What acts as the mark of newly replicated DNA for histone chaperones to interact with?
Sliding clamp
100
What are some sources of DNA damage?
Hydrolysis, UV light, methylation, etc.
200
What is a DNTP? What is its function???
It is a deoxynucleoside triphosphate; it is the building block of DNA in DNA synthesis.
200
What are the 2 active sites on the polymerase?
The base-incorporating part and the proofreading part.
200
List the steps of initiation of the replication origin in bacteria.
Initiator binds to A-T rich sequence, DNA is destabilized, DNA helicase is loaded on, DNA primase is loaded on, the rest of the replication machinery does its thing.
200
What happens to the H3-H4 tetramers and the H2a-H2b dimers as DNA is replicated? What do the tetramers carry?
Tetramers stay loosely associated to the strand and either go with the parent or the daughter strand (randomly), dimers fall off completely. Tetramers carry memory of modifications.
200
What is DNA damage v. DNA mutation?
Damage is reparable, mutation is permanent.
300
A woman has a genetic mutation where her eyes are purple. Her child also has this mutation where her eyes are purple. Was the mutation in the germline or in the somatic cells?
Germline
300
What does Topoisomerase I do? What does Topoisomerase II do?
Topo. I makes a cut in front of the fork to prevent supercoiling; Topo. II creates a double strand break to unhook the DNA from one another.
300
How is replication controlled in bacteria?
Replication won't begin until sufficient nutrients are available; there is a refractory period because replication won't start again until the DNA is methylated on both strands, and the Dam methylase is slow to methylate.
300
What is a telomere? Why do we need them? What is the link between telomere length and health?
A telomere is a tandem repeat of base pairs at the end of a DNA strand. We need them because the ends of DNA strands don't have enough room for polymerase to replicate the tiny stretch at the end, so if we didn't extend with telomeres, the chromosome would lose genetic material and get shorter and shorter each time. Longer telomere=ya good. Shorter=ya dead.
300
How does the mismatch repair system work?
MutS scans, MutL cuts, polymerase fills the gap, ligase seals the nick. In bacteria, mute H marks the unmethylated, new strand with a lil nick.
400
What are the 5 requirements for DNA synthesis?
Primer, template, DNTPs, polymerase, divalent cations.
400
Name the order of replication proteins at the replication fork.
ORC binding sight, easily meltable unwinding region, binding site for "helper" ORC protein.
400
What is the phase of the cell cycle that DNA replicates in??
S phase
400
What is a direct repair process that only occurs in bacteria? How does this work? Contrast it with demethylation in prokaryotes.
Photoreactivation. Protein DNA photolyase attaches to dimer in the dark, uses the light to be able to undimerize it.
Photophosphorylation-protein can be reused, demethylation, expensive, one use protein.
500
What was the experiment that allowed us to determine DNA is semi-conservative? What happened in it?
Meselston and Stahl. They produced some DNA in a heavy medium, then moved it into a lighter DNA medium, and they observed how the heavy parental and the light daughter strands paired. By centrifuging them out, they were able to see that the first round were all hybrids, and the subsequent rounds were hybrids and light DNA. This allowed them to observe that one strand of the parental heavy DNA paired with one light strand of the daughter DNA.
500
What direction does DNA polymerase proofread? How does it correct wrong base pairs?
3'-5'. An exonuclease attached to the polymerase chews it back and then the polymerase goes on its merry way.
500
What's in a PreRC? What prevents the formation of another PreRC during synthesis and G2?
It is an ORC+helicase; High Cdk activity and phosphorylation of the ORC.
500
Why is the mutation rate in DNA so low?
DNA damage repair mechanisms, Dna polymerase proofreading (think of other examples you smart people)
500
What damage does UV light do? Intercalating agents? How would each be fixed in a eukaryote?
UV light=dimers. Intercalating=space in backbone. Dimer=nucleotide excision repair, intercalating=translesion.