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

Ch. 14 Repair Systems (Exam 2) Flashcards

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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
Q

What does the mismatch repair system detect?

A

Mismatched nucleotide and the absence of base pairing in general

25
Q

What chemical term is used to describe the strands that are often targeted for mismatched base repair?

A

Nonmethylated. Nonmethylated strands are often targeted

26
Q

What is the purpose of the dam gene?

A

It converts adenines to 6-methyl adenines in the sequence 5’-GATC-3’

27
Q

What enzyme does the dam gene use to convert adenines to 6-methyladenines?

A

DNA methyltransferase

28
Q

Why can the dam gene be likened to a beaver dam?

A

It plugs the 6-methyladenine into the nonmethylated strand, which improves the overall flow

29
Q

Why aren’t methylations via the dam gene mutagenic?

A

The modified nucleotides have the same base-pairing properties as the unmodified versions

30
Q

In mismatch repair, sometimes an entire strand needs to be excised. Should it be the methylated or nonmethylated strand?

A

Nonmethylated

31
Q

What is the purpose of mut genes in prokaryotes?

A

Encode mismatch repair proteins

32
Q

What is the first step of mut gene mismatch repair?

A

MutS dimer binds to mismatch

33
Q

After the MutS dimer binds to the mismatch, what is the next step in mut gene mismatch repair?

A

MutL dimer binds with MutS dimer to form tetramer

34
Q

After forming the tetramer, what happens next in mut gene mismatch repair?

A

MutS finds GATC sequence

35
Q

What happens after the GATC sequence is found in mut gene mismatch repair?

A

MutH endonuclease joins the tetramer and cleaves the unmethylated strand

36
Q

After the unmethylated strand is removed, what happens in the final step of mut gene mismatch repair?

A

DNA polymerase III synthesizes a new strand

37
Q

What is the eukaryotic homolog to the prokaryotic mut gene?

A

Msh2 (MutS homolog 2)

38
Q

Eukaryotic MutS/L systems repair mismatches and insertion/deletion (indel) loops caused by replication…

A

Slippage

39
Q

What is replication slippage?

A

Misalignment of DNA strands during replication of repeated sequences i.e. the DNA literally slacks/slips down and misaligns base pairing

40
Q

What is single-strand exchange in recombination-repair systems?

A

The retrieval of a normal nucleotide sequence from a healthy, homologous strand and placing it into the damaged strand

41
Q

What is the mechanism behind single-strand recombination repair?

A

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
Q

What 2 recombination repair pathways fix double-strand breaks?

A

1) Homology-directed recombination-repair (HRR)

2) Nonhomologous end joining (NHEJ)

43
Q

Why is HHR the ideal pathway for repairing DSBs?

A

It ensures that no genetic info is lost from the breakpoint

44
Q

Why is genetic info lost with nonhomologous end joining (NHEJ)?

A

The protein Artemis has nuclease activities that trim overhangs during the rejoining process

45
Q

What 2 proteins recognize DSBs in NHEJ?

A

Ku70 & Ku80

46
Q

What does the MRN complex do in NHEJ?

A

Bridges the DSB strands together

47
Q

What does DNA-dependent protein kinase (DNA-PK) do in NHEJ?

A

Phosphorylate protein targets like Artemis

48
Q

DNA ligase IV functions with this protein to join the ends together in NHEJ…

A

XRCC4

49
Q

What are the 3 proteins of the MRN complex in NHEJ?

A

1) Mre11 (meal-ready-to-eat)
2) Rad50 (radical)
3) Nbs1 (No bullshit)

50
Q

Homology-directed recombination repair requires the use of a { } to fix a DSB.

A

Double Holliday junction

Molecular Biology (21 decks)

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