DNA Replication Flashcards

Learn about DNA Replication

1
Q

Function: DnaA

A

oriC recognition protein - bind at DnaA box next to oriC and melt DNA after oligomerization

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2
Q

Function: DnaB

A

bacterial replicative helicase - unwind DNA at replication fork

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3
Q

Function: DnaC

A

helicase (DnaB) loader - loads helicase (lol)

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4
Q

Function: DnaG

A

bacterial primase - make RNA primer

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5
Q

Prokaryotic Replication Initiation Steps

A

1) DnaA binds upstream oriC and oligomerizes
2) oligomerization melts oriC by making solenoidal supercoil
3) DnaC loads DnaB onto bubble
4) DnaC comes off

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6
Q

Function: ORC

A

initiator protein, recognizes origin of replications

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7
Q

Function: MCM2-7

A

eukaryotic replicative helicase - unwind DNA at replication fork

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8
Q

Function: Cdc6

A

Co-initiator, helicase loader - helps MCM2-7 bind properly to ORC

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9
Q

Function: Cdt1

A

Helicase loader - loads MCM2-7 onto ORC and origin of replication

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10
Q

Function: Pol α

A

eukaryotic primase - make RNA primer

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11
Q

Eukaryotic Replication Initiation Steps

A

1) ORC binds to origin of replication
2) With ATP, Cdc6 binds (coinitiator)
3) With ATP, Cdt1 loads MCM2-7 to ORC
4) with ATP, Cdc45 causes maturation of MCM2-7

Note: MCM2-7 is loaded as dodecamer, splits into hexameric rings on maturation

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12
Q

Function: HDA

A

hydrolyzes ATP-DnaA to prevent oligomerization, stops reinitiation

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13
Q

Function: CLP

A

Converts ADP-DnaA to Apo-DnaA

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14
Q

Function: SeqA

A

binds hemimethylated DNA post replication initation to prevent origin refiring

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15
Q

Bacterial Replication Initiation Regulation

A

Hda dephosphorylates ATP-DnaA, CLP replaces ADP-DnaA with Apo-DnaA, Apo-DnaA can get recycled to ATP-DnaA

SeqA can bind hemimethylated DNA

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16
Q

Eukaryotic Replication Initiation Regulation

A

Post-Translational Modifications
Proteolysis
Nuclear Export

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17
Q

Function: The CMG

A

Elongation Helicase

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18
Q

Function: Pol III

A

Bacteria DNA Polymerase

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19
Q

Function: Pol ε, Pol δ

A

Eukaryotic DNA Polymerase

20
Q

CMG vs DnaB Difference in Directionality

A

DnaB - 5’ -> 3’ movement on lagging strand template

CMG - 3’ -> 5’ movement on leading strand template

21
Q

Why so many Polymerase families?

A

Many functions to perform, such as priming, leading/lagging strand synthesis, repair

22
Q

Function: Translesion (TLS) polymerases

A

cannot fix damage, has to just make an error and move on

23
Q

Polymerase Fidelity

A

“Steric gate”
Snug active site - sense shape complimentarity
Disfavor rNTP binding
Exclude wobble/mispairs

24
Q

Function: β protein

A

Bacterial clamp

25
Function: PCNA
Eukaryotic clamp
26
Function: RFC
Eukaryotic Clamp Loader
27
Function: the τ complex
Bacterial clamp loader
28
Function: Ssb
Bacterial single strand binding protein
29
Function: RPA
Eukaryotic single strand binding protein
30
What does the clamp do during replication?
Increase processivity of DNA pol
31
Clamp Loader Mechanism
1) ATP binding opens clamps 2) 3' end of primer enters clamp loader 3) ATP hydrolysis closes clamp closes,
32
Leading/Lagging Strand Linking
Bacteria: clamp loader connects helicase + polymerase Eukaryote: Helicase binds pol + scaffold factor
33
Function: Ctf4
Scaffold factor that tethers lagging strand to helicase
34
How do cells deal with Okazaki Fragments?
3'->5' degradation RNase H cleaves primer, extend with Pol, ligate Dna2/FenI mechanism through flap formation
35
RNase H Mechanism
2-metal ion mechanism | Mg ion goes into high energy state when nucleotide binds
36
DNA Ligase mechanism
Charge ligase with AMP through ATP hydrolysis AMP transferred to 5' phosphate 3' OH of acceptor will attack 5' phosphate Ligase encircles DNA
37
Premature Termination Mechanisms
Protein mediated block, Fork collision, superhelical strain
38
What are catenanes?
interlocking rings of DNA that cannot be separated without breaking covalent bonds, formed during replication/transcription Need to unlink
39
Type I Topo vs Type II Topo
Type 1 cuts 1 strand, type 2 cuts 2 strands Both go through tyrosyl-DNA intermediate
40
Type 1B Topo Mechanism
Nick-and-Swivel Too lazy to explain
41
Topo IIA Mechanism
1) ATP binds and traps gate segment 2) cleaves and pulls another DNA strand through 3) Releases ADP and can accept another G segment processive, can unlink catenanes
42
What type of supercoils do histones stabilize?
Stabilize solenoidal supercoils, negative
43
Histone Modifications for Replication
H4K20me2 -> ORC
44
Histone Segregation
Mcm2 has H3-H4 chaperdone domain that aids apportionment. Equal apportionment of old and new nucleosomes
45
T/F. Initiation, elongation and termination factors are all broadly conserved.
False, initiation machineries are broadly conserved, but elongation and termination factors are not