Brainscape's Knowledge GenomeTM

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


See full index

Molecular Biology - 3550 > slides exam 2 > Flashcards

slides exam 2 Flashcards

1
Q

What is DNA replication?

A
  • Duplication of the cellular genome
  • Stored genetic information passed to next generation
  • Highly regulated
  • Requires sufficient resources
  • Loss of control leads to cancer—uncontrolled cell division
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

DNA replication is said to be __________

A

semiconservative

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

How do we know about semiconservative replication?

A

Meselson and Stahl performed an experiment with 2 types of DNA
•DNA contains: C, H, O, N, P
•1 type of DNA contained the abundant isotope: N-14
•1 type of DNA contained a less abundant isotope: N-15

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

How did this lead to a discovery of semiconservative replication?

A

Different densities of DNA allows for separation by centrifugation

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

DNA replication is said to be _______

A

bidirectional

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

What is involved in prokaryotic replication?

A 
1 Origin of replication
1 bubble
2 replication forks
Semiconservative
Bidirectional
Sometimes called θ replication
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is involved in eukaryotic replication?

A 
Multiple origins of replication
Multiple bubbles
2 replication forks/bubble
Bidirectional
Semiconservative
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What are the exceptions to bidirectionality?

A

Unidirectional replication occurs in some:
• Prokaryotes
•BacteriophageΦ29
•Plasmids
•Viruses
•Adenovirus
•Respiratory illnesses: common cold, pneumonia, croup, and bronchitis

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

DNA replication is _______

A

semi-discontinuous

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

Does replication have directionality?

A

Yes 5’ and 3’ ends.

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

Which direction does DNA polymerase only synthesize?

A

5’ to 3’ direction.

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

Can both daughter strands be synthesized in the same direction?

A

No

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

Can DNA polymerase initiate synthesize of a daughter strand?

A

NO, dna polymerase requires an RNA primer than is placed by primate.

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

What does DNA polymerase require to initiate synthesis of a daughter strand?

A

RNA primer that is placed by primase

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

Is DNA replication continuous?

A

no

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

What strand is synthesized continuously with the direction of the replication fork opening?

A

Leading strand

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

What strand is synthesized discontinuously in the opposite direction the replication fork is opening?

A

Lagging strand

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

What is the meaning behind discontinuous replication?

A

One strand (leading strand) is synthesized continuously whereas one strand (lagging strand) is synthesized discontinuously into fragments that must be glued together with ligase.

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

What are the fragments of the lagging strand called?

A

Okazaki fragments

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

Each Okazaki fragments starts with an RNA primer that is how many nucleotides long?

A

10-13 nucleotides

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

What is the fragment length in eukaryotes?

A

100-200 nucleotides

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

What is the fragment length in prokaryotes?

A

1000-2000 nucleotides

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

Summarize the 3 big takeaways of dna replication:

A

DNA replication is

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

Summarize DNA polymerase

A
  • Template: DNA
  • Synthesizes: DNA
  • Reading direction: 3’  5’
  • Synthesizing direction: 5’  3’
  • CANNOT initiate DNA chains
  • Requires an RNA primer placed by primase
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

In what direction does DNA polymerase read the strand?

A

3’ to 5’ direction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What process is RNA polymerase involved in?

A

Transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What is RNA polymerases template?

A

DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What does RNA polymerase synthesize?

A

RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What direction does RNA polymerase read?

A

3’ to 5’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What direction does RNA polymerase synthesize a strand?

A

5’ to 3’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What process is the ribosome involved in?

A

Translation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

What is a ribosomes template?

A

RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What does a ribosome synthesize?

A

A polypeptide

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

What direction does a ribosome read the template?

A

5’ to 3’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

What is the synthesizing direction of a ribosome?

A

N –> C-terminus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What does DNA polymerase require?

A

an RNA primer

37
Q

What is a template strand + a primer strand called?

A

A primed template

38
Q

What is an example of an RNA primer?

A

OH-

39
Q

What would an example of a primer terminus be?

A

3’ hydroxyl end

40
Q

How many DNA polymerases does E. coli have?

A

5

41
Q

Name the 5 DNA polymerases of E. coli

A 
Poly I
Pol II
Pol III
Pol IV
Pol V
42
Q

What is the function of E. coli DNA Poly I?

A

Okazaki fragment processing and DNA repair

43
Q

What is the function of E. coli DNA Poly II?

A

Translation Synthesis

44
Q

What is the function of E. coli DNA Poly III?

A

Chromosome replication

45
Q

What is the function of E. coli DNA Poly IV?

A

Translesion synthesis

46
Q

What is the function of E. coli DNA Poly V?

A

Translesion synthesis

47
Q

What are the 3 DNA polymerases of E. coli that are 3’ –> 5’ exonucleases?

A

DNA poly I, II, and III

48
Q

What is the only DNA polymerase of E. coli that functions as a 5’ –> 3’ exonuclease?

A

DNA polymerase I

49
Q

What happens while adding nucleotides?

A
  • DNA polymerase incorporates nucleotides 1 at a time
  • Mistakes every 105-106 nucleotide additions
  • Mistake can be removed
50
Q

How often do mistakes occur while adding nucleotides? (how many nucleotides before a mistake)

A

about every 105-106 nucleotide additions there will be a mistake

51
Q

Can mistakes be removed once they occur?

A

yes

52
Q

How many nucleotides are added at a time?

A

DNA polymerase incorporates 1 nucleotide at a time

53
Q

Specifics of adding nucleotides:

A
  • 3’ OH— of the RNA primer attacks the α phosphate of the incoming dNTP
  • β and γ phosphate leave as a pyrophosphate (PPi)
  • dNMP is incorporated to the growing chain
54
Q

What is the overall reaction of nucleotide addition?

A

•(dNMP)n + dNTP –> (dNMP)n+1 + PPi

55
Q

What is the (dNMP)n represent in the reaction of nucleotide addition?

A

Existing chain

56
Q

What does dNTP represent in the reaction of nucleotide addition?

A

incoming nucleotide

57
Q

What does (dNMP)n+1 represent in the reaction of nucleotide addition?

A

Chain length +1

58
Q

What does PPi represent in the reaction of nucleotide addition?

A

Pyrophosphate

59
Q

What does magnesium facilitate on DNA polymerase?

A

The 3’ OH- attack of the α phosphate andthe removal of PPi are facilitated by 2 Mg2+ ions on

60
Q

What are the 2 polymerase sites?

A

post insertion and insertion site

61
Q

What happens at DNA polymerases sites? Which one translocates to the other one?

A

After a new dNMP is incorporated at the insertion site, the polymerase translocates (moves) until the dNMP is in the postinsertion site

62
Q

What is pyrophosphorylation?

A

A nucleotide is release from a polymer by adding PPi

  • reverse of an elongated chain
  • dNMP is freed from a chain as dNPT when PPi is added
63
Q

What is the formula for pyrophosphorylation?

A

(dNMP)n+ PPi (dNMP)n-1+ dNTP

64
Q

What does pyrophosphatase do?

A

PREVENT phosphorylation

65
Q

How does pyrophosphatase do its job?

A

By hydrolyzing PPi into Pi + Pi

66
Q

What does the hydrolization of PPi into Pi + Pi explain?

A

This explains why dNTP is favored over dNDP or dNMP; dNTP + hydrolysis of PPi prevent the chain from undergoing pyrophosphorylation…
In other words, after making the chain longer, you don’t want it to fall apart

67
Q

T/F Most DNA polymerases have nuclease activity

A

TRUE

68
Q

What is a nuclease?

A

something that cuts phosphodiester bonds in nucleic acids

69
Q

What are the 2 types of nucleases?

A

Exonucleases and Endonucleases

70
Q

What is the difference between the 2 types of nucleases?

A
  • Endonuclease cuts a strand internally

* Exonuclease cuts a nucleotide from the terminus of a strand

71
Q

Name the 2 types of exonucleases and explain the difference:

A
  • 3’  5’ nuclease = nuclease that cuts at the 3’ end
  • 5’  3’ nuclease = nuclease that cuts at the 5’ end
  • DNA Pol I has both 3’  5’ and 5’  3’ exonuclease activity
72
Q

Which polymerase has activity both exonucleases?

A

DNA poly I

73
Q

Define Proofreading:

A

When the wrong nucleotide is incorporated it can be removed and replaced with a different one

74
Q

The error rate of mismatch was every 10^4-10^5 bases…

___________ exonuclease activity improves the error rate to ____________

A

3’ to 5’

10^6 - 10^8

75
Q

What exonuclease activity is facilitated by magnesium ions?

A

3’ to 5’ exonuclease activity

76
Q

Is proofreading the same as pyrophosphorolysis?

A

NO

77
Q

Mismatched nucleotides are released as what?

A

dNMPs

78
Q

Why does mismatch occur?

A

Tautomers can “fool” the enzyme into an incorrect base pair..
When tautomers revert back to their normal structure, polymerase can detect the mismatch

79
Q

FUN FACT:

A

• Remember DNA pol I has 3’  5’
and 5’  3’ exonuclease activity
• 5’  3’ exonuclease activity can function at the same time as its polymerase activity

80
Q

What is Nick Translation?

A
  • Allows the degradation of RNA primers at the same time they are replaced with DNA
  • RNA primers are degraded from the 5’ end while new DNA is added to the 3’ end
  • Nicks are repaired by DNA ligase
81
Q

Which DNA polymerases intentionally allow mistakes?

A

DNA Pol IV and V

82
Q

Which DNA poly is responsible for DNA repair?

A

II

83
Q

What does the polymerase crystal structure consist of?

A
  • fingers
  • thumb
  • palm
  • DNA
  • polymerase sites
84
Q

When the correct dNTP is added a ____ degree conformation change is undergone by polymerase

A

40 degree

85
Q

What happens when an incorrect base pair tries to attach to polymerase?

A
  • Polymerase cannot fully close with incorrect base pair
  • This incorrect base pairing is up to 1000x slower
  • Allows time for wrong dNTP to disassociate
  • Or allows time for 3’  5’ exonuclease activity
  • Also, a mismatched 3’ terminal nucleotide adds the next nucleotide more slowly  more time (6 in the next figure)
86
Q

What is distributive synthesis?

A

DNA polymerase adds a nucleotide, fully disassociates then rebinds DNA

87
Q

What is processive synthesis?

A

DNA continually adds nucleotides without disassociating

88
Q

What is the processivity number?

A

average nucleotides incorporated before polymerase disassociates
• Pol I: 10-100nt
• Pol III: 1000s (more in the next section)

Molecular Biology - 3550 (8 decks)

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