05a: DNA Replication

Question 1

T/F: DNA replication is the most accurate biological process.

Answer 1

True

Question 2

DNA replication uses (non-activated/activated) substrates, (X).

Answer 2

Activated;

X = dNTPs

Question 3

4 steps for DNA replication. In what order do they occur?

Answer 3

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

All occur simultaneously

Question 4

Bacterial DNA has (X) shape and how many start sites for replication?

Answer 4

X = circular

One start site (oriC)

Question 5

OriC is recognized by:

Answer 5

DnaA (initiator protein)

Question 6

Prok:

Initiator protein, (X), combines with (Y) and interacts with DNA in what way?

Answer 6

X = DnaA

Y = Histone-like proteins (and ATP)

Tight association with DNA, so bends it

Question 7

Why does replication bubble form?

Answer 7

DnaA bends DNA and AT-rich repeats near OriC open to form bubble

Question 8

Prok:

DnaB is called (X) and forms complex with (Y), which helps it bind the DNA.

Answer 8

X = helicase

Y = DnaC

Question 9

Prok:

When does DnaA displace from DNA?

Answer 9

Once helicase binds

Question 10

Prok:

(X) bind(s) DNA, preventing its coiling, once primase, aka (Y), binds.

Answer 10

X = SSBs

Y = DnaG

Question 11

T/F: in bacteria, binding of each DNA replication protein to DNA requires ATP.

Answer 11

True

Question 12

Which DNA polymerase initiates strand synthesis in bacteria?

Answer 12

None! No DNA pol can initiate new strand synthesis

Question 13

RNA primer is created in which direction? About how long is it?

Answer 13

5’ to 3’ direction;

5-10 NT

Question 14

There are (X) number of prokaryotic DNA polymerases. Which ones are critically mainly for panicked cell?

Answer 14

X = 5

DNA polymerase 2, 4, 5

Question 15

DNA polymerase I is known for:

Answer 15

Primer excision (and some repair) in prokaryotes

Question 16

DNA polymerase 3 is known for:

Answer 16

Replication chain elongation (and some repair) in prokaryotes

Question 17

List activities of DNA pol 1.

Answer 17

(Prokaryotes)

1. Polymerase
2. 3’ exonuclease (repair)
3. 5’ exonuclease (primer excision)

Question 18

What does a polymerase’s processivity signify?

Answer 18

Number of NT it can add before dissociating from DNA

Question 19

Which prokaryotic DNA polymerase has the greatest processivity?

Answer 19

DNA pol 3

Question 20

Replication bubble has how many DNA polymerase 3?

Answer 20

2 (one at each end of fork)

Question 21

Which subunit on DNA pol 3 is responsible for proof reading? What’s its specific function?

Answer 21

Epsilon (3’ exonuclease)

Question 22

Which subunit on DNA pol 3 is responsible for primer excision? What’s its specific function?

Answer 22

DNA pol 3 doesn’t remove primer - DNA pol 1 does that (5’ exonuclease)

Question 23

How many different subunits does DNA pol 3 have?

Answer 23

10

Question 24

Which subunit on DNA pol 3 is responsible for replicating strands?

Answer 24

Polymerase (alpha subunits)

Question 25

T/F: in DNA pol 3, the clamp loader is separate from the core enzyme.

Answer 25

True

Question 26

Which subunit on DNA pol 3 is the sliding clamp?

Answer 26

Beta subunit

Question 27

Which subunit on DNA pol 3 is the clamp loader?

Answer 27

Gamma complex

Question 28

DNA pol 3 replicates (leading/lagging) strand first.

Answer 28

Neither - replicates both strands simultaneously

Question 29

The sliding clamp for DNA pol 3 has inner diameter of (X) and mainly (negative/positive/neutral) AA on inside.

Answer 29

X = 3.5 nm Negative

Question 30

How can DNA pol 3 detect mismatched bases and correct itself?

Answer 30

Defects change in DNA structure

Question 31

In bacteria, where is the termination site, wrt OriC?

Answer 31

180 degrees from it

Question 32

Nick translation, carried out by (X), removes how many (Y) at a time?

Answer 32

X = DNA pol 1 Y = RNA primer 1 at a time

Question 33

T/F: Nick translation requires ATP.

Answer 33

False - DNA pol 1 uses water (hydrolysis) for 5' exonuclease

Question 34

The nick after primer removal is sealed by:

Answer 34

DNA ligase

Question 35

What's the final step in bacterial termination of DNA synthesis?

Answer 35

Type 2 topoisomerase separates the two interlinking strands of replicated circles and refolds DNA into supercoils

Question 36

DNA pol gamma is responsible for:

Answer 36

Eukaryotic DNA replication in mitochondrion

Question 37

Eukaryotic equivalent to beta subunit on prokaryotic DNA pol (X).

Answer 37

X = 3 Beta subunit is clamp; PCNA in euk

Question 38

DNA pol epsilon is responsible for:

Answer 38

Eukaryotic DNA synthesis of leading strand

Question 39

DNA pol delta is responsible for:

Answer 39

Eukaryotic DNA synthesis of lagging strand

Question 40

Primer removal in eukaryotes is carried out by:

Answer 40

Rnase H and Fen1

Question 41

Helicase in eukaryotes is called:

Answer 41

MCM

Question 42

Origin of replication in euk is called:

Answer 42

ARC (autonomous replicating sequences)

Question 43

T/F: Topoisomerase II requires ATP for its function.

Answer 43

True

Question 44

What makes DNA Pol (X) better suited for primer excision than DNA Pol (Y)?

Answer 44

``` X = 1 Y = 3 ``` Low processivity

Question 45

T/F: Type II Topoisomerase only adds negative supercoils.

Answer 45

False