DNA damage and Repair Flashcards
How many errors does DNA polymerase make?
10^4 to 10^5 nucleotides
How many errors are left after repair mechanisms?
1 in 10^9 nucleotides are errors.
Which types of abnormalities need repair?
Base mismatches
Damage to the structure of the DNA itself (break in the chromosome or pyrimidine dimers)
What does mismatch repair do?
repairs replication errors: mispaired bases and strand slippage.
What does direct repair do?
repairs pyrimidine dimers and other specific types of alterations
What does base excision do?
repairs abnormal bases, modified bases and pyrimidine dimers.
What does nucleotide excision do?
Repairs DNA damage that distorts the double helix, including abnormal bases, modified bases and abnormal dimers.
Which enzyme repairs nicks in the DNA strand?
DNA ligase
How are chemically modified bases repaired?
Base excision repair: removal of base-specific DNA glycolase.
How are mismatched bases repaired?
Corrected by mismatch repair: excision and resynthesis.
What does the AP endonuclease repair system do?
Fixes apurining or apyrimidinic sites.
How is a damaged region of DNA fixed?
Nucleotide excision repair (excision and resynthesis across partner strand)
How are pyrimidine dimers fixed?
enzymatically reversed.
Describe direct repair in detail.
Damaged nucleotide, chemically damaged and abnormal: it is not chemically stable in relation to the rest of the DNA molecule. Not a standard ATCG. Direct repair would be to chemically modify the damaged nucleotide (little evidence of occurring substantially). For example, is deamination of thymidine occurs, forming uracil, one cannot just go back and add an amine groupe.
Describe excision repair in detail.
A damaged nucleotide not forming the standard ATCG can excise a region: the sugar phosphate backbone is removed and the missense strand is used as a template by DNA polymerase. DNA ligase then reforms the backbone.
Describe mismatch repair in detail.
Occurs when either a missing base has occurred or a mis-matching of DNA bases. A segment of DNA is excised and the other strand is used as a template to add newly synthesised nucleotides whilst reforming the sugar phosphate backbone. Can be as much as 500 bases excised.
Describe recombination repair.
Double strand break: hard to repair as there are no sticky ends. Recombination repair involves two molecules (via the other chromosomes) to direct the process of joining these two broken DNA strands.
What is required for DNA ligase to operate?
Requires a function 5’-phosphate and 3’hydroxyl group.
How are alkyl groups repaired?
This is a highly specific removal of chemical groups: O6-methylguanine-DNA methyltransferase (MGMT)
How does photoreactivation occur?
DNA photolyase is stimulated by 300-500 nm light. It is not present in humans but is found in plants.
How is base-excision repair performed?
Specific DNA glycosylases cut between the base and the sugar backbone (or cut out the whole backbone or remove th bases that reside within the DNA molecule, glycosylases will further remove the bases, leaving the backbone intact. This creates and AP site, AP endonucleases cut the backbone and resynthesis by DNA polymerase, with the damaged strand acting as a primer and original strand as a template.
How does nucleotide-excision repair differ from base excision repair?
They are very similar, however NER does not require initial removal of damaged base. There is recognition of damaged region, followed by excision of up to 12 nucleotides. Excised region is replaced by DNA polymerase/DNA ligase. Regions up to 2kb may be excised and repaired.
Why is mismatch repair difficult?
It is difficult to tell which was the original base and which needs to be retained. Mismatch repair specifically repairs errors of replication where the bases are normal. Excision of daughter strand followed by new polymerisation.
What is replication slippage?
It is expansions of repeats (mostly microsatellites: AAA homopolymer or GCGCGCGCG; the simpler they are the more difficult they are to replicate.
Expansions are common but sometimes retractions can occur. Expansion/contraction may depend on the parent of origin. The larger the repeat gets, the more they expand from one generation to the next.
