Chapter 6

Question 1

Describe the three possible models of DNA replication

Answer 1

Semiconservative (1 old 1 new strand)

Dispersive (mix of old and new)

Conservative (1 old DNA, 1 new DNA)

Question 2

What model of DNA replication did Watson and Crick like?

Answer 2

Semiconservative

Question 3

Describe the experiment used to determine the basic model of DNA replication

Answer 3

Grow bacteria in 15N medium, then grow for 1 generation in 14N medium

Centrifuge to produce bands based on density (light higher in tube)

One generation of growth → One intermediate band → Ruled out conservative

2+ generations → One intermediate and one light strand → Ruled out dispersive

Question 4

What would the results of the experiment to determine the basic model of DNA replication be if the other models were correct?

Answer 4

Conservative would have produced one light and one heavy band for both

Dispersive would have produced an intermediate band for both

Question 5

What are the four enzymes required for the synthesis of lagging strands? What do they each do?

Answer 5

DNA primase, DNA polymerase, nuclease, and ligase

Primase to provide 3* OH

DNA polymerase to add new nucleotides

Nuclease to remove the RNA primer

Ligase to seal nicks by forming phosphodiester bonds via ATP hydrolysis

Question 6

What are RNA primers for? How are they made? How many does each strand type need?

Answer 6

RNA primers are synthesized by primase, a type of DNA polymerase

One primer is required for the leading strand, and one primer is needed for each lagging strand

The primers provide a starting place (3* Hydroxyl) for DNA replication to begin

Question 7

What is the role of the sliding clamp in DNA replication?

Answer 7

Hold RNA polymerases onto DNA

Question 8

What is the role of the DNA helicase in DNA replication?

Answer 8

Unwinds double-stranded DNA with energy from ATP hydrolysis

Question 9

What is the role of the single-stranded binding proteins in DNA replication?

Answer 9

Maintain strand separation

Prevents refolding and regenerating of H-bonds

Question 10

What is the role of topoisomerases in DNA replication?

Answer 10

Relieve tension in front of the replication fork by breaking phosphodiester bonds (also catalyze reformation of that bond)

Question 11

Why are linear chromosomes problematic?

Answer 11

Replication of linear chromosomes would shorten the DNA strands because the final RNA primer in lagging strands cannot be replaced with DNA (no starting point)

Question 12

What are telomeres? What is their purpose?

Answer 12

Telomeres are repetitive G-rich sequences at the end of linear DNA that are heterochromatic and non-coding. They also prevent the ends of the chromosomes from fusing together

Question 13

What does telomerase do?

Answer 13

Telomerase is a protein active in germline and cancer cells that prevents shortening of the telomeres and loss of genetic information by adding an RNA template to the template strand, allowing DNA polymerase to finish the lagging strand

Question 14

Which direction relative to the origin do the leading and lagging strands go? What direction relative to 5/3?

Answer 14

Leading strand goes towards replication fork, lagging strand goes away from replication fork, towards origin (first one is next to the origin, pointing towards it)

Both synthesized 5-3

Question 15

Describe the area where DNA replication begins

Answer 15

DNA replication begins at AT rich replication origins

Contain sequences recognized by initiator/helicase proteins that bind and open up DNA

Question 16

Describe how the number of replication origins affects replication (include prokaryotic, eukaryotic

Answer 16

Bacterial chromosomes only have 1 origin, Eukaryotes have many

more origins, faster replication

Question 17

Describe the two catalytic sites of DNA polymerase and their direction (5/3)

Answer 17

Synthesis goes 5* to 3* (new strand)

Nuclease/Proofreading goes 3* to 5* (compare with template strand)

Question 18

How is DNA proofread?

Answer 18

Recognize mismatched bases by bond angles and repairs by removing newly synthesized DNA strand (identified by nicks), which is replaced by DNA polymerase and ligase.

Question 19

What is correct repair so important?

Answer 19

Unrepaired DNA will produce 50% mutant/nonmutant, repair of template strand will produce 100% mutant

Question 20

Describe the chemical mechanism of DNA synthesis

Answer 20

Polymerase must undergo condensation reactions and add to 3*, where there is no phosphate and the incoming deoxyribonucleoside triphosphate can hydrolyze (cleave phosphoanhydride bond, release pyrophosphate group) to provide energy for polymerization.

Question 21

Give an overview of the direction of DNA synthesis and its effects on evolution

Answer 21

Synthesis must go 5→3 or replication would stop during proofreading when removal of an incorrect base would produce a phosphate on 5* end.