DNA REPAIR OVERVIEW

DNA Repair Overview

  • DNA is a relatively stable molecule but can suffer damage from various sources.

Types of Damage to DNA

  • Sources of Damage:

    • Thermal fluctuations (common)

    • Metabolic accidents (unintended oxidations)

    • Radiation (UV, X-ray)

    • Environmental toxins (mutagens, carcinogens)

  • Note: These are different from replication errors.

DNA Repair Mechanisms

  • Effectiveness: Approximately 99.9% of DNA damage is identified and repaired by cells.

  • Function of Repair Proteins: Cells synthesize many repair proteins which often use a template for guidance, explaining the universality of double-stranded DNA as the hereditary material.

Common DNA Repair Mechanisms

  • Base Excision Repair

  • Nucleotide Excision Repair

  • Double-Strand Break Repair

Base Excision Repair

  • Process:

    • DNA glycosylases identify and separate damaged bases from DNA strands.

    • At least 6 different glycosylases exist, each recognizing specific altered bases.

    • When an altered base is detected, it leads to a conformational change and initiation of repair, where the base is removed via a hydrolytic reaction.

    • Other enzymes then remove the backbone of the strand, replacing the removed section with a new base.

  • **Specific Enzymes: **

    • DNA Glycosylases: Remove damaged bases.

    • AP Endonuclease: Cuts one side of the sugar-phosphate bond.

    • Phosphodiesterase: Cuts the other side of the bond.

    • DNA Polymerase: Replaces the damaged base.

    • DNA Ligase: Seals the remaining bonds.

Base Chemistry Facilitating Repair

  • Deamination: Refers to an altered base, involving a different glycosylase for each altered base.

  • Note on Bases: Cytosine (C) can be deaminated to Uracil (U), resulting in DNA damage as U is typically not present in DNA.

Nucleotide Excision Repair (NER)

  • Function: Repairs larger areas of damage, such as bulky lesions (e.g., covalent hydrocarbon attachments and dimerization).

  • Mechanism:

    • A multi-enzyme complex binds to distorted regions on DNA.

    • Phosphodiester (PD) bonds around the lesion are cut allowing helicase to separate the damaged strand.

    • DNA polymerase and ligase then perform the repair.

Double-Strand Breaks (DSBs)

  • Severity: DSBs are serious as both strands of the helix are damaged, complicating repair efforts.

  • Repair Mechanism:

    • Non-Homologous End Joining (NHEJ): Simply rejoins broken ends, resulting in deletion mutations.

Homologous Recombination (HR)

  • Characteristics:

    • Preserves the original DNA sequence, requiring a sister chromatid and occurs after replication (S and G2 phases).

    • Functional Mechanism: Involves single-stranded regions invading homologous double-stranded DNA.

    • Proteins involved: RecA (in E. coli) and RAD51 (in eukaryotes).

Recombination Processes

  • Types:

    • Homologous recombination, transposition, and site-specific recombination involve DNA strand invasion.

    • Useful in repairing DSBs and allowing genetic exchange during meiosis (crossing over).

Consequences of Crossing Over

  • Results: New combinations of alleles, gene conversion can occur leading to an unequal contribution of parental alleles.

Mobile Genetic Elements

  • Move from one region of the genome to another, do not require homology between the sites, and can remain fixed in genomes (approx. 45% of human DNA).

Types of Transposable Elements

  • Transposition: Involves both DNA-only and retroviral-like retrotransposons.

  • Mechanism: DNA-only transposons utilize transposase; retrotransposons rely on reverse transcriptase for “copy and paste” movement between locations.

True Retroviruses

  • Use a similar mechanism to retrotransposons but include proteins for moving between cells (e.g., viral coats).

Evolutionary Context

  • All labeling of DNA repair, homologous recombination, and transpositional processes share similar biochemical mechanisms involving specific enzymes like endonucleases, exonucleases, and ligases.

robot