Chapter 12

Question 1

What is semi-conservative replication?

Answer 1

the DNA double helix unwinds, and each single strand serves as a template for a new DNA strand

Question 2

What is conservative replication?

Answer 2

the original DNA double helix serves as a template for a whole new DNA double helix

Question 3

What is dispersive replication?

Answer 3

the original DNA double helix breaks apart into fragments, and each fragment then serves as a template for a new DNA fragment; each strand after replication is a hybrid of old and new DNA fragments

Question 4

How did Meselson and Stahl show that replication takes place in a semiconservative manner?

Answer 4

They took e. coli were grown in 15N media then transferred to 14N media. The e. coli was then subjected to equilibrium density centrifugation. After the first round of replication, there was an intermediate band, but after the second there was an intermediate band and a light band because it stayed in the light band medium

Question 5

What are the three major requirements for replication?

Answer 5

needs to have a DNA template, need the building blocks (dNTPs), and need enzymes for replication

Question 6

What substrates are used in DNA synthesis reactions?

Answer 6

dNTPs, deoxynucleotide triphosphates

Question 7

What is a replicon?

Answer 7

a segment where replication takes place

Question 8

What is used for primer synthesis?

Answer 8

NTPs/rNTPs

Question 9

What is the replication origin?

Answer 9

the initiation sites on a DNA molecule (there are thousands)

Question 10

What is the replication bubble?

Answer 10

separated complementary strands

Question 11

What is the replication fork?

Answer 11

actual site of DNA replication

Question 12

How does a phosphodiester bond form?

Answer 12

The 3’-OH of the last nucleotide on the new strand (dNMP) attacks the 5’ phosphate group of the incoming dNTP.
A phosphodiester bond forms between the two nucleotides and the phosphate ions are released

Question 13

Describe the difference between dNTPs and dNMPs.

Answer 13

dNTPs - free monomers before they are added to the polymer of DNA
dNMP - the nucleotides that are part of the polymer of DNA

Question 14

How does DNA polymerase add nucleotides?

Answer 14

replication can only move 5’ to 3’ direction and the DNA polymerase adds the monomer nucleotides to only the 3’ prime OH end of the growing strand

Question 15

During DNA replication, DNA polymerase adds:

Answer 15

dNTPs to the 3’ hydroxyl group on the growing strand

Question 16

How do phosphodiester bonds form?

Answer 16

the 3’-OH of the last nucleotide on the new strand(dNMP) attacks the 5’-phosphate group of the incoming NTP and the bond forms between the two as two phosphate ions are released

Question 17

How do the leading and lagging strand work?

Answer 17

the leading strand goes towards the replication fork and the lagging strand goes away from the replication fork

Question 18

What is the direction in linear eukaryotic DNA replication?

Answer 18

two forks at the replication bubble and each fork moves in opposite directions (bidirectional)

Question 19

What is continuous vs discontinuous replication?

Answer 19

continuous is what happens in the leading strand and discontinuous is what happens in the lagigng strand

Question 20

Discontinuous replication is a result of which property of DNA?

Answer 20

antiparallel nucleotide strands

Question 21

How does bacterial DNA replication work?

Answer 21

they have a single origin and a single initiator protein and then DNA helicase unwinds the double helix and single-strand-binding proteins keep the bubble open. There is only one bubble in bacterial

Question 21

What happens during the initiation phase of DNA replication?

Answer 21

the initiator protein unwinds a short stretch of DNA, which allows helicase and other single-strand binding proteins and initiate replication. DNA helicase unwinds the DNA by breaking the hydrogen bonds. DNA gyrase relieves the torsion on the strand

Question 22

What do primers do during elongation?

Answer 22

gives the first DNA nucleotides somewhere to attach - they allow the DNA to get DNA nucleotides attached

Question 23

What are primers?

Answer 23

an existing group of RNA nucleotides with a 3’-OH group to which a new nucleotide can be added

Question 24

Where are primers located?

Answer 24

at the start of each DNA replication

Question 25

What is primase: RNA polymerase?

Answer 25

uses a template to make an RNA copy

Question 26

Why are RNA primers needed?

Answer 26

DNA polymerase can not copy a single strand of DNA unless it has a free 3'OH on the growing replicated strand to which to add new dNTPs. RNA polymerases can add the first NTP to a single strand piece of DNA that is copying

Question 27

What is elongation carried out by?

Answer 27

DNA polymerase III

Question 28

What does DNA polymerase III do?

Answer 28

removes incorrectly paired nucleotides by backing up and taking it out then adds the new nucleotide. It moves 3'-5'

Question 29

What does DNA polymerase I do?

Answer 29

removes RNA primers from the newly copied DNA strand and replaces those primers with DNA nucleotides - moves 5'-3' and puts DNA nucleotides into place and can remove incorrect nucleotides by backing up and replacing them

Question 30

What does DNA ligase do?

Answer 30

catalyzes the formation of a phosphodiester bond along the DNA backbone (seals up the connecting nick after the RNA primer is removed)

Question 31

What are the three steps to getting correct DNA?

Answer 31

nucleotide selection, proofreading, and mismatch repair

Question 32

What do single-strand-binding proteins do?

Answer 32

attach to single-stranded DNA an prevent secondary structures from forming

Question 33

What does DNA polymerase III do?

Answer 33

elongates a new nucleotide from the 3'

Question 34

What does DNA polymerase I do?

Answer 34

removes RNA primers and replaces them with DNA

Question 35

What is the difference between 5’ to 3’ exonuclease activity versus 3’ to 5’ exonuclease activity? What does each do? Which Polymerases have these activities?

Answer 35

5' to 3' exonuclease activity is responsible for removing the RNA nucleotides of the primer and is done by DNA polymerase I. 3' to 5' exonuclease activity is responsible for proofreading activity - removing incorrect nucleotides in a backwards direction. Both DNA polymerase I and III do this activity