Test 3_DNA Damage and Repair

Question 1

Spontaneous Lesion

Answer 1

1. consist of depurination or deamination reactions

Question 2

Depurination

Answer 2

Hydrolysis of a purine to release nucleic acid and a purine

Question 3

Deamination

Answer 3

conversion of cytosine into uracil.

Question 4

Bulky Lesions

Answer 4

1. covalent linkages formed by reactive oxygen, sunlight, or carcinogens.
2. bond forms between adjacent nucleotides

Question 5

Copy Errors.

Answer 5

Occurs when DNA polymerase introduces the improper base

Question 6

Mutagens

Answer 6

a physical or chemical agent that alters the structure or sequence of DNA

Question 7

Base analog

Answer 7

1. chemical mutagen.

2. Resembles purine/pyrimidines and is incorporated into DNA during replication

Question 8

Intercalating Agents

Answer 8

1. chemical mutagen
2. inserts into doube helix and causes stretching on one side, leading DNA pol to add more nuecleotides to the other strand

Question 9

Direct acting Agents

Answer 9

1. chemical mutagen
2. chemically reacts with DNA
   (base analogs/intercalating agents???)

Question 10

Indirect Acting Agents

Answer 10

1. chemical mutagen

2. requires metabolic conversino by P-450 to actively alter DNA.

Question 11

UV Radiation

Answer 11

1. physical mutagen
2. changes energy level or electrons, allowing it to act irradically.

short wavelength=higher energy=more damage

Question 12

UV-A radiation

Answer 12

1. 320-400nm

2. cause ds breaks and oxidation

Question 13

UV-B Radiation

Answer 13

1. 280-320nm

2. forms pyrimidine dimers

Question 14

UV-C Radiation

Answer 14

1. 180-290nm

2. germicidal and ozone filters out the majority of it.

Question 15

Rank the UV-A,B,C in order from highest to lowest energy.

Answer 15

C > B > A in terms of energy.

energy and wavelength are inversely related.

Question 16

Rank the UV radiation from highest to lowest in terms of frequency.

Answer 16

A > B > C

Question 17

What is ionizing radiation?

Answer 17

1.loss of an electron creating an unstable radical.

Question 18

What are the types and subtypes of ionizing radiation?

Answer 18

1. electromagnetic (x-ray, gamma ray)

2. particulate ( decay of radioactive material)

Question 19

Where do beta particles come from?

Answer 19

1. ionizing radiation

2. these are high speed energy electrons from a decaying particle

Question 20

What are alpha particles?

Answer 20

1. ionizing radiation chemical

2. helium nuclei from a decaying particle.

Question 21

What types of damage are common with ionizing radiation?

Answer 21

1. cross-linking
2. ss/ds breaks
3. base damage

Question 22

DNA repair

Answer 22

correction of accidental lesions made in DNA during replication or sustained from the environment

Question 23

Types of DNA repair?

Answer 23

can repair the damaged bases or repair the bases that were incorrectly paired during replication.

Question 24

Base excision repair is used when?

Answer 24

for small, spontaneous lesions

Question 25

What is the process of Base excision repair?

Answer 25

1. 6+ DNA glycosylases look for damaged bases by "flipping out" 2. base is removed by base-sugar cleavage. 3. AP endonucleases locate missing base, remove phosphodiester backbone. 4. DNA pol adds correct nucleotide. 5. DNA ligase seals the nick.

Question 26

When is nucleotide excision repair used?

Answer 26

to repair large sections of DNA bulky lesions

Question 27

What is the process of Nucleotide excision repair?

Answer 27

1. multienzyme complex scans ds, and cleaves backbone on both sides of mutation. 2. DNA helicase required to remove damaged section 3. DNA polymerase adds nucleotide sequence. 4. DNA ligase seals nick.

Question 28

When is mismatch repair used?

Answer 28

This is a method AFTER dna replication, to resolve the errors of DNA pol.

Question 29

What is the process of mismatch repair?

Answer 29

1. MutS and MutL bind the improper base, and control excision of DNA between the ss break and the mismatched sequence.

Question 30

What is the role of MutS?

Answer 30

recognizes and binds to mispaired nucleotides and allows further action of MutL

Question 31

What is the role of MutL?

Answer 31

eliminate a portion of newly synthesized DNA strand containing the mispaired base

Question 32

What methods are used for replicative repair?

Answer 32

1. proofreading (3'-->5') | 2. back-up polymerase

Question 33

What is the role of back-up polymerases?

Answer 33

1. DNA polymerase stalls when DNA is too severely damaged to replicate. 2. release of back-up polymerase provides terrible accuracy of repairing DNA. 3. DNA is repaired so transcription can still occur.

Question 34

Why can back-up polymerases be used if they have such poor accuracy with repairing DNA BEFORE it is transcribed?

Answer 34

1. the DNA contains large cast regions of introns that do not code for specific proteins, therefore it is assumed these mutations will take time before a coding region is actually affected.

Question 35

What is post-replicative repair?

Answer 35

1. transcription-coupled repair | 2. double strand break repair.

Question 36

What is transcription coupled repair?

Answer 36

1. RNA pol 2 stalls on template DNA strand pulling "TCR machinery" to site 2. RNA is remodeled. 3. The lesion is repaired 4. RNA pol restarts active transcription of genes

Question 37

What makes up "TCR machinery"?

Answer 37

1. CSB: locates stalled RNA; recruits TFIIH 2. TFIIH: remodels RNA Pol 3. XPG: cuts the DNA

Question 38

What causes ds breaks?

Answer 38

1. radiation 2. errors 3. oxidation

Question 39

How are ds breaks fixed using nonhomologous end joining?

Answer 39

1. Ku70/80 locates free ds ends, and pull them together. 2. DNA-PK acts like kinase to activate the DNA ligase * *very inaccurate due to loss of nucleotide sequences but is fast and most commonly used in mammalian**

Question 40

How are ds breaks fixed using homologous recombination?

Answer 40

1. Rad51 pairs and guides the 3' overhanging ss to homologue on sister chromatid. 2. Homologue template allows DNA synthesis to occur 3. leads to formation of Holliday Junction. 4. Junction is cleaved and 2 strands of DNA produced. * *high accuracy, more energy required**

Question 41

What is a Holliday Junction?

Answer 41

1. the results of 2 ds DNA strands that are interwoven to form a 4-way intersection. 2. Essentially 4 ds arms of DNA that join together.

Question 42

What are the DNA damage checkpoints?

Answer 42

1. G1 to S phase 2. Middle of S phase (error of synthesis/replication) 3. S to M phases

Question 43

What is the ATM protein?

Answer 43

1. kinase released with DNA damage that phosphorylates specific kinases to promote cell cycle arrest.

Question 44

When would you expect to see the highest amounts of ATM protein?

Answer 44

1. G1 to S phase 2. during S pahse 3. S to M phase.

Question 45

What does ATM protein target specifically?

Answer 45

1. p53

Question 46

What happens if p53 is phosphorylated?

Answer 46

1. will ditch the Mdm2. | 2. stimulate p21 xcription

Question 47

What is the role of p21, after it has been activated by p53?

Answer 47

1. bind to G1/S Ckd or S-Cdks to inhibit them; prevent cell cycle progression. 2. technically CKI=p21

Question 48

What is the role of Chk1 and Chk2 in the ATM/DNA damage pathway?

Answer 48

1. block the activation of M-Cdk | 2. transmit the signal from ATM/ATR protein to the p53 protein

Question 49

What happens if p53 is not phosphorylated?

Answer 49

1. it remains bound to Mdm2 and will be targeted for ubiquitination. 2. this will occur when there is no DNA damage in the cell, allowing cell cycle to occur

Question 50

What event in a normal, healthy individual will lead to p53 activation to promote cell cycle arrest and therefore apoptosis?

Answer 50

1. telomere shortening.