Ch. 8a DNA Replication (Exam 2)

Question 1

What is the formal name for the synthesis of DNA?

Answer 1

DNA replication

Question 2

What is the result of the conservative replication mechanism?

Answer 2

One DNA molecule w/ 2 OG strands and another w/ completely new DNA

Question 3

What is the result of the semi-conservative mechanism?

Answer 3

Two molecules each w/ one OG strand and one new strand

Question 4

What is the result of the dispersive replication mechanism?

Answer 4

Two DNA molecules w/ a patchwork of OG and new DNA

Question 5

Who confirmed that DNA replication was semi-conservative?

Answer 5

Meselson & Stahl

Question 6

How did Meselson & Stahl determine that DNA replication was semi-conservative?

Answer 6

They set up an experiment using N-15 (heavy) & N-14 (light) isotopes

Question 7

In which phase of the cell cycle does replication take place for eukaryotes?

Answer 7

S

Question 8

What happens in the G1 phase?

Answer 8

Everything expect for DNA is doubled

Question 9

What phase starts the cell cycle?

Answer 9

G1

Question 10

For what 2 reasons is there a checkpoint between the G1 and S phases?

Answer 10

1) Damaged DNA
2) Too little growth

Question 11

Define replicon.

Answer 11

Genomic unit in which DNA is replicated

Question 12

In which phase does the first replicon activate?

Answer 12

S

Question 13

What is the origin of replication?

Answer 13

Site in DNA sequence where replication occurs

Question 14

What structures form at the origin of replication?

Answer 14

2 replication forks

Question 15

Which way does replication occur?

Answer 15

Replication is bi-directional

Question 16

How do eukaryotic chromosomes differ from prokaryotic ones with respect to their origins of replication?

Answer 16

Eukaryotes have multiple

Question 17

What is a replication bubble?

Answer 17

Bulge in DNA resulting from replication

Question 18

Generally describe the formation of replication bubbles in two steps starting with the formation of the replication forks.

Answer 18

1) Replication forks form at both sides of replication origin
2) Bubbles form along molecule as it replicates in opposite directions.

Question 19

When do replication bubbles stop growing?

Answer 19

When the bubbles join together at the end of replication

Question 20

When do replication bubbles stop growing?

Answer 20

When they join together at the end of replication

Question 21

Bi-directional replication of the circular bacterial chromosome begins at this single origin of replication.

Answer 21

What is OriC?

Question 22

Why do eukaryotic chromosomes have multiple origins of replication?

Answer 22

Eukaryotic chromosomes are huge and take time to replicate

Question 23

In order for the initiation of replication to occur, does DNA need to be supercoiled or relaxed?

Answer 23

Relaxed

Question 24

What general enzyme is responsible for the alteration of chromosomal structure?

Answer 24

Topoisomerase

Question 25

How do DNA topoisomerases solve the topological issues associated with replication?

Answer 25

They introduce temporary single- or double-stranded breaks in DNA

Question 26

What topological issues arise in replication?

Answer 26

DNA is being unwound, which messes with its structure and ultimately its various functions (recombination, transcription, etc.)

Question 27

What is initiation in terms of replication?

Answer 27

The start of replication

Question 28

Initiation involves recognition of an origin by a...

Answer 28

Protein complex

Question 29

What 3 things must happen to the parental strands before replication occurs?

Answer 29

Separation, strand stabilization, and forming a replication bubbles

Question 30

What is a replisome?

Answer 30

Protein complex associated with the structure of DNA at the replication fork

Question 31

How does the replisome aid in replication?

Answer 31

The replisome moves along the DNA, unwinding it and synthesizing daughter strands

Question 32

What is meant by the term "de novo" when referring to the replisome?

Answer 32

It reassembles at the origin for each replication cycle

Question 33

Can the replisome exist as independent protein units?

Answer 33

No

Question 34

Why does the replisome have to assemble at the origin of each replication cycle?

Answer 34

All parts of the protein complex have to work together to function

Question 35

What is helicase?

Answer 35

The enzyme that separates DNA strands using energy from ATP

Question 36

What protein is responsible for maintaining the integrity of separated DNA strands?

Answer 36

Single-stranded DNA binding protein

Question 37

What does single-stranded DNA binding protein do to help the DNA polymerases?

Answer 37

It binds to the single strands very well to allow the DNA polymerases to bind to their substrate

Question 38

What are three key enzymes that you'll find in a replisome?

Answer 38

1) Helicase 2) Primase 3) DNA polymerase

Question 39

To reiterate, DNA replication as we know it is... (HINT: replication mechanism)

Answer 39

Semi-conservative

Question 40

What does DNA polymerase do?

Answer 40

Synthesizes 5' - 3' daughter strands

Question 41

What synthetic activity do all prokaryotic and eukaryotic DNA polymerases share?

Answer 41

Antiparallel synthesis from 5' to 3' from a 3' to 5' template

Question 42

Although there are many DNA polymerases, there is only { } replication enzyme.

Answer 42

One

Question 43

Which DNA polymerase is the replication polymerase responsible for de novo synthesis of new DNA strands?

Answer 43

DNA polymerase III

Question 44

Which 2 DNA polymerase classes are required for nuclear replication?

Answer 44

Delta and epsilon

Question 45

What are holoenzymes?

Answer 45

Replication polymerases incorporated into large protein assemblies

Question 46

If the DNA-synthesizing subunit is only one of several functions of the holoenzyme, what functions do other subunits serve?

Answer 46

Making sure that template replication is accurate e.g. proofreading

Question 47

Which end of the parental strand does DNA polymerase add nucleotides to?

Answer 47

3' end

Question 48

DNA polymerase has both polymerase (synthesis) and { } activity (HINT: the blank refers to its enzymatic, degradative properties).

Answer 48

Nuclease

Question 49

Nuclease has the ability to break this type of bond between nucleotides...

Answer 49

What is phosphodiester?

Question 50

DNA polymerase I uses this enzyme to perform nick translation...

Answer 50

5'-3' nuclease

Question 51

What is the function of 5'-3' exonuclease?

Answer 51

To remove the RNA primers

Question 52

What are the 2 primary functions of DNA polymerase I?

Answer 52

Repair damaged DNA and remove RNA primers, replacing them with DNA

Question 53

What is the function of 3'-5' exonuclease?

Answer 53

To remove incorrectly paired bases at the 3' end, effectively proofreading

Question 54

In which direction is DNA synthesized?

Answer 54

5' to 3'

Question 55

In which direction is the DNA template strand?

Answer 55

3' to 5'

Question 56

The leading strand synthesizes...

Answer 56

Continuously from 5' to 3' toward the replication fork

Question 57

The lagging strand quite literally...

Answer 57

Lags

Question 58

Why does the lagging strand lag?

Answer 58

DNA is antiparallel, and there is only one free 3' end in synthesis, but it is already occupied with synthesizing the leading strand

Question 59

What does it mean for the lagging strand to lag?

Answer 59

This strand is synthesized away from the replication fork, so it is synthesized in fragments

Question 60

What is the official name for the fragments created by the lagging strand?

Answer 60

Okazaki fragments

Question 61

What is a primer?

Answer 61

A short nucleic acid (RNA) sequence with an open 3' OH end that serves as the starting point for DNA synthesis

Question 62

What is RNA primase?

Answer 62

A special RNA polymerase that synthesizes primers

Question 63

What enzyme extends the primer?

Answer 63

DNA polymerase

Question 64

In terms of the initiation of priming activity, how does the lagging strand differ from the leading strand?

Answer 64

The leading strand only requires one initiation event to get its primers going while the lagging strand requires multiple initiation events

Question 65

Why does the lagging strand require multiple initiation events for its priming activity?

Answer 65

The Okazaki fragments require the primer activity to start and restart (de novo) for each strand

Question 66

What is the function of DNA ligase?

Answer 66

To form phosphodiester bonds between Okazaki fragments

Question 67

What intermediate molecule works alongside DNA ligase in forming the phosphodiester bonds?

Answer 67

Adenosine monophosphate (AMP)

Question 68

What is termination?

Answer 68

The completed replication of the parent molecule

Question 69

When does bidirectional replication terminate?

Answer 69

When two replication forks meet halfway around the circle

Question 70

What are the sites that cause termination called?

Answer 70

Ter sites

Question 71

How does the Meselson-Stahl experiment start?

Answer 71

The N-15 (heavy) isotope is used to label the parental DNA molecule, so it is now a duplex of "heavy" strands

Question 72

After the N-15 isotope labels the parental DNA molecule, what happens next in the Meselson-Stahl experiment?

Answer 72

The molecule spends a generation in the N-14 (light) isotope

Question 73

What is the result of the parental DNA molecule (N-15-labeled) growing a generation in the N-14 isotope?

Answer 73

The parental molecule spawns a hybrid consisting of one N-14 strand and one N-15 strand

Question 74

In the Meselson-Stahl experiment, the N-14, 15 hybrid strand is cultivated in more N-14 isotope for another generation of replication. What is the result?

Answer 74

Semi-conservative replication such that the N-14 strand is paired with another N-14 strand, and the N-15 strand is paired with an N-14 as well