Lecture 3: DNA repair, and homologous recombination Flashcards
how many errors per nucleotide added between each combined. replication step
1 in 10^10 nt copied
what are the 3 most common dna damages
- depurination
- depyrimidination
- cytosine deamination
what are different kinds of spontaneous nucleotide modifications
- oxidative damage
- hydrolytic attack like depurination, depyrimidaytion, and C deamination
- methylation
true/false without DNA repair, spontaneous DNA damage would rapidly change DNA sequences
true
what does depurination do to a dna strand
- the N‐glycosidic bonds are cleaved to release the corresponding adenine or guanine from DNA
- the purines
what does deamination do to a dna strand
- converts cytosine to uracil
- can occur on other bases as well
- removes amines, and adds oxygen
what base is formed if adenine is deaminated
hypoxanthine
what base is formed if guanine is deaminated
xanthine
what base is formed if cytosine is deaminated
uracil
what base is formed if thymine is deaminated
thymine cannot be deaminated (no amine group)
what is a thymine dimer
a photolesion produced by UV radiation in sunlight and is considered as a potential factor causing skin cancer
how is a thymine dimer formed
formed as a covalently bonded complex of two adjacent thymines on a single strand of DNA
what does uracil DNA glycosylase do
removed deaminated cytosine
describe what happens when a 5-methyl C nucleotide is deaminated
- about 3% of the C nucleotides are methylated to help control gene expression
- when they are accidentally deaminated, they form the natural T
- this T will be paired w a G, making a mismatched base pair
describe how base excision repair works
- uracil dna glycosylase removed the deaminated cytosine
- AP endonuclease recognizes a deoxyribose sugar with a missing base (the gap thats formed from removing the cytosine)
- the sugar phosphate with a missing base is cut out by sequential action of AP endonuclease and a phosphodiesterase
- the gap of a single nucleotide is then filled and sealed by DNA polymerase and DNA ligase
describe how nucleotide excision repair works
- a multi-enzyme complex recognizes a lesion such as a pyrimidine dimer
- a cut is made on each side of the lesion
- a DNA helicase then removes the entire portion of the damaged strand
- DNA polymerase and DNA ligase fills in the missing DNA
what process is nucleotide excision repair coupled to and why
- transcription
- to ensure fidelity
when are translesion DNA polymerases used, explain the process
- when there is damage on a dna strand
- this can stall replicative dna polymerases
- covalent modifications will happen to the sliding clamp when the polymerase encounters DNA damage
- the replicative dna polymerase will be released, and the translesion one will load on
- its more versatile and less accurate
- once the damage is bypassed, replicative polymerase will return
are double-strand breaks common
yes
what are 2 ways to repair a double-strand break
- nonhomologous end joining
- homologous recombination
desribe non-homologous end joining
- broken ends are ligated without the need for a homologous template
- typically uses short-homologous DNA sequences (microhomologies) to guide repair, present in single-strand overhands on the ends of double strand breaks
- Ku protein grasps the broken chromosome ends
- additional proteins hold the broken ends together while they are processed and joined together covalently
what is a repurcussion of non-homologous end joining
repaired DNA has generally suffered a deletion of nucleotides
describe how homologous recombination works
- nuclease digests 5’ ends of broken strands, creating an overhang
- one broken strand attaches the overhang part to the homologous piece of DNA
- repair polymerase synthesizes DNA using undamaged DNA as a template
- the damaged DNA is then released once the replication has happened
- this extended damaged DNA is then used as a template for the other strand of the damaged DNA
- dna ligation will occur
when is homologous recombination used
when there is a homologous piece of DNA present in the nucleus (ie during DNA replication time of cell cycle)
