Lecture 20: DNA Replication

Question 1

Who discovered that the specific pairing in DNA suggests a possible copying mechanism for genetic material?

Answer 1

Watson and Crick

Question 1

What results would you expect for the gen 2 sample of the pulse-chase experiment if DNA replication was conservative?

Answer 1

3/4 of the sample would be low density and 1/4 high density

Question 2

What results would you expect for the gen 2 sample of the pulse-chase experiment if DNA replication was dispersive?

Answer 2

100% would be of intermediate density

Question 3

What are the by-products of polymerization using activated nucleotides?

Answer 3

pyrophosphate, H2O and energy

Question 4

What is the function of DNA polymerase?

Answer 4

catalyzes DNA synthesis

Question 5

Does only one type of DNA polymerase exist in organisms?

Answer 5

No, DNA Polymerases are a family of enzymes with specialized functions in DNA synthesis during replication and repair

Question 6

How many types of DNA polymerases exist in E.coli versus in humans?

Answer 6

5 versus a dozen

Question 7

Three properties of DNA polymerization contribute to
fidelity

Answer 7

1. H-bonding between A and T and G and C are stable
   interactions.
2. Active site of DNA polymerase is unlikely to catalyze
   bond formation if mismatched base pair is formed.
3. DNA polymerase can proofread.

Question 8

How does DNA polymerase proofread?

Answer 8

• If the enzyme finds a mismatch, it pauses and removes the mismatched base that was just added.
• DNA polymerase III can do this because its e (epsilon) subunit acts as an exonuclease that removes a mismatched deoxyribonucleotides from DNA.

Question 9

When does DNA replication happen in the cell cycle?

Answer 9

Synthesis phase

Question 10

What makes a DNA
sequence an origin of
replication?

Answer 10

AT-Rich Regions: Origins of replication often have sequences rich in adenine (A) and thymine (T) because A-T base pairs are easier to separate than G-C pairs.

Question 11

How does DNA replication proceed?

Answer 11

Question 12

What is the difference between the number of origins of replication in a bacterial chromosome vs. a eukaryotic chromosome?

Answer 12

Question 13

What are the leading and lagging strands?

Answer 13

leading strand builds a new strand towards the replication fork (5’ to 3’ direction)

lagging strand builds a new strand in the opposite direction as the replication fork (5’ to 3’ direction)

Question 14

What’s the function of helicase?

Answer 14

Question 15

What’s the function of single-strand -DNA-binding proteins?

Answer 15

Question 16

What’s the function of topoisomerase?

Answer 16

Question 17

What’s the function of primase? (leading strand vs lagging strand)

Answer 17

leading strand: catalyzes the synthesis of an RNA primer

lagging strand: catalyzes the synthesis of RNA primer of an okazaki fragment

Question 18

What’s the function of DNA polymerase III? (leading strand vs lagging strand)

Answer 18

leading strand: extends leading strand in the 5’ to 3’ direction

lagging strand: extends okazaki fragements

Question 19

What’s the function of the sliding clamp?

Answer 19

Holds DNA polymerase in place during extension

Question 20

What’s the function of DNA polymerase I? Which strand synthesis needs it?

Answer 20

the lagging strand needs it to remove RNA primers et replace it with DNA

Question 21

What’s the function of DNA ligase? Which strand synthesis needs it?

Answer 21

catalyzes the joining of okazaki fragments together in the lagging strand

makes a continuous strand of new DNA

Question 22

Which three proteins in DNA replication require ATP to function? Which one can use other types of energy?

Answer 22

helicase, topoisomerase and DNA ligase

Question 23

DNA ligase joins the fragments through a covalent bond between nucleotides and closes gap in sugar-phosphate backbone.

What is the name of this covalent bond formed by ligase?

Answer 23

phosphodiester bond

Question 24

What is the replisome

Answer 24