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Unformatted text preview: 4.12.2007 AP endonucleases makes one knick, exonuclease removes a handful of nucleoutides, DNA pol fills in the gap, ligase fills the last phoshopdiester bond Excision repair system repairs more than one kind of problem and this is true also for AP endonuclease type repairdeamination is also done Deamination of cytosine by nitrous acid gives deoxyuridine (rare base) this rare base is recognized by a particular enzyme (glycosylase) glycosylase recognizes uracil bound to deoxyribose and it breaks a bond between the uracil and the deoxyribosethis creates an AP site because the base is gone which is recognized by AP endonucleases and is fixed subsequently by exonuclease, DNA polymerase, and ligase. There is not just one glycosylase there are a number of them in the cell. The one we just talked about is a uridine glycosylase. When other bases are deaminated the result is some other rare base and there is a specific glycosylase for each one of those and does the same exact thing. Another excision repair system o Mismatch repair o It is used to fix the misincorporated nucleotide that is caused by a tautomeric shift (cause transitions in replication) o Cant recognize a tautomeric shift because they shift and shift back in the moments before replication and so looking at the nucleotides themselves on the strandthe one consistent rule is that the one that is wrong is the one that was on the new strand. o Methylase will put a methyl group on both strands at the same location (opposite each other) this is what DNA looks like most of the time. At replication (replication is semiconservative) and the two strands separate from each other so that each one can be used as a template, DNA polymerase will make a new strand that is complimentary to each one but DNA pol can only incorporate the normal nucleotides (not methylated nucleotides) so the new strand is not methylated. The methyl group will be added to the new strand but it must be done by methylase not by DNA polymerase. So the methylase comes along after replication, it takes a few minutes for it to get around to this so there is a window of time between replication and methylation when the old strand is methylated (because it already was methylated from before) and the new strand is not yet methylated. This is when mismatch repair occurs o Weve always talked about repair happening before replication, before a lesion can cause a mutation. But here it must be repaired after replication because there was no lesion before replication and the mutation happens after replication. o At the mismatch, is where there is a repulsion of two nucleotides that cant base pair to each other. It is recognized by a protein called mutS . mutS on its own cannot do the repair, it just recognizes the bulge so it recruits another protein called mutH ....
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