Notes on DNA Mutation and Repair

Mutation

  • Mutation: Refers to any hereditary change in the base sequence of DNA.
  • Mutant: A genetic state of an organism with characters different from the 'wild type'.

Types of Mutations

A. Based on the number of bases changed:
  1. Point Mutation: a) Base Substitution: i. Transition: Change between two purines or two pyrimidines. ii. Transversion: Change between a purine and a pyrimidine.
    1. Multiple/Chromosomal Mutations:
      • Inversions, Translocations.
    2. Frameshift Mutation:
      i. Base Addition: Insertions.
      ii. Base Deletion: Deletions, Duplications.
    3. Numerical Chromosomal Aberrations:
      • Aneuploidy, Euploidy.
B. Based on consequences to amino acid sequence:
  1. Silent Mutation: No change in amino acid.
  2. Neutral Mutation: No significant effect on the organism.
  3. Missense Mutation: Change in one amino acid.
  4. Nonsense Mutation: Premature stop codon.

Mutagenesis

  • Mutagenesis: Process of producing a mutation.
    1. Spontaneous: Occurs naturally without mutagen.
    2. Induced: Mutation caused by an external agent (mutagen).

Spontaneous Mutagenesis

  1. Uncorrected Mismatches: Errors during DNA replication.
  2. Tautomerization/Tautomeric Shift: Base shifts into tautomeric forms affect pairings.
  3. Replication Slippage: Misalignment during replication of short tandem repeats.
  4. Spontaneous Depurination: Loss of purine bases, creating gaps.
  5. Spontaneous Deamination: Loss of an amino group converting cytosine (C) to uracil (U).

Induced Mutagenesis

A. Chemical Mutagens

  1. Base Analogs: Similar to standard bases, lead to point mutations.
    • Example: 5-bromouracil (analog of T).
  2. Base-Modifying Agents: a) Deaminating Agents:
    • Nitrous acid deaminates A, C, G.
      b) Hydroxylating Agents:
    • Hydroxylamine hydroxylates C.
      c) Alkylating Agents:
    • Methylating and ethylating agents modify bases, causing mutations.
  3. Intercalating Agents: Insert between base pairs, causing distortion.
    • Examples: Ethidium bromide, proflavin.

B. Physical Mutagens

  1. UV Radiation: Creates pyrimidine dimers.
  2. Ionizing Radiation: More potent than UV, causes various mutations.
  3. Heat: Induces tautomeric shifts and damages.

C. Biological Agents

  1. Transposable Elements: Mobile DNA segments causing mutations.
  2. Viruses: Insert viral DNA disrupting host genes.
  3. Bacteria: Cause inflammation and produce DNA-damaging oxidants.

Consequences of Mutation

  • Impact on DNA, mRNA, and protein can lead to functional alterations depending on the type of mutation.

Types of mutations in context:

  • Point Mutation & Insertion: Can lead to changes in protein sequence affecting functionality.

DNA Repair Mechanisms

A. Direct Repair/Direct Reversal

  • Acts on damaged nucleotides directly.
    • Three types: Nicks, Alkylation damage, Cyclobutyl damage.

B. Base Excision Repair (BER)

  • Corrects specific chemical damage.
    • Involves excision of damaged segment and resynthesis using DNA glycosylase and AP endonuclease.

C. Nucleotide Excision Repair (NER)

  • Repairs extensive damage (2-30 bases).
    • Involves recognition, excision, and replacement of damaged DNA.

D. Mismatch Repair (MMR)

  • Corrects mismatched nucleotides in daughter strand.
    • In prokaryotes and eukaryotes involves specific sets of proteins like MutS, MutL, hMSH2.

E. Double-Strand Break Repair

  1. Homologous Recombination: Requires identical sequences.
  2. Non-Homologous End-Joining: Does not require sequence homology, directs sealing of DNA breaks.

F. SOS Response

  • Bacterial mechanism allowing error-prone DNA replication through damage, involving key proteins that regulate the response.