Chapter 14 lecture (repair systems)

Question 1

two types of nucleotide excision repair

Answer 1

global genome repair
transcription-coupled repair

Question 2

three types of excision repair

Answer 2

nucleotide
base
mismatch

Question 3

nucleotide excision repair

Answer 3

recognizes bulky lesions in DNA

Question 4

global genome repair

Answer 4

repairs damage everywhere in the genome

Question 5

transcription-coupled repair

Answer 5

repairs damage in the transcribed strand of active genes

Question 6

base excision repair

Answer 6

recognizes damage to individual nitrogenous bases

Question 7

mismatch excision repair

Answer 7

A type of repair that corrects mispaired bases
Usually immediately following replication
Preferentially corrects the sequence of the daughter strand
Distinguishes between the daughter strand and parental strand
Sometimes based on methylation status
Also recognizes insertion and deletion hairpin loops

Question 8

single base changes

Answer 8

Affect the DNA sequence but don’t greatly distort the structure
May occur due to in situ mutations or replication errors
Mismatch persists only until the next replication
Limited time for repair

Question 9

structural distortions

Answer 9

Provide a physical impediment to replication or transcription
Pyrimidine dimers
Alkylation
Nitrogenous base removal

Question 10

repair system recognition

Answer 10

single base changes
structural distortions

Question 11

short patch repair

Answer 11

The Uvr system makes incisions approximately 12 bases apart on both sides of damaged DNA
99% of repair
DNA between the incisions is then removed
Excision
New DNA is synthesized to fill the gap

Question 12

long patch repair

Answer 12

Remaining 1%
1500-9000 nucleotides removed and repaired
Decision mechanism of short- versus long-patch are unknown

Question 13

Base excision repair is triggered by direct removal of

Answer 13

a damaged nitrogenous base from DNA

Question 14

The enzymes that remove bases from DNA are called

Answer 14

glycosylases

Question 15

Glycosylases sometimes also have …. activity that cleaves the ring structure of the deoxyribose sugar

Answer 15

lyase

Question 16

glycosylase action alone

Answer 16

leads to the DNA Pol gamma epsilon pathway that results in the replacement of a long stretch of nucleotides
Long-patch pathway

Question 17

both glycosylase and lyase action

Answer 17

leads to the DNA Pol beta pathway that results in the replacement of a short stretch of nucleotides
Short-patch pathway

Question 18

Damaged DNA that has not been repaired causes

Answer 18

DNA Polymerase III to stall during replication

Question 19

DNA polymerase V or DNA polymerase IV can temporarily

Answer 19

replace polymerase III and synthesize a complement to the damaged strand

Question 20

Error-prone polymerases add

Answer 20

random nucleotides to daughter strand at site of damage

Question 21

error prone synthesis

Answer 21

The DNA synthesized by repair DNA polymerases often have errors in their sequence

Question 22

Methylation and directionality of mismatch

Answer 22

The strand lacking methylation at a Me-A/T is usually replaced in prokaryotes
Repair must be completed before daughter strand is methylated
Methylation status is not used by eukaryotic repair enzymes

Question 23

Nuclease enzymes that resect 5’ ends of broken strands become very active in

Answer 23

S and G2
When sister chromatids are present

Question 24

In G1 phase,

Answer 24

no sister chromatids are present, so recombination repair would use homologous chromosome for repair
Loss of heterozygosity

Question 25

CRISPR

Answer 25

A Cas9 transgene can be transferred into a cell along with a guide RNA that targets a specific DNA sequence in the genome and the gene
Cas9 and guide RNA are usually included together on an expression vector
The Cas9/guide RNA complex binds to the target sequence in the genome and creates a DbSB
DbSB is repaired using recombination repair mechanism
If homologous sequence is present, it will replace the damaged region
Gene editing
Homologous sequence is sometimes introduced into the cell on same vector as Cas9 and guide RNA

Question 26

If the homologous recombination DbSB repair mechanisms cannot find an identical or homologous sequence to use as a template for repair, then the cell will use the

Answer 26

nonhomologous end-joining (NHEJ) pathway

Question 27

nonhomologous end-joining (NHEJ) pathway

Answer 27

Primary pathway used to repair DsDB in mammalian somatic cells
Spend most of their time in G1 when identical or homologous sequence is less available

Question 28

The NHEJ pathway is error-prone and usually results in

Answer 28

errors in the repaired DNA

Question 29

the NHEJ pathway is acceptable in what cells

Answer 29

Acceptable in somatic cells because most of the mammalian genome is not essential for life and can tolerate NHEJ errors

Question 30

NHEJ mechanism

Answer 30

Ku complex binds to ends and bridges them
Initial ends are not completely blunt
Some nucleotides are lost from each strand after breakage
Leads to small, irregular non-complimentary single stranded overhangs
Initial bridging is facilitated by tiny stretches of short (as little as 1 bp) complimentary sequences

Question 31

Insertions and deletions commonly result from

Answer 31

NHEJ

Question 32

Different patterns of histone modification may distinguish different

Answer 32

repair pathways or stages of repair

Question 33

H2AX phosphorylation is a conserved double-strand break-dependent modification that

Answer 33

Recruits chromatin modifying enzymes
Facilitates assembly of repair factors

Question 34

Remodelers and chaperones are required to reset chromatin structure after

Answer 34

completion of repair