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32 Cards in this Set
- Front
- Back
what are the 3 components that contribute to base-pairing/structure stability?
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H-bonds, stacking, steric interactions/shape complimentarity
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DNA Pol I can be found where and what is its functions?
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-E. coli
-polymerize DNA in 5'->3' direction -exonuclease in both 5'->3' and 3'->5' -low processivity -slow polymerization rate -strand displacement synthesis (replication) -nick translation (recombination) |
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What are the subunits of DNA Pol III?
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alpha: polyermase activity
epsilon: proofreading, 3'->5' exonuclease beta clamp: increases processivity by binding DNA to DNA Pol III clamp loading complex: links the 2 core domains together and puts new beta clamp on core after each OF is added |
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activity of alpha subunit of DNA Pol III?
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polymerase activity
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activity of epsilon activity of DNA Pol III?
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proofreading; 3'->5' exonuclease
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activity of beta clamp subunit of DNA Pol III?
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increases processivity by binding DNA to DNA Pol III
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activity of clamp loading complex of DNA Pol III?
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links 2 core polymerization domains of DNA Pol III and puts new beta clamp on core after each OF added
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DnaB helicase is found in which organism and what does it do?
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-E. coli
-helicase, so unwinds and separates dsDNA -binds to DNA Pol III |
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DnaA protein is found in which organism and what is its functions?
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-E. coli
-binds tightly to R and I sites on DNA and causes DNA separate upstream in AT rich area (DUE) so helicase can bind -released after DnaB binds and DNA Pol III recruited |
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DnaB helicase is found in which organism and what is its function?
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-E. coli
-unwinds and separates dsDNA; binds at DUE (2 at a time because 2 replication forks at each origin) -constitutes beginning of 2 replication forks -recruits DNA Pol III |
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DnaC protein is found in which organism and what is its function?
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-E. coli
-facilitates DnaB helicase binding to DUE |
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what are the functions of topoisomerase type I?
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relieves torsional strain (positive supercoiling) by cutting one strand of dsDNA
-tyrosine attacks phosphodiester bond -ligates break |
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what are the functions of topoisomerase type II?
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-relieve and induce torsional strain (maintain underwound state to make strand separation easier)
-cuts both strands of dsDNA |
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what is the function of primase?
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lays down RNA primer so that there is a 3'-OH end for DNA Pol to build off of
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what are the functions of single strand DNA binding proteins (SSB)?
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keeps strands apart, from annealing to each other, and protect ssDNA from nucleases
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how is DNA replication terminated in E. coli?
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Tus proteins binding to ter sites (tus-ter complexes)
-trap replication fork moving in one direction; when fork moving in other direction collides with trapped fork DNA pol comes off and replication terminated |
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topoisomerase IV is found in which organism and what does it do?
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e. coli, separates replicated dsDNA from original circular DNA
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how is DNA replication terminated in eukaryotes?
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when the 2 replication forks collide into each other
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ORC protein is found in which organism and what does it do?
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-eukaryotes
-binds to replication initiation site -present throughout cell cycle regulated by Cdk; Cdk phosphorylates it during replication to prevent another round of replication from starting before completion |
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Cdc6 and Cdt1 are found in what organisms and what do they do?
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-eukaryotes
-2 of each bind to ORC origin complex and recruits Mcm helicase -equivalent to DnaC proteins of prokaryotes |
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Mcm is found in what organisms and what does it do?
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-eukaryotes
-helicase activity equivalent to DnaB helicase of prokaryotes |
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after proteins are bound to DNA replication site, how is it initiated?
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-dependent on cell cycle
-Cdk phosphorylates ORC origin complex, Cdc6 adn Cdt1 fall off and polymerase and other proteins recruited -ORC phosphorylated so new round of replication doesn't start before previous round is complete |
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PCNA is found in which organisms and what is its function?
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-eukaryotes
-similar to beta clamp of prokaryotes; binds DNA to polymerase to increase processivity |
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RPA is found in which organisms and what is its function?
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-eukaryotes
-similar to SSB of prokaryotes -keeps ssDNA separated and protects strands from nuclease degradation |
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RFC is found in which organisms and what is its function?
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-eukaryotes
-similar to clamp loading complex of prokaryotes -puts new beta clamp on polymerase after each OF added |
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where is pol-alpha-primase found and what does it do?
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-eukaryotes
-primase and polymerase -low processivity, no proofreading |
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where is pol-delta found and what does it do?
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-eukaryotes
-lagging strand synthesis -proofreading and high processivity due to PCNA |
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where is pol-epsilon found and what does it do?
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-eukaryotes
-leading strand synthesis -proofreading, high processivity |
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where is DNA pol beta found and what does it do?
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-eukaryotes
-DNA repair -no proofreading, low processivity, low fidelity |
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what does reverse transcriptase do?
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RNA dependent DNA polymerase
-makes RNA-DNA hybrid -degrades RNA component -Dna-dept DNA synthesis to make dsDNA that can be incorporated into host DNA genome |
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what does telomerase do and what is its mechanism?
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restores 3' ends of linear DNA (chromosome telomeres)
-has intrinsic RNA template that it uses to synthesize DNA |
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what is targeted in HIV drug therapy? Why?
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reverse transcriptase
-has higher affinity for nucleotide analogs instead of dNTPs, so can use AZT and DDI which don't have 3'-OH end for extension |