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Molecular Biology Test 3 > Chapter 16 - Repair Systems > Flashcards

Chapter 16 - Repair Systems Flashcards

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1
Q

Direct Repair

A

LEAST COMMON. Reversal/Removal of the damage.

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2
Q

Excision Repair

A

One strand of DNA is directly excised and then replaced by resynthesis using the complementary strand as template.

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3
Q

Mismatch Repair

A

MOST COMMON. Corrects recently inserted bases that do not pair properly.

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4
Q

Recombination Repair

A

Filling a gap in one strand of duplex DNA by retrieving a homologous single strand from another duplex.

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5
Q

Nonhomologous end joining

A

Rejoins broken DSB.

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6
Q

Deamination of cytosine

A
  • Creates a U-G base pair.
  • Uracil is preferentially removed from the mismatched pair.
  • Minor structural distortion with pyrimidine-purine pair (U-G).
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7
Q

Replication Error

A
  • Causes a mismatched pair.
  • Corrected by replacing one base.
  • Greater structural distortion with purine-purine pair (A-G).
  • If uncorrected, a mutation is fixed in one daughter duplex.
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8
Q

Ultraviolet irradiation

A
  • Thymine dimer formation.
  • Corrected by excision.
  • The dimer blocks replication and transcription.
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9
Q

Methylation of the Base

A
  • Causes mispairing at replication.

* Corrected by dealkylation.

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10
Q

Depurination

A
  • Removes a base from DNA.
  • Corrected by insertion
  • Blocking replication and transcription.
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11
Q

Nucleotide excision repair removes

A

a stretch of DNA that includes the damaged base.

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12
Q

Incision

A

Requires the activity of an endonuclease to recognize and cut on both sides of the damaged DNA.
Distinguishes nucleotide from Base Excision Repair.

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13
Q

Excision & Synthesis

A

Removal and replacement often occur concurrently and

require an exonuclease/helicase (excision) and DNA polymerase (synthesis).

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14
Q

Ligation of Nicks

A

Requires DNA ligase to covalently link the 3’-ends of the new DNA strand with the original DNA.

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15
Q

Uvr repair system

A 
In E. coli, the Uvr repair system accounts for almost all of the excision repair events.  
Uvr complex can be directed to sites of damage by other proteins.
1. UvrAB dimer recognizes and binds
damaged DNA.
2. UvrA released (ATP-dependent) and
UvrC binds.
3. UvrC nicks 10-11 bases around the
damage site; ATP-dependent
(Incision).
4. UvrD is the helicase that unwinds
the DNA to release ssDNA strand.
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16
Q

UvrAB

A

Dimer recognizes and binds damaged DNA.

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17
Q

UvrA

A

UvrA released (ATP-dependent)

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18
Q

UvrC

A

Nicks 10-11 bases around the damage site; ATP-dependent

Incision

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19
Q

UvrD

A

Helicase that unwinds the DNA to release ssDNA strand.

20
Q

Mfd

A

Recognizes a stalled RNA polymerase (transcription) and
directs the repair complexes to the damaged template strand.
Displaces the ternary RNA polymerase from the DNA.
Promotes UvrA/B recruitment.

21
Q

Human excision repair mechanism

A

In eukaryotes, a complex of proteins including XP products and the transcription factor TFIIH.

22
Q

Nucleotide excision repair occurs via 2 major pathways:

A
  1. Global Genome Repair

2. Transcription-coupled Repair

23
Q

Global Genome Repair

A

Recognizes damage anywhere in the genome.

24
Q

Transcription-coupled Repair

A

Preferentially repairs transcriptionally active genes.

25
Q

Shared components of the 2 pathways (Global Genome Repair, Transcription-coupled Repair) include:

A
  • Transcription factor TFIIH
  • XPB and XPD
  • XPF and XPG
  • DNA synthesis
  • Nicks are ligated via DNA ligase II and XRCC1.
26
Q

XPB and XPD

A

Helicase components; exhibit activity to unwind around

the damaged site in Global Genome Repair, Transcription-coupled Repair.

27
Q

XPF

A

5’ exonuclease for incision around the damaged base in Global Genome Repair, Transcription-coupled Repair.

28
Q

XPG

A

3’ exonuclease for incision around the damaged base in Global Genome Repair, Transcription-coupled Repair.

29
Q

DNA ligase II and XRCC1

A

Ligate nicks in Global Genome Repair, Transcription-coupled Repair.

30
Q

Base excision repair

A

Removes the individual damaged base from DNA by excision and then re-synthesis (not “flipping”).
Base removal triggers the removal and replacement of a stretch of polynucleotides.
The nature of the base removal reaction determines which of two pathways for excision repair is activated.

31
Q

Glycosylase

A

Hydrolyzes the bond between base and deoxyribose (using H2O).

32
Q

Lyase

A

Take the reaction further by opening the sugar ring (using NH2).
Attack of the deoxyribose ring recruits the polβ pathway to replace a short stretch.

33
Q

Trigger for mammalian excision-repair pathways

A

Single base removal by glycosylase or lyase action.

34
Q

Examples of enzymes that remove/modify an individual base from DNA by “flipping” the base directly out of the
DNA duplex.

A

Alkyladenine DNA glycosylase for alkylated bases (methylated).
Uracil-DNA glycosylase.
Photolyase for pyrimidine dimers.
Yeast Rad4 - flips 2-A bases complementary to T-dimers.

35
Q

Damaged DNA that has not been repaired

A

Causes DNA polymerase III to stall during replication.

36
Q

Prokaryotes DNA polymerase V and
IV or eukaryotic DNA polymerases Eta
and Zeta

A

Can synthesize a complement to a damaged strand in order to bypass a lesion.

37
Q

Replication polymerase

A

Stalls at the site of damage; is displaced by a trans-lesion polymerase; commences DNA synthesis.

38
Q

MutS

A

Recognizes a mismatch and translocates to a GATC site.
Bound to both the mismatch site and to DNA as it
translocates, and as a result it creates a loop in the DNA.
Endonucleases degrade the strand from the GATC to the mismatch site.

39
Q

MutH

A

Cleaves the un-methylated strand at the GATC.

40
Q

MutS/L systems

A

Initiates repair of mismatches in eukaryotic systems produced by replication slippage. Do not use DNA methylation to select the daughter strand for repair. Not fully understood how eukaryotes recognize the daughter
strand during mismatch repair.

41
Q

Replication fork stalls when it encounters a damaged site/nick in DNA will:

A
  • May reverse by pairing between the two newly synthesized strands.
  • May restart after repairing the damage and use a helicase to move the fork forward.
  • May initiate translesion/excision repair or recombination repair to correct DNA damage.
42
Q

Recombination repair

A

Preferred mechanism for repairing DSB.
Works analogous to Homologous Recombination in Meiotic
cells. Homologous recombination ensures no genetic
information is lost from a broken DNA end.

43
Q

Double-strand breaks

A

One of the most severe types of DNA damage that can occur, particularly in eukaryotes.
Can be caused by ionizing radiation, oxygen radicals generated by cellular metabolism, or action of endonuclease.

44
Q

Ku70 and Ku80

A

Recognize broken ends by Ku70/Ku80 heterodimer and formation of a scaffold.
An unknown DNA polymerase fills in any remaining ssDNA protrusions.

45
Q

DNA-dependent protein kinase (DNA-PK)

A

Activated by DNA to phosphorylate protein targets like

Artemis, which exhibits nuclease activity to trim overhanging ends.

46
Q

What different mechanisms of recognition do global genome repair and transcription-coupled repair use? (XPC vs. RNA polymerase II).

A

Global genome repair - XPC

Transcription coupled repair - RNAP II

47
Q

Glycosylase-mediated APE1 recruitment initiates

A

The polδ/ε pathway to replace a long polynucleotide stretch.

Molecular Biology Test 3 (5 decks)

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