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DNA replication Flashcards

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1
Q

what are the 3 fundamental condition of DNA replication?

A

semiconservative
bidirectional
semi discontinuous

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2
Q

What does it mean when DNA replication is semiconserative?

A

The two DNA stands separate and each is copied so the new DNA double helices contain one original strand and one newly synthesized strand

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3
Q

What does it mean when DNA replication is bidirectional?

A

Replication proceeds in both directions from an origin of replication

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4
Q

What does it mean when DNA replication is semidiscontinuous?

A

One of the two strands is copied discontinuously as a set of fragments called Okazaki fragments which are then joined to form an intact strand

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5
Q

How many nucleotides long are Okazaki fragments in Ecoli?

A

1000-2000 nucleotides long

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6
Q

How many nucleotides long are Okazaki fragments in eukaryotes?

A

100,000 nucleotides

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7
Q

How many replication origins are there?

A

30,000

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8
Q

in the semi conservative method, one strand of the newly synthesized strand is ____ to the original

A

complementary (A-T, C-G)

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9
Q

okazaki fragments are liked via ____ bonds

A

covalent

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10
Q

in what direction is the leading strand synthesized?

A

5’ to 3’

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11
Q

what enzyme synthesizes DNA?

A

DNA polymerase

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12
Q

What two things cause semi-discontinuous DNA replication?

A
  1. DNA polymerases only synthesize DNA 5’ to 3’
  2. The two DNA strands of the double helix must be in opposite directions
    (one 5’ to 3’, one 3’ to 5’)
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13
Q

what are the 3 phases of DNA replication?

A

initiation, elongation, termination

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14
Q

what is the initiation factor that binds to OriC to separate the strands of the double helix?

A

DnaA protein

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15
Q

DnaB protein is a ____, or DNA-unwinding protein

A

helicase

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16
Q

what is the role of DnaA protein?

A

bind to oriC to separate the strands of the double helix

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17
Q

what helicase binds to the separated strands and moves alone the DNA to unwind the DNA double helix?

A

DnaB protein

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18
Q

what is the role of DnaB protein?

A

bind to the separated strands to unwind the double helix

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19
Q

what is the protein that prevents the two unwound DNA strands from coming back together?

A

SSB (single-stranded DNA binding protein)

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20
Q

what is the role of SSB (single-strand DNA binding protein)?

A

prevent the separated strands from coming back togehter

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21
Q

what protein relieves stress in the helical DNA caused by the unwinding?

A

DNA gyrase (DNA topoisomerase 2)

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22
Q

DnaA protein binds to the ___ __ ____

A

origin of replication (oriC)

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23
Q

The binding of DnaA protein ____ ____ at the origin of replication

A

separates the strands

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24
Q

DnaB protein is delivered to the replication forks by ___ and ___ proteins

A

DnaC and DnaT

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25
DnaB protein moves along the DNA, unwinding the __ __
double helix
26
what two proteins are responsible for bringing in the DnaB protein?
DnaC and DnaT
27
DnaB subunits come in the form of a ____
hexomere
28
DnaB subunits come in the form of a ____
hexamer
29
SSB subunits come in the form of _____
tetromers
30
SSB subunits come in the form of _____
tetramers
31
what are the two enzymes responsible for DNA unwinding during the elongation phase?
DNA helicase (DnaB), gyrase (topoisomerase 2)
32
what enzyme is responsible for synthesizing an RNA primer that is needed for DNA replication in the elongation phase?
primase enzyme
33
what enzyme is used in the elongation phase to synthesize the new DNA strands?
DNA polymerase 3 holoenzyme
34
What seven proteins replicate the DNA double helix?
1. DNA polymerase lll holoenzyme 2. DNA helicase 3. DNA gyrase 4. primase 5. single stranded DNA binding protein 6. DNA polymerase l 7. DNA ligase
35
what subunit of DNA polymerase 3 acts as a “sliding clamp” that hold the DNA polymerase onto the DNA strand?
beta
36
what second enzyme is associated with DNA polymerase 1?
DNA ligase
37
what enzyme during elongation is responsible for binding to the region of the primers that will begin the Okazaki fragment to cut it out and replace it with a patch of DNA?
DNA polymerase 1
38
how many subunits are a part of DNA polymerase 3 holoenzyme?
10
39
what part of DNA polymerase 3 holoenzyme is involved in polymerase activity of linking new nucleotides to the end of the growing chain via covalent linkages?
alpha
40
what part of DNA polymerase 3 holoenzyme has 3’ to 5’ proofreading activity?
episilon
41
What is the main subunit of DNA polymerase lll?
alpha
42
what part of DNA polymerase 3 holoenzyme stimulates the proofreading activity?
theta
43
How many subunits does the "core" DNA polymerase lll have?
3 subunits (alpha, episilon, theta)
44
In DNA polymerase 3 holoenzyme, how many core units of A,E,T are present?
2
45
what is the middle core of DNA polymerase 3 holoenzyme?
gamma
46
what complex keeps together the 2 A,E,T cores?
gamma complex
47
what are the components of the gamma complex?
gamma, delta, delta prime, chi, si
48
how many tau and beta are present at each A,E,T core?
1 tau, 2 beta
49
what is the role of tau in DNA polymerase 3 holoenzyme?
to bring about proper assembly
50
at termination, what is the name of the termination region?
ter
51
what is the termination protein that is bound to the termination region (ter) to help bring about termination?
tus
52
In termination, the two bidorectional replication forks continue to move around the circular E.coli chromosome until they meet at a ____ ____ and replication is terminated
termination region (Ter region)
53
DNA in higher cells interact with ____ proteins to form ______ and ______ ______
histones, nucleosomes, chromatin fibers
54
The beads on a string nucleosome fiber is ___ nm
10
55
The beads on a string nucleosome fiber with DNA is wrapped around ___ _____
histone proteins
56
A chromatin fiber is __ nm
30
57
A chromatin fiber is produced by helical coiling of the ___ ____
nucleosome fiber
58
are histones positively or negatively charged?
positively charged to bind to the negatively charged DNA
59
What Eukaryotic DNA polymerase is the principal DNA polymerase in eukaryotic DNA replication?
Polymerase delta
60
What Eukaryotic DNA polymerase functions in the initiation of nuclear DNA replication?
Polymerase alpha
61
What Eukaryotic DNA polymerase cooperates with DNA polymerase delta?
Polymerase epsilon
62
What Eukaryotic DNA polymerase functions in DNA repair?
Polymerase beta
63
What Eukaryotic DNA polymerase DNA replicating enzyme of mitochondria?
Polymerase gamma
64
How many DNA polymerases are needed in eukaryotic DNA replication?
5
65
What two eukaryotic DNA polymerases work together to synthesize most of DNA?
Polymerase delta and epsilon
66
What eukaryotic DNA polymerase forms primers and begins to add DNA nucleotides?
Polymerase alpha
67
What eukaryotic DNA polymerase synthesizes short patches of DNA?
Polymerase beta
68
polymerase ___ has 4 subunits with 2 involved in DNA replication and 2 involved in primase (RNA) synthesis
alpha
69
what eukaryotic DNA polymerase has the 4 subunits of PolA1, PolA2, Prim1, and Prim2?
alpha
70
what eukaryotic DNA polymerase has the 5 subunits of PolyD1, PolyD2, PolyD3, PolyD4, and PCNA (clamp)?
delta
71
what eukaryotic DNA polymerase has the 3 subunits of Pole, Pole2, and Pole3?
epsilon
72
what eukaryotic DNA polymerase has the 2 subunits of PolG and PolG2?
gamma
73
what eukaryotic DNA polymerase has low fidelity?
beta
74
what eukaryotic DNA polymerases have low processivity?
alpha, beta
75
what is the eukaryotic protein that bind to to the replication origins and is important to bringing about the assembly of the pre-replicative complex?
ORC
76
what is the eukaryotic protein that acts as a helicase to unwind the double helix at replication origins and separate DNA strands?
MCM (replaces DnaA and DnaB)
77
what is the eukaryotic protein that brings about the binding of the MCM proteins to the replication origins?
Cdc6 (no active role)
78
what is the eukaryotic protein that is a kinase complex that initiates DNA replication by adding phosphate groups to ORC, MCM, and Cdc6 proteins?
cyclin CDK (negative charged phosphate changes protein folding and activates them)
79
in eukaryotes, a pre-replication complex is formed by the binding of ____ and ____ proteins to the replication origin where ____ protein is bound
Cdc6, MCM, ORC
80
ORC is duplicated during the ___ phase
S phase
81
a gap is produced at the ___ end by the removal of the RNA primer
5’
82
_____ is the enzyme responsible for extending the 3’ end in eukaryotes by adding TTAGGG repeats so that DNA polymerase can extend the 5’ end
telomerase
83
Cyclin-CDK initiates DNA replication by adding ___ ___ to ORC, MCM, and Cdc6 proteins
phosphate groups
84
telomerase adds sequences of ______ bases
TTAGGG
85
A gap is produced at the 5' end by removal of the ____ ____
RNA primer
86
Telomerase extends the 3' end by adding ______ repeats
TTAGGG
87
DNA polymerase can then extend the __ end
5'

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