Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BISC 320 > DNA Replication and Telomeres > Flashcards

DNA Replication and Telomeres Flashcards

1
Q

What direction is DNA replication?

A

bi-directionally away from origins

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

Where is the DNA double-helix opened?

A

at the origin of replication and unwound to form replication forks

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

What are exposed at replication forks?

A

single stranded DNA is exposed and DNA synthesis can occur

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

What are the continuous and discontinuous strands called?

A

the leading strand and lagging strand

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

What is the function of helicase?

A

begins bi-directional DNA unwinding creating two forks

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

What does DNA polymerase need?

A

a primer

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

What is DNA primase?

A

a specialized RNA polymerase that synthesizes RNA primers for DNA replication

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

Does RNA polymerase need primers?

A

do not need primers to begin RNA synthesis (same as transcription)

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

What is a primer?

A

a short (<10 base) RNA strand complementary to the template

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

What are the three steps of DNA replication?

A
  1. sliding clamp is recruited to primer
  2. DNA polymerase is recruited to sliding clamp
  3. All DNA synthesis occurs in 5’ to 3’ direction
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What are Okazaki fragments?

A

nascent lagging strands (~0.2 kb in eukaryotes/ ~2kb in prokaryotes)

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

When does termination occur?

A

when two different forks meet, when the fork reaches the end of a linear chromosome, or when polymerase meets the previously replicated strand (as above)

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

What happens to RNA primers after termination?

A

removed and replaced with DNA

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

What are the main polymerases in DNA replication for bacteria?

A

polymerase III

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

What are the main polymerases in DNA replication for eukaryotes?

A

polymerase δ and ε

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

What is proofreading?

A

polymerases are highly conserved and composed of multiple subunits that have different functions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What is processivity?

A

DNA polymerases attach to DNA for long stretched before dissociation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

After each nucleotide is added, DNA polymerase has the potential to _

A

fall off the DNA

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

What is proccessive synthesis?

A

replicative polymerases stay attached for many 1000s of nucleotides

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

What is distributive synthesis?

A

DNA polymerases involved in repair, only add a few nucleotides before falling off

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

What is tautomerization?

A

the isomerization of each base between its tautomeric forms

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

What causes improper incorporation?

A

the less common tautomer can pair with the wrong bases

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

What happens to misshapen DNA?

A

moves from the polymerase active site to a second enzymatic site on the protein that contains 3’ to 5’ exonuclease

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

What is the function of proofreading exonuclease?

A

removes the termine 3’ ase, thus restoring the correct geometry of the primer-template junction, which can move back to the polymerase site

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What are the chances for incorrect nucleotide polymerization?

A

~10^-5

26
Q

What are the chances for incorrent nucleotide after moving to a second enzymatic site?

A

~10^-7

27
Q

What are chances for incorrect nucleotide after Mismatch Repair?

A

10^-9

28
Q

The active sites of polymerases are _

A

highly conserved

29
Q

How are polymerases grouped?

A
  1. group according to the evolutionary lineage of the rest of the protein
  2. in groups A, C, D, X, and Y
30
Q

What suggests the early divergence of polymerase groups?

A

are more similar within groups than within organisms

31
Q

What catalyzes unwinding?

A

catalyzed by ATP-hydrolysis-driven DNA helicases, which open up the helix and travel along the DNA, continuously unwinding it at the replication form

32
Q

What direction does bacterial helicase move?

A

5’ to 3’ along the lagging strand template

33
Q

What direction does eukaryotic move?

A

moves 3’ to 5’ along the leading strands

34
Q

What does the crystal structure of helicase and DNA show?

A

a single strand of DNA within a hexamer of helicase subunits

35
Q

How many subunits does E. coli helicase, DnaB, have?

A

six subunits

36
Q

What is the helicase in euakroyres and archea called?

A

MCM complex and is formed of different, but related subunits MCM2-7

37
Q

What makes copying by polymerase difficult?

A

single stranded DNA can form secondary structures that would make copying by polymerase difficult

38
Q

What is the function of single-stranded binding proteins?

A

single-stranded binding proteins (SSA in bacteria and replication protein A, in eukaryotes) bind to the displaced single stranded DNA

39
Q

SSB proteins keep _ and interact with the _

A

open, DNA synthesis machinery

40
Q

What happens as DNA is unwound?

A

torsional stress is introduced into the DNA - strand separation at the fork results in overwinding ahead of the fork

41
Q

What do torsional stresses lead to?

A

changes in DNA supercoiling - overwinding makes the DNA ahead of the for more difficult to unwind

42
Q

What is the function of topoisomerases?

A

resolve the overwinding by transiently breaking DNA and allowing supercoils ro relax

43
Q

What is the function of Type IA and IB topoisomerases?

A

break one of the two DNA strands and do not require ATP

44
Q

What is the function of Type II topoisomerases?

A

use atp to separate two tangled helices by cutting both. strands of one helix and passing the other helix through the gap, ligates the two ends

45
Q

What is the function of Type I topoisomerase?

A

cleaves one DNA strand and becomes covalently bonded to one end through phospho-tyrosine bond

46
Q

What happens to the uncut strand after Topo I cleaves one DNA strand?

A

passed through the cut strands (Type Ia), or rotation occurs around the phosphodiester bond of the uncleaved strand (Type Ib), to relive tension (pos. or neg)

47
Q

What ligates the two DNA ends?

A

topo I

48
Q

What is the function of Topo II?

A

separates two tangled helices by cutting both strands of one helix and passing the other helix through the gap; ligates two ends

49
Q

What is the high processivity of replicative DNA polymerase due to?

A

the sliding clamp that keeps it tethered to DNA

50
Q

Both _ and _ are highly conserved in bacteria, archaea, and eukaryotes

A

clamp and clamp loader

51
Q

What is a sliding clamp?

A

a ring shape with 35 A hole that encloses the DNA - it is highly stable and stays associated with DNA once loaded

52
Q

What is a bacterial sliding clamp?

A

the beta protein; in eukaryotes it is PCNA

53
Q

What is an E.coli ring?

A

a homodimer of two proteins with three similar domains; in the pCNA three proteins of two similar domains come together

54
Q

How does the clamp bind DNA polymerase?

A

through an 8 amino acid motif

55
Q

What is the mechanism of clamp loading (6)?

A
  1. the clamp loader has a low affinity for the sliding clamp until the loader is bound to ATP
  2. the clamp loader binds to the sliding clamp, forming a spiral shape
  3. the clamp loader-sliding clamp complex has a high affinity with the primer-template junction
  4. binding of the complex to the primer-template junction stimulates ATPase activity, which closes the sliding clamp and releases the clamp loader
  5. sliding clamp remains associated with DNA
  6. the clamp loader must be recharged with ATP in order to repeat the cycle
56
Q

What happens during polymerase switching (2)

A
  1. after the polymerase alpha subunit of the primase complex makes a short stretch of DNA, replicative polymerases take over
  2. after the clamp loader releases, replicative polymerase binds to the sliding clamp in the position where the loader was previously bound
57
Q

How often does polymerase switching occur?

A

every time a new strand is started

58
Q

How is replicative polymerase recruited?

A

by the sliding clamp

59
Q

What are joined after synthesis?

A

okazaki fragments - okazaki fragment maturation

60
Q

What happens to DNA polymerase III in E. coli?

A

dissociates from the DNA when it reaches the next RNA primer. The sliding clamp remains attached

61
Q

What does DNA polymerase I have?

A

a 5’ exonuclease that degrades RNA primer while its DNA polymerase activity fills in the gap with DNA. This results in “nick translation” because the nick has been moved along the DNA

62
Q

What seals the DNA nick?

A

DNA ligase

BISC 320 (20 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions