Dna Replication

Front 1

what are the 3 components that contribute to base-pairing/structure stability?

Back 1

H-bonds, stacking, steric interactions/shape complimentarity

Front 2

DNA Pol I can be found where and what is its functions?

Back 2

-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)

Front 3

What are the subunits of DNA Pol III?

Back 3

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

Front 4

activity of alpha subunit of DNA Pol III?

Back 4

polymerase activity

Front 5

activity of epsilon activity of DNA Pol III?

Back 5

proofreading; 3'->5' exonuclease

Front 6

activity of beta clamp subunit of DNA Pol III?

Back 6

increases processivity by binding DNA to DNA Pol III

Front 7

activity of clamp loading complex of DNA Pol III?

Back 7

links 2 core polymerization domains of DNA Pol III and puts new beta clamp on core after each OF added

Front 8

DnaB helicase is found in which organism and what does it do?

Back 8

-E. coli
-helicase, so unwinds and separates dsDNA
-binds to DNA Pol III

Front 9

DnaA protein is found in which organism and what is its functions?

Back 9

-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

Front 10

DnaB helicase is found in which organism and what is its function?

Back 10

-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

Front 11

DnaC protein is found in which organism and what is its function?

Back 11

-E. coli
-facilitates DnaB helicase binding to DUE

Front 12

what are the functions of topoisomerase type I?

Back 12

relieves torsional strain (positive supercoiling) by cutting one strand of dsDNA
-tyrosine attacks phosphodiester bond
-ligates break

Front 13

what are the functions of topoisomerase type II?

Back 13

-relieve and induce torsional strain (maintain underwound state to make strand separation easier)
-cuts both strands of dsDNA

Front 14

what is the function of primase?

Back 14

lays down RNA primer so that there is a 3'-OH end for DNA Pol to build off of

Front 15

what are the functions of single strand DNA binding proteins (SSB)?

Back 15

keeps strands apart, from annealing to each other, and protect ssDNA from nucleases

Front 16

how is DNA replication terminated in E. coli?

Back 16

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

Front 17

topoisomerase IV is found in which organism and what does it do?

Back 17

e. coli, separates replicated dsDNA from original circular DNA

Front 18

how is DNA replication terminated in eukaryotes?

Back 18

when the 2 replication forks collide into each other

Front 19

ORC protein is found in which organism and what does it do?

Back 19

-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

Front 20

Cdc6 and Cdt1 are found in what organisms and what do they do?

Back 20

-eukaryotes
-2 of each bind to ORC origin complex and recruits Mcm helicase
-equivalent to DnaC proteins of prokaryotes

Front 21

Mcm is found in what organisms and what does it do?

Back 21

-eukaryotes
-helicase activity
equivalent to DnaB helicase of prokaryotes

Front 22

after proteins are bound to DNA replication site, how is it initiated?

Back 22

-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

Front 23

PCNA is found in which organisms and what is its function?

Back 23

-eukaryotes
-similar to beta clamp of prokaryotes; binds DNA to polymerase to increase processivity

Front 24

RPA is found in which organisms and what is its function?

Back 24

-eukaryotes
-similar to SSB of prokaryotes
-keeps ssDNA separated and protects strands from nuclease degradation

Front 25

RFC is found in which organisms and what is its function?

Back 25

-eukaryotes
-similar to clamp loading complex of prokaryotes
-puts new beta clamp on polymerase after each OF added

Front 26

where is pol-alpha-primase found and what does it do?

Back 26

-eukaryotes
-primase and polymerase
-low processivity, no proofreading

Front 27

where is pol-delta found and what does it do?

Back 27

-eukaryotes
-lagging strand synthesis
-proofreading and high processivity due to PCNA

Front 28

where is pol-epsilon found and what does it do?

Back 28

-eukaryotes
-leading strand synthesis
-proofreading, high processivity

Front 29

where is DNA pol beta found and what does it do?

Back 29

-eukaryotes
-DNA repair
-no proofreading, low processivity, low fidelity

Front 30

what does reverse transcriptase do?

Back 30

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

Front 31

what does telomerase do and what is its mechanism?

Back 31

restores 3' ends of linear DNA (chromosome telomeres)
-has intrinsic RNA template that it uses to synthesize DNA

Front 32

what is targeted in HIV drug therapy? Why?

Back 32

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