RR2

Question 1

True or False? “DNA remains the same throughout time”

Answer 1

False. It’s constantly changing (deamination, oxidation, methylation, hydrolytic depurination, etc.)

Question 2

What’s a mutagen?

Answer 2

Chemical compounds or UV and ionizing radiations that increase mutation risks.

Question 3

What’s a mutation?

Answer 3

Permanent, transmissible changes to the genetic material. Can occur spontaneously, by transposable elements or by replication errors.

Question 4

What’s a carcinogen?

Answer 4

Cancer causing agent (often a mutagen).

Question 5

True or False? “DNA polymerases are error-proof”

Answer 5

False. They have a 1/10 000 mistake rate.

Question 6

Do cells have mechanisms to protect itself against DNA replication errors?

Answer 6

Yes. Proofreading exonuclease (decreases to 1/1 000 000) and mismatch repair (1/1 000 000 000).

Question 7

True or False? “All polymerases can proofread”

Answer 7

False. For example, eukaryotes only have pol epsilon and delta that can proofread (alpha can’t).

Question 8

Describe the MMR process

Answer 8

MSH2 and MSH6 bind to newly synthesized strand. // Leads to MLH1 endonuclease binding (comes with PMS2). // Helicase unwinds DNA and exonuclease digests daughter strand. // The gap is repaired by pol delta and ligase.

Question 9

Describe the BER process

Answer 9

A specific DNA glycosylase hydrolyzes the bond between wrong base and backbone // APE1 cuts the backbone // Pol beta (AP lyase) removes dNP and fills the gap // Ligase seals the nicks.

Question 10

What’s the main difference between MMR and BER?

Answer 10

MMR recognizes distortions and removes chunks of newly synthesized strands. BER only recognizes a specific faulty base.

Question 11

Give an example for a mistake picked up by BER

Answer 11

Cytosine can spontaneously deaminate into uracil. If methylated, it turns into thymine which BER recognizes as wrong.

Question 12

Describe the NER process

Answer 12

23B/XP-C complex recognize the lesion // TFIIH catalyzes unwinding of the surroundings // RPA and XP-G help out during the unwinding // XP-F and XP-G have endonuclease activities (cut the lesion) // polymerase and ligase fill the gap.

Question 13

When does NER come into play?

Answer 13

When dealing with bulky damages such as T-T dimer formation.

Question 14

What’s the difference between endonuclease and exonuclease?

Answer 14

Endonucleases cut the middle of a DNA strand along with its backbone while exonuclease usually cuts a single dNTP at the end of the strand.

Question 15

What’s a difference between BER and NER?

Answer 15

The surroundings come off during NER so it’s not as localized.

Question 16

What’s the danger of single and double-strand breaks?

Answer 16

There’s a chance for NHEJ which is a “repair” type that leads to genomic rearrangements and translocations.

Question 17

True or False? “Single strand breaks are more common than double strand breaks”

Answer 17

True

Question 18

True or False? “Single strand breaks can turn into double strand ones during replication”

Answer 18

True

Question 19

Describe the HR process

Answer 19

After or at replication // Ends are digested by 5’-exonucleases, leaving ss 3’-ends // RecA or Rad51 finds homologous chromosome in nucleus // 3’-ends are extended by Pol // 5’ ends are ligated and form Holiday structures // Holiday structures are resolved

Question 20

Describe the NHEJ process

Answer 20

Before replication // DNA-PK/Ku80/Ku70 complex binds to ends // Nucleases digest ends // Ends are ligated

Question 21

What’s the point of double strand breaks?

Answer 21

Generate genetic variability (if cut and ligated a certain way)