Term
| What is the substrate for the DNA synthesis? |
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Definition
|
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Term
| What is necessary about the DNA primer in order to continue extension of the DNA? |
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Definition
|
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Term
| How is the phosphiester backbone created? (mechanism) |
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Definition
| SN2 reaction in which the hydroxyl group at the 3' end of the primer strand attacks the a-phosphoryl group group of the incoming nucleoside triphosphate |
|
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Term
| Which phosphates leave as pyrophosphate? |
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Definition
| B-phosphate and y-phosphate |
|
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Term
| What is the enzyme that hydrolyzes the released pyrophosphate into two phosphate molecules? |
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Definition
|
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Term
| which are more present in the cell? rNTPs or dNTPs? |
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Definition
|
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Term
| What is the secondary structure of the palm domain? |
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Definition
|
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Term
| which region of the DNA polymerase (palm, fingers, thumb) can you find the divalent cations? |
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Definition
|
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Term
| What does each metal cation do in DNA polymerase? |
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Definition
| the first one reduces the affinity of the 3'-OH of the primer for it H. the second one coordinates the negative charge of the beta and gamma phosphates of the dNTP and stabilizes the pyrophosphate |
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Term
| What are the roles of the finger and thumb? |
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Definition
| fingers bind to the incoming dNTP and encloses it. thumb interacts with the newly synthesized DNA. |
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Term
| define "degree of processivity" |
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Definition
| the initial binding of polymerase to the primer:template unction that is rate-limiting for DNA synthesis. |
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Term
| What is the rate limiting step for DNA synthesis? |
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Definition
| the binding of the polymerase to the primer:template junction |
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Term
| What is the primary conformational change of the DNA polymerase when it binds DNA? |
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Definition
| the O helix rotates (helix in finger domain) 40 degrees closer to the incoming dNTPs |
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Term
| Does DNA polymerase use the same active site for polymerization as exonuclease activity? |
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Definition
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Term
| Which enzyme removes the RNA primer? |
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Definition
|
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Term
| What are four enzymes that function at the replication fork? |
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Definition
| ssb, primase, DNA helicase, topo |
|
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Term
| What are primases called in E. coli, Yeast, and human?> |
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Definition
e. coli: DNAG
yeast: Primase 1 and 2
human: Primase |
|
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Term
| What are the DNA helicases called in E. coli, yeast, and human? |
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Definition
e.coli: DnaB
yeast: McM2-7 complex
human: McM2-7 complex |
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Term
| What are the SSb proteins called in E. coli, yeast, and human? |
|
Definition
e. coli: SSB
yeast: RPA
human: RPA |
|
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Term
| What are topoisomerases called in e. coli, yeast, human? |
|
Definition
e. coli: Topo I, Gyrase
Yeast: Topo I, II
Human: Topo I, II |
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Term
| In bacteria, which is the main polymerase that replicates the chromosome ? |
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Definition
|
|
Term
| What is DNA Pol I used for? |
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Definition
|
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Term
|
Definition
| lagging strand DNA syntehsis |
|
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Term
|
Definition
|
|
Term
|
Definition
|
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Term
|
Definition
| primer synthesis during DNA replication |
|
|
Term
| What makes of the DNA Pol II holoenzyme? |
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Definition
| three copies of DNA Pol III core enzyme, one copy of sliding clamp |
|
|
Term
| how many DNA polymerases work on the lagging strand in the E. coli replisome? |
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Definition
|
|
Term
| What is the error rate of DNA polymerase? |
|
Definition
|
|
Term
| What happens when manganese is incorporated into DNA polymerase as a divalent cation ? |
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Definition
|
|
Term
| What is the speed of DNA polymerasE? |
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Definition
|
|
Term
| How does the exonuclease activity increase the fidelity of the polymerase? |
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Definition
|
|
Term
| Why do we use an RNA primer as opposed to a DNA primer? |
|
Definition
| it's easier to cut out of the sequence |
|
|
Term
| When does primes become activated? |
|
Definition
| when it associates with helices |
|
|
Term
| which protein at the replication fork is a hexameric protein? |
|
Definition
|
|
Term
| Does SSB protein needs a specific sequence to bind? |
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Definition
|
|
Term
|
Definition
| antibiotic target for topoisomerase |
|
|
Term
| which polymerases in human can be used for repair? |
|
Definition
|
|
Term
| what catalyzes the placement of the sliding clamp onto the double stranded helix of DNA? |
|
Definition
| sliding clamp loader using ATP hydrolysis |
|
|
Term
| can the sliding clamp loader and DNA polymerase interact with the sliding clamp at the same time? |
|
Definition
| no--because their binding sites are the same. |
|
|
Term
| what removes the hairpins in the sand newly synthesized? |
|
Definition
|
|
Term
| how long are okazaki fragments? |
|
Definition
|
|
Term
|
Definition
| cis-acting DNA sequence, initiator recognition site, AT-rich sequence for DNA unwinding |
|
|
Term
| What is the Initiator in the replicon model? |
|
Definition
| proteins recognizes DNA (replicator) sequence, activates the initiation of replication |
|
|
Term
|
Definition
| the single replicator in E. coli that is needed for replication |
|
|
Term
| How many binding sites are there for DnaA, the E. coli initiator? |
|
Definition
|
|
Term
| how many binding sites are there for T-antigen, the initiator in the eukaryotic virus? |
|
Definition
|
|
Term
| Which DNA polymerase is utilized in the holoenzyme? |
|
Definition
|
|
Term
| The replicator sequence is rich in what? |
|
Definition
|
|
Term
|
Definition
| release of the helicase loader? |
|
|
Term
| How is DNA Pol II holoenzyme recruited to the origin? |
|
Definition
| through interactions between primer:template junction and helicase |
|
|
Term
| What happens first at the origin? DNA polymerases engage the leading strand, or RNA primers are added to the lagging strand? |
|
Definition
| DNA polymerases engage leading strand |
|
|
Term
| What are the three functions that DnaA can perform? |
|
Definition
1. bind to the replicator
2. unwind a region of DNA
3. recruit other proteins to the replicator |
|
|
Term
| What can ORC not do that DnaA can do? |
|
Definition
| it can not act as a DNA topoisomerase |
|
|
Term
| Explain the order of proteins binding in the initiation of replication |
|
Definition
| DnaA binds to OriC, and ssDNA and DnaA recruit DnaB and DnaC (helicase and loader) . Together they both recruit primase. Helicase loader leaves. Primase recruits holoenzyme and sliding clamp. |
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|
Term
| When does helices loading occur in the eukaryotic organism? At which point in the cell cycle? |
|
Definition
|
|
Term
| In eukaryotes, at which point in the cell cycle does helices actually become active? |
|
Definition
|
|
Term
| In eukaryotic replication, when are the kinases activated? |
|
Definition
| only when cells enter S phase. activate the helices |
|
|
Term
| What is the eukaryotic initiator called? |
|
Definition
|
|
Term
| How does the eukaryotic cell control each origin of replication is only activated once in the cell cycle? |
|
Definition
| helicase loading is inhibited upon entering S, M phase |
|
|
Term
| What kind of sequence are telomeres rich in? |
|
Definition
|
|
Term
| what do telomeres consist of ? |
|
Definition
|
|
Term
| is telomerase activity higher in somatic or germ cells? |
|
Definition
|
|
Term
| Is the activity of telomere binding proteins an example of a positive or negative feedback loop? |
|
Definition
|
|
Term
| Which type of topoisomerase can separate two linked circular chromosomes? |
|
Definition
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