Lecture 10 Flashcards
1
Q
specific sequence in the genome in which dsDNA is first opened up for replication
A
origin of replication
2
Q
most prokaryotes have – per circular genome
A
one replicon
3
Q
agrobacteria have linear chromosomes and –
A
multiple replicons
4
Q
E. coli – has 245 bp
A
OriC
5
Q
OriC has a – followed by –
A
tandem array of three A-T rich 13-mer regions followed by five 9-mer DnaA binding sites
6
Q
origin of replication of yeast
A
ARS1
7
Q
core sequence of ARS1
A
A/TTTTAA/GTTTA/T
8
Q
ori-binding proteins of E. coli
A
DnaA
9
Q
ori-binding proteins in yeast
A
ORC
10
Q
methylate all E. coli GATC sequence
A
Dam methylase
11
Q
methylation of E. coli replication origin creates a – for DNA synthesis initiation
A
refractory period
12
Q
approximately – origins of replication are used each time a human cell divides
A
30,000-50,000
13
Q
Different cell types use – sets of origin of replications
A
different
14
Q
a eukaryotic genome have many origins of replication per –
A
chromosome
15
Q
timing of origin activation is related to the –
A
packing of the local chromatin
16
Q
dsDNA contains two – but DNA synthesis can only be 5’ to 3’
A
antiparallel ssDNA
17
Q
Which of the following is correct for the replication direction?
- 2 origins and 2 growing ends
- 1 origin and 1 fork
- 1 origin and 2 forks
A
1 origin and 2 forks (bidirectional)
18
Q
replication bubble gets increasingly longer from both directions but the center is –
A
constant
19
Q
one replication bubble has two forks growing in –
A
the opposite direction
20
Q
At each replication fork, two ssDNA are replicated in the –
A
5’ to 3’ direction
21
Q
labeled replicating DNA show many – fragments being formed (termed Okazaki fragments)
A
1-2 kb
22
Q
strand that is synthesized continuously
A
leading strand
23
Q
strand that is synthesized discontinuously
A
lagging strand
24
Q
– are needed for DNA replication
A
RNA primers
25
DNA polymerase can only synthesize DNA if there is --
an existing polynucleotide primer...short RNA sequences
26
T/F: RNA primers are needed in both prokaryotes and eukaryotes
true
27
-- is the RNA polymerase that synthesizes the short RNA primer
primase
28
DNA replication is a -- process
DNA template-dependent polymerization
29
replication of sDNA proceeds in -- directions
opposite (bidirectional)
30
DNA replication starts from replication origins that possess --
specific DNA sequences
31
T/F: each strand of DNA is synthesized continuously and discontinuously
true
32
required substrates for DNA synthesis
dNTP and primer
33
DNA is synthesized by extending the -- of the primer
3' end
34
The DNA catalyzes the -- of a deoxyribonucleotide to the 3' OH end of a polynucleotide chain
stepwise addition
35
the DNA pol synthesizing reaction is driven by a large, favorable free-energy change cause by the release of -- and its subsequent hydrolysis to 2 molecules of inorganic phosphate
pyrophosphate
36
DNA polymerase has -- ability
proofreading
37
can remove wrong nucleotide one at a time from the ends of polynucleotides
exonuclease
38
pretty good but not perfect DNA pol proofreading ability is one of the reasons for -- in the genome
"spontaneous" mutations
39
there is about 1 error for every -- polymerization event during RNA or protein synthesis
10^4
40
there is about 1 error for every --polymerization event during DNA replication
10^10
41
A -- suggests why DNA is always synthesized from 5' to 3'
need for proofreading
42
helicase binds to -- to unwind dsDNA to create ssDNA at the replication fork
replication origins
43
topoisomerase release supercoil that results from --
DNA unwinding
44
-- stabilize ssDNA before replication
SSB proteins/RPA
45
primase is a --
DNA dependent RNA polymerase
46
primase uses -- to make short RNA primers
DNA as a template
47
in eukaryotes, -- synthesizes short DNA from the RNA primer, resulting in an RNA-DNA hybrid
DNA pol alpha
48
eukaryotic primers has -- nucleotides
10
49
one RNA primer is made every -- nucleotides on lagging strand
200
50
DNA ligase connects
backbone of DNA
51
DNA ligase uses -- to activate the 5' end at the neck before forming the new bond
a molecule of ATP
52
The energetically unfavorable nick-sealing reaction is driven by being -- to the energetically favorable process of ATP hydrolysis
coupled
53
holds DNA polymerase on the DNA
regulated sliding clamp
54
ATP binding to clamp loader -->
opens sliding clamp
55
ATP hydrolysis locks sliding clamp around DNA and -- clamp loader
releases
56
sliding clamps -- the DNA polymerase processivity
increase
57
main synthesizing enzymes in prokaryotes
DNA pol III
58
main synthesizing enzymes in eukaryotes (lagging)
DNA pol delta
59
main synthesizing enzymes in eukaryotes (leading)
DNA pol epsilon
60
prokaryotic clamp and loader
B clamp and gamma clamp loader
61
eukaryotic clamp and loader
PCNA (proliferating cell nuclear antigen) and RFC (replication factor C)
62
remove RNA primers in prokaryotes
DNA pol I
63
remove RNA primers in eukaryotes
RNase H and FEN1
64
fill in gaps from removed RNA primer in prokaryotes
DNA pol I
65
fill in gaps from removed RNA primer in eukaryotes
DNA pol delta
66
connects the Okazaki fragments
DNA ligase
67
if DNA cannot rapidly rotate -->
torsional stress will build up
68
some of the tension can be taken up by -- whereby the DNA double helix twists around itself
supercoiling
69
If the tension continues to build up, the replication fork will eventually stop because further unwinding require -- energy than the helicase can provide
more
70
T/F: Topoisomerase I cleave one strand of DNA and ligates the two ends of the broken strand
true
71
topoisomerase I has -- at the active site
tyrosine
72
DNA topoisomerase -- attaches to a DNA phosphate thereby breaking a phosphodiester bond linkage in one strand
covalently
73
original phosphodiester bond energy is stored in the -- making the reaction reversible
phosphotyrosine linkage
74
-- of the phosphodiester bond regenerates both the DNA helix and the DNA topoisomerase
spontaneous reformation
75
topoisomerase II is used to separate --
2 double helices that are interlocked
76
topoisomerase II make as reversible covalent attachment to the two strands of one of the double helices creating a double-strand break and forming a --
protein gate
77
prokaryotic DNA replication begins at the
OriC
78
around 10 DnaA moleucules bind to the DnaA binding sites which wrap around the DnaA proteins causing the DNA at the -- to unpair
13-mer region
79
denatured 13-mer region recruits
DnaB (helicase) and DnaC (helicase loader) complex
80
DnaC helps DnaB bind to the -- at the 13-mer regino
ssDNA
81
helicase loading proteins prevent the -- from inappropriately entering other single-stranded binding proteins
replicative DNA helices
82
-- inhibit the helices until they are properly loaded at the replication origin
helicase loaders
83
helicase and primase form
primosome
84
-- of the primase produces the short RNA primers that generate the Okazaki fragment
periodic binding
85
-- is kicked out before DNA pol comes in
SSB proteins
86
DNA polymerase machinery on each strand work together as part of --
a single complex
87
the template with the lagging strand -- in order for the DNA pol complex to travel in the same direction...towards the replication fork
loops back
88
prokaryotic helicase
DnaB
89
eukaryotic helicase
Mcm
90
prokaryotic helicase loaders
DnaC
91
eukaryotic helicase loaders
Cdc6 and Cdt1
92
-- stay behind after helices moves on to prevent another round of replication before mitosis is finished
ORC
93
Mcm helicase + ORC -->
prereplicative complex
94
an origin of replication can only be used if a -- forms in G1 phase
prereplicative complex
95
At the beginning of S phase, kinases phosphorylate Mcm and ORC, -- the former and -- the latter
activate Mcm
| inactivate ORC
96
A new pre replicative complex cannot form at the origin until the cell progresses to the next G1 phase, when the bound ORC has been --
dephosphorylated
97
Mcm helicase moves along the --
leading strand template
98
bacterial helicase moves along the --
lagging strand template
99
-- synthesizes short RNA-DNA primers on each strand, which mark the starting points to be replicated
primase-DNA pol alpha complex
100
-- replaces the primase-DNA pol alpha complex generating the leading strand
Pol epsilon PCNA-Rfc complex
101
-- synthesize the Okazaki fragment
pol delta PCNA-Rfc complex
102
RNA-DNA primers are removed by
RNaseH and FEN1
103
in eukaryotes -- fill in gaps with dNTPS
DNA pol delta
104
the two DNA pol complexes on both strand work together and move --
in the same direction (lagging stand loops back to accommodate)
105
histones are mainly synthesized in
S phase
106
physical ends of linear chromosoe
telomeres
107
3' end of G rich strand extends -- beyond the 5' end of the complementary C-rich strand
12-16 nucleotides
108
3' overhand region is bound by specific proteins that serve to protect the ends of linear chromosomes from
attack by exonuclease
109
last regions of DNA to be replicated
telomere
110
-- resulting from lagging strand synthesis would become shorter at each cell division
daughter DNA strand
111
adds telomeric sequences to the ends of each linear chromosome
telomerase
112
telomerase is a large --
protein-RNA complex
113
telomerase has -- activity that can synthesize DNA from its RNA template
reverse transcriptase
114
stem cells divide slowly but don't
shorten telomere
115
single stranded 3' end will fold into a T loop with specialized telomere binding proteins -- to protect the end of the DNA molecule
shelterin
116
T/F: most adult somatic cells lack telomerase
true
117
what has telomerase activity?
stem cells, germ line cells, tumor cells
118
somatic cells with short telomeres cease dividing
replicative cell senescence
