • Defect → Xeroderma Pigmentosum (XP).
  • Mismatch Repair (MMR): For replication errors. MSH, MLH proteins.
    • Defect → Lynch Syndrome (HNPCC).
  • Double-Strand Break (DSB) Repair:
    • Homologous Recombination (HR): Error-free. S/G2 phase. Proteins: BRCA1/2, RAD51.
    • Non-Homologous End Joining (NHEJ): Error-prone. G1 phase. Proteins: Ku70/80.
  • Translesion Synthesis (TLS): Error-prone bypass polymerases.

⭐ Xeroderma Pigmentosum (XP) results from NER defects, causing extreme UV sensitivity and high skin cancer risk.

Clinical Correlates & Inhibitors - Healing Code Glitches

• Repair Defect Syndromes:
  • Xeroderma Pigmentosum (XP): NER defect; UV hypersensitivity, ↑ skin Ca.
  • Lynch Syndrome (HNPCC): MMR (MSH2, MLH1) defect; ↑ colorectal, endometrial Ca.
  • Ataxia-Telangiectasia (AT): ATM gene (NHEJ) defect; ataxia, telangiectasias, immunodeficiency.
  • Fanconi Anemia: DNA crosslink repair defect; pancytopenia, congenital anomalies.
• Key Replication Inhibitors:
  • Antimetabolites: Cytarabine (DNA Pol), Methotrexate (DHFR), 5-FU (Thymidylate Synthase).
  • Topoisomerase Inhibitors:
    • Type I: Irinotecan, Topotecan.
    • Type II: Etoposide, Doxorubicin.

⭐ Quinolone antibiotics (e.g., Ciprofloxacin) target bacterial DNA gyrase (Type II topoisomerase).

High‑Yield Points - ⚡ Biggest Takeaways

• DNA replication: semiconservative, bidirectional, S phase. Key enzymes: Pol III/δ/ε, helicase, ligase.
• Okazaki fragments form on the lagging strand, joined by DNA ligase.
• Telomerase (reverse transcriptase) maintains eukaryotic telomere length, preventing degradation.
• Mismatch Repair (MMR) corrects post-replication errors; defects cause Lynch syndrome.
• Nucleotide Excision Repair (NER) removes UV-induced pyrimidine dimers; defects cause Xeroderma Pigmentosum.
• Base Excision Repair (BER) corrects single damaged bases like deamination.