Chapter 5: DNA Replication, Repair, and Recombination

Question 1

What is the error rate of P activity in DNA polymerase?

Answer 1

1 x 10^5

Question 2

What is the error rate of E activity in DNA polymerase?

Answer 2

1 x 10^2

Question 3

What is the combined error rate of total DNA polymerase activity?

Answer 3

1 x 10^7

Question 4

This function occurs at the E site of DNA polymerase; identifies the polymerization of incorrect nucleic acids

Answer 4

exonucleolytic proofreading

Question 5

This process occurs soon after DNA replication and before ligase activity seals the “nicks” of Okazaki fragments

Answer 5

Eukaryotic strand-directed mismatch repair

Question 6

What is the error rate of eukaryotic strand-directed mismatch repair?

Answer 6

1 x 10^3

Question 7

these are a common artifact after DNA synthesis that serve as markers to identify new strands

Answer 7

“nicks”

Question 8

What is the total combined error rate of DNA synthesis/replication?

Answer 8

1 X 10^10 (1 in 10 billion)

Question 9

What are the two challenges of maintaining chromosome ends

Answer 9

1. break/error repairs
2. shortening telomeres with replication

Question 10

What are 3 things done to prevent the breakage-repair of chromosome ends?

Answer 10

1. 5’ end removal (via nuclease)
2. addition of protruding 3’ end (telomere)
3. shelterin protein protection

Question 11

What are the bases of the protruding 3’ repeat sequence added to the ends of chromosomes?

Answer 11

TTAGGG

Question 12

about how many times are the telomere sequences repeated on a chromosome end?

Answer 12

~3000x

Question 13

What are 3 outcomes of telomere shortening?

Answer 13

1. loss of coding DNA
2. triggering of cellular senescence
3. telomerase restoration

Question 14

What is cellular senescence?

Answer 14

the ceasing of cell division; not synonymous with cell death

Question 15

How does telomerase extend the 3’ end of chromosomes?

Answer 15

uses RNA template to complete synthesis of the lagging strand (via DNA pol)

Question 16

This is a method of DNA repair that excises ALL bases to look for errors (via 6 different enzymes)

Answer 16

Base excision repair

Question 17

What are the 5 steps of base excision repair?

Answer 17

1. error base recognition
2. base removal
3. phosphate backbone removal
4. nucleotide replacement (via DNA pol)
5. nick sealing (via ligase)

Question 18

what are the most common DNA errors that are not caught during replication (via endonuclease activity/eukaryotic strand-directed repair)

Answer 18

deaminations

Question 19

This is a method of post-replication DNA repair that removes whole chunks of polynucleotides

Answer 19

nucleotide excision repair

Question 20

When does nucleotide excision repair occur most frequently? why?

Answer 20

during RNA transcription; RNA pol II gets stalled by bulky lesions

Question 21

What is the enzyme used in nucleotide excision repair?

Answer 21

excision nuclease

Question 22

Double-stranded break repair that occurs post-DNA replication is a subtype of what other DNA repair?

Answer 22

HDR (homology-directed repair)

Question 23

What are the only times double-stranded break repair can occur?

Answer 23

during cell division (after DNA replication, before nuclear division)

Question 24

what are the 3 additional methods of DNA repair that usually occur post-DNA replication?

Answer 24

1. base excision repair
2. nucleotide excision repair
3. double-stranded break repair

Question 25

What are the 3 main classes of transposable elements?

Answer 25

1. transposases 2. reverse transcriptase (+integrase) 3. reverse transcriptase (+endonuclease)

Question 26

What are the 3 methods of transposing elements?

Answer 26

1. DNA-only transposons 2. Retroviral-like transposons 3. non-retroviral-like retrotransposons

Question 27

transposase is coded by DNA/RNA to move the transposable elements in which method of transposition?

Answer 27

DNA-only transposition

Question 28

DNA-only transposons are found in which organisms?

Answer 28

bacteria/prokaryotes ONLY

Question 29

What are the 5 steps of DNA-only transposons?

Answer 29

1. coded transposase from DNA/RNA 2. transposase binds to target DNA 3. target DNA is looped + broken 4. target DNA is integrated into a new location 5. donor region is repaired

Question 30

What are the 4 steps of retroviral-like transposition?

Answer 30

1. reverse transcriptase codes DNA from vRNA 2. retrotransposon integrates DNA into new location 3. copies of viral sequence are made 4. protein synth from viral sequence (replication occurs)

Question 31

What are the 4 steps of nonretroviral retrotransposition?

Answer 31

1. L1 RNA sequence synthesizes reverse transcriptase 2. rt protein binds to 5' of L1 + DNA target 3. rt is primed 4. sequence transcribes (+ is integrated into new location)

Question 32

about how many transposable elements are present in the human genome?

Answer 32

~3,000,000

Question 33

LINE elements compose about what percentage of the human genome?

Answer 33

~50%

Question 34

about how many nonretroviral retrotransposons are active in the human genome?

Answer 34

80-100

Question 35

What is the TATA box?