Lecture 30

Question 1

How many hours does a human cell take to divide?

Answer 1

18-24 but intestine can take around 9-10 hours. E coli. can take 20-30 mins.

Question 2

What are the four phases of the cell cycle?

Answer 2

G1, S, G2, M

Question 3

How is DNA copied during replication?

Answer 3

In a semi conservative way and happens during the S phase

Question 4

How does replication happen in E coli.?

Answer 4

It happens in a bidirectional way because the chromosome is circular

Question 5

How does replication happen in bacterias?

Answer 5

In a 5 to 3

Question 6

Where does replication happen in E coli. ?

Answer 6

It happens in the OriC

Question 7

What is true about the replication sites in eukaryotes?

Answer 7

They have multiple sites in each chromosomes(bc linear) and because it is slower process to replicate

Question 8

What is the replication fork strand form?

Answer 8

It is a Y shape

Question 9

What is the role of helicase?

Answer 9

unwinds and separates the 2 DNA strands by breaking the
weak hydrogen bonds

Question 10

What is the single strand binding proteins?

Answer 10

attach and keep the 2 DNA strands separated and untwisted (they stabilize the single strand of DNA)

Question 11

What is topoisomerase?

Answer 11

attaches to the 2 forks of the bubble to relieve stress
on the DNA molecule as it separates

Question 12

What is primase?

Answer 12

the enzyme that synthesizes the RNA Primer

Question 13

What is DNA polymerase?

Answer 13

can only add nucleotides to the 3’ end of the template DNA

Question 14

What is ligase?

Answer 14

joins the Okazaki fragments together to make one strand

Question 15

What functions does DNA polymerase carry out?

Answer 15

specialized functions (Pol I, II and III) and require Mg2+

Question 16

What are the substrates of DNA Pol III?

Answer 16

dATP, dCTP, dGTP and dTTP. These are added during the base portion

Question 17

What does DNA Pol need?

Answer 17

Mg and DNA temp strand

Question 18

What does the 3’ exonuclease do in DNA Pol 1?

Answer 18

It is the proofreading function to make sure DNA temp is copied correctly

Question 19

What is the function of the 5’ exonuclease in DNA Pol 1?

Answer 19

functions both in replication and in DNA repair.

Question 20

What happens when DNA primer binds to the template?

Answer 20

Pol III adds dNTPs and the 3 OH primer forms a phosphodiester with the a-phosphate

Question 21

What happens after the Pol 3/dNTP reaction?

Answer 21

Pyrophosphate and water exit the reaction. Hydrolysis of pyrophosphate drives the reaction

Question 22

What needs to happen during the 3 OH/dNTP/a-phosphate reaction? What needs to happen to the charge?

Answer 22

There needs to be Mg+2 because both the 3 OH and a-phosphate have negative charge. This is what makes it a phosphodiester bond.

Question 23

What does Mg do during the phosphodiester bond?

Answer 23

stabilizes these transition states which then enables the daughter strand to be synthesized in the 5’- 3’ direction

Question 24

How does DNA Pol correct mismatch bases?

Answer 24

The incorrect base pair moves from the polymerase active site to a second enzymatic site on the protein that contains 3’ to 5’ exonuclease activity

Question 25

What initiates DNA synthesis?

Answer 25

It is initiated by RNA primer which is synthesized by primase which is a RNA polymerase that can begin without a primer

Question 26

How does primase begin the DNA replication process?

Answer 26

It begins a synthesizing a short (5-10 base) RNA molecule complementary to the template

Question 27

What is the leading strand?

Answer 27

It is the left hand template and is the easiest to be synthesized

Question 28

What is the lagging strand?

Answer 28

It is the right hand strand and is harder to synthesized because the DNA is opening at the 5' end

Question 29

What does Pol 1 do in prokaryotes?

Answer 29

Synthesis of lagging strand repair(removes RNA primers)

Question 30

What does Pol 2,4,and 5 do in prokaryotes?

Answer 30

Repair under unique conditions

Question 31

What does Pol 3 do in prokaryotes?

Answer 31

primarily responsible for new synthesis

Question 32

How is the lagging strand problem solved?

Answer 32

Primase lays down primers as DNA is unwound. Primase lays down lagging strand primer DNA Pol III synthesizes from primer, DNA Pol I replaces RNA primer with DNA

Question 33

How is the leading strand replicated?

Answer 33

Replicated in the same direction as the fork as one long continuous strand of nascent DNA

Question 34

How is the lagging strand replicated?

Answer 34

Replicated in the opposite direction, and is synthesized discontinuously as Okazaki fragments

Question 35

What does the lagging strand need to do?

Answer 35

All DNA Pol synthesize in the 5 to 3 direction but the lagging strand has to loop around in order to come back through the second pol in the correct direction and have a similar polarity to the leading strand

Question 36

What does Tau do in prokaryotes?

Answer 36

Tau proteins link Pol III subunits to the clamp loader complex and Tau also links helicase to polymerases

Question 37

What is the sliding clamp in DNA Pol 3?

Answer 37

It is a ring clamp that makes sure polymerase it binded to the DNA and copies correctly

Question 38

What is true about the clamp form in prokaryotes?

Answer 38

It is a dimer(B protein) in E coli.

Question 39

What is true about the clamp in eukaryotes?

Answer 39

It is a trimer (PCNA)

Question 40

What is the clamp a part of?

Answer 40

It is a part of the holoenzyme complex

Question 41

What opens the clamp?

Answer 41

The clamp loader protein complex to load it onto DNA

Question 42

Does the sliding clamp need energy?

Answer 42

Yes. It needs ATP binding and hydrolysis to load the clamp

Question 43

What are the subunits in the clamp in e coli.?

Answer 43

gamma, delta, and delta prime

Question 44

What is true about ATP in the clamp?

Answer 44

It increases affinity of the clamp loader for closed sliding clamp. ATP is super active and ADP is inactive.

Question 45

What is the shape of DNA Pol 1?

Answer 45

It is in the form of a hand that only closes on the correct base-pair. It allows the enzyme to hold on to the DNA to repeat catalytic cycle

Question 46

What is the geometric problem?

Answer 46

Where an incorrect nucleotide is polymerized into DNA that inhibits further synthesis due to incorrect structure of the mispaired base

Question 47

What does the proofreading exonuclease do?

Answer 47

Removes the terminal 3’ base, thus restoring the correct geometry of the primer-template junction, which can move back to the polymerase site

Question 48

What replicated leading and lagging strands are in prokaryotes?

Answer 48

Pol 3

Question 49

What is true about the Pol 3 clamp in how it binds? How many times does it bind?

Answer 49

It binds only once in the leading and many times in the lagging for DNA synthesis to begin.

Question 50

What does single-stranded binding do?

Answer 50

It keeps DNA unwound for DNA synthesis.

Question 51

Where does SSB bind?

Answer 51

Near replication for to stabilize single strand

Question 52

What does SSB prevent?

Answer 52

Prevents intramolecular base-pairing and keeps the DNA in an extended conformation with the bases exposed to facilitate synthesis

Question 53

Does helicase use energy?

Answer 53

Yes. Lots of it to unwind DNA helix

Question 54

What is the form of helicases?

Answer 54

It has the form of a hexamer that forms a circle around DNA to keep it bound

Question 55

How does helicase move?

Answer 55

In a one direction in one strand because of polarity

Question 56

How does DNA Pol 1 work in replication?

Answer 56

3 to 5 exo