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MBG Flashcards > DNA Replication > Flashcards

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
Q

Function: PCNA

A

Eukaryotic clamp

26
Q

Function: RFC

A

Eukaryotic Clamp Loader

27
Q

Function: the τ complex

A

Bacterial clamp loader

28
Q

Function: Ssb

A

Bacterial single strand binding protein

29
Q

Function: RPA

A

Eukaryotic single strand binding protein

30
Q

What does the clamp do during replication?

A

Increase processivity of DNA pol

31
Q

Clamp Loader Mechanism

A

1) ATP binding opens clamps
2) 3’ end of primer enters clamp loader
3) ATP hydrolysis closes clamp closes,

32
Q

Leading/Lagging Strand Linking

A

Bacteria: clamp loader connects helicase + polymerase
Eukaryote: Helicase binds pol + scaffold factor

33
Q

Function: Ctf4

A

Scaffold factor that tethers lagging strand to helicase

34
Q

How do cells deal with Okazaki Fragments?

A

3’->5’ degradation
RNase H cleaves primer, extend with Pol, ligate
Dna2/FenI mechanism through flap formation

35
Q

RNase H Mechanism

A

2-metal ion mechanism

Mg ion goes into high energy state when nucleotide binds

36
Q

DNA Ligase mechanism

A

Charge ligase with AMP through ATP hydrolysis
AMP transferred to 5’ phosphate
3’ OH of acceptor will attack 5’ phosphate

Ligase encircles DNA

37
Q

Premature Termination Mechanisms

A

Protein mediated block, Fork collision, superhelical strain

38
Q

What are catenanes?

A

interlocking rings of DNA that cannot be separated without breaking covalent bonds, formed during replication/transcription

Need to unlink

39
Q

Type I Topo vs Type II Topo

A

Type 1 cuts 1 strand, type 2 cuts 2 strands

Both go through tyrosyl-DNA intermediate

40
Q

Type 1B Topo Mechanism

A

Nick-and-Swivel

Too lazy to explain

41
Q

Topo IIA Mechanism

A

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
Q

What type of supercoils do histones stabilize?

A

Stabilize solenoidal supercoils, negative

43
Q

Histone Modifications for Replication

A

H4K20me2 -> ORC

44
Q

Histone Segregation

A

Mcm2 has H3-H4 chaperdone domain that aids apportionment.

Equal apportionment of old and new nucleosomes

45
Q

T/F. Initiation, elongation and termination factors are all broadly conserved.

A

False, initiation machineries are broadly conserved, but elongation and termination factors are not

MBG Flashcards (12 decks)

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