Chapter 11 repair

Question 1

The most direct way to repair DNA lesions is to identify and then reverse the DNA damage, proofreading activity of _______ can fix some errors immediately

Answer 1

DNA polymerase
3’ -> 5’ exonuclease activity

Question 2

Pyrimidine dimers can be directly repaired by _______ in bacteria single-celled euks, plants, and some animals
- but not humans :(

Answer 2

photoreactive repair

Question 3

The enzyme _______ uses energy from visible light to break the bonds between pyrimidine dimers

Answer 3

photolyase

Question 4

What is photolyase encoded by in Ecoli?

Answer 4

phr (photoreactive repair) gene

Question 5

DNA damage by_______ is repaired by enzymes that remove the added chemical groups, restoring the nucleotide to its normal form

Answer 5

alkylating agents

Question 6

Enzymes that repair DNA damaged by alkylating agents are called _______

Answer 6

alkyltransferases

Question 7

Alkyltransferases are permanently _______ after one repair/conversion reaction
ex) O6-methylguaninemethyltransferase

Answer 7

inactivated

Question 8

_______ is a multistep process that may repair damage to a nitrogenous base or replace an incorrect base

Answer 8

Nucleotide base excision repair (BER)

Question 9

What are the steps to base excision repair (BER)? (4)

Answer 9

1) DNA glycosylases recognizes bp mismatch and removes incorrect bp creating an AP site
2) AP endonuclease creates nick on 5’ side
3) Nick translation occurs replacing several nucleotides
4) ligase seals the backbone

Question 10

_______ is often used to repair UV-induced damage to DNA so it is also known as ultraviolet repair

Answer 10

Nucleotide excision repair

Question 11

What are the 4 proteins that are involved in UV-damage repair?

Answer 11

uvrA, uvrB, uvrC, uvrD

Question 12

What are the steps to UV repair? (5)
- also known as NER

Answer 12

1) UVR AB complex bind opposite of photoproduct
2) UVR A disassociates and UVR C binds
3) UVR BC complex cuts 3’ and 5’
4) UVR D helps remove the DNA fragment
5) DNA polymerase and ligase fix the strand

Question 13

UVR D (a _______) helps remove the DNA fragment containing the photoproduct

Answer 13

helicase

Question 14

Xeroderma Pigmentosa is caused by mutations of any of seven different genes involved in _______

Answer 14

NER

Question 15

mismatched nucleotides that escape DNA polymerase proofreading may be detected and repaired by ________

Answer 15

mismatch repair

Question 16

In mismatch repair, repair enzymes distinguish between the original, correct nucleotide and the new, mismatched nucleotide using the presence of _______ on the original strand

Answer 16

methylation

Question 17

What are the 3 proteins specified for mismatch repair?

Answer 17

1) MutH
2) MutS
3) MutL

Question 18

What are the steps to mismatch repair? (7)

Answer 18

1) MutH binds to hemimethylated DNA region
2) MutS binds to DNA mismatch
3) MutL forms complex with MutS and the complex binds to MutH
4) MutH protein breaks phosphodiester bond on 5’ end of unmethylated daughter strand (~GATC)
5) exonuclease enzymes digest nucleotides from the “nick”
6) DNA polymerase and DNA ligase fill in the gap
7) Dam methylase methylates adenine of GATC of daughter strand

Question 19

Biochemical mechanisms to recognize the presence of _______ and initiate a _______ consist of a tightly regulated genetic process

Answer 19

DNA lesions
repair response

Question 20

_______ plays a pivotal role in communicating DNA damage, to activate the transcription of the _______ gene

Answer 20

ATM
p53

Question 21

The p53 repair pathway controls cell responese to mutation by deciding to either: (2)

Answer 21

1) pause the cell cycle (g1-s phase)
2) initiate apoptosis

Question 22

p53 initiates G1 arrest by inducing synthesis of _______ that inhibits formation of cyclin-CDK complexes

Answer 22

p21

Question 23

p53 also activitates transcription of _______ gene, which encodes a slowly acting inhibitor of _______

possible apoptosis

Answer 23

BAX gene
BCL2

Question 24

In damaged cells, if the p53-induced pause of the cell cycle persists too long, the _______ pathway is induced when BCL2 is inhibited

Answer 24

apoptotic

Question 25

The ________ system can be activated in response to heavily damaged DNA in E.coli cells

Answer 25

SOS repair

Question 26

SOS repair is accomplished by activation of translesion or bypass polymerases (_______)

Answer 26

DNA pol V

Question 27

How does SOS repair work? (3)

Answer 27

1) Rec A proteins coat the template strand ahead of the lesion (forms DNA-RecA-SSB-complex)
2) DNA pol V replaces pol III
3) Once normal replication can occur DNA pol III replaces pol V

Question 28

What are the two mechanisms that carry out repair on double-stranded break repair?

Answer 28

1) non-homologous end joining
2) synthesis-dependent strand annealing (HDR)

Question 29

Nonhomologous end joining allows cells to _______ the ability to complete DNA replication, though the process inevitably leads to mutation. When does NHEJ usually take place?

Answer 29

regain
after G1 before DNA replication (S)

Question 30

What is the process of nonhomologous end joining?

Answer 30

1) double stranded break in DNA
2) PKcs, Ku70, and Ku80 complex attach to the broken ends of DNA
3) the complex trims free ends of the break
4) blunt ends ligated by ligase IV

Question 31

what are the 3 proteins that make up the complex in nonhomologous end joining?

Answer 31

1) PKcs
2) Ku70
3) Ku80

Question 32

Double-stranded breaks that occur after replication can be repaired by an error-free process called _______

Answer 32

synthesis-dependent strand annealing

Question 33

synthesis-dependent strand annealing is also known as _______

Answer 33

homology dependent repair (HDR)

Question 34

What are the steps to SDSA? (4)

Answer 34

1) broken edges are trimmed
2) Rad51 is attached to broken ends and intact sister chromatid
3) Strand invasion process creates displacement (D) loop
4) sister chromatids reform and fixed strands are annealed with original fragment