Genome integrity Flashcards
(65 cards)
six basic forms of DNA repair
nucleotide excision repair, base excision repair, recombination (NHEJ), direct reversal repair, mismatch repair, recruit mutagenic pols to get through stalled fork
what is most frequent form of spontaneous damage?
spontaneous depurination of guanine to O6-methylguanine
how to tell which strand is newly synthesized in bacteria?
methylation patterns, newly synthesized is unmethylated, recognized by MutSHL proteins
how do photolyases work?
use light energy to become activated, break up thymidine dimers
for what are XP genes named?
Xeroderma pigmentosum
what are some ways you can get mispairing?
misincorporation, tautomer incorporation, spontaneous hydrolysis
what is translesion DNA synthesis?
process that permits synthesis across unrepaired lesions, carried out by error prone polymerases. Members of polymerase Y family
what is translesion DNA synthesis?
process that permits synthesis across unrepaired lesions, carried out by error prone polymerases. Members of polymerase Y family
how do you repair double stranded breaks?
two broad pathways - non-homologous end joining and homology directed repair
which DSB repair pathway is highly preferred by the cell?
NHEJ > HDR, although it is almost always an imprecise join
T/F. Homology directed repair has a strong cell cycle dependence
True, it is almost completely absent during G1, pops up in S phase
T/F. NHEJ and Crispr knockouts are related
True, you cut with Crispr and rely on the cell to repair the break via NHEJ, which introduces mutations at the site and often causes a frameshift
what are the NHEJ mammalian proteins and what do they do?
Ku binds broken ends, recruits DNA-PKcs, Artemis nuclease which trims single stranded tails, DNA ligated by ligase 4
synthesis dependent strand annealing is the mechanism for what repair pathway?
homology-directed repair
strand exchange in homologous recombination is mediated by what types of proteins?
specialized recombinases, RecA in Ecoli, Rad51 in eukaryotes, and Dmc1 in meiosis
how does stretching/underwinding of DNA by specialized recombinases affect melting temperature
it lowers it
how are single stranded tails at DSBs generated?
by RecBCD, is a bidirectional helicase that melts/separates DNA strand while the RecB degrades both strands, hits a chi site that induces RecBCD to only chew up one strand, leaving the tail which is the invading entity
T/F. In ecoli as much as half cells require replication fork restoration in each round of chromosome duplication
True, they requires homology directed repair to rescue them
holliday junction
formed and resolved during homologous recombination, due to reciprocal exchange of strands between homologous DNA duplices
how can homologous recombination occur?
between plasmid, viral and host chromosomes, during mitosis, transformation, and most importantly ) meiosis in eukaryotes, during transduction/conjugation etc in prokaryotes
what are two ways holliday junctions can resolve and what are their consequences?
horizontal, no exchange and non-recombinant product
vertical, exchange and recombinant product
T/F. Homologous recombination involves formation of a single Holliday junction
False, you need a double junction in reality
why is sliding of holliday junction energetically possible?
because you pair a base for every one you break, driving the reaction
loss of heterozygosity can be caused by (2)
homologous recombination or break induced replication
