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MCBM Exam 5 > DNA Replication > Flashcards

DNA Replication Flashcards

1
Q

What is semiconservative replication?

A

When DNA replicates, one template strand pairs with a new daughter strand, so that there is always one “old” strand in the helix

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2
Q

The structure of DNA accounts for what?

A

The storage and transmission of genetic information

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3
Q

What did Meselson and Stahl prove?

A

That DNA replication is semiconservative

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4
Q

What did Meselson and Stahl use to prove that DNA replication is semiconservative?

A

They grew E. coli in radioactive nitrogen

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5
Q

What happened after 1 generation of the Meselson and Stahl experiment?

A

Half of the E. coli had the heavy nitrogen, and the other half had “light” nitrogen

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6
Q

What did Kornberg discover?

A

That DNA is synthesized from nucleotide triphosphate precursors by DNA polymerases

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7
Q

What are the 4 deoxyribonucleotide triphosphate precursors?

A

dGTP
dATP
dCTP
dTTP

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8
Q

What did Cairns discover?

A

The theta structure of replicating chromosomes in E. coli

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9
Q

How does replication occur in bacteria?

A

Begins at a single origin, and proceeds bidirectionally

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10
Q

What is occurring at the replication fork?

A

DNA is being unwound and daughter strands are being synthesized using a parent strand as a template

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11
Q

What is a primer?

A

A segment of nucleic acid (RNA or DNA) base paired to the template, having a free 3’ OH

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12
Q

DNA replication by polymerases require what two things?

A

Template

Primer

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13
Q

What is processivity?

A

The number of bases synthesized before the DNA polymerase enzyme dissociates from the template
(How long it stays on the template and adds bases)

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14
Q

What occurs during polymerization to make it thermodynamically favorable?

A

Hydrolysis of PPi and base pairing + stacking

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15
Q

How do DNA polymerases become more accurate?

A

Use of mismatch repair mechanisms

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16
Q

What is the overall polymerase accuracy?

A

1 error per 10^6-10^8 bases

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17
Q

How do errors in replication occur?

A

The chemical structure of a base is not stable in solution, so proton rearrangement can lead to tautomer formation

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18
Q

What is a tautomer?

A

A chemical with the same atomic composition, but a slightly different chemical structure

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19
Q

1 in how many molecules are tautomeric?

A

1 in 10,000

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20
Q

A vytosine tautomer will accurately base pair with what?

A

Adenine, not guanine

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21
Q

What does DNA polymerase I use to proofread its activity?

A

3’ to 5’ exonuclease

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22
Q

On which bases does the 3’ to 5’ exonuclease act?

A

Only on the one just incorporated

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23
Q

How does DNA polymerase I proofread?

A

After adding a base, polymerase pauses. If the base doesn’t match, the nuclease moves backward and cuts out the base, then the polymerase resumes.

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24
Q

DNA polymerase I has a ___ function.

A

Repair

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25
Q

DNA polymerase II has a ___ ___ function

A

Specialized repair

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26
Q

What is the main DNA replication enzyme in E. coli?

A

DNA polymerase III

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27
Q

How many subunits does DNA polymerase III have?

A

At least 10 subunits

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28
Q

How many subunits does DNA polymerase II have?

A

7

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29
Q

In which E. coli DNA polymerases is a 3’ to 5’ exonuclease found?

A

DNA polymerase I, II and III

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30
Q

In which E. coli DNA polymerase is a 5’ to 3’ exonuclease found?

A

DNA polymerase I

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31
Q

Which of the E. coli DNA polymerases has the highest processivity?

A

III - greater than 500,000

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32
Q

What are the three stages of DNA replication?

A

Initiation
Elongation
Termination

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33
Q

Where does DNA replication begin?

A

At the origin of replication (ORI)

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34
Q

How many proteins are involved in E. coli DNA replication?

A

Over 20

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35
Q

What proteins are required to initiate replication at the E. coli origin?

A

DnaA, DnaB, DnaC, HU, DnaG, SSB, DNA gyrase, Dam methylase

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36
Q

What does DnaA do?

A

Recognises ORI; opens duplex at specific sites

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37
Q

What is the other name for DnaB? What does it do?

A

Helicase

Unwinds DNA

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38
Q

What is the function of DnaC?

A

Required for DnaB binding at origin

39
Q

What is HU?

A

A histone-like protein

40
Q

What is the other name for DnaG? What is its function?

A

Primase

Synthesizes RNA primers

41
Q

What does SSB do?

A

Binds single-stranded DNA to stabilize it

42
Q

What is the function o f DNA gyrase

A

Relieves torsional strain generated by DNA unwinding

43
Q

What is the function of Dam methylase?

A

Methylates 5’ GATC sequences at ORI

44
Q

How is an open complex formed during replication?

A

By local denaturation

45
Q

What do DnaB and DnaC bind to, and why?

A

Bind to an open complex and unwind the DNA to expose a single strand template

46
Q

What is the prepriming complex?

A

The portion of unwound DNA opened by DnaB and DnaC

47
Q

What stabilizes single stranded DNA?

A

The binding of single-strand binding proteins (SSBs)

48
Q

Which steps of the initiation of replication require ATP?

A

All of them

49
Q

What do all synthesizing enzymes require?

50
Q

Where can a primer be added?

A

Only to the 3’ end of an existing strand - cannot initiate a new strand

51
Q

What does primase bind to?

A

DnaB/DnaC on DNA templates

52
Q

What is a primosome?

A

When other proteins add to the primase/DnaB/DnaC complex at the replication fork

53
Q

What is primase?

A

A specialized RNA polymerase

54
Q

What does primase do?

A

Synthesizes a short 15 nt stretch of RNA on DNA template which remains base paired

55
Q

What creates the primer for DNA polymerase?

56
Q

How is a replisome formed?

A

By DNA polymerase III binding to the primosome

57
Q

What things are required to begin leading strand synthesis?

A

1 DNA polymerase III, RNA primer, leading strand template

58
Q

How does DNA replication carry on?

A

Bidirectional replication from a fixed origin

59
Q

In which direction is DNA synthesized?

A

5’ to 3’

60
Q

Why is the 5’ to 3’ synthesizing of DNA a problem?

A

There is no way to achieve continuous synthesis on the lagging strand without leaving long stretches of single stranded DNA

61
Q

How is the lagging strand synthesized?

A

Discontinuously in short stretches - Okazaki fragments

62
Q

How many base pairs are in an Okazaki fragment?

A

Several hundred to a few thousand

63
Q

As helicase unwinds the double helix, what is introduced in front of the replication fork?

A

Supercoiling

64
Q

What is the function of DNA gyrase and topoisomerase I?

A

To maintain the chromosome negatively supercoiled

65
Q

Certain antibiotics stop DNA gyrase and topoisomerase I. What does that cause during replication?

A

Allows supercoiling in front of the replication fork, ceasing replication

66
Q

In order to synthesize the lagging strand template, what must occur first?

A

A loop has to form of the lagging strand template on the replisome - reverses the orientation of the lagging strand template

67
Q

After several hundred bases have been synthesized, what happens to the loop of the lagging strand?

A

It drops out of the replisome forming an Okazaki fragment, and a new loop is initiated

68
Q

Okazaki fragments are not ___ linked to one another.

A

Covalently

69
Q

Each Okazaki fragment has what at its 5’ end?

A

An RNA primer

70
Q

What repairs the Okazaki fragments to produce a continuous DNA lagging strand?

A

DNA polymerase I and DNA ligase

71
Q

What does the 5’ to 3’ exonuclease function of DNA polymerase I do to the Okazaki fragments?

A

Removes RNA from the 5’ end

72
Q

What does DNA ligase do to the Okazaki fragments?

A

Covalently seals gaps in the backbone after the exonuclease removes the RNA from the 5’ end

73
Q

How does DNA replication terminate in E. coli?

A

Replication forks meet, and the topoisomerases allow the two double helices to separate

74
Q

How many polymerases are found in eukaryotes?

A

At least 5

75
Q

How many polymerases are found in eukaryotic mitochondria?

76
Q

In eukaryotes, replication is initiated roughly every __-__ kb.

77
Q

In mammals, what is DNA polymerase alpha?

78
Q

In mammals, what does DNA polymerase beta do?

A

BE repair and meiotic recombination

79
Q

In mammals, what does DNA polymerase gamma do?

A

Mitochondrial replication

80
Q

In mammals, what does DNA polymerase delta do?

A

Nuclear replication, NER and MMR

81
Q

In mammals, what does DNA polymerase epsilon do?

A

Nuclear replication, NER and MMR

82
Q

Instead of being circular like bacterial DNA, eukaryotic DNA is ___.

83
Q

What issue does linear DNA cause?

A

Causes a problem replicating the ends of the DNA molecule

84
Q

What are telomeres?

A

The buffer ends of eukaryotic chromosomes

85
Q

What allows linear molecules to be replicated without a loss of information?

86
Q

What do telomeres contain?

A

Hundreds of tandem repeated copies of a GT-rich sequence, usually 6-8 bases long

87
Q

What is used to synthesize telomeres?

A

Telomerase

88
Q

What is telomerase?

A

A specialized reverse transcriptase with an RNA component for a template to synthesize the GT-rich DNA sequence

89
Q

What is the sequence of bases found in human telomeres?

90
Q

What are the functions of telomeres?

A

To seal chromosomal ends, preventing undesirable fusion of chromosomes and aberrant recombination
Attach chromosomes to nuclear envelope
Facilitate replication
Serve as “mitotic clock”

91
Q

What do shorter telomere induce?

A

Senescense and/or apoptosis

92
Q

Where is there no detectable telomerase activity?

A

In differentiated cells

93
Q

In which cells is telomerase active?

A

Germ cells
Stem cells
Tumors

94
Q

Telomeres in the fibroblasts of the elderly are ___ then those in children.

MCBM Exam 5 (11 decks)

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