DNA Replication

Question 1

Three fundamental rules of DNA replication

Answer 1

1) DNA replication is semi-conservative
2) Replication begins at an origin and proceeds bidirectionally
3) DNA synthesis proceeds in a 5’-> 3’ direction and is semidiscontinuous

Question 2

Which drug can target viral DNA polymerases specifically, such as in herpes simplex, whose structure resembles a guanine attached to an incomplete ribose ring

Answer 2

Acyclovir

Question 3

What sort of sequences are good as origins of replication and why?

Answer 3

AT base pair rich sequences because they only form two bonds and therefore are easier to melt into ssDNA.

Question 4

True or false: DNA replication is only bidirectional in prokaryotes

Answer 4

False

Question 5

Protein which forces DNA strands apart to create origin of replication

Answer 5

DnaA

Question 6

Enzyme which couples energy from ATP cleavage to produce a conformational change in DnaA, thus forcing the strands apart

Answer 6

AAA+ ATPase

Question 7

Creates phosphodiester bonds to seal nicks in the DNA strand

Answer 7

DNA Ligase

Question 8

Enzyme responsible for strand elongation, requiring ssDNA template and an RNA primer

Answer 8

DNA Polymerase

Question 9

Unwind DNA double strands in helix

Answer 9

Helicase

Question 10

Responsible for sythesizing RNA complementary to the template DNA strand to start DNA synthesis

Answer 10

Primase

Question 11

Enzymes which adjust the supercoiling of DNA double helices

Answer 11

topoisomerase

Question 12

Type I Topoisomerase

Answer 12

cleave one of the strands of the double helix

Question 13

Type II Topoisomerase

Answer 13

cleave both strands to perform its function

Question 14

binds to the single-stranded portion of each
DNA strand, preventing the strands from reannealing and protecting them from degradation
by nucleases

Answer 14

Single-stranded DNA binding protein (SSB)

Question 15

What do we call the Type II topoisomerase which alleviates positive supercoiling imposed by strand unwinding

Answer 15

DNA gyrase

Question 16

Three aspects of genome fidelity

Answer 16

1) geometry of the active site of DNA Polymerase (purine-pyrimidine pairing)
2) Proofreading (3’->5’ exonuclease activity)
3) mismatch repair and DNA methylation

Question 17

How does DNA methylation factor into mismatch repair?

Answer 17

Methylation marks the parent strand so repair functions know which side to fix

Question 18

Three prokaryotic DNA Polymerases involved just in DNA repair

Answer 18

DNA Polymerase II, IV, and V

Question 19

Prokaryotic DNA polymerase involved in DNA repair and also removes RNA primers during replication

Answer 19

DNA Polymerase I

Question 20

Prokaryotic DNA polymerase responsible for synthesizing most of the DNA during replication. High proccessivity

Answer 20

DNA Polymerase III

Question 21

Which prokaryotic DNA Pol(s) have 5’->3’ exonuclease activity?

Answer 21

DNA Polymerase I

Question 22

Which prokaryotic DNA Pol(s) have 3’->5’ exonuclease activity?

Answer 22

DNA Polymerase I and III

Question 23

3 major causes of mtDNA depletion

Answer 23

1) Issues with mitochondrial fusion / fission
2) Availability (rather lack) of nucleotides
3) Presence of machinery to replicate

Question 24

A given cell contains multiple types of mitochondrial DNA, with varying levels of each from one cell to the next.

Answer 24

heteroplasmy

Question 25

Mitochondrial DNA Maintenance Defects affect which three groups the most?

Answer 25

1) children
2) those treated for HIV-1 and hepatitis B virus infections
3) young adults

Question 26

Why do MDMDs exhibit autosomal inheritance patterns?

Answer 26

Most mitochondrial proteins are nuclear-encoded and all known mutations occur there.

Question 27

Eukaryotic DNA Polymerase containing primase and initiating DNA synthesis

Answer 27

Pol alpha

Question 28

Eukaryotic DNA Polymerase whose function is repair

Answer 28

Pol beta

Question 29

Eukaryotic DNA Polymerase responsible for replicating mtDNA

Answer 29

Pol gamma

Question 30

Eukaryotic DNA Polymerase thought to elongate Okazaki fragments of the lagging strand

Answer 30

Pol delta

Question 31

Eukaryotic DNA Polymerase thought to elongate the leading strand

Answer 31

Pol epsilon

Question 32

Which eukaryotic DNA polymerases have 3’ -> 5’ exonuclease/proofreading activity

Answer 32

Polymerase gamma, delta, and epsilon

Question 33

Are eukaryotic origins of replication specific or non-specific?

Answer 33

Non-specific. They’re just AT rich and occurs ~30-300 kbp

Question 34

Which is faster: eukaryotic or prokaryotic DNA synthesis?

Answer 34

prokaryotic

Question 35

What type of enzyme is telomerase a special type of?

Answer 35

Reverse Transcriptase