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MCBM Exam 5 Kat > DNA Replication > Flashcards

DNA Replication Flashcards

0
Q

Who proposed that DNAs structure allowed it to be replicated?

A

Watson and Crick

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1
Q

Define semi conservative replication.

A

Each newly replication DNA helix consists of one strand from the parent helix and one newly synthesized daughter strand.

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2
Q

What does the structure of DNA account for?

A

Storage and transmission of genetic material.

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3
Q

What did Meselson and Stahl prove in 1957?

A

They proved that DNA replication is semiconservative.

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4
Q

What did Kornberg describe in 1958?

A

The purification of DNA polymerase I from E. Coli which synthesizes DNA.

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5
Q

How does replication in bacteria begin?

A

At a single origin

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6
Q

How does replication of bacteria proceed from its single origin?

A

Bidirectionally

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7
Q

What is a replication fork?

A

The point where replicating bacterias loops end.

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8
Q

What does replication via DNA polymerases require?

A

A template and a primer

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9
Q

What is a template?

A

A DNA strand used to specify the nucleotides to be incorporated into the daughter strand

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10
Q

What is a primer?

A

A segment of nucleic acid bases paired to the template and with a free 3’-OH

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11
Q

Define processivity.

A

The number of bases synthesized before the DNA polymerase enzyme dissociates from the template.

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12
Q

Is polymerization thermodynamically favored?

A

Yes

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13
Q

Are DNA polymerases accurate?

A

Yes

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14
Q

What form of repair makes DNA polymerases more accurate?

A

Mismatch repair

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15
Q

How do errors in replication occur?

A

Incorrect base pairing

Creation of tautomers

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16
Q

Define tautomers?

A

Same atomic composition, slightly different chemical structure.

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17
Q

How does DNA polymerase I proofread?

A

With 3’ - 5’ exonuclease activity which acts only on base just incorporated, no others

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18
Q

What is the function of DNA polymerase I?

A

Repair

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19
Q

What is the function of DNA polymerase II?

A

Specialized repair

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20
Q

What is the function and structure of DNA polymerase III?

A

Main DNA replication enzyme which clamps on DNA.

Has 10 subunits

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21
Q

What are the 3 stages of replication?

A

Initiation
Elongation
Termination

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22
Q

Where does DNA replication begin?

A

At the ORI or Origin of Replication

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23
Q

What’s the function of DnaA?

A

Recognizes ORI; opens duplex at specific sites

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24
Q

What is the function of DnaB (helicase)?

A

Unwinds DNA

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25
Q

What is the function of DnaC?

A

Required for DnaB binding at origin

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26
Q

What is the function of HU?

A

Histone like protein

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27
Q

What is the function of DnaG (primase)?

A

Synthesize RNA primers

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28
Q

What is the function of SSB?

A

Binds single stranded DNA

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29
Q

What is the function of DNA gyrase?

A

Relieves torsional strain generated by DNA unwinding

30
Q

What is the function of Dam methylase?

A

Methylated 5’ GATC sequences at ORI

31
Q

What is the prepriming complex?

A

DnaB/DnaC dimmers bind to open complex created by DnaA and unwind origin DNA to expose single strand template.

32
Q

(T/F) All steps of initiation of replication require energy.

A

True

33
Q

What is a problem for the initiation of DNA replication?

A

All synthesized enzymes require a primer: they can only add to the 3’ end of an existing strand and cannot initiate a new strand.

34
Q

What binds to the DnaB/DnaC complex?

A

Primase

35
Q

What forms the primosome?

A

When other proteins add to the primase/DnaB/DnaC complex.

36
Q

What does the primosome do?

A

It creates a 15nt stretch of RNA on the DNA template also known as the primer.

37
Q

What happens when the DNA polymerase III dimer binds to the primosome?

A

It becomes the replisome

38
Q

What happens when the replisome is created?

A

It begins to move around the chromosome creating bidirectional replication from a fixed origin.

39
Q

What is a problem for DNA elongation?

A

DNA polymerase only adds bases to the 3’ end but DNA can only be synthesized in the 5’ to 3’ direction.

40
Q

What is the physical direction of movement of the replication fork on the leading strand?

A

In the 5’ to 3’ direction which is the same direction of synthesis

41
Q

What is the physical direction of fork movement of the lagging strand?

A

In the opposite direction of the leading strand or 3’ to 5’.

42
Q

How do we synthesize the lagging strand without leaving long stretches of single stranded DNA?

A

With Okazaki fragments

43
Q

What are Okazaki fragments?

A

How we synthesize the lagging strand discontinuously.

Short stretches of several hundred to a few thousand bases.

44
Q

As the replisome moves along helicase unwinds the double helix and induces what?

A

Positive supercoiling in front of the replication fork.

45
Q

What is the function of DNA gyrase and topoisomerase I in elongation?

A

To maintain the chromosome negative supercoiling.

46
Q

What would happen if the negative supercoiling was not maintained?

A

Replication would cease

47
Q

How is elongation of the lagging strand different from that of the leading strand?

A

A loop is made which locally reverses the orientation of the lagging strand with respect to the movement of the replisome. Primase creates an additional primer and another DNA polymerase III binds the primer and begins synthesis.

48
Q

How long does the lagging strand loop continue to get fed through the replisome?

A

Until several hundred bases have been synthesized. Then a new loop so initiated.

49
Q

Where is the RNA primer attached on each Okazaki fragment?

A

At its 5’ end

50
Q

Are Okazaki fragments covalently linked?

A

No, not until DNA ligase comes through.

51
Q

What two enzymes repair the Okazaki fragments to make them continuous?

A

DNA polymerase I and DNA ligase

52
Q

What is the third enzymatic activity of DNA polymerase I?

A

It’s a 5’ to 3’ exonuclease meaning it removes RNA from the 5’ end of the Okazaki fragment in front of the DNA polymerase I molecule

53
Q

What exactly does DNA ligase do?

A

Covalently seals gaps in the backbone of the Okazaki fragments

54
Q

What is known about the termination of DNA replication?

A

The replication forks meet then topoisomerases allow two double helicase to seperate.

55
Q

Is DNA replication in eukaryotes more or less complex than prokaryotes?

A

More complex but the same principles apply

56
Q

How many polymerases are used in eukaryotes?

A

At least 5, 1 in mitochondria

57
Q

How is chromosomal replication in eukaryotes kept from taking many days?

A

It is initiated at multiple origins (~40-100kb)

58
Q

What is the function of DNA polymase alpha?

A

Primase

59
Q

What is the function of DNA polymerase beta?

A

BE repair and Meiotic recombination

60
Q

What is the function of DNA polymerase gamma?

A

Mitochondrial replication

61
Q

What is the function of DNA polymerase delta and epsilon?

A

Nuclear replication, NER and MMR

62
Q

In eukaryotic replication what creates a problem for replicating the ends of the DNA molecule?

A

DNA in eukaryotes are linear molecules

63
Q

What are the end of eukaryotic chromosomes called?

A

Telomeres

64
Q

What do telomeres allow?

A

Allow linear molecules to be replicated without loss of information

65
Q

What do telomeres contain?

A

Hundreds of Tandem repeated GT rich sequences usually 6-8 bases long

66
Q

What do these GT rich sequences usually form?

A

Non-helical structures

67
Q

Are telomeres synthesized with a DNA template?

A

No

68
Q

What do telomeres use as a template?

A

An RNA component that extends to the end of the chromosome.

69
Q

Where does priming occur for telomerase?

A

In the telomere, not coding DNA.

70
Q

What is telomerase?

A

A specialized reverse transcriptase

71
Q

What are the functions of telomeres?

A

Seal chromosome ends
Attach chromosomes to nuclear envelope
Facilitate replication
Serve as mitotic clock

72
Q

What does sealing chromosomal ends do?

A

Prevents undesirable fusion of chromosomes

Avoids aberrant recombination

73
Q

What does serving as “mitotic clock” mean?

A

Short telomeres induce senescence and/or apoptosis
No detected telomerase activity in differentiated cells
Telomerase active in germ cells, stem cells and tumors
Telomeres in fibroblasts from elderly patients are shorter than those from children

MCBM Exam 5 Kat (15 decks)

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