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Biochem 275: Exam 2
DNA bound to a nucleosome is not _______ |
accessible |
Nucleosomes can be positioned by what? |
DNA binding proteins |
Acetylation of lysines does what? |
Reduces the interaction of the histone with the DNA phosphate backbone |
What directs the binding of proteins that modify nearby histones? |
Modification of histones |
What happens to old histones? |
They're reused at the point of replication |
What does RNase H do? |
It removes RNA primer |
DNA directed DNA polymerase is used in.. |
Replication |
DNA directed RNA polymerase is used in.. |
Transcription |
Primer extension occurs where? |
In the active site of the DNA polymerase |
Can an a ribose fit into the active site of the DNA polymerase? |
No |
What are the error rates for proofreading? |
1/100,000 w/o and 1/10,000,000 w/PR |
What does the DNA helicase do? |
Unwinds the DNA |
What do Topoisomerases do? and how do they do it? |
They relieve supercoiling ahead of the replication fork By cutting DNA and resealing it |
SSBs do what? |
interact w/phosphate backbone (electrostatic) and stacking interactions (Van der Waals) with the bases |
What does the polymerase need? |
Template DNA, Primer, dNTPs, Mg^2+ |
How does the sliding clamp help polymerase synthesize more than 20-100 base pairs at a time? |
By preventing the polymerase from drifting away from the DNA |
Where are sliding clamp loaders located? |
Primer template junctions |
What two protein-protein interactions are critical for rapidfork progression? |
Helicase interaction with primase
Polymerase holoenzyme interaction with helicase |
What does polymerase holoenzyme interaction with helicase do? |
Increases activity of the helicase |
What does the replisome include? |
Helicase, toposomerase, primase, DNA pol III holoenzyme, DNA pol I, ligase, SSB, sliding clamp, RNase H |
What is included in the replicator? |
Binding site for initiator, regions rich in T's and A's |
List the differences between the telomerase and the DNA pol III |
Telomerase has an enzyme complex that inlcudes an RNA, can use RNA as a template, brings its own template.
DNA Pol III requires a template, only makes DNA to 5' to 3' direction. Uses dNTPs. |
What protects the ends of chromosomes? |
Telomerase |
What type of polymerase is telomerase? |
RNA directed DNA polymerase |
What strand does telomerase bind to? |
The leading strand |
What stops the telomerase? |
A high amount of telomere binding proteins |
What actually adds the primer? |
Primase |
Can DNA pol I move in 3' to 5' direction |
Yes |
What recruits RNase H? |
PCNA |
What proteins don't need PCNA interaction? |
Helicase and Primase |
How fast does DNA pol III add dNTPs |
1000 bp/sec |
What keeps the helicase near the replication fork? |
the holoenzyme |
What is the first step in replication? |
The initiator protein binds to the origin of replication |
Nucleosome remodeling complexes use what to break bonds and move nucleosomes? |
ATP |
What is responsible for acetylation? |
Histone acetyl transferases |
What phosphorylates amino acids? |
Kinases |
What does modification of histones provide for other proteins? |
Binding sites |
Bromodomains move __________ |
Acetylated histones |
Chromodomains move _________ |
Methylated histones |
H2A H2B dimers interact with ________ |
NAP-I |
H3 H4 tetramers interact with ________ |
CAF-I |