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MCBM Exam 5 > DNA Replication > Flashcards

DNA Replication Flashcards

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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
DNA polymerase II has a ___ ___ function
Specialized repair
26
What is the main DNA replication enzyme in E. coli?
DNA polymerase III
27
How many subunits does DNA polymerase III have?
At least 10 subunits
28
How many subunits does DNA polymerase II have?
7
29
In which E. coli DNA polymerases is a 3' to 5' exonuclease found?
DNA polymerase I, II and III
30
In which E. coli DNA polymerase is a 5' to 3' exonuclease found?
DNA polymerase I
31
Which of the E. coli DNA polymerases has the highest processivity?
III - greater than 500,000
32
What are the three stages of DNA replication?
Initiation Elongation Termination
33
Where does DNA replication begin?
At the origin of replication (ORI)
34
How many proteins are involved in E. coli DNA replication?
Over 20
35
What proteins are required to initiate replication at the E. coli origin?
DnaA, DnaB, DnaC, HU, DnaG, SSB, DNA gyrase, Dam methylase
36
What does DnaA do?
Recognises ORI; opens duplex at specific sites
37
What is the other name for DnaB? What does it do?
Helicase | Unwinds DNA
38
What is the function of DnaC?
Required for DnaB binding at origin
39
What is HU?
A histone-like protein
40
What is the other name for DnaG? What is its function?
Primase | Synthesizes RNA primers
41
What does SSB do?
Binds single-stranded DNA to stabilize it
42
What is the function o f DNA gyrase
Relieves torsional strain generated by DNA unwinding
43
What is the function of Dam methylase?
Methylates 5' GATC sequences at ORI
44
How is an open complex formed during replication?
By local denaturation
45
What do DnaB and DnaC bind to, and why?
Bind to an open complex and unwind the DNA to expose a single strand template
46
What is the prepriming complex?
The portion of unwound DNA opened by DnaB and DnaC
47
What stabilizes single stranded DNA?
The binding of single-strand binding proteins (SSBs)
48
Which steps of the initiation of replication require ATP?
All of them
49
What do all synthesizing enzymes require?
A primer
50
Where can a primer be added?
Only to the 3' end of an existing strand - cannot initiate a new strand
51
What does primase bind to?
DnaB/DnaC on DNA templates
52
What is a primosome?
When other proteins add to the primase/DnaB/DnaC complex at the replication fork
53
What is primase?
A specialized RNA polymerase
54
What does primase do?
Synthesizes a short 15 nt stretch of RNA on DNA template which remains base paired
55
What creates the primer for DNA polymerase?
Primase
56
How is a replisome formed?
By DNA polymerase III binding to the primosome
57
What things are required to begin leading strand synthesis?
1 DNA polymerase III, RNA primer, leading strand template
58
How does DNA replication carry on?
Bidirectional replication from a fixed origin
59
In which direction is DNA synthesized?
5' to 3'
60
Why is the 5' to 3' synthesizing of DNA a problem?
There is no way to achieve continuous synthesis on the lagging strand without leaving long stretches of single stranded DNA
61
How is the lagging strand synthesized?
Discontinuously in short stretches - Okazaki fragments
62
How many base pairs are in an Okazaki fragment?
Several hundred to a few thousand
63
As helicase unwinds the double helix, what is introduced in front of the replication fork?
Supercoiling
64
What is the function of DNA gyrase and topoisomerase I?
To maintain the chromosome negatively supercoiled
65
Certain antibiotics stop DNA gyrase and topoisomerase I. What does that cause during replication?
Allows supercoiling in front of the replication fork, ceasing replication
66
In order to synthesize the lagging strand template, what must occur first?
A loop has to form of the lagging strand template on the replisome - reverses the orientation of the lagging strand template
67
After several hundred bases have been synthesized, what happens to the loop of the lagging strand?
It drops out of the replisome forming an Okazaki fragment, and a new loop is initiated
68
Okazaki fragments are not ___ linked to one another.
Covalently
69
Each Okazaki fragment has what at its 5' end?
An RNA primer
70
What repairs the Okazaki fragments to produce a continuous DNA lagging strand?
DNA polymerase I and DNA ligase
71
What does the 5' to 3' exonuclease function of DNA polymerase I do to the Okazaki fragments?
Removes RNA from the 5' end
72
What does DNA ligase do to the Okazaki fragments?
Covalently seals gaps in the backbone after the exonuclease removes the RNA from the 5' end
73
How does DNA replication terminate in E. coli?
Replication forks meet, and the topoisomerases allow the two double helices to separate
74
How many polymerases are found in eukaryotes?
At least 5
75
How many polymerases are found in eukaryotic mitochondria?
1
76
In eukaryotes, replication is initiated roughly every __-__ kb.
40-100
77
In mammals, what is DNA polymerase alpha?
Primase
78
In mammals, what does DNA polymerase beta do?
BE repair and meiotic recombination
79
In mammals, what does DNA polymerase gamma do?
Mitochondrial replication
80
In mammals, what does DNA polymerase delta do?
Nuclear replication, NER and MMR
81
In mammals, what does DNA polymerase epsilon do?
Nuclear replication, NER and MMR
82
Instead of being circular like bacterial DNA, eukaryotic DNA is ___.
Linear
83
What issue does linear DNA cause?
Causes a problem replicating the ends of the DNA molecule
84
What are telomeres?
The buffer ends of eukaryotic chromosomes
85
What allows linear molecules to be replicated without a loss of information?
Telomeres
86
What do telomeres contain?
Hundreds of tandem repeated copies of a GT-rich sequence, usually 6-8 bases long
87
What is used to synthesize telomeres?
Telomerase
88
What is telomerase?
A specialized reverse transcriptase with an RNA component for a template to synthesize the GT-rich DNA sequence
89
What is the sequence of bases found in human telomeres?
AGGGTT
90
What are the functions of telomeres?
To seal chromosomal ends, preventing undesirable fusion of chromosomes and aberrant recombination Attach chromosomes to nuclear envelope Facilitate replication Serve as "mitotic clock"
91
What do shorter telomere induce?
Senescense and/or apoptosis
92
Where is there no detectable telomerase activity?
In differentiated cells
93
In which cells is telomerase active?
Germ cells Stem cells Tumors
94
Telomeres in the fibroblasts of the elderly are ___ then those in children.
Shorter

MCBM Exam 5 (11 decks)

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