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Molecular Biology > Replication > Flashcards

Replication Flashcards

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1
Q

DNA Replication is…

A

Semi-conservative, bi-directional, and semi-discontinuous

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2
Q

What are the three stages of prokaryotic DNA replication?

A

Initiation, elongation, and termination

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3
Q

What is the origin of replication called in prokaryotic DNA?

A

oriC (a sequence of 245 bp)

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4
Q

The OriC contains what?

A

It contains and DNA Unwinding Element (DUE) and 5 bind sites (R sites)

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5
Q

Step 1 of prokaryotic DNA replication (initiation)

A
  1. 8 ATP-bound DnaA proteins bind to the oriC sequence at the R sites
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6
Q

Step 2 of prokaryotic DNA replication (initiation)

A
  1. DNA wraps around DnaA proteins inducing a positive, right-handed, solenoidal coil
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7
Q

Step 3 of prokaryotic DNA replication (initiation)

A
  1. DUE sequence begins to unwind due to strain due to solenoidal coiling
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8
Q

the DNA unwinding element is rich in what?

A

A and T base pairs (weaker IMFS)

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9
Q

Step 4 of prokaryotic DNA replication (initiation)

A

DnaC loads DnaB onto unwound DNA and DnaB unwinds it further

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10
Q

DnaC uses what?

A

Uses the hydrolysis of ATP to bind DnaB to DNA strand

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11
Q

DNA polymerase III requires what 3 things?

A

A primer, template, and magnesium ions

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12
Q

What are the two steps that occur in the active site DNA polymerase III

A
  1. insertion 2. Translocation
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13
Q

DNA polymerase III has what amino acids residues that catalyze elongation? Name the cofactor and it use.

A

2 aspartate residues. Magnesium ions and they coordinate the aspartate and deprotonated 3’ hydroxyl group

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14
Q

explain DNA polymerase III mechanism.

A

The enzyme brings in a dNTP to the active site (insertion) and the nucleophilic 3’ hydroxyl group attacks the phosphate group of the dNTP. it releases pyrophosphate which catalyzes the reaction.

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15
Q

What is fidelity?

A

Fidelity of replication means replication of DNA and the production of accurate daughter DNA using the parental DNA as a template. Ensures accurate DNA bp is chosen.

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16
Q

What is Processivity?

A

The rate at which bp are added to DNA strand

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17
Q

DNA polymerase III contains many subunits list the three that you were taught.

A

Polymerase III core, b-sliding clamp, and clamp loader

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18
Q

What is the function of polymerase III core?

A

The core catalyzes polymerization and added base pair to the growing 5’->3’ strand

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19
Q

What is the function of the b-sliding clamp?

A

“clamps” and holds polymerase to DNA

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20
Q

What is the function of the clamp loader?

A

“loads” beta clamps near core and holds core polymerases together. As well is removes beta clamps from completed Okazaki fragments

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21
Q

What other three proteins assist in prokaryotic replication

A
  1. DNA gyrase 2. Primase 3. Single-stranded binding proteins (SSB)
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22
Q

What does gyrase do?

A

gyrase is a topoisomerase that relieves supercoiling generated by strand separation

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23
Q

What do SSBs do?

A

Prevents DNA from reannealing

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24
Q

What is a exonuclease?

A

Cleaves phosphodiester linkages

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25
Once elongation is complete what two proteins complete the process
1. DNA polymerase 1 2. DNA ligase
26
What does DNA polymerase 1 do?
removes short RNA primer
27
What does DNA ligase do?
removes the nick in the newly synthesized DNA strand. Meaning it forms the final phosphodiester bond
28
prokaryotic DNA replication termination step 1
1. A Tus protein binds to one of several Ter sequences on chromosome
29
prokaryotic DNA replication termination step 2
2. Tus-Ter complex traps a replication fork
30
prokaryotic DNA replication termination step 3
3. second replication fork stalls when reaches first stalled fork
31
prokaryotic DNA replication termination step 4
4. replication ceases with two linked circular catenanes
32
prokaryotic DNA replication termination step 5
5. topoisomerase VI cleaves and re-ligates one chromosome allowing for separation
33
G1
Rapid growth and metabolic activity
34
S
DNA replication and growth
35
G2
growth and preparation for cell division
36
M
mitosis
37
Late M and early G1 is?
when licensing of replication occurs or when the proteins bind to origin
38
S phase is when
Actual replication begins
39
Cell Cycle progression is regulated by...
Cyclins and Cyclin-dependent kinases
40
How does CDK regulation work
Cyclins bind to a Cyclin-dependent kinase and then bind to a target protein. The cyclin complex phosphorylates. MUST BE APART OF THE COMPLEX TO PHOSPHORYLATE
41
S-CDKs induce what
the switch from G1 to S phase
42
Eukaryotes polymerases are what
slower and have shorter s phases
43
Initial players in Pre-replication complex
ORC (origin recognition complex), helicase loaders, and helicase
44
Phosphorylation of MCM2-7 by S-CDKS does what
recruits DNA Polymerase to the origin
45
Polymerase epsilon does?
leading strand synthesis
46
polymerase delta does?
lagging strand synthesis
47
polymerase alpha acts as?
primase and polymerase
48
RPA does?
prevents reannealing
49
PCNA does?
increases polymerase processivity
50
ORC does?
acts as a "landing pad" for proteins at origin of replication
51
CDC6 and CDT1 do?
load the helicase
52
MCM proteins do?
act as helicase and unwind DNA
53
PCNA does?
holds polymerase to template strand
54
RPA does?
stabilizes single stranded DNA
55
RFC does?
loads loads clamp (PCNA) on to replicating DNA
56
DNA polymerase beta does?
proofreading and repair
57
Telomere installation step 1
1. telomerase binds to the end of the overhanging strand with RNA sequence in its active site
58
Telomere installation step 2
2. telomerase translocates
59
Telomere installation step 3
3. telomerase dissociates and rna primase adds primer and the end of the strand
60
Telomere installation step 4
4. DNA polymerase fills gap and DNA ligase closes nick
61
Telomere installation step 5
RNA primer is removed by RNAase
62
Telomere installation step 6
the remaining overhand is bound by proteins TRF1 and TRF2 to protect overhang
63
telomerase acts as reverse transcriptase
RNA template to DNA

Molecular Biology (1 decks)

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