16: DNA repair Flashcards
What is DNA damage?
any unintended physical or chemical change in DNA
template for repair?
Complementary strand
What is a copying mistake?
DNA polymerase makes an error once every ~107 nucleotides in insertion, deletion, or mismatch
What is depurination?
spontaneous loss of A or G base; forms abasic site (sugar and phosphate but no base)
if depurination happens before replication? solution?
loss of base in template strand = normal replicative DNA poly stalls, replication stops, –> issue bc cell is committed to cell division
solution: A translesion DNA polymerase skips past abasic site and continues replication bc it is more flexible than normal DNA poly
Why can’t we always use translesion DNA?
flexible active site = more mistakes
What is deamination?
spontaneous loss of amine in a C and conversion to carbonyl (converts C->U)
What are pyrimidine dimers?
UV light catalyses 4 membered ring formation between adjacent pyrimidines (T) (double bond)
blocking DNA rep and requires translesion poly to condition past damage site, but cause mutation in new strand
What are some Other base modifications?
- Ionizing radiation (x rays)
- Chemical mutagens
What are causes of Breakage of sugar-phosphate backbone?
Ionizing radiation (UV, x-ray)
* Reactive oxygen species
* Mechanical stress (DNA strand separation)
can be:
* Single-strand or double-strand
What are DNA repair systems?
- proofreading during replication by DNA poly
- mismatch repair: repair replication mistakes shortly after replication
- direct repair: enzymes specific to particular base
modifications
What is the mismatch repair mechanism In bacteria?
- bacteria methylates DNA at specific locations on both strands
- determine new strand by seeing which one is not methylated (this will be the one that gets fixed) - hemi-methylated
- endonuclease nicks new strand at the methylated site
- exonuclease cutes from methylated site to site of mismatch – costly!
- DNY poly 1 and ligase
catches 99% of DNA poly mistakes (3 mistakes/3 billion remain)
what is the difference between base excision repair and direct repair?
BER is more general
What are the two types of base excision repair?
short patch and long patch (both one damaged base); long patch occurs when something goes wrong in sealing backbone
What is the base excision repair short patch mechanism?
- DNA glycosylase breaks N-glycosidic bond, doesn’t break backbone and only removes base from backbone
- AP endonuclease breaks backbone (makes a nick at abasic site)
- DNA poly synthesizes single base (need to remove extra sugar phosphate with nuclease) and DNA ligase
What is the base excision repair long patch mechanism?
- bae removal from glycosylase
- abasic site made
- endonuclease nicks backbone
- DNA polymerase adds a base and extra sugar phosphate is pushed BUT nuclease CANT cut
- DNA poly adds more bases of DNA that are already there (repeat) and redundant DNA pushes normal DNA out (2-10 bases added)
- endonuclease removes normal DNA flap
- nick and endonuclease cut site ligated with DNA ligase
What is the Nucleotide excision repair mechanism?
- damaged nucleotide
- helicase separates stands at and around site of damage
- different from BER endonuclease cutes on either site of damage and damaged fragments is released
- DNA poly and DNA ligase
What is Homologous recombination (HR)?
Repair of double-strand breaks
* Slow, but accurate (used in smaller organisms - if another copy of chromosomes in DNA with exact sequence is near right after replication of daughter cells)
What is Non-homologous end joining (NHEJ):
Repair of double- strand breaks
* Fast, but inaccurate
What is Base excision repair (BER):
Repair of modified bases (deamination), abasic sites, single-strand breaks
What is Nucleotide excision repair (NER):
Repair of pyrimidine dimers and damage that
disrupts double helix (+1 base)
