13 A Notes on Mutation Proofreading and Repair

Introduction to Mutations

• Mutations are rare, random alterations in the genetic material.
• They can lead to deleterious effects, impairing gene function or products.
• Role of Mutations: Generate inherited genetic diversity, fueling evolutionary change.

Types of Mutations

General Types

• Mutations can substitute or delete one or more DNA base pairs.

Point Mutations

• Defined as a mutation occurring at a specific identifiable position in a gene.
• Mutation Rates Across Organisms:
  • E. coli mutation rate: 1 imes 10^{-7} to 1 imes 10^{-9} per replication.
  • Human mutation rate: 1 imes 10^{-4} to 1 imes 10^{-6}.

Base Pair Substitution Mutations

1. Types:
   • Transition Mutations: Purine to purine or pyrimidine to pyrimidine (e.g., adenine to guanine).
   • Transversion Mutations: Purine to pyrimidine or vice versa (e.g., adenine to cytosine).
2. Tautomeric Shifts: These shifts in base pairing can lead to mutations with a mispairing probability of 10^{-4} mutations per base pair.

Categories of Base Pair Substitution Mutations

• Silent Mutations: No change in amino acid sequence (e.g., A to T with no effect on resulting protein).
• Missense Mutations: Change in amino acid (e.g., cytosine to adenine, changing proline to threonine).
• Nonsense Mutations: Introduces a premature stop codon, shortening the protein significantly.

Frameshift Mutations

• Occur upon adding or deleting one or more base pairs, altering the reading frame of the gene.
• Altered reading frame can produce entirely different polypeptide sequences or lead to premature stop codons.
• Example: Deleting two bases changes the reading frame and the resulting protein structure.

Regulatory Mutations

• These mutations affect gene regulation rather than protein sequence itself and include:
  • Promoter Mutations: Affect efficient transcription initiation.
  • Splicing Mutations: Affect intron-exon splicing, possibly creating new splice sites or preventing normal splicing.

DNA Proofreading and Repair Mechanisms

DNA Polymerase Function

• Intrinsic Proofreading: DNA polymerase checks nucleotides after addition, correcting errors using its 3' to 5' exonuclease activity.
• Cleavage of mismatched nucleotides allows correct base pairing.

Induced Mutations

• Caused by various agents (chemical & radiation), affecting the DNA sequence.
• Mutagens: Cause DNA damage.
  • Examples of Chemical Mutagens: Nucleotide analogs, intercalating agents (e.g., Acridine).

Irradiation Effects

• UV light can cause photoproducts, which disrupt replication and permeability of DNA polymerase.
• Common photoproducts: Thymine dimer and 6-4 photoproduct.

Testing for Mutagens

Ames Test

• Tests for mutagenicity using Salmonella typhimurium, particularly in the context of human exposure.
• Involves observing the reversion of histidine auxotrophs when exposed to potential mutagens.

Repair Mechanisms for Mutations

1. Nucleotide Excision Repair: Repairs UV-induced damage by removing damaged bases.
2. Photoreactivation: Direct repair mechanism that restores DNA from photoproducts.
3. Mismatch Repair: Enzymes distinguish between the correct and mismatched nucleotide after DNA replication.
4. Direct Repair: Enzymes fix mismatches by identifying and correcting errors based on DNA template integrity.

Clinical Relevance of Repair Deficiencies

• Defects in repair mechanisms can lead to disorders like Xeroderma Pigmentosa, associated with severe skin abnormalities due to UV damage.

Conclusion

• Mutations can arise from various sources, but cellular mechanisms exist for proofreading and repairing DNA damages. Understanding these processes is vital to grasp genetic stability and variations in living organisms.

• For any queries or further explanations, feel free to reach out directly.