Chapter 14 Repair Systems

Question 1

What is mismatch repair (MMR)?

Answer 1

A type of repair that corrects mis-paired bases, typically immediately following replication.
(A process that corrects the sequence of the daughter strand by distinguishing the daughter strand and the parental strand from each other, sometimes on the basis of their states of methylation.)
(Repair systems can be classified into pathways that use different mechanisms to reverse or bypass damage to DNA)

Question 2

What is photoreactivation?

Answer 2

A repair mechanism
(Uses a white light-dependent enzyme to split cyclobutane pyrimidine dimers formed by ultraviolet light.)

Question 3

What is excision repair?

Answer 3

A type of repair system
(In which one strand of DNA is directly excised and them replaced by resynthesis using the complementary strand as template)
Excision repair directly replaces damaged DNA and then resynthesizes a replacement stretch for the damaged strand.

Question 4

What is base excision repair (BER)?

Answer 4

A pathway of excision repair
(Recognizes damage to single bases, such as deaminiation or alkylation, and either repairs the base alone (short patch repair) or replaces 2-10 nucleotides (long patch repair))

Question 5

What is nucleotide excision repair (NER)?

Answer 5

An excision repair pathway
(Recognizes bulky lesions in DNA = such as = UV-induced pyrimidine dimers)
Divided into two subpathways:
TC-NER ———- GG-NER

Question 6

Sub-pathway of NER: (TC-NER) ( Transcription-coupled repair)

Answer 6

Repairs damaged in the transcribed strand of active genes

Question 7

Sub-pathway of NER: (GG-NER) (Global genome repair)

Answer 7

Repairs damage anywhere in the genome

Question 8

Repair system

Answer 8

Recognize DNA sequences that do not conform to standard base pairs

Question 9

Excision system

Answer 9

Remove one strand of DNA at the site of damage and then replace it

Question 10

What does recombination-repair systems do?

Answer 10

Uses recombination to replace the double-stranded region that has been damaged
(*risk= all the systems may introduce errors during the repair process)

Question 11

What is photoreactivation?

Answer 11

Is a non mutagenic repair system that acts specifically on pyrimidine dimers

Question 12

Methytransferase enzymes do what?

Answer 12

Can directly reverse alkylation damage in a suicide reaction.

Question 13

What does dimers block?

Answer 13

Replication and transcription

Question 14

What does ultraviolet irradiation causes what?

Answer 14

Dimer formation ——> between adjacent thymines

Question 15

Step by step of the UVR system

Answer 15

1: Damage structure
2: Incision —> endonuclease cleaves on both sides of damaged base (12 bases apart on both sides of damage DNA)
3: Excision —> exonuclease or helicase removes DNA between nicks (removes the DNA between them)
4: Synthesis —> polymerase synthesizes replacement DNA (resynthesizes new DNA)

Question 16

Figure 14.0.10 UVR system stages: UVRAB ——- UVRBC ——- UVRD

Answer 16

UVRAB: recognizes damage
UVRBC: nicks the DNA
UVRD: unwinds the marked region

Question 17

What is (XP) Xeroderma pigmentosum?

Answer 17

A human disease that’s caused by mutations in any one of several nucleotide excision repair genes
(Affecting numerous proteins, XP products, and the transcription factor (TF2H))

Question 18

Nucleotide excision repair occurs via what two major pathways?

Answer 18

Global genome repair (recognizes damage anywhere in the genome using XPC as its mechanisms of damage recognition)
Transcription-coupled repair (uses RNA polymerase 2 as its mechanisms of damage recognition) (transcriptionally active genes are preferentially repaired via this pathway)

Question 19

What 3 different human diseases are caused by mutations in the XPD component of TF2H?

Answer 19

Xeroderma pigmentosum
Cockayne syndrome (neurodegenerative disease)
Trichothiodystrophy

Question 20

TF2H

Answer 20

Provides the link to a complex of repair enzymes

Question 21

Base excision repair system step by step

Answer 21

1.Base excision: is triggered by directly removing a damaged base from DNA
2. 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)
3. Polo/£ pathway replaces a long polynucleotide
Polo/§ pathway replaces a short stretch

Question 22

Glycosylases recognizes what bases?

Answer 22

Uracil and alkylated bases then are removed directly from DNA

Question 23

What does glycosylases and photolyase do?

Answer 23

Act by flipping the base out of the double helix, where, depending on the reaction, it is either removed or modified and returned to the helix.

Question 24

Glycosylases vs. photolyase

Answer 24

Glycosylase hydrolyzes the bond between base and deoxyribose
Photolyase (lyase) takes the reaction further by opening the sugar ring

Question 25

Base excision repair systems require glycosylases

Answer 25

Picture

Question 26

Terms review

Answer 26

Nucleotide excision repair- UV damaged DNA Transcription coupled repair- RNA polymerase, TF2H Global genome repair- XPC, TF2H Base alone- lyase, Pol§ Base excision repair 2-10 nucleotide Pol/£

Question 27

DNA polymerase V and DNA polymerase IV

Answer 27

Can synthesize a complement to the damaged strand DNA polymerase V = codes for umuCD DNA polymerase IV = codes for dinB

Question 28

Error-prone repair and translesion synthesis

Answer 28

Damaged DNA that has not been repaired causes prokaryotic DNA 3 to stall during replication The DNA synthesized by repair DNA polymerase often has errors in its sequence

Question 29

Mutator

Answer 29

A mutation or a mutated gene that increases the basal level of mutation Such genes often encode proteins that are involved repairing damaged DNA The prokaryotic must genes encode a mismatch repair system that deals with mismatched base pairs