DNA Replication

Question 1

List and explain the proposed mechanisms for DNA replication.

Answer 1

1. Conservative model - both strands of parental duplex remain intact
   • New DNA copies consist of all new molecules
   • No conservation from parental templates
2. Semiconservative model - each daughter duplex consist of one parental strand and one new strand
   • Hybrid molecule of new and old strand
3. Dispersive model - new DNA is dispersed through each strand of both daughter duplexes after replication

Question 2

Describe semi-conservative replication through first and second replication.

Answer 2

First replication: half and half
Second replication: half and half with one with new material

Question 3

Describe dispersive replication through first and second replication.

Answer 3

First replication: new DNA dispersed within daughter strand

Old material keeps shrinking for each generation

Question 4

Explain the methods of the Meselson and Stahl experiment

Question 5

What were the results from Meselson and Stahl’s experiment?

Question 6

DNA synthesis produced a __________ of the template strand

Answer 6

Reverse complement

Question 7

Where does DNA synthesis begin?

Answer 7

Replication origins

Question 8

Replication origin are A-T rich, meaning?

Answer 8

More As and Ts in this region
Easier to break hydrogen bonds

Question 9

How many replication forks form at each replication origin?

Answer 9

2

Question 10

DNA replication in both prokaryotes and eukaryotes is _________.

Answer 10

Bidirectional

Question 11

Why is the rate of replication slower in eukaryotes?

Answer 11

No histones in bacteria (no heterochromatin)

Eukaryotes: levels of compaction that has to be dealt either (e.g., moving histones

Question 12

What does DNA polymerase do?

Answer 12

Synthesizes DNA by adding nucleotides to 3’ end of growing chain

Question 13

DNA (and RNA) is always synthesized in the _______ direction

Answer 13

5’-3’

Question 14

Where does the energy for polymerization by DNA polymerase come from?

Answer 14

Hydrolysis of incoming dNTP

Question 15

What is the by product of using hydrolysis of dNTP as energy?

Answer 15

Pyrophosphate

Question 16

What kind of metabolic process is DNA synthesis? Anabolic or catabolic?

Answer 16

Anabolic

Question 17

T or F: DNA replication is continuous

Answer 17

F: DNA replication is semidiscontinuous

Question 18

What does DNA ligase do?

Answer 18

Join Okazaki fragments together

Question 19

Short Okazaki fragments are formed on the _______

Answer 19

Lagging strand

Question 20

Explain DNA polymerase’s proofreading mechanism

Answer 20

Contains 3’ to 5’ exonuclease activity (removes improperly added dNTP)

Question 21

What is primase and what does it do?

Answer 21

• Type of RNA polymerase
• Puts down temporary RNA primers

Question 22

T or F: DNA polymerase can initiate DNA synthesis without a primer

Answer 22

F: DNA polymerase cannot initiate DNA synthesis without a primer

Question 23

What is the difference between the leasing and lagging strand when it comes to primers?

Answer 23

Leading strand: only requires one primer

Lagging strand: continuously requires new primers to generate new Okazaki fragments

Question 24

What does DNA helicase do?

Answer 24

Pries apart double helix

Question 25

What is the function of single strand binding proteins?

Answer 25

Prevent two strands (on lagging template) from rebinding back together

Question 26

What is the function of the sliding clamp?

Answer 26

Holds DNA polymerase onto DNA strand

Question 27

What is processivity? How does it relate to the sliding clamp and its loader?

Answer 27

Processivity - being able to stay engaged with DNA before it falls off Sliding clamp has high processivity No sliding clamp = DNA polymerase would fall off more often

Question 28

T or F: Clamp loader requires ATP

Answer 28

True

Question 29

What does semicontinuous replication mean? How does replication of the lagging strand differ from the leading strand? How is this coordinated?

Question 30

What are the two ways that torsional strain resulting from DNA unwinding be relieved during replication? What enzyme is involved?

Answer 30

1. DNA supercoiling - temporarily relieves tension 2. DNA topoisomerase - relieves tension long term • Two enzymatic activity: nuclease and ligase

Question 31

1. How does telomerase replicate the ends of eukaryotic chromosomes? 2. Is telomerase required in non dividing cell? Why?

Answer 31

(1) • Repetitive DNA sequences added to telomeres • This is done using its own RNA template 2. Yes

Question 32

Bacteria don’t require telomerase. Why?

Answer 32

Chromosomes are circular (do not require telomeres)

Question 33

Where does DNA replication occur in mitosis?

Answer 33

S phase

Question 34

What is a replication fork?

Answer 34

Y-shaped junction at site where DNA is being replicated

Question 35

What is meant by DNA replication being bidirectional?

Answer 35

Two replication forks move away from replication origin in opposite directions

Question 36

What is DNA polymerase?

Answer 36

Enzyme that catalyzes addition of nucleotides to 3’ end of growing DNA strand

Question 37

What is primase?

Answer 37

Enzyme that synthesizes RNA primers

Question 38

What is the function of the sliding clamp?

Answer 38

Keep DNA polymerase firmly attached to template

Question 39

What is the function of the clamp loader?

Answer 39

Lock sliding clamp around DNA