DNA Replication

Question 1

What are the four steps of DNA synthesis?

Answer 1

1. Initiation
2. Priming
3. Synthesis
4. Termination

Question 2

How many initiation sites are there in prokaryotes?

Answer 2

1

Question 3

Is prokaryotic synthesis unidirectional or bidirectional?

Answer 3

bidirectional

Question 4

Why are AT rich repeats important for initiation?

Answer 4

They are less stable than native DNA and can open to form the replication bubble

Question 5

What MUST come before DNA polymerase?

Answer 5

RNA primase!!

Question 6

In what direction is DNA made?

Answer 6

5’ to 3’

Question 7

What is the function of DNA pol III?

Answer 7

Replicative chain elongation

Question 8

What is the function of DNA pol I?

Answer 8

Primer excision (nick translation) and DNA repair

Question 9

Does DNA pol I or III have higher processivity?

Answer 9

Pol III

Question 10

What does the beta subunit of Pol III do?

Answer 10

A sliding clamp that encircles DNA and holds the polymerase onto the DNA

Question 11

What does the alpha subunit of Pol III do?

Answer 11

Polymerize DNA

Question 12

What does the epsilon “ε” subunit of Pol III do?

Answer 12

Proof reading/ 3’ to 5’ exonuclease

Question 13

How many Pol III complexes will you have?

Answer 13

2! One at each replication fork

Question 14

On the leading strand DNA is synthesized in the _____ direction as the replication fork and on the lagging strand DNA is synthesized in the _______ direction as the rep fork.

Answer 14

Leading = same

Lagging = opposite

Question 15

Single strand binding proteins protect open DNA on the _____ strand.

Answer 15

Lagging

Question 16

What does the gamma complex do in DNA Pol III?

Answer 16

It loads the beta subunit clamp

Question 17

How are RNA primers removed from the lagging strand?

Answer 17

DNA Polymerase I in a process called Nick Translation

Question 18

How does Nick Translation work?

Answer 18

DNA Pol I uses 5’ to 3’ exonuclease activity to hydrolyze primers and simultaneously the 3’ end of the Okazaki fragment is extended by incorporation of dNTPs. The nick is then sealed by DNA ligase

Question 19

What enzyme joins all the okazaki fragments?

Answer 19

DNA ligase

Question 20

What is the final step of e. coli DNA synthesis?

Answer 20

Type II topoisomerase separates interlinking strands of the replicated circles and refolds the DNA into supercoils

Question 21

What does DNA polymerase alpha do in eukaryotic DNA?

Answer 21

Makes the RNA primer at both leading and lagging strand

Question 22

Rnase H is defective in Aicardi-Goutieres syndrome. What is Rnase H responsible for?

Answer 22

Removal of RNA primer during eukaryotic DNA replication

Question 23

What is the diagnostic feature of Aircardi-Goutieres syndrome?

Answer 23

INF alpha in CSF

Question 24

What is the electrostatic charge of the inside of the inside of the Pol III B-subunit?

Answer 24

Negative–has a low affinity for DNA and keeps from sticking

Question 25

What is the origin of replication called in prokaryotes and eukaryotes?

Answer 25

OriC | ARS--autonomous replicating sequences

Question 26

What binds the origin of replication and initiates replication in prokaryotes and eukaryotes?

Answer 26

dnaA complex | ORC--origin of replication complex

Question 27

What helicase is used in prokaryote and eukaryote DNA replication?

Answer 27

dnaB/dnaC complex | MCM--minichromosome maintenance proteins

Question 28

What stabilizes single stranded DNA in prokaryotes and eukaryotes?

Answer 28

SSB's | RPA--replication protein A

Question 29

What increases the processivity DNA replication?

Answer 29

B-subunit of Pol III | PCNA-proliferating cell nuclear antigen--of DNA Pol delta 𝛿

Question 30

What serves as the clamp loader in DNA replication in prokaryotes and eukaryotes?

Answer 30

γ gamma subunit | RFC-replication factor C

Question 31

What makes the RNA primer in prokaryotes and eukaryotes?

Answer 31

dnaG | DNA Pol α alpha

Question 32

What removes the RNA primers in prokaryotes and eukaryotes?

Answer 32

DNA Pol I (nick translation) | Rnase H and FEN1 (flap endonuclease)

Question 33

What eukaryotic polymerase is responsible for synthesizing DNA on the leading strand?

Answer 33

DNA Pol ε epsilon

Question 34

What eukaryotic polymerase is responsible for synthesizing DNA on the lagging strand?

Answer 34

DNA Pol δ delta

Question 35

What eukaryotic polymerase is responsible for synthesizing mitochondrial DNA?

Answer 35

DNA Pol γ gamma

Question 36

What are the two components of telomerase?

Answer 36

hTERT--protein component--reverse transcriptase | hTR--RNA component--serves as template

Question 37

What type of structure stabilizes the binding of telomere-binding proteins?

Answer 37

D-loop-T-loop

Question 38

What is the difference between exonucleases and endonucleases?

Answer 38

Exo--cleave at the end of polynucleotide chain | End--cleave in the middle of polynucleotide chain

Question 39

Describe the structure of DNA polymerase III

Answer 39

Consists of a core enzyme (theta, sigma, alpha, beta, tau) and a gamma-complex clamp loader