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Ann's M2M Cards - weeks 1, 2 > Replication (Huang) > Flashcards

Replication (Huang) Flashcards

1
Q

DNA replication is bi or uni - directional

A

Bidirectional

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2
Q

How many origins in prokaryotes?

A

One

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3
Q

How many origins in eukaryotes?

A

Hundreds

some used more than others

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4
Q

Define semiconservative

A

Each new strand is one old strand and one new strand.

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5
Q

Replication fork

A

Site where replication is occurring

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6
Q

What recognizes and binds to origin?

A

Origin binding proteins

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7
Q

Where are origins likely to be?

A

AT rich sequences

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8
Q

What unwinds the parental strands?

A

Helicase

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9
Q

What prevents super coiling?

A

Topoisomerases in eukaryotes

Gyrase in prokaryotes

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10
Q

What inhibits dna gyrase?

A

quinolones

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11
Q

what are quinolones?

A

class of broad spectrum antibiotics

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12
Q

Direction of DNA replication?

A

5’ —> 3’

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13
Q

What catalyzes the synthesis of DNA?

A

DNA polymerase

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14
Q

How does DNA polymerase work?

A

adds deoxyribonucleotides to the 3’- OH of RNA primers then to 3’- OH of growing DNA strands

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15
Q

How many DNA polymerases in prokaryotic DNA replication?

A

2

Pol I and Poll III

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16
Q

Which is used more? Pol I or Pol III

A

Poll III

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17
Q

Why is Poll III used more in prok. DNA repl

A

has a sliding clamp so can work over a longer distance (more processive manner)

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18
Q

What does Pol I do?

A

Clean-up work during DNA replication and repair

Replaces RNA primers via
5’ - 3’ exonuclease activity
5’ - 3’ DNA polymerase activity

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19
Q

How many polymerases in Eukaryotic DNA replication?

A

3
Pol alpha
Pol delta
Pol epsilon

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20
Q

What does Pol alpha do?

A

is a holoenzyme - multi-protein complex

Primase activity
DNA polymerase activity

Synth. first ~20 residues after RNA primer

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21
Q

Does Pol alpha have proofreading activity?

A

No

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22
Q

What does Pol delta do?

A

Synthesis of lagging strand

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23
Q

What does Pol epsilon do?

A

Synthesis of leading strand

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24
Q

Can DNA replication start ‘de novo’?

A

No. Requires an RNA primer

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25
What prepares the RNA primer?
primase
26
What does SBB do?
Single Strand Binding protein holds and protects the single strands unwound by helicase during replication
27
What does helicase do?
unwinds parent DNA strand
28
What does origin binding protein do?
recognizes and binds to origin
29
What serves as primer for DNA synth?
RNA
30
How long is the primer?
~10 residues of RNA
31
What synthesizes the first ~20 DNA residues onto the primer?
Pol alpha
32
What synthesizes the leading strand in eukaryotes?
Pol epsilon
33
What synthesizes the lagging strand in eukaryotes?
Pol delta
34
What does primase do?
synth the RNA primer
35
How do the RNA primers get chosen?
use the DNA template
36
Replication fork?
place where DNA replication is ocurring simultaneously on both parent strands but in opp. directions e.g. both grow in 5' - 3' direction along the growing strand but spatially opposite direction
37
Which strand grows towards replication fork?
leading strand
38
Leading strand grows _______________.
continuously
39
Lagging strand grows _____________.
discontinuously. e.g. okazaki fragments
40
Which strand grows away from the replication fork?
lagging strand
41
What are okazaki fragments?
short fragments of DNA formed in synth of lagging strand
42
how long are okazaki fragments?
Euk: 100-200 bp Prok: 1000 - 2000 bp
43
How are RNA primers removed?
5' - 3' exonuclease (DNA pol I in e.coli)
44
How are gaps from RNA primers filled?
with appropriate DNA using template (by pol I in e.coli)
45
In E. Coli what are the functions of Pol I?
1. 5' - 3' DNA polymerase activity requiring 3'-OH primer 2. 5' - 3' exonuclease activity to remove RNA primer 3. 3' - 5' exonuclease activity for proofreading
46
How are okazaki fragments joined?
by DNA ligase
47
What does DNA ligase do?
forms phosphodiester bonds between 3'-OH and 5'-phosphate of two polynucleotide chains to join okazaki fragments
48
Overall fidelity of DNA replication?
error rate of 10^-9 to 10^-10
49
2 ways polymerases discriminate between correct and incorrect nucleotide?
1. Hydrogen bonding between complimentary nucleotides (A-T, C-G) 2. Geometry of the A-T and C-G base pairs that allow them to fit into the active site of polymerase
50
H-bonding and bp geometry account for what level of accuracy?
1 error in 10,000 to 100,000 correct nucleotieds
51
If an error occurs, how is it fixed during replication?
Proofreading during replication by 3'-5' exonuclease activity associated with polymerase complex
52
Proofreading increases the accuracy of replication by 100 - 1,000 fold. What is the final error rate?
1 error per million to 100 million correct nucleotides
53
How else can DNA repair occur other than during replication?
Post-replicational repair...see DNA repair lecture
54
What is synthesis of DNA from RNA?
reverse transcription
55
Name two instances where reverse transcription takes place?
1. Retroviruses | 2. Telomerase activity
56
What does telomerase do?
has reverse transcriptase activity carries its own RNA template restores ends of chromosome (telomeres) in human cancer and stem cells
57
What is the end replication problem?
leading strand can be synthesized to the very end but the lagging strand cannot
58
Why can the lagging strand NOT be synthesized to the very end?
Need an RNA primer ot begin synth. of each piece. | The last piece has no attachment for primer
59
What is result of lagging strand not going to the very end of replication?
Telomere gets shorter with each round of replication.
60
In cancer cells is telomerease turned on or off?
On. (de-repressed) Bad. | blocks normal cell death promoting tumor growth.
61
In normal cells is telomerase on or off?
Off (repressed)
62
What is added to the CTD of poll II and what is its function?
The CTD of pol II is phosphorylated. This attaches to the 5'-cap on the growing RNA strand and serves as a "landing pad" for the incoming nucleotides
63
What protein is a trimer of the PCNA protein and what is its function?
The DNA "sliding clamp" holds DNA template in the polymerase aids in processivity
64
What is the ORC?
Origin recognition complex

Ann's M2M Cards - weeks 1, 2 (16 decks)

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