Biochem DNA Damage

Mutation

An accidental, permanent change in a DNA sequence

Silent Mutation

Change is a base at the DNA level - No change at the protein level

Nonsense Mutation

Results in a non-functional protein

Frameshift Mutation

• Insertion or deletion that is not a multiple of 3 bases

• Often leads to an early stop codon

• Mutations that affect RNA splicing often generate these

In-Frame Deletion

• Adding or removing a multiple of 3 bases

• Seen in cystic fibrosis mutation

DNA Damage

• Abnormal chemical structure of DNA

• Can be spontaneous or caused by environmental factors

• Can result in mutations

_____ promote changes in DNA sequences and are often _______ .

Mutagens; carcinogens

Ames Test

Determines if a compound is a mutagen

Deamination

• Of C → U and 5-meC → are most common

• Can occur spontaneously

Reactive Oxygen Species

• Generated by cellular respiration

• OH radical inserts into G or T

• Can result in DNA strand breaks

Depurination

Hydrolysis of glycosidic bond linking purine to sugar-phosphate backbone

• Creates an abasic site → site without a base

_____ agents covalently modify bases in DNA and distort DNA helix.

Alkylating

Alkylating Agents Examples

1. Sulfur Mustard

2. SAM (G→ 7-methylguanine)

Thymine Dimers

Most common DNA damage caused by UV radiation

Ionizing Radiation

• High-energy radiation that can release electrons from atoms generating ions which can break covalent bonds

• Cosmic rays, X-rays, Radioactive material

• Damages bases at breaks (single or double strand breaks)

  • DNA ligase cannot repair

Mismatch Repair

Corrects mismatched base pairs mainly from errors in replication

• MutL-MutS recognizes the mismatch

• MutH has endonuclease activity - digests nick from mismatch

• DNA Pol 3 fills gap

• DNA ligase seals

Base Exclusion Repair

Repairs mismatches resulting from damaged bases, depurination, and single-stranded breaks in DNA

DNA Glycosylase

• Cleaves glycosidic bond in base excision repair

• Creates an abasic site

Nucleotide Excision Repair (NER)

Repairs lesions that distort DNA double helix like thymine dimers or alkylation

Excinuclease

• Hydrolyze 2 phosphodiester bonds

• Eukaryotes use XP excinuclease

• In NER

Non-Homologous End Joining

• Predominant mechanism in G0 and G1 for repair of double-stranded breaks in mammals

• Error prone repair

• Error Prone terminal transferases add in random bases after physical contact between break of double strands

Homologous Recombination Repair

• Can also repair double stranded breaks in DNA after it has been replicated

• Template is sister chromatid

• BRCA ½ involved in strand invasion

• error-free repair mechanism