Instability of Human Genome

Question 1

In the reading, what leads to increase frequencies of nucleotide changes?

Answer 1

colorectal pancreatic cancer cells with mutation in MutL gene

Question 2

In the reading, what is the most frequent altered gene in breast & cervical cancer?

Answer 2

• breast -> PIK3CA
• cervical -> STK2

Question 3

What are mutations?

Answer 3

• type of DNA damage
• ex: switching one base out for another
• possibility of distorting helix

Question 4

What are thymine dimers?

Answer 4

• covalent attachment between 2 thymines
• caused by UV light
• target for DNA repair
• ALWAYS distorts helix

Question 5

What is cis configuration?

Answer 5

• causes less disruption in helix
• harder to recognize & fix repair

Question 6

What is trans configuration?

Answer 6

• bigger disruption -> more noticeable to repair
• more severe -> better response

Question 7

What are the sources of DNA damage?

Answer 7

• UV light
• X-rays
• beta-emissions
• gamma-rays

Question 8

What are the repairs involving hydrolysis of phosphodiester bonds?

Answer 8

• NER -> global genome (GGR) and transcription coupled repair (TCR)
• MMR -> MutL & MutS
• RR -> BRCA2, deals with double stranded DNA

Question 9

What are the steps to GGR repair?

Answer 9

1. defect in xeroderma pigmentosa
2. XPC identifies distortions and recruits TF2H -> thymine dimer
3. TF2H, XPA, & RPA open helix
4. XPG hydrolyzes phosp bond
5. XPF hydrolizes second phospho bond
6. gap is filled -> synthesis of leading strand of DNA; PCNA with DNA poly delta

Question 10

What are the steps for TCR repair?

Answer 10

1. RNA poly 2 gets stopped by DNA damage
2. CSB recognizes distortion and recruits CSA
   * coupled with transcription*

Question 11

What are the symptoms of xeroderma pigmentosum?

Answer 11

• severe light sensitivity
• frequent neurological defects

Question 12

What are the steps of mismatch repair?

Answer 12

1. error noticed BEFORE okazaki fragments
2. exonuclease used to access ends
3. MutS recognizes helix distortion and recruits MutL
4. MutL recruit exonuclease to go back on okazaki fragments
5. DNA poly delta, PCNA, & ligase resynthesize

Question 13

What is MMR a defect in?

Answer 13

nonpolyposis colorectal cancer

Question 14

What syndrome does MLH1 cause?

Answer 14

lynch syndrome -> version of nonpolypoptosis

Question 15

What is the difference between MMR and NER?

Answer 15

• MMR -> bp errors during replication
• NER -> DNA damage like thymine dimers

Question 16

What are the subunits of MutS?

Answer 16

MSH2 & MSH6

Question 17

What is a subunit of MutL?

Answer 17

MLH1 -> defective in HNPCC

Question 18

What 2 things stimulate strand invasion and form the triple helix?

Answer 18

BRCA2 & RAD51

Question 19

From the case, what is a leading cause of death in blacks?

Answer 19

colorectal cancer

Question 20

In the colorectal article, what types of sequencing were used?

Answer 20

exome & illumina

Question 21

From the case, what polypeptides constitue MutS & MutL?

Answer 21

• MutS = MSH2 & MSH6
• MutL = MLH1 & PMS2

Question 22

From the case, what is the significance of a mutation in MLH1 that could interfere with a MLH1-EX01?

Answer 22

Could not mismatch repair error and can lead to cancer (bc w/ mutation can’t cut ends to repair)

Question 23

From the case, what other MMR proteins might not interact with mutated forms of MLH1? Which proteins would you test?

Answer 23

Exonuclease, DNA polymerase delta, PCNA, Ligase