DNA Repair Flashcards
Methods of DNA proofchecking
H bonding, then DNA pol can “double check”
- conformational changes in DNA pol
- 3’-5’ exonuclease activity (DNA pol)
- strand directed mismatch repair (after rep)
Exonuclease activity
DNA pol can hydrolyze in the 3-5 direction that has just been covalently bound. mismatched nucleotides do not H bond and free OH groups in wrong position, leaving abnormal geometry, inducing cleavate.
DNA pol makes 1 in 100K , but in proofreading 1 in 10bil
DNA Damage
spontaneously or chemical, metabolics can produce damaging products
- mutations
- can become permenant in replication chain
Mechanisms of Repair
removal of bases and replaced with new DNA
a base excision
b mucleotide excision
c mismatched repair
or double stranded breaks
a NHEJ
b HR
Base Excision Repair
DNA glycosylases
deamination events to remove unnatural bases or repair missing bases (depurinations)
travel along DNA helix to probe
lesion specific
8 different types
- recognition
- glycosylase cleaves off base from deoxyribise
- abasic sugar left behind
- AP endonuclease removes the sugar phosphate backbone
- DNA pol adds new nucleotides, ligase seals
Nucleotide Excision repair
NEr recognizes distortions (damaged bases, pyrimidine dimers)
- recognition, by multienzyme complex for distortion
- nuclease cleaves on both sides including lots of bases
- helicase separates the two strands
- gap repaired DNApol, ligase
Strand directed Mismatch repair
used for mistakes made by DNA pol proofreading
-looks for distortions caused by misfit of non complimentary base pairs
- MSH binds to bulge
- Mlh binds to Msh at the DNA and scans for a nick (where Okazaki frag will be)
- Mlh trigger dgredation all the way back to mismatch
- gap filled by pol and ligase
HR
double stranded break
-primarily used to repair DS breaks during cell division when duplicated chromosomes have not split
- single strand end invade the other double helix of the sister chrom or hom chromosome
- ss DNA strands from damaged use complimentary of undamaged as a template to elongate 5-3.
- elongation complete, disengage and pair with DNA pol and ligase
G2 cell cycle only when sister chromatids available
NHEJ
exonuclease activity removes protion of ends
3’ ends pair with eachother, using others as template.
ligase fills gap.
missing bases are introduced.
ERROR PRONE
3’ ends must overlap. loss of one or more bases during resection
DNA DAMAGE
endo
deamination
base hydrolysis
oxidation
Exo
UV damage
Carcinogens
-DNA adducts
deamination
nitrous acid or nitrite (preservative in food) alters structure for incorrect pairing
cytosine to uracil 100bp/genome/day
uracil DNA glycosylase to remove bases
Base hydrolysis
glycosidic bond between purine base and sugar in a nucleotide can spontaneously hydrolyze leavine the ribose sugar without a base (apurinic site
dypyrimidination does also occur but lower rate.
loss of base with no repair: DELETION
Oxidation
metabolites release Oxygen.
causes mispairing by adding O to bases, ruins h bonding
UV radiation
pyrimidine dimers. adjacent thymine. CYCLOBUTANE ring.
repair: NER, covalent bond requires NER for fix
carcinogens
Add bulky adducts to DNA.
NER repair, but if too bulky it is ineffective.
