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Molecular Biology > Ch. 14 Repair Systems (Exam 2) > Flashcards

Ch. 14 Repair Systems (Exam 2) Flashcards

1
Q

Generally speaking, what does direct repair do?

A

Act directly on damaged nucleotide and converts each once back to original structure

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2
Q

Generally speaking, what does base excision repair do?

A

Removes damaged nucleotide base

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3
Q

Generally speaking, what does nucleotide excision repair do?

A

Acts on greater damaged areas of DNA i.e. removing nucleotide sequences

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4
Q

Generally speaking, what does mismatch repair do?

A

Corrects nucleotide base mispairs

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5
Q

Generally speaking, what does recombination repair do?

A

Fixes double-strand breaks (DSBs)

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6
Q

What is the mechanism behind direct repair systems?

A

Nicks are filled in with DNA ligase to correct nucleotide modification without excision

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7
Q

What chemical agents do direct repair systems work on?

A

Ubiquitous alkylating agents

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8
Q

What two enzymes are responsible for the mechanism behind base excision repair (BER) systems?

A

Glycosylates & lyases

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9
Q

How much damage is required to initiate the glycosylates?

A

Relatively minor damage

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10
Q

How do glycosylates act on damaged bases?

A

Cleaving the beta N-glycosidic bond between the damaged base and deoxyribose

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11
Q

How do lyases act on damaged bases?

A

Using an amino group to attack the deoxyribose ring

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12
Q

What 3 nucleotide base conditions do glycosylates remove?

A

1) Deaminated bases
2) Alkylated bases
3) Oxidized bases

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13
Q

What is the difference between the short-patch BER pathway and the long-patch BER pathway?

A

Short-patch BER removes a single nucleotides while long-patch removes a series of 2 to 10 nucleotide bases

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14
Q

Seeing that nucleotide excision repair (NER) systems target greater areas of nucleotide sequences, give 2 examples of damages they fix.

A

1) Intrastrand crosslinks
2) Attachment of large chemical groups

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15
Q

What are the 4 steps of NER systems?

A

1) Incision
2) Excision
3) Synthesis
4) Ligation

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16
Q

What is the UvrABC endonuclease?

A

Protein complex that initiates short-patch NER

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17
Q

What is the function of the UvrAB dimer?

A

Recognize pyrimidine dimers and other bulky legions

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18
Q

What is the function of the UvrBC dimer?

A

Make incision on each side of damaged site i.e. 2 cuts

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19
Q

What does UvrD do?

A

Helicase activity to unwind DNA and release the single strand between the 2 cuts created by UvrBC

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20
Q

What is xeroderma pigementosum (XP)?

A

Recessive disease resulting in sensitivity to sunlight

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21
Q

What is the cause of XP?

A

Deficiency in NER

22
Q

What is the result of XP?

A

Skin disorders, cancer, etc.

23
Q

What are the 2 major NER pathways?

A

1) Global genome (GG-NER)
2) Transcription-coupled repair (TC-NER)

24
Q

What’s the difference between GG-NER & TC-NER?

A

GG-NER uses XPC protein to recognize damage anywhere in the genome while TC-NER uses RNA polymerase in the transcribed strand of active genes

25
What does the mismatch repair system detect?
Mismatched nucleotide and the absence of base pairing in general
25
What chemical term is used to describe the strands that are often targeted for mismatched base repair?
Nonmethylated. Nonmethylated strands are often targeted
26
What is the purpose of the dam gene?
It converts adenines to 6-methyl adenines in the sequence 5'-GATC-3'
27
What enzyme does the dam gene use to convert adenines to 6-methyladenines?
DNA methyltransferase
28
Why can the dam gene be likened to a beaver dam?
It plugs the 6-methyladenine into the nonmethylated strand, which improves the overall flow
29
Why aren't methylations via the dam gene mutagenic?
The modified nucleotides have the same base-pairing properties as the unmodified versions
30
In mismatch repair, sometimes an entire strand needs to be excised. Should it be the methylated or nonmethylated strand?
Nonmethylated
31
What is the purpose of mut genes in prokaryotes?
Encode mismatch repair proteins
32
What is the first step of mut gene mismatch repair?
MutS dimer binds to mismatch
33
After the MutS dimer binds to the mismatch, what is the next step in mut gene mismatch repair?
MutL dimer binds with MutS dimer to form tetramer
34
After forming the tetramer, what happens next in mut gene mismatch repair?
MutS finds GATC sequence
35
What happens after the GATC sequence is found in mut gene mismatch repair?
MutH endonuclease joins the tetramer and cleaves the unmethylated strand
36
After the unmethylated strand is removed, what happens in the final step of mut gene mismatch repair?
DNA polymerase III synthesizes a new strand
37
What is the eukaryotic homolog to the prokaryotic mut gene?
Msh2 (MutS homolog 2)
38
Eukaryotic MutS/L systems repair mismatches and insertion/deletion (indel) loops caused by replication...
Slippage
39
What is replication slippage?
Misalignment of DNA strands during replication of repeated sequences i.e. the DNA literally slacks/slips down and misaligns base pairing
40
What is single-strand exchange in recombination-repair systems?
The retrieval of a normal nucleotide sequence from a healthy, homologous strand and placing it into the damaged strand
41
What is the mechanism behind single-strand recombination repair?
Upon recognition of a damaged base, the repair system forms a gap opposite of the damaged base, and this gap is where the normal sequence is placed
42
What 2 recombination repair pathways fix double-strand breaks?
1) Homology-directed recombination-repair (HRR) 2) Nonhomologous end joining (NHEJ)
43
Why is HHR the ideal pathway for repairing DSBs?
It ensures that no genetic info is lost from the breakpoint
44
Why is genetic info lost with nonhomologous end joining (NHEJ)?
The protein Artemis has nuclease activities that trim overhangs during the rejoining process
45
What 2 proteins recognize DSBs in NHEJ?
Ku70 & Ku80
46
What does the MRN complex do in NHEJ?
Bridges the DSB strands together
47
What does DNA-dependent protein kinase (DNA-PK) do in NHEJ?
Phosphorylate protein targets like Artemis
48
DNA ligase IV functions with this protein to join the ends together in NHEJ...
XRCC4
49
What are the 3 proteins of the MRN complex in NHEJ?
1) Mre11 (meal-ready-to-eat) 2) Rad50 (radical) 3) Nbs1 (No bullshit)
50
Homology-directed recombination repair requires the use of a { } to fix a DSB.
Double Holliday junction

Molecular Biology (21 decks)

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