Chapter 2 Molecular Mechanism of DNA damage and Repair

Question 1

Name 2 single ringed pyrimidines and 2 double ringed purines?
Name complement base pairs?

Answer 1

Thymine and Cytosine
Adenine and Guanine

Adenine_=Thymine
Guanine=Cytosine

Question 2

Number of DNA lesions per cell detected immediately after X-ray D0 dose(between 1-2Gy) in mammalian cells?
Base ?
SSBs ?
DSBs ?

Answer 2

1000
1000
40

Question 3

Define D0?

Answer 3

Dose of radiation that induce average of one lethal event per cell that leaves 37% still viable.

Question 4

Define DSBs?

Answer 4

Break in two strands are opposite one another or separated by only few base pairs.

Question 5

Diameter, energy and number of ion pairs in Spur and Blobs?

How much is the diameter of DNA double helix?

Answer 5

Spur 4nm/ 100eV / 3 ion pairs
Blobs 7nm / 100-500eV / 12 ion pairs

2nm

Question 6

In X-rays and gamma rays, 95% of energy deposition event takes place in which form?

In densely ionizing radiations, Neutron and alpha-particles, greater proportion of energy deposition event takes place in which form?

Answer 6

Spur

Blobs

Question 7

Clustered lesion could spread out up to how many base pairs?

Answer 7

20 base pairs

Question 8

Which method is most widely used to measure DNA strand breaks?

Answer 8

Pulsed-Field Gel Electrophoresis(PFGE)

Question 9

What does PGFE detect?

Answer 9

Induction and repair of DNA DSBs

Question 10

What is advantageous of Single-cell Electrophoresis(Comet assay)?

Answer 10

Biopsy specimen from tumors in which a relatively small number of cells can be assayed to determine DNA damage and repair.

Question 11

What does comet assay detect?

Answer 11

High sensitivity and specificity for SSBs and alkaline sensitive sites
Lesser degree to DNA DSBs

Question 12

Name 6 assayed proteins for foci formation in DNA damage-induced nuclear foci assay(radiation-induced foci assay)

Answer 12

H2AX - most common 
53BP1 - most common
ATM(Ataxia telangiectasia mutated)
RPA(Replication Protein A)
RDA51
BRCA1

Question 13

Name enzymes used in following steps of Base Excision Repair

1. Removal of sugar residue?
2. Replacement with correct nucleotide?
3. Completed by?

Answer 13

1. Apurinic endonuclease 1(APE1)
2. DNA polymerase
3. DNA ligase III - XRCC1(X-ray cross complementing factor 1 gene)mediated ligation

Question 14

Name enzymes used in repair of more than one nucleotide in Base Excision Repair

1. Removal of sugar residue?
2. Repair synthesis?
3. Removal of overhanging flap structure?
4. Completed by?

Answer 14

1. APE1
2. Complex of replication factor C(RFC)/proliferating cell nuclear antigen(PCNA)/DNA polymerase
3. Flap endonuclease 1 (FEN 1)
4. DNA ligase I

Question 15

Name 2 pathways of nucleotide excision repair?

Answer 15

Global Genome Repair(GGR or GG-NER)

Transcription-Coupled Repair(TCR or TC-NER)

Question 16

How does GG-NER and TC-NER differ in mechanism of NER?

Answer 16

Differs at initial damage recognition step

Question 17

How does GGR recognize lesion?

Answer 17

Through XPC-XPE complex
XPC xeroderma pigmentosum complementation group C
XPE xeroderma pigmentosum complementation group E

Question 18

How does TCR recognize lesion?

Answer 18

NER proteins are recruited by the stalled RNA polymerase in cooperation with CSB and CSA
CSB Cockayne Syndrome B gene
CBA Cockayne Syndrome A gene

Question 19

Name 5 essential steps in pathway of NER?

Answer 19

1. Damage recognition
2. DNA incisions that bracket lesion, usually between 24-32 nucleotides in length
3. Removal of region containing the adducts
4. Repair synthesis to fill in the gap region
5. DNA ligation

Question 20

Name the enzyme that incise DNA lesion in NER?

Germline mutations in NER gene lead to which human DNA repair deficiency disorder?

Answer 20

XPG and XPF-ERCC1 endonuclease
XPG/XPF Xeroderma Pigmentosum complementation group G/F
ERCC1 Excision Repair Cross Complementation group 1 gene

Xeroderma Pigmentosum

Question 21

Name the enzyme that fills gap at incised region in NER?

Answer 21

Polymerase aided by RFC and PCNA
RFC Replication Factor C
PCNA Proliferating Cell Nuclear Antigen

Question 22

Name 2 types of DNA double strand break repair

Answer 22

Homologous Recombination Repair(HRR)

Non Homologous End-Joining(NHEJ)

Question 23

HRR occurs in which phase of cell cycle and why?

Answer 23

Late S/G2 phase

Because undamaged sister chromatid is available to act as template (before mitosis)

Question 24

NHEJ occurs in which phase of the cell cycle?

Answer 24

G1 phase

It has been found to be active in late S and G2 phase of cell cycle, is yet to identify cause!

Question 25

Which is prone to error in between HRR and NHEJ?

Answer 25

NHEJ, accounts for many premutagenic lesions

Question 26

Name protein kinase which act as sensor in immediate response of cell to DNA DSB?

Answer 26

APR(ATM and Rad3-related) belongs to PIKK(Phosphotidylinositol-3-Kinase related Kinase) family

Question 27

Name the protein that regulates competition for repair by HRR vs NHEJ?

Answer 27

53BP-1

Question 28

Describe 5 essential steps of NHEJ?

Answer 28

1. End recognition by Ku binding 2. Recruitment of DNA dependent protein kinase catalytic subunit (DNA-PKcs) 3. End processing 4. Fill-in-synthesis or end bridging(DNA Polymerase) 5. Ligation(Ligase 4)

Question 29

Name key protein in HRR which mediates invasion of homologous strand of sister chromatid leading to formation of Holliday junction?

Answer 29

RAD51

Question 30

Name the combination repair pathways needed to repair DNA crosslinks

Answer 30

NER and HRR

Question 31

Name the disease hypersensitive to crosslinking agent?

Answer 31

Fanconi Anemia

Question 32

Describe 4 essential steps of Mismatch Repair?

Answer 32

1. Mismatch identified by sensor 2. MMR factors recruited 3. Newly synthesized strand harboring mismatch identified and incorrect/altered nucleotides are excised 4. Resynthesis and ligation of excised DNA tract completed

Question 33

Name the cancer due to mutation in mismatch repair genes?

Answer 33

HNPCC(Hereditary Nonpolyposis Colon Cancer)

Question 34

Enumerate essential features in Interphase of cell cycle

Answer 34

Largest phase of cell cycle Quantity of DNA in nucleus doubles Presence of nuclear membrane Presence of nucleoli

Question 35

Enumerate essential features of prophase in cell cycle

Answer 35

Thickening of chromatin and increased stainability of chromosome Chromosome has centromere Nuclear membrane disappears Nucleoli disappears

Question 36

Enumerate essential features of Metaphase in cell cycle

Answer 36

Chromosome move to cells equator Spindles appears Centromere divides

Question 37

Enumerate essential features of Anaphase in cell cycle

Answer 37

Movement of chromosome towards the pole

Question 38

Enumerate essential features of Telophase in cell cycle

Answer 38

Chromosome at poles begins to uncoil Nuclear membrane reappears Nucleoli reappears

Question 39

Define the role of telomere

Answer 39

It cap and protect the terminal ends of chromosome

Question 40

What comprise of base repeats in mammalian telomere?

Answer 40

TTAGGG in 1.5 to 150 kilobases

Question 41

After how many cell divisions does telomeric DNA is lost to undergo senescence?

Answer 41

40-60 cell divisions

Question 42

In hypothesis,Immortalization and carcinogenesis are associated with expression of what enzyme?

Answer 42

Telomerase

Question 43

What are 2 classes of radiation induced aberrations seen in metaphase?

Answer 43

Chromosome aberration | Chromatid aberration

Question 44

Chromosome aberration occurs in what phase of cell cycle?

Answer 44

Early in interphase before chromosome material has been duplicated

Question 45

Chromatid aberration occurs in which phase of cell cycle?

Answer 45

Later in interphase after DNA material has doubled and chromosome consists of two strands of chromatin

Question 46

Name 3 lethal and 2 non-lethal examples of radiation induced aberration

Answer 46

Dicentric(grossly distorted chromosome with 2 centromere) Ring Anaphase bridge Symmetric translocation Small interstitial deletion

Question 47

Ring aberration and Anaplastic bridge falls under which class of radiation induced aberration?

Answer 47

Ring - Chromosome aberration | Anaplastic - Chromatid aberration

Question 48

Symmetric translocation is observed in which technique of preparation?

Answer 48

FISH or chromosomal painting

Question 49

Name disease associated with symmetric translocation

Answer 49

Burkitt lymphoma | Leukemia

Question 50

What is widely used biomarkers of radiation exposure?

Answer 50

Chromosome aberration in peripheral lymphocyte

Question 51

Give an example of unstable aberration that decline with time after irradiation

Answer 51

Dicentric aberration

Question 52

Give an example of stable aberration that persist for many years and pass on aberration to their progeny

Answer 52

Symmetric translocation

Question 53

Two strands of DNA are joined by which bond?

Answer 53

Hydrogen bond