Lec 4. DNA Replication & Repair

Question 1

Which of the three DNA replication complications are Eukaryote specific problems?

Answer 1

Heterochromatin (histones) and Linear chromosomes

Question 2

What are the three problems encountered during DNA replication?

Answer 2

Heterochromatin (histones), linear chromosomes and incorrect nucleotide added

Question 3

For Higher Fidelity Repairs what repair mechanisms are used?

Answer 3

Base Excision Repair (BER) and Nucleotide Excision Repair(NER)

Question 4

For Lower Fidelity Solutions what repair mechanisms are used?

Answer 4

Translesion Synthesis (TLS) and Nonhomologous End Joining (NHEJ)

Question 5

Why is there a problem with Heterochromatin during DNA replication?

Answer 5

The histones have to be replaced, so theres a mix of new and old histones.

Question 6

What do recycled histones do?

Answer 6

They retain their marks and thus tell the new histones what marks are needed.

Question 7

What does the FACT complex do?

Answer 7

Facilitates chromosome transcription by associating with the CMG helicase to displace histones in front of the replication fork

Question 8

What do chaperone proteins do?

Answer 8

Help histones find their new homes

Question 9

What is ASF1 stand for?

Answer 9

Anti-silencing function protein 1

Question 10

What does ASF1 do?

Answer 10

binds H3-H4 dimers and delivers them to the CAF1 complex

Question 11

What does the CAF1 complex do?

Answer 11

associates with PCNA

Question 12

Besides during replication what other times do histones need to be remodeled?

Answer 12

Repair, transcription and protein turnover

Question 13

Why is linear DNA a problem during DNA replication?

Answer 13

DNA polymerase cant fill in the gaps at the ends of chromosomes

Question 14

What does Telomerase do?

Answer 14

Deals with the linear DNA problem by filling gaps and preventing the shortening of chromosomes

Question 15

How does Telomerase prevent shortening of chromosomes?

Answer 15

Telomerase is a reverse transcriptase, uses RNA to template DNA. The ssDNA end of the chromosome can invade the upstream telomere sequence.

Question 16

Which polymerases have an exonuclease domain?

Answer 16

α, δ, ε

Question 17

What does an exonuclease domain allow?

Answer 17

For proofreading capabilities

Question 18

Which pol is the best proofreader?

Answer 18

δ

Question 19

Which pol is the worst proofreader?

Answer 19

α

Question 20

True or False? Proofreading means that both strands of DNA are synthesized in a discontinous fashion

Answer 20

True

Question 21

What are the proofreading steps?

Answer 21

Sense incorrect shape, Stall replication fork, Move the nucleotide to exonuclease domain, cleave phosphodiester bond, move growing strand back to polymerase domain.

Question 22

What mutations are caused by changes in hydrogen bonding potential?

Answer 22

Unfavored Tautomers and modified nitrogenous bases

Question 23

How are mutations caused by changes in hydrogen bonding potential corrected?

Answer 23

By proofreading and base excision repair

Question 24

What mutations result from error-prone repair of roadblocks?

Answer 24

Depurination, Covalent adducts with chemicals or between nitrogenous bases

Question 25

How are mutations that result from error-prone repair of roadblocks corrected?

Answer 25

Translesion synthesis and nucleotide excision repair

Question 26

How does Base Excision Repair work?

Answer 26

Glycosylases recognize modified nucleotides, nitrogenous base is swung out and clipped off at the glycosidic bond. AP Endonuclease cleaves the phosphodiester bond on either side of the abasic site, single stranded break is created. Pol β or Pol λ add a complementary nucleotide. DNA ligase reforms phosphodiester bonds

Question 27

How does nucleotide excision repair work?

Answer 27

UV repair enzymes recognize distortion of helix, cleaves some nt surrounding the lesion on single strand. TFII is the helicase that unwinds the region to be cleaved. Pol ε ( replicating cells) or Pol δ (quiescent cells) add back to the complementary nucleotides. DNA ligase reforms phosphodiester bonds.

Question 28

How does Translesion Synthesis work?

Answer 28

Translesion polymerases take over DNA synthesis at stalled replication forks, each accommodates a particular structure type, does not remove damage, returns control to regular replicative polymerases once lesion is passed. Inserters pick a base to add, extenders continue synthesis.

Question 29

During Translesion synthesis which are inserters?

Answer 29

Rev1, Pol η, Pol lota

Question 30

During Translesion synthesis which are extenders?

Answer 30

Pol η, Pol ζ

Question 31

During Translesion Synthesis what does Rev1 insert?

Answer 31

Can only insert dC, at abasic sites

Question 32

During Translesion Synthesis what does Pol η insert?

Answer 32

Can insert bases opposite TT dimer (UV rad)

Question 33

During Translesion Synthesis what does Pol lota insert?

Answer 33

Insert bases opposite snyA and 8-oxoG (ROX)

Question 34

How are double stranded breaks repaired?

Answer 34

Nonhomologous End Joining and Homologous Recombination

Question 35

What is Nonhomologous End Joining?

Answer 35

Basically a non-discriminate cut-and-paste event.

Question 36

How does Nonhomologous End Joining work?

Answer 36

Ends must be prepared for ligation. Double stranded break is recognized by Ku heterodimers, Artemis nuclease cuts at ssDNA-dsDNA junction, TdT, Pol μ and Pol λ bridge the gap, DNA ligase IV adds the final phosphodiester bond

Question 37

What does TdT do?

Answer 37

Performs untemplated synthesis