WVSOM: Biochem test 2, Thatcher Replication
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| Replication occurs where in Prokaryotes? eukaryotes? | pro: cytoplasm, euk: nucleus
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| this polymerase synthesizes the leading strand, is able to proofread, uses an RNA primer | DNA polymerase delta
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| this polymerase synthesizes the lagging strand, cannot proofread, uses an RNA primer | DNA polymerase alpha
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| this polymerase fills in the of DNA for repair. It does not proofread or use an RNA primer | DNA Pol. beta
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| this polymerase is found in the mitochondrai and is used to synthesize both leading and laging strand. it contains a proofreading fxn, but does not use an rna primer | DNA pol gamma
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| the metalic cofactor necessary for activation of DNA polymerase? | Mg++
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| DNA synthesis always proceeds in which direction? | 5' to 3'
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| Proofreading (exonuclease activity) occurs in which direction? | 3' to 5'
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| which pols. are able to perform exonuclease activity? | dna pols delta and gamma are able to proofread their dna scripts.
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| which model of dna synthesis is followed? | semiconservative: one strand of daughter chrome is newly synthesized, the other template is inherited intact from the parental chrome
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| decribe the difference between the leading and lagging strands... | the leading strand is continuously synthesized in the 5'-3' direction by dna pol. delta while the lagging strand is synthesized 5'-3' in short fragments by dna pol. alpha
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| what is the name of the fragments of the lagging strand? | okazaki fragments
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| what are "ori" and how many of them are present on each chrome? | "ori" are origins of replication, and there are many of them for every chromosome. this speeds the process of replication up dramatically.
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| prokaryotic vs. eukaryotic ori | pro: one; euk: many... this is why it only takes a little longer for the latter to replicate a genome that is dramtically larger
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| what it a replicon? | a region of euk genome that is replicated as a unit from one central ori (avg. is 200 kb)
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| this enzyme binds an ori and serves to open the double helix so the dna pol. can begin replication? | helicase
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| this cluster of factors stabilizes the single stranded DNA and prevents it from "winding back up" | SSBs (single stranded binding protein)
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| a cluster of factors assembled around helicase that serves to replicate DNA. | DNA replication apparatus (this includes DNA pols. alpha, delta, the "beta clamp", and primase... it does not include SSBs)
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| this ringl like protein wraps around the dna to stabilize the association of the replication apparatus. | Beta clamp. (this is required for dna pol. delta which will "fall off" w/out it)
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| this enzyme binds the unwound lagging strand template and transcribes short stretches (<15 bp) of RNA primer that provides the necessary 3'OH for DNA pol. alpha. | primase
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| this enzyme removes the rna primer laid down by primase, leaving chunks of missing bps | RNA-ase
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| this polymerase fills in the chunks/ gaps of missing bps that were removed by RNA-ase | DNA polymerase beta (these chunks are roughly 20 bp long)
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| this enzyme seals the nicks btwn the 3' OH and 5' phosphate | DNA ligase (this happens not only after the replacement of DNA for RNA in the lagging strand, but also after DNA excisional repair)
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| this enzyme is reponsible for fixing the supercoiling caused by the unwinding of DNA (helicase) during replication | topoisomerase
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| this enzyme fxns to synthesize the telomere, it contains an rna reverse transcriptase. its activity decreases with age, and increased activity of this enzyme is associated with cancer | telomerase
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