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