Wk 13&14 Lecture 5: DNA Repair

DNA Fidelity and Repair

  • Importance of DNA integrity

    • DNA serves as a permanent copy of the cellular genome, so maintaining integrity is crucial for survival and cellular function.

    • Damage can arise from replication errors or external factors.

  • Mechanisms of DNA Repair

    • The cell employs several mechanisms to repair DNA, highlighting biological systems' evolution to manage stress.

    • If damage is not repaired prior to replication, errors can be passed to daughter cells, affecting gene functions.

Types of DNA Damage

  • Categories of Damage

    • Exogenous Damage: Originates from external factors.

      • Examples include UV light and radiation, leading to thymine dimers which interfere with replication.

      • Chemicals (like alkylating agents) can cause modifications to bases, e.g., methylation and carcinogen interactions (e.g., benzopyrene).

    • Endogenous Damage: Originates within the cell.

      • Occurs from spontaneous reactions (e.g., deamination) or reactive oxygen species generated during metabolism.

DNA Lesions and Mutations

  • Lesions: Actual damages or structural changes in DNA caused by various factors (e.g., breaks, bulky additions, dimerization).

  • Mutations: Sequence changes in DNA bases, commonly GC to AT transitions.

    • Types of mutations: substitutions, insertions, deletions.

    • Mutations can be silent, harmful, or lethal and mostly offer no benefit to the organism.

DNA Repair Mechanisms

  1. Mismatch Repair (MMR)

    • Fixes mismatches left after DNA replication.

    • Utilizes hemimethylation to differentiate between template and newly synthesized strands.

    • In E. coli, methylation of adenine in the GATC sequence aids in strand identification.

    • Key proteins involved:

      • MutS: Recognizes mismatches.

      • MutL: Coordinates the repair process.

      • MutH: Cleaves unmethylated strand.

    • Repair Process:

      • MMR increases fidelity by correcting missed errors post-replication, utilizing energy from ATP hydrolysis.

  2. Direct Repair (Doctor)

    • Removes base modifications directly without excising entire bases.

    • MGMT (O6-methylguanine methyltransferase): Transfers methyl group from damaged guanine, sacrificing itself in the process.

    • This mechanism highlights the need for DNA fidelity by sacrificing enzymes to repair bases.

  3. Base Excision Repair (BER)

    • Removes specific damaged bases, using small lesions and chemical changes as targets.

    • Key enzymes:

      • DNA Glycosylases: Recognize and remove damaged bases.

    • The process:

      • Removal leaves an abasic site, followed by actions of endonucleases and DNA polymerase to fill in the gaps.

    • Endogenous threats like oxidative stress (producing radicals) and spontaneous deaminations target critical bases (e.g., guanine to 8-oxoG).

      • MMR can further address mismatched bases derived from mispaired oxidative damage.

  4. Nucleotide Excision Repair (NER)

    • Targets bulky DNA adducts and helix-distorting lesions (e.g., thymine dimers from UV radiation).

    • NER's versatility allows for the repair of multiple bases, often involving a larger 12-nucleotide segment.

    • Enzymes in this process effectively remove damaged regions, allowing for subsequent repair by DNA polymerases.

Summary of Repair Processes

  • Functions of Repair Mechanisms:

    • All four mechanisms (MMR, direct repair, BER, NER) safeguard the genome's integrity, ensuring proper cellular function and minimizing mutations.

    • Efficiency and redundancy are crucial, as different types of damage require distinct repair strategies to maintain fidelity.

    • Understanding how these systems work provides insights into genetic stability and the potential implications when repair processes fail.