Genetics test 2 > DNA replication > Flashcards

DNA replication Flashcards

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1
Q

Where is the site where DNA strands are made?

A

DNA replication fork.

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2
Q

What is the process in which original DNA strands are used as templates for the synthesis of new DNA strands?

A

DNA Replication

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3
Q

What provides the basis for DNA replication

A

the DNA double helix and the complementarity of DNA strands based on the AT/GC rule.

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4
Q

A strand of DNA that is used to synthesize a complementary strand of DNA or RNA.

A

template strand/parental strand

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5
Q

What are the two newly made strands of DNA called?

A

Daughter strands

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6
Q

What features of the structure of DNA enable it to be replicated?

A

its double stranded structure and the base pairing between A and T and G and C

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7
Q

In the late 1950’s there were 3 different mechanisms/models that scientists used to explain DNA replication. What are these 3 models?

A

Conservative model, Semiconservative model, and dispersive model.

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8
Q

An incorrect model of DNA replication in which both parental strands of DNA remain together following DNA replication.

A

Conservative model

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9
Q

The correct model for DNA replication in which the newly mad dsDNA contains one parental strand and one daughter strand.

A

Semiconservative model

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10
Q

An incorrect model for DNA replication in which segments of DNA and newly made DNA are interspersed in both strands following the replication process.

A

Dispersive model

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11
Q

Meselson and Stahl’s hypothesis

A

Based on Watson and Crick’s ideas, the hypothesis was that DNA replication is semiconservative.

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12
Q

How was Meselson and Stahl’s hypothesis tested? What were the steps of the experiment?

A
  1. Add an excess of 14N- contains compounds to the growth medium so that all of the newly made DNA will contain 14N
  2. Incubate the cells for various lengths of time. Note: the 15N-labled DNA is shown in purple, and the 14N labeled DNA is shown in blue.
  3. Lyse the cells by adding lysozyme and detergent, which disrupt the bacterial cell wall and cell membrane, respectively.
  4. Load a sample of the lysate onto a CsC1 gradient. Note: The average density of DNA is around 1.7g/cm cubed, which is sufficiently different from other cellular macromolecules.
  5. Centrifuge the gradients until the DNA molecules reach their equilibrium densities.
  6. DNA within the gradient can be observed under UV light.
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13
Q

To make a new DNA strand, what is necessary?

A

A template strand and nucleotides

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14
Q

Where does DNA synthesis begin in a bacterial chromosome?

A

Origin of Replication

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15
Q

The manner in which two replication forks move, in opposite directions outward from the origin; refers to a regulatory element that can function in either the forward or reverse direction.

A

bidirectional

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16
Q

Replication fork

A

is teh region where two DNA strands have separated and new strands are being syntehsized.

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17
Q

What are the three types of DNA regions found within oriC

A

An AT rich region, DnaA box sequences, and GATC methylation sites.

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18
Q

AT-rich region

A

a region a bacterial origin of replication that contains high amounts of Adenine and Thymine, and is the site where the DNA strands initially separate.

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19
Q

DnaA box

A

A DNA sequence that serves as a recognition site for the binding of DnaA protein, which is involved in the formation of a replication fork.

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20
Q

What is the protein that binds to a DnaA box sequence at the origin of replication in bacteria and initiates DNA replication?

A

DnaA protein

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21
Q

DNA helicase

A

an enzyme that separates two strands of DNA.

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22
Q

Bidirectional replication

A

the phenomenon in which two DNA replication forks move in opposite directions from an origin of replication.

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23
Q

What are the 4 steps that occur to form two DNA replication forks?

A
  1. DNA réplication begins with the binding of DnaA proteins with DnaA boxes within the origin of replication. When DnaA proteins are in their ATP-bound form, they bind to the five DnaA boxes in orin to imitate DNA replication. DnaA proteins ind to eachother to form a complex.
  2. Other DNA-binding proteins are HU and IHF which cause the DNA to bend around the complex of DnaA proteins, this results in the separation of strands at the AT-rich region. Because only two hydrogen bonds form between the bases A and T, whereas three hydrogen bonds occur between G and C, the DNA strands are more easily separated at an AT-rich region.
  3. Following the separation at the AT-rich region, the DnaA proteins with the help of the DnaC proteins, recruit DNA helicase to the site. When DNA helicase encounters a double stranded region, it breaks the hydrogen bond between the two strands, thereby generating two single strands.
  4. Two DNA helicases begin strand separation within the orin region and continue to separate the DNA strands beyond the origin. These proteins use the energy from ATP hydrolysis to catalyze the separation of the double-stranded parental DNA. In E. coli, DNA helices bind to single-stranded DNA and travel along the DNA in a 5’ to 3’ direction to keep the replication fork moving. The action of DNA helicases promotes the movement of two replication forks outward from the oriC in opposite directions. This initiates the replication of the bacterial chromosome in both directions, a phenomenon coined bidirectional replication.
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24
Q

Why is primase needed for DNA replication?

A

because DNA polymerase cannot initiate DNA replication on a bare template strand.

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25
DnaA proteins
Bind to DnaA box sequence within the origin of replication to initiate DNA replication.
26
DnaC proteins
Aid DnaA in the recruitment of DNA helicase to the origin.
27
DNA helicase (DnaB)
separates dsDNA into single strands by breaking the hydrogen bonds between the strands.
28
DNA Gyrase (Topoisomerase II)
removes positive supercoiling ahead of the replication fork.
29
Single-strand binding proteins
Bind to single stranded DNA and prevent it from reforming a double stranded structure.
30
Primase
Synthesizes short RNA primers
31
DNA polymerase III
Synthesizes DNA in the leading and lagging strands
32
DNA polymerase I
Removes RNA primers, fills in gaps with DNA.
33
DNA ligase
Covalently attaches adjacent Okazaki fragments
34
Tus
Binds to ter sequence and prevents the advancement of the replication fork.
35
RNA primers
A short strand of RNA, made by primase, that is used to elongate a strand of DNA during DNA replication.
36
What strand during DNA replication is synthesized continuously toward the replication fork?
Leading strand
37
What is the strand that during DNA replication that is synthesized as short Okazaki fragments in the direction away from the replication fork?
Lagging strand
38
DNA polymerase
an enzyme that catalyzes the formation of covalent bonds between nucleotides to form a strand of DNA
39
α subunit of DNA polymerase III
Synthesizes DNA
40
ε subunit of DNA polymerase III
Contains the 3' to 5' exonuclease site that removes mismatched nucleotides (proofreading).
41
θ subunit of DNA polymerase III
Accessory protein that stimulates the proofreading function.
42
β subunit of DNA polymerase III
Clamp protein, which allows DNA polymerase to slide along the DNA without falling off.
43
the remaining subunits of DNA polymerase III
Clamp loader complex, involved with helping the clamp protein bind to the DNA.
44
What are the differences between the synthesis of the leading and lagging strands?
The leading strand is synthesized as one, long continuous strand in the same direction in which the replication fork is moving. The lagging strand is formed from Okazaki fragments produced in the direction away from the replication fork.
45
During DNA replication, what is the role of the GATC methylation site within the oriC
Regulate DNA replication initiation
46
At a single origin of replication, how many leading strand primers are required for the complete replication of the DNA strand (assume bidirectional replication)?
Two (There are two replication forks. At each replication fork there is one lagging strand so two total primers are needed.)
47
The name of the enzyme that methylates the GATC methylation site within the oriC is
Dam
48
Small segments of DNA that are synthesized on the lagging strand of DNA are called ...?
Okazaki fragments
48
Before the lagging strand can begin assembling new DNA nucleotides, what must occur?
RNA primase constructs a short RNA primer.
49
A complex consisting of DNA helicase and primase is called ...?
primosome
50
Okazaki fragments are required during DNA replication to
allow synthesis of the lagging strand
51
What removes RNA primers?
DNA polymerase I
52
Replisome
A complex that consists of a primosome and dimeric DNA polymerase.
53
What is a complex of two DNA polymerase holoenzymes that move as a unit during replication?
Dimeric DNA polymerase
54
Termination sequences (ter sequences)
In E.coli, a pair of sequences in a chromosome that bind a protein known as the termination utilization substance (Tus), which stops the movement of replication forks.
55
Catenanes
intertwined circular molecules
56
How are catenanes separated?
by the action of DNA Gyrase
57
Is DNA strand breakage necessary for catenane separation?
Yes, it is necessary so that the strands can move relative to each other and the catenanes can separate.
58
Conditional mutant
a mutant whose phenotype depends on environmental conditions, such as temperature-sensitive (ts) mutant
59
temperature-sensitive mutant
a mutant that has a normal phenotype at a permissive temperature but a different phenotype, such as failure to grow, at a nonpermissve temperature.
60
What are the three mechanisms that ensure fidelity of DNA replication
1. Stability of base pairings 2. the active site structure of DNA polymerase 3. The process of DNA proofreading
61
DNA polymerase III is a ...?
processive enzyme
62
proofreading function
the ability of a DNA polymerase to remove mismatched bases from a newly made strand.
63
What are some features that make DNA replication in eukaryotes more complex?
larger linear chromosomes, chromatin is tightly packed within nucleosomes, and cell-cycle regulation is more complicated.
64
Who provided evidence for multiple origins of replication?
Huberman and Riggs
65
Why do Eukaryotes need multiple origins of replication?
Due to the fact that Eukaryotic chromosomes are so large, multiple origins of replication are needed so that the DNA can be replicated in a reasonable length of time.
66
ARS elements (Autonomously replicating sequence)
DNA sequences found in yeast that function as origins of replication
67
ARS element properties
- 100-200bp in length and are necessary for the initiation of DNA replication - Contain a high percentage of A and T bases. - Have a copy of the ARS Consensus Sequence (ACS) which is ATTTAT(A or ) TTT A along with/ additional sites, such as B1 and B, that also enhance the function of the origin of replication. - This arrangement in building yeast is similar to that in bacterial origins of replication, which also have an AT-rich region and specific elements such as DnaA boxes.
68
α
Initiate DNA replication
69
ε
Replication of the leading strand
70
δ
Replication of the lagging strand
71
γ
Replication of mitochondrial DNA
72
G4 motifs
G rich sequences
73
G-quadruplex
a four stranded structure in DNA that is stabilized by hydrogen bonding between four guanines.
74
prereplicaiton complex (preRC)
in eukaryotes, an assembly of at least 14 different proteins, including a group of proteins called the origin recognition complex (ORC) that are required to initiate DNA replication.
75
origin recognition complex
a group of proteins found in eukaryotes that acts as the first initiator of preRC assembly to begin DNA replication.
76
MCM helicase
a group of six proteins needed to complete a process called DNA replication licensing, which is necessary for the formation of of two replication forks at an origin of replication in eukaryotes.
77
DNA réplication licensing
in eukaryotes, occurs when MCM helicase is bound at an origin of replication, enabling the formation of two replication forks.
78
Polymerase switch
an exchange of one type of DNA polymerase for another type during DNA replication.
79
translesion-replicaitng polymerase
a type of DNA polymerase that can replicate over a DNA region that contains an abnormal structure (i.e., a lesion).
80
What is an enzyme that removes small RNA flaps that are generated by the action of DNA polymerase δ on an RNA primer during DNA replication?
Flap endonuclease
81
telomeres
specialized repeated sequences of DNA found at the ends of Eukaryotic Chromosomes. Have a 3' overhang that is 12-16 nucleotides in length.
82
What is the enzyme that recognizes telomeric sequences at the ends of eukaryotic chromosomes and synthesizes additional repeats of those sequences? It also prevents the ends of eukaryotic chromosomes from shortening.
telomerase
83
Who discovered telomerase?
Greider and Blackburn
84
telomerase RNA component (TERC)
the RNA component of telomerase
85
Which characteristics of DNA polymerase prevent the enzyme from replicating the 3' ends of DNA strands?
- DNA polymerase synthesizes DNA only in a 5' to 3' direction. - DNA polymerase can only elongate an existing nucleotide strand.
86
senescent
cell that is no longer capable of dividing
87
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