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Molecular Biology > Ch. 8a DNA Replication (Exam 2) > Flashcards

Ch. 8a DNA Replication (Exam 2) Flashcards

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1
Q

What is the formal name for the synthesis of DNA?

A

DNA replication

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2
Q

What is the result of the conservative replication mechanism?

A

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

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3
Q

What is the result of the semi-conservative mechanism?

A

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

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4
Q

What is the result of the dispersive replication mechanism?

A

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

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5
Q

Who confirmed that DNA replication was semi-conservative?

A

Meselson & Stahl

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6
Q

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

A

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

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7
Q

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

A

S

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8
Q

What happens in the G1 phase?

A

Everything expect for DNA is doubled

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9
Q

What phase starts the cell cycle?

A

G1

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10
Q

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

A

1) Damaged DNA
2) Too little growth

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11
Q

Define replicon.

A

Genomic unit in which DNA is replicated

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12
Q

In which phase does the first replicon activate?

A

S

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13
Q

What is the origin of replication?

A

Site in DNA sequence where replication occurs

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14
Q

What structures form at the origin of replication?

A

2 replication forks

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15
Q

Which way does replication occur?

A

Replication is bi-directional

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16
Q

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

A

Eukaryotes have multiple

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17
Q

What is a replication bubble?

A

Bulge in DNA resulting from replication

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18
Q

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

A

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

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19
Q

When do replication bubbles stop growing?

A

When the bubbles join together at the end of replication

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20
Q

When do replication bubbles stop growing?

A

When they join together at the end of replication

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21
Q

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

A

What is OriC?

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22
Q

Why do eukaryotic chromosomes have multiple origins of replication?

A

Eukaryotic chromosomes are huge and take time to replicate

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23
Q

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

A

Relaxed

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24
Q

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

A

Topoisomerase

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25
Q

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

A

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

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26
Q

What topological issues arise in replication?

A

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

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27
Q

What is initiation in terms of replication?

A

The start of replication

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28
Q

Initiation involves recognition of an origin by a…

A

Protein complex

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29
Q

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

A

Separation, strand stabilization, and forming a replication bubbles

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30
Q

What is a replisome?

A

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

31
Q

How does the replisome aid in replication?

A

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

32
Q

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

A

It reassembles at the origin for each replication cycle

33
Q

Can the replisome exist as independent protein units?

A

No

34
Q

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

A

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

35
Q

What is helicase?

A

The enzyme that separates DNA strands using energy from ATP

36
Q

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

A

Single-stranded DNA binding protein

37
Q

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

A

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

38
Q

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

A

1) Helicase
2) Primase
3) DNA polymerase

39
Q

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

A

Semi-conservative

40
Q

What does DNA polymerase do?

A

Synthesizes 5’ - 3’ daughter strands

41
Q

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

A

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

42
Q

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

A

One

43
Q

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

A

DNA polymerase III

44
Q

Which 2 DNA polymerase classes are required for nuclear replication?

A

Delta and epsilon

45
Q

What are holoenzymes?

A

Replication polymerases incorporated into large protein assemblies

46
Q

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

A

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

47
Q

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

A

3’ end

48
Q

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

A

Nuclease

49
Q

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

A

What is phosphodiester?

50
Q

DNA polymerase I uses this enzyme to perform nick translation…

A

5’-3’ nuclease

51
Q

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

A

To remove the RNA primers

52
Q

What are the 2 primary functions of DNA polymerase I?

A

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

53
Q

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

A

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

54
Q

In which direction is DNA synthesized?

A

5’ to 3’

55
Q

In which direction is the DNA template strand?

A

3’ to 5’

56
Q

The leading strand synthesizes…

A

Continuously from 5’ to 3’ toward the replication fork

57
Q

The lagging strand quite literally…

A

Lags

58
Q

Why does the lagging strand lag?

A

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

59
Q

What does it mean for the lagging strand to lag?

A

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

60
Q

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

A

Okazaki fragments

61
Q

What is a primer?

A

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

62
Q

What is RNA primase?

A

A special RNA polymerase that synthesizes primers

63
Q

What enzyme extends the primer?

A

DNA polymerase

64
Q

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

A

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

65
Q

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

A

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

66
Q

What is the function of DNA ligase?

A

To form phosphodiester bonds between Okazaki fragments

67
Q

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

A

Adenosine monophosphate (AMP)

68
Q

What is termination?

A

The completed replication of the parent molecule

69
Q

When does bidirectional replication terminate?

A

When two replication forks meet halfway around the circle

70
Q

What are the sites that cause termination called?

A

Ter sites

71
Q

How does the Meselson-Stahl experiment start?

A

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

72
Q

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

A

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

73
Q

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

A

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

74
Q

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?

A

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

Molecular Biology (21 decks)

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