dna replication and structure

Question 1

What were the possible modes of DNA replication?

Answer 1

conservative - original helix is conserved and new one is made
semi conservative - each replicated dna molecule is made of one old strand and one new strand
dispersive - parental strands are dispersed into two new double helices

Question 2

What did messelson and Stalh do?

Answer 2

used 15N E. coli grown in medium containing 14N

Starts off as 15N/15N, cells replicate once to form 15N/14N, then a second time to form 15/14 and 14/14, showing semiconservative replication

Question 3

What did Taylor Woods-Hughes do?

Answer 3

used broad bean to show semiconservative replication in eukaryotes

At metaphase II, reciprocal regions of both chromatids were labeled

Question 4

What is the replication fork?

Answer 4

Created by unwound helix where replication is occurring, there are two since replication is bidirectional

Question 5

What is a replicon?

Answer 5

length of DNA that is replicated following one initiation event at a single origin

Entire bacterial chromosome only contains one

Question 6

What does dna polymerase require to start DNA synthesis?

Answer 6

DNA template, deoxyribonucleoside triphosphate, free 3’OH to extend

Question 7

How is 3’OH group exposed?

Answer 7

When nucleotide is added, two terminal phosphates are cleaved off

Question 8

Compare the three DNA polymerases

Answer 8

Only DNA polymerase 1 demonstrates 5’ to 3’ exonuclease activity, excising primers and filling in gaps left behind

All three elongate primers but can’t initiate DNA synthesis

All three have 3’ to 5’ exonuclease activity allowing them to proofread newly synthesized DNA and remove and replace incorrect nucleotides

Question 9

What does DNA polymerase III do?

Answer 9

DNA polymerase III is the enzyme responsible for the 5’ to 3’ polymerization essential in vivo

ONLY synthesized 5’ to 3’

Question 10

What is a holoenzyme and what does it consist of?

Answer 10

Active form of DNA pol III, contains core enzyme complexes

Question 11

What are the core subunits of DNAPIII and their function?

Answer 11

alpha - 5’-3’ polymerization

E - 3’-5’ exonuclease

0 - core assembly

y complex - loads enzyme on template

B- Sliding clamp structure

T- dimerizes core complex

Question 12

What is dnaA?

Answer 12

binds to origin of replication causes helix to destabilize and open up

Question 13

What is DNA helicase?

Answer 13

Made of DnaB polypeptides

Subsequently recruits holoenzyme to bind replication fork and initiate replication

Question 14

What is DNA gyrase?

Answer 14

a type of DNA topoisomerase that relieves tension from unwinding of helix

makes single or double stranded cuts

Question 15

What is RNA Polymerase?

Answer 15

recruited to replication fork by helicase, synthesizes RNA primer and provides free 3’OH end required by DNAPIII for elongation

Question 16

What does DNA polymerase I do?

Answer 16

Removes primer on lagging strand and replaces it with DNA

Question 17

What are Okazaki fragments and DNA ligase?

Answer 17

OF - manner in which lagging strand is synthesized with RNA primer

DNA ligase - catalyzes formation of phosphodiester bonds, seals nicks and joins fragments

Question 18

What is the function of the DNA clamp?

Answer 18

prevents core enzyme dissociation from template

Question 19

Compare Eukaryotic and Prokaryotic DNA

Answer 19

Both double stranded DNA unwound at replication origins

both have replication forks and bidirectional synthesis creating leading/lagging strands,
both require DNTPs, template and primer

Eukaryotic: There is more eukaryotic DNA, DNA is complexed with proteins, chromosomes are linear, multiple origins of replication

Eukaryotic DNA replication is more complex

Question 20

What is the prereplication complex and origin recognition complex?

Answer 20

prereplication complex - assembles replication origins

origin recognition complex -tags origin at site of initiation

Question 21

What do alpha, epsilon, and delta DNA do?

Answer 21

Pol alpha, epsilon and delta are involved in initiation and elongation

pol a - rna primer synthesis

delta synthesizes lagging

epsilon synthesizes leading

Pol A has low processivity so pol E and d replace it for elongation

Question 22

What is chromatin?

Answer 22

Eukaryotic D N A complexed with binding proteins (chromatin)

Question 23

What is the problem with the lagging strand and telomeres?

Answer 23

When the RNA primer is removed, there is no free 3’ hydroxyl group from which to elongate, so telomeres, which preserve integrity of chromosomes, erode.

Telomerase directs synthesis of telomere repeat sequence through reverse transcription.