Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

MBG > DNA replication > Flashcards

DNA replication Flashcards

1
Q

three phases of replication

A

initiation, elongation, termination

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

what is origin of replication

A

where fork is initiated, bound by a trans acting factor, contains signal seqs and stimulates replication

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

T/F. All organisms have a single replication origin

A

False. Although most bacteria have a single ori, eukaryotes have more and humans have thousands

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

what are some techniques to look at replication fork structure (3)?

A

2D gels to view topology, EdU labeling/fiber combing, pull out Okazaki fragments with specific antibody

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

what are some initiation factors (4)

A

helicase, helicase loader, primase, initiators

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

how are helicase rings activated

A

accessory subunits Cdc45 and GINS activate to begin DNA unwinding

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

T/F. Helicase is the fastest part of the motor

A

False, synthesis proceeds faster through the combinatorial action of multiple components

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

How do eukaryotes prevent fork reinitation?

A

DnaA is a product inhibited enzyme - so when it hydrolyzes ATP to ADP, the assembly becomes destabilized and prevents reinitiation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

what are two challenges facing the replication fork?

A

topology, chromatin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

what are some characteristics of human replication?

A

replication initiates stochasticalyy, initiates within non-transcribed, up to 150kb zones, and terminates dispersively

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What does the initiator do, and what is it called in bacteria and eukaryotes?

A

Binds origins/recruits helicase, DnaA in bacteria and ORC in eukaryotes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What does the helicase do, and what is it called in bacteria and eukaryotes?

A

Unwinds DNA, called DnaB in bacteria and CMG (MCM2-7/Cdc45/GINS) in eukaryotes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What does the helicase loader do, and what is it called in bacteria and eukaryotes?

A

Loads Helicase, called DnaC in bacteria and Cdc6/CdtI in euk

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What does primase do, and what is it called in bacteria and eukaryotes?

A

Makes RNA primers, DnaG in bacteria and Pol-alpha (Pri1, Pri2, PolAI, PolA2) in euk

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

T/F. All initiator components of the replication fork use NTPs

A

True

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What are the 4 steps of helicase loading in bacteria?

A
  1. DNA initiator binds to DnaA, bends DNA at rep ori
  2. DNA bending allows local unwinding at AT-rich region
  3. DnaC assembles onto DnaB helicase, binds to DnaA
  4. DnaC loads DnaB helicase on, disassembles
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What are the 4 steps of helicase loading in eukaryotes?

A
  1. Origin binding (ORC, coinitiates with Cdc6)
  2. Loading (Mcm2-7, Cdt1)
  3. Activation (Cdc45, GINS, DDK kinase)
  4. Unwinding (CMG)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

If MCM loading were not limited to G1, what might be a potential problem in S phase?

A

Potentially deleterious re-replication of certain genomic loci

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What prevents eukaryotic origins from re-firing?

A

Post translational modifications, proteolysis, nuclear export

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Six types of replication elongation proteins

A

helicase, polymerase, clamp, clamploader, primase, SSBs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Helicase in bactera and eukaryotes?

A

DnaB, the “CMG”

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Polymerase in bacteria and eukaryotes?

A

Pol III, pol epsilon/pol delta

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Clamp in bacteria and eukaryotes?

A

Beta protein, PCNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Clamp loader in bacteria and eukaryotes?

A

The theta complex, RFC

25
Primase in bacteria and eukaryotes?
DnaG, Pol-alpha
26
SSBs in bacteria and eukaryotes?
Ssb, RPA
27
T/F. DnaB/CMG encircle and move along both strands
False, they move along single DNA strands, in opposite directions
28
What are the members and roles of DNA pol family A?
T7 pol, Ecoli pol I, mito pol gamma. Replication, and repair of short segments - the "classic polymerase"
29
What are the members and roles of DNA pol family B?
High fidelity replication, 3-5' exo, members are eukaryotic pols alpha, delta, epsilon, called the "A family catalytic center"
30
What are the members and roles of DNA pol family C?
Members E.coli pol III, is a high fidelity, highly processive enzyme class with 3'-5' exo
31
What are the members and roles of DNA pol family D?
PolD, archaeal replication?
32
What are the members and roles of DNA pol family X?
Repair pol, low fidelity/processivity, lesion bypass. Members are eukaryotic pols n, i , k and bacterial pols IV, V
33
What are the members and roles of DNA pol family RT?
RNA dependent DNA synthesis, viral replication, telomere synthesis - members are the HIV RT and telomerase
34
T/F. DNA pol families A, B, D, Y, and RT are related, but C and X are not.
False - A, B, D, Y, and RT are related, and C and X are also related
35
Why do eukaryotes need so many polymerases?
Bc there are so many functions they need to perform -priming, making okazaki fragments, repair, mito replication, lagging/leading strand synthesis,
36
What structural feature do pols have to ensure fidelity?
"steric gate", with a snug active site that matches watson/crick pair, disfavors rNTP binding and excludes wobbles/mispairs
37
What two structural features do steric gates of DNA pols contain?
A selectivity residue, and a 2'C on ribose
38
T/F. Polymerases read hydrogen bonding to recognize sequence motifs.
False, they sense shape complementarity, which is indicative of base-stacking interactions and proper H-bonding, but not H-bonds directly
39
T/F. dNTPs are 50-100X more abundant than rNTPs.
False, rNTPs are 50-100X more abundant than dNTPs
40
Why is rNTP misincorporation a problem? (3)
U can mispair with G, RNA is more prone to backbone cleavage, and the 2' OH deforms the DNA helix to alter protein binding
41
Why is rNTP misincorporation a problem? (3)
U can mispair with G, RNA is more prone to backbone cleavage, and the 2' OH deforms the DNA helix to alter protein binding
42
T/F. ATP turnover controls clamp opening and release
True, ATP binding leads to conformational change, causing clamp binding/opening, and then ATP hydrolysis causes clamp closure and clamp loader release
43
How do lagging and leading strand polymerases maintain speed with each other in eukaryotes?
Random pausing/dissociation events maintain synchrony, it is *not* directly coupled
44
How are okazaki fragments removed/patched?
3 mechanisms: 1. 3' - 5' degradation, nicking and ligase 2. RNA cleavage with RNaseH, nick and ligase 3. Flap formation, Dna2/Fen1 cleave, nick and ligase
45
What is the substrate and geometry for RNAse H nuclease action?
Substrate - 2 metal ions, strained geometry and incomplete liganding
46
DNA ligase mechanism
encircles DNA, ATP hydrolysis to power nick healing
47
how large is the E. coli replisome, and how fast can the fork move?
300-400A, and moves at a speed of up to 1kb/s
48
What are three things that can cause forks to terminate prematurely?
Protein mediated block, fork collision, and superhelical strain
49
What are catenanes?
Interlocking rings of DNA which cannot be separated without breaking covalent bonds, formed during strain of DNA replication and transcription
50
What happens if you don't resolve catenanes?
You get gene misexpression and DNA breakage
51
What is the difference between type I and type II topoisomerases?
Type I cuts one strand, and type II cuts both, all form covalent enzyme-DNA intermediates
52
If type IA topos preferentially relax negatively supercoiled DNA, and IIA topos positively supercoiled, where would you expect these two classes to act during transcription
The type IA topo would be acting ahead of the RNA polymerase, and IIA would be acting behind.
53
T/F. nucleosomes stabilize positive supercoils
False, they stabilize negative supercoils
54
What are 4 types of histone modifications?
acetylation, methylation, phosphorylation, and ubiquitylation - make up a "histone code"
55
what are a few things the histone code affects?
chromatin accessibility, origin usage, fork speed
56
T/F. The histone code is relatively fixed.
False, it is in constant flux
57
How are old and new histones apportioned between daughter nucleosomes
Mcm2 has a histon H3-H4 chaperone domain that aids apportionment, preserves epigenetic information between cell divisions, but the segregation mechanism itself is not understood
58
What are 4 characteristics of nucleosomes?
Octamer of histones wrapped by DNA, packages DNA in eukaryotes, affects protein recruitment to DNA, and can be post-translationally modified
59
T/F. Initiation, elongation and termination factors are all broadly conserved.
False, initiation machineries are broadly conserved, but elongation and termination factors are not

MBG (13 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions