In-Depth Notes on DNA Repair Mechanisms

DNA Repair Overview

  • Importance of DNA Repair: Critical for the survival of organisms; systems to prevent errors during DNA replication and to repair mutations are essential.

Multi-step Process of DNA Repair

  1. Detection of DNA Irregularities: Identifying the abnormal structure in DNA.
  2. Removal of Abnormal DNA: Eliminating the section of the DNA that contains the error.
  3. Synthesis of Normal DNA: Filling in the gap with correct nucleotides.

Types of Mutations

  • Spontaneous Mutations:
    • Arise from errors during natural biological processes, e.g., DNA replication.
  • Induced Mutations:
    • Caused by environmental mutagens, including:
    • X-rays
    • UV light
    • Certain chemicals

Direction of DNA Strand Replication

  • Addition of nucleotides occurs only in the 5' to 3' direction during DNA replication.

DNA Polymerases and Proofreading

  • Domains of DNA Polymerase:
    • Polymerase domain: Synthesizes new DNA strands.
    • 3'–5' exonuclease domain: Responsible for proofreading and correcting errors.
    • 5'–3' exonuclease domain: Removes RNA primers left during replication.
  • Not all polymerases possess these domains.

Importance of Proofreading

  • Proofreading is vital; most DNA polymerases possess a 3'–5' proofreading ability to identify and correct mismatches.
  • Without effective proofreading, a larger mutation rate occurs, particularly with DNA polymerases V, IV, and II in E. coli.

Mismatch Repair Systems

  • Function: Corrects base pair mismatches and operates when proofreading fails.
  • Mismatch repair systems can distinguish between parental and daughter strands due to methylation patterns:
    • Newly synthesized strands are initially unmethylated, while parental strands are methylated.
  • Key proteins in E. coli involved in mismatch repair: MutL, MutH, MutS.

DNA Methylation

  • Methylation is a process where methyl groups (–CH3) are added to DNA bases:
    • Unmethylated: Newly synthesized daughter strand after replication.
    • Hemimethylated: Parental strand is methylated while daughter is not immediately after replication.
    • Fully Methylated: Both strands are methylated after some time.

Types of DNA Damage and Repair Mechanisms

  1. Thymine Dimers:

    • Caused by UV light leading to cross-linking of thymine bases, which must be repaired to maintain DNA integrity.
    • Repair Enzyme: Photolyase can directly reverse thymine dimers.

  2. Deamination of Cytosine:

    • Loss of amino group results in uracil, which must be removed by repair enzymes.

  3. Base Excision Repair:

    • Targets and removes damaged or abnormal bases via DNA N-glycosylases that cleave the bond between the abnormal base and the sugar.
    • Process: Removal of the damaged base → AP endonuclease cuts DNA backbone → Repair by DNA polymerase and ligase.

  4. Nucleotide Excision Repair:

    • Removes larger segments of damaged DNA, such as thymine dimers and other chemically modified bases.
    • Requires proteins: UvrA, UvrB, UvrC, UvrD in E. coli.

Double-Strand Break Repair Mechanisms

  • Homologous Recombination:
    • Uses a sister chromatid as a template for accurate repair; involves proteins such as RecA, RecB, RecC, RecD.
  • Nonhomologous End Joining:
    • Directly joins broken DNA ends, which may lead to minor deletions.

Implications of DNA Repair Mechanisms

  • Defects in DNA repair mechanisms can lead to diseases, e.g., xeroderma pigmentosum and Cockayne syndrome, characterized by increased sensitivity to UV light.