DNA replication

Question 1

replication fork

Answer 1

“growing fork” - site of active DNA synthesis (helix unwound creates a fork)

Question 2

leading strand

Answer 2

continuous synthesis in direction of replication fork opening (5’–> 3’)

Question 3

lagging strand

Answer 3

discontinuous synthesis in direction opposite of replicaiton fork, Okazaki fragments

Question 4

semi-conservative DNA replication

Answer 4

each new double strand of DNA has a parent and a daughter strand (one old and one new)

Question 5

origin of replication

Answer 5

starting site for replication on the chormosome, replication occurs bidirectionally

Question 6

DNA Ligase

Answer 6

1. joins fragments together in lagging strand (any gap between a 5’ end and a 3’ end) 2. can only join DNA to DNA, not RNA to DNA or RNA to RNA

Question 7

reverse transcriptase

Answer 7

enzyme that creates DNA from an RNA template, requires template, primer, and nucleosides, no exonuclease activity makes it error prone (Telomerase and retroviruses)

Question 8

okazaki fragments

Answer 8

series of discontinuous framents synthesized from multiple primers on laggin strand (still primase and DNA Polymemrase at work - 5’ –> 3’)

Question 9

3 Steps for DNA replication initiation

Answer 9

1. single-stranded DNA 2. RNA primer (DNA polymerases cannot start synthesis w/o a template) 3. deoxynucleotides

Question 10

Differences of Mitochondrial DNA Replication (3)

Answer 10

1. circular DNA (no telomeres) 2. replication form is unidirectional (no okazaki fragments) 3. not cell cycle regulated (can have lots of different genomes and multiple mitochondria)

Question 11

Differences of Eukaryotic DNA replication (5)

Answer 11

1. many origins of replication 2. Replication is regulated by the cell cycle 3. Mitochondrial DNA replication 4. Telomeres bc chromosomes are linear 5. Chromatin/organization is different

Question 12

What are the Watson-Crick nucloetide base pairings?

Answer 12

A–T, C—G

Question 13

What is the structure or DNA

Answer 13

antiparallel double stranded helix

Question 14

What is the most prevelant non-covalent bond in DNA secondary structure?

Answer 14

Hydrogen bonding between base pairs (A-T has 2, C-G has 3)

Question 15

What is the direction of DNA synthesis?

Answer 15

5’–>3’ for the new strand

Question 16

Which end are bases added to in a growing polynucleotide chain?

Answer 16

3’

Question 17

4 Steps of initiation of DNA replication in Prokaryotes

Answer 17

1. DNAA binds origin or replication and uses ATP to part the strands 2. 2 Helicases (DNAB) bind each single strand and continue to unwind using ATP 3. single stranded binding proteins (ssb) stabilize single strands 4. Primase (RNA polymerase) synthesizes primer for DNA polymerase

Question 18

Is DNA Polymerase processive?

Answer 18

Yes. It is able to stay attached and carry out multiple rounds of nucleotide addition and not fall off thanks to Beta clamp subunit (on lagging strand, clamp goes on and off to move DNA Pol up)

Question 19

Explain the DNA Polymerase “dimer.”

Answer 19

DNA Polymerase on the lagging strand is linked to the DNA Pol on the leading strand by a protein , this helps for coordinated synthesid of both strands

Question 20

DNA Polymerase 3

Answer 20

fastest rate (30,000 nucleotides/min), polymerizes 5’->3’, exonuclease 3’->5’

Question 21

DNA Polymerase 1

Answer 21

slower rate (600 nu/min), polymerizes 5’->3’, exonuclease 5’->3’ and 3’->5’ (removes RNA primers on lagging strand and replaces it with DNA)

Question 22

Topoisomerase

Answer 22

enzyme to untagle DNA, nicks one strand and passes the other through it and reseals it

Question 23

Error rate of DNA polymerases

Answer 23

1 in 100,000 bases

Question 24

How can DNA polymerase correct errors?

Answer 24

DNA polymerase has 2 active sites (synthesis and exonuclease), it can exonuclease back a few bases and resynthesize that area

Question 25

Telomere

Answer 25

repeat of simple sequences at the 3’ ends of chromosomes, few thousand pairs, non-coding, form a protein bound loop to protect ends, added by Telomerase

Question 26

telomerase

Answer 26

enzyme containing an RNA template to add repeats to 3’ end of lagging strand, TERT (protein) and TERC (RNA) components, not active in cells that have reached their terminal state