3 - DNA Damage and Repair

Question 1

What are mobile genetic elements?

Answer 1

viruses

Question 2

What is endonuclease?

Answer 2

cuts between phosphodiester bond | cuts DNA

Question 3

What is glycosylase?

Answer 3

pulls out the bases = separates base from DNA strand

Question 4

What are the 2 DNA repair pathways for excision repairs?

Answer 4

BER (bases) | NER (nucleotides)

Question 5

What is the function of methylation?

Answer 5

deactivates gene | happens on specific sites of DNA

Question 6

What is CpG?

Answer 6

areas in the DNA where Cs and Gs are next to each other

Question 7

Where in the DNA would methylation ONLY occur?

Answer 7

on a C that is next to a G (CpG)

Question 8

How likely is demethylation?

Answer 8

rare

Question 9

Where are CpG islands located?

Answer 9

promoter regions of housekeeping and tissue specific genes

Question 10

What does CpG-island methylation lead to?

Answer 10

inhibits transcription factors from accessing it bc a bunch of proteins jump onto methylated site = silences gene

Question 11

How can CpG methylation lead to cancer?

Answer 11

if the wrong genes are silenced/turned off

Question 12

How can CpG methylation be used as a cancer therapy?

Answer 12

can silence the proto-oncogenes or mutated genes that cause the cell to run wild

Question 13

What is Base Excision Repair (BER)?

Answer 13

removes the damaged base | more active | transcription-coupled repair pathway

Question 14

What is Nucleotide Excision Repair (NER)?

Answer 14

removes a stretch of nucleotides | more specific | can be coupled with transcription

Question 15

What are the enzymes used in BER?

Answer 15

glycosylase, endonuclease, exonuclease, DNA pol beta, ligase

Question 16

What is the function of glycosylase in the “flipping out” mechanism?

Answer 16

flips one of the bases out and clips it = abasic site

Question 17

What is the function of endonuclease in the “flipping out” mechanism?

Answer 17

clips on 5’ or 3’ BUT nicks DNA in ine space

Question 18

Which polymerase fills out the clipped spot from endonuclease in the “flipping out” mechanism?

Answer 18

DNA polymerase beta

Question 19

What is the function of ligase in the “flipping out” mechanism?

Answer 19

fixes by reforming the phosphodiester bonds

Question 20

What are scaffolding genes?

Answer 20

proteins that bring in other proteins involved in the DNA repair

Question 21

What kind of gene are the BRCA1 (breast cancer) genes?

Answer 21

scaffolding genes

Question 22

What does a mutation in the BRCA1 gene indicate?

Answer 22

something going on in the DNA repair mechanisms

Question 23

What does NER fix?

Answer 23

thymine dimers | big adducts causing bulky lesions blocking DNA replication

Question 24

What are the enzymes used in NER?

Answer 24

endonuclease, DNA polymerase, ligase

Question 25

What is the process for NER?

Answer 25

nick, nick between lesion (endonuclease) >>> lift lesion strand out >>> fill (DNA polymerase and ligase)

Question 26

What results from a mutation in a protein involved in the NER pathway?

Answer 26

xeroderma pigmentosum

Question 27

What is xeroderma pigmentosum?

Answer 27

person sensitive/allergic to UV light = can only come out at night = skin cells cannot repair thymine dimers

Question 28

What is the difference between xeroderma pigmentosum variant and classical?

Answer 28

biochemical: classical = defect in early step of NER | variant = defect in translesion bypass

Question 29

What is Trichothiodystrophy?

Answer 29

scaly skin due to dying skin cells from a mutation in one of the parts of the NER mechanism

Question 30

What are the 5 recombinational DNA repair mechanisms?

Answer 30

daughter strand gap repair | homologous recombination (HR) | non-homologous end-joining (NHEJ) | break-induced repair (BIR) | interstrand-crosslinks

Question 31

What brings in the BRCA proteins?

Answer 31

checkpoint proteins

Question 32

What does sporadic mean?

Answer 32

accumulation of mutation throughout our lifetime

Question 33

What would NHEJ repair mechanism be used for?

Answer 33

if chromosome cannot find its partner | not preferable because results in many mismatches

Question 34

In NHEJ repair mechanism, how is it trying to fix a mutation?

Answer 34

cell is looking for 2 areas that are closely complimentary = give it enough H-bonds to stick

Question 35

Why are lesion-replication polymerases error prone to normal DNA?

Answer 35

they have loose specificity