16: DNA repair

Question 1

What is DNA damage?

Answer 1

any unintended physical or chemical change in DNA

Question 2

template for repair?

Answer 2

Complementary strand

Question 3

What is a copying mistake?

Answer 3

DNA polymerase makes an error once every ~107 nucleotides in insertion, deletion, or mismatch

Question 4

What is depurination?

Answer 4

spontaneous loss of A or G base; forms abasic site (sugar and phosphate but no base)

Question 5

if depurination happens before replication? solution?

Answer 5

loss of base in template strand = normal replicative DNA poly stalls, replication stops, –> issue bc cell is committed to cell division

solution: A translesion DNA polymerase skips past abasic site and continues replication bc it is more flexible than normal DNA poly

Question 6

Why can’t we always use translesion DNA?

Answer 6

flexible active site = more mistakes

Question 7

What is deamination?

Answer 7

spontaneous loss of amine in a C and conversion to carbonyl (converts C->U)

Question 8

What are pyrimidine dimers?

Answer 8

UV light catalyses 4 membered ring formation between adjacent pyrimidines (T) (double bond)

blocking DNA rep and requires translesion poly to condition past damage site, but cause mutation in new strand

Question 9

What are some Other base modifications?

Answer 9

• Ionizing radiation (x rays)
• Chemical mutagens

Question 10

What are causes of Breakage of sugar-phosphate backbone?

Answer 10

Ionizing radiation (UV, x-ray)
* Reactive oxygen species
* Mechanical stress (DNA strand separation)

can be:
* Single-strand or double-strand

Question 11

What are DNA repair systems?

Answer 11

1. proofreading during replication by DNA poly
2. mismatch repair: repair replication mistakes shortly after replication
3. direct repair: enzymes specific to particular base
   modifications

Question 12

What is the mismatch repair mechanism In bacteria?

Answer 12

1. bacteria methylates DNA at specific locations on both strands
2. determine new strand by seeing which one is not methylated (this will be the one that gets fixed) - hemi-methylated
3. endonuclease nicks new strand at the methylated site
4. exonuclease cutes from methylated site to site of mismatch – costly!
5. DNY poly 1 and ligase

catches 99% of DNA poly mistakes (3 mistakes/3 billion remain)

Question 13

what is the difference between base excision repair and direct repair?

Answer 13

BER is more general

Question 14

What are the two types of base excision repair?

Answer 14

short patch and long patch (both one damaged base); long patch occurs when something goes wrong in sealing backbone

Question 15

What is the base excision repair short patch mechanism?

Answer 15

1. DNA glycosylase breaks N-glycosidic bond, doesn’t break backbone and only removes base from backbone
2. AP endonuclease breaks backbone (makes a nick at abasic site)
3. DNA poly synthesizes single base (need to remove extra sugar phosphate with nuclease) and DNA ligase

Question 16

What is the base excision repair long patch mechanism?

Answer 16

1. bae removal from glycosylase
2. abasic site made
3. endonuclease nicks backbone
4. DNA polymerase adds a base and extra sugar phosphate is pushed BUT nuclease CANT cut
5. DNA poly adds more bases of DNA that are already there (repeat) and redundant DNA pushes normal DNA out (2-10 bases added)
6. endonuclease removes normal DNA flap
7. nick and endonuclease cut site ligated with DNA ligase

Question 17

What is the Nucleotide excision repair mechanism?

Answer 17

1. damaged nucleotide
2. helicase separates stands at and around site of damage
3. different from BER endonuclease cutes on either site of damage and damaged fragments is released
4. DNA poly and DNA ligase

Question 18

What is Homologous recombination (HR)?

Answer 18

Repair of double-strand breaks
* Slow, but accurate (used in smaller organisms - if another copy of chromosomes in DNA with exact sequence is near right after replication of daughter cells)

Question 19

What is Non-homologous end joining (NHEJ):

Answer 19

Repair of double- strand breaks
* Fast, but inaccurate

Question 20

What is Base excision repair (BER):

Answer 20

Repair of modified bases (deamination), abasic sites, single-strand breaks

Question 21

What is Nucleotide excision repair (NER):

Answer 21

Repair of pyrimidine dimers and damage that
disrupts double helix (+1 base)