CH.12 Flashcards
(131 cards)
1
Q
plasmids are self replicating circular genomes that maintain a relatively _______ copy number
A
constant
2
Q
explain what low copy of plasmids are?
A
1-10 copies per cell. have a segregation mechanism
3
Q
explain high copy in plasmids
A
more than 10 copies, sometimes up to 100 or more. are distributed between the daughter cells randomly
4
Q
episome
A
a plasmid that can integrate into the host chromosome
5
Q
phages are self replicating entities that produce _________________. may be ______ or ______, _____ or ______.
A
infectious particles. circular, linear, DNA OR RNA
6
Q
lysogenic
A
phages that can integrate into the host genome
7
Q
immunity
A
ability of a phage or plasmid to exclude reinfection by similar entity
8
Q
the transfer of phages occurs through _______
A
infectious particles
9
Q
the transfer of plasmids occurs through _______
A
conjugation
10
Q
plasmids are always ________, but phages may exist as either _______ or _______.
A
circular. linear or circular
11
Q
DNA pol usually binds region
that _______ origin
A
surrounds
12
Q
what is the linear template called?
A
adenovirus
13
Q
bottom strand is used as _______ and the top strand is _______
A
template, displaced
14
Q
top strand forms ______ before initiating DNA synthesis..
A
terminal duplex
15
Q
duplex origin formed by _________
A
base pairing
16
Q
what is an example of a small protein that intervenes with the problem of linear replication?
A
adenovirus DNA
17
Q
protein intervenes are often used by ____________ that have proteins linked to the 5’ terminal base
A
viral nucleic acids
18
Q
during strand displacement for linear DNA replication, the first synthesis uses a _______________.
A
normal double- stranded linear template
19
Q
the displaced strand mimics a____________ by forming what?
A
linear double strand, hairpin structure
20
Q
terminal protein ______ binds to the 5’ end of the ______ of adenovirus DNA between ____ and _____ nucleotides
A
dCTP, top strand, 9-18
21
Q
host protein ______ is essential for the _______. it binds between ___ and ____ nucleotides
A
nuclear factor 1, initiation. 17-48
22
Q
initiation complex forms between positions __ and ___= ___________ from the actual DNA end
A
9 and 48. a fixed distance
23
Q
what serves as a primer for DNA synthesis in strand displacement?
A
3, OH of dCTP
24
Q
new strand is _________ to the initiating dCTP
A
covalently
25
old TP is _______ by the new TO fir each new replication cycle
displaced
26
does TP remain attached during elongation?
yes
27
name two of the solutions
hairpins, and telomere( repetitive sequences)
28
another solution used is converting ______ to _______ or multimeric molecules.
linear to circular
29
lambda phage is an example of what?
| T4 phage is an example of what?
circular, multimeric
30
rolling circle generate what?
single stranded multimers of the original sequence
31
rolling circle is an example of what?
each strand being replicated independently
32
what does the nicking in rolling circle?
protein A which is a endonuclease (cuts in the middle)
33
what does an exonuclease do
cuts on the ends
34
ϕX A protein is a cis acting _______. what does it do?
relaxase. generates single stranded circles from the tail produced by rolling circle replication
35
A protein has multiple functions, what are the three?
origin recognition, endonuclease, and ligas
36
rolling circle replication is a model for what?
leading strand synthesis
37
plus strand is what? when it replicates it becomes what?
single stranded, minus strand
38
is the replicative form double stranded or single ?
double
39
rolling circle is used by ______ to do what?
plasmids to transfer themselves and host chromosome sequences to other bacteria during conjugation
40
F factor replication system is ________
surpressed
41
F plasmid is an example of a ______ in E.coli
episome
42
F plasmid is a large circular plasmid ______kb.
only ______ genes have been mapped.
_____kb is organized as a unit to transfer its genome to another bacteria. (___________ or ____ genes)
100.
60.
32.
transfer region or tra
43
three methods of replication?
oriV, oriC, oriT
44
____ as free plasmid (one copy/bacterial chromosome)
oriV
45
uses e.coli chromosomal origin when integrated is called what? ____ is surpressed
oriC,OriV
46
______ during conjugation
oriT
47
discrete regions that has transfer genes?
TRA
48
simple transposons- encode transposase. used to insert into host chromosomes (integration)
IS
49
used to initiate plasmid replication- vegetative
oriV
50
where are tra and trb loci?
40 genes
51
used to initiate replication for transfer ( in conjugation- rolling circle model)
OriT
52
which bacteria is F +
the one that has F factpr
53
outer membrane protein that blocks mating pair formation?
T
54
blocks DNA transfer?
S
55
covalently attaches to 5' end of DNA and unwinds (relaxase)
I
56
recruits TraI to 5' end of DNA
Y
57
what proteins are involved with immunity?
s AND t
58
DNA nicking and unwinding?
Y and I
59
pilin-
A
60
SENSES THAT MATING PAIR FORMED
m
61
transfer of an F factor is initiated when rolling circle replication begins at _______
oriT
62
the free 5' end initiates what? what is bound to the 5' end?
transfer into the recipient bacterium. traI
63
transferred DNA is converted into __________ in the recipient bacterium?
double stranded
64
when F factor is ____, conjugation "infects" the recipient bacterium with a copy of the F factor
free
65
when F factor is _________, conjugation causes transfer of the bacterial chomosome
integrated
66
pilus is composed of what?
pilin subunits
67
DNA transferred through channel formed by the _________system._______ coupling protein which directs the 5' end of the DNA to the channel. ______ and _____ may also participate
T4SS. traD, tra N and G
68
transfer begins from _____ which is nicked by ______ complex at a ____ site. ( what usually does the nicking)
OriT. traY/traI. traI
69
how many unit lengths are transferred in conjugation?
one
70
plasmids can be either mobilizable or self transmissible. a mob plasmid only contains an _______. a self transmissible plasmid contains a ____ region
oriT. tra
71
tra systems are linked to their what?
incompatibility group
72
plasmids that allow transfer ofr DNA to unrelated species are known as what? and they recognize a range of oriT?
promiscuous
73
name this process: pore formed between two cells and only one strand of DNA is passed through to the other cell (5' end first). the single strand in each cell undergoes replication to form double stranded DNA.
self transmissible
74
name this process: another plasmid is needed for this process. (helper plasmid must contain tra functions)
mobilization
75
binds near oriT and recruits TraI (relaxase),
traY
76
has nuclease & helicase (ATP) activity. Function enhanced by TraY & IHF (integration host factor);
traI
77
is a transferase covalent attachment of the 5’ end of the DNA to the protein (serves as the pilot protein)
traI
78
active transport, binds DNA, ATP/GTP binding sites, inner membrane protein, necessary for DNA transfer, directs 5’ end to the T4SS channel.
traD
79
protein A has the combined activities of _____ and _____. it recognized the ____ like traY and does nicking like traI
traY and traI, ori
80
blocks DNA transfer, inner membrane
TraS
81
outer membrane protein that blocks mating-pair formation
traT
82
name the two mechanisms of DNA integration in bacteria
homologous recombination and transposisiton
83
what does the Hfr cell contain?
an integrated F plasmid
84
F+ cell contains what?
episomal F plasmid
85
after integration, F plasmid ______________________________________________________. and _____ is suppressed
replicates as part of the host replicon. oriV
86
the donor chromosome is transferred as what?
single stranded DNA starting at the origin of transfer oriT
87
which gene is transferred first between bacteria?
the one closest to the origin
88
the integrated F plasmid is found when transferring into another bacteria?
both at the beginning and at the end of the DNA being transferred
89
does the F- strand stay -
yes it does
90
the transfer process using Hfr uses the _____ method or replication.
rolling circle
91
how long does it take to transfer entire chromosome of E.coli?
100 min
92
the double stranded transferred DNA is _____ into the recipient chromosome by __________.
integrated, double recombintation
93
F+ strains containf the integrated plasmid supports _______ and are described as _____ strains which stands for what?
high levels or recombination. Hfr, high frequency of recombination
94
the transfer of the host chromosome is ____ from the tra region and F- plasmid. except for a small part around _____.
away, oriT
95
in host chromosome transfer, donor DNA integrates into the host genome by _______ and _______.
recombination and transposition
96
most transfers are near the site of _____, which causes what to be formed?
insertion. gradient of transfer frequencies
97
plasmids that leave the genome carrying chromosomal DNA are called what? they leave by ______, resulting in a deletion in the ________.
F' plasmid, homologous recombination. chromosome
98
A. timefaciens can transform plant cells into tumors. the infectious agent is a ______ carried by the ______.
plasmid, bacterium
99
is produced by wounded plant cells (phenolic compound).
Acetosyringone
100
Agrobacterium infection succeeds only on
wounded plants
101
what uses opines as nutrients in the soil?
agrobacterium
102
what transfers T DNA to the plant cell?
agrobacterium in tumor at wound sitt
103
opines are made up of what?
basic amino acids and alpha ketogluterate
104
encodes all of the functions required for the transfer of the T-strand to the plant
Virulence region( Vir)
105
23 kb region that is transferred to the plant (only the T-strand actually transferred)
T-DNA
106
T DNA is involved with the synthesis of what two things?
opine synthesis and plant hormone synthesis
107
allows the bacterium to use octopine and nopaline nutrient (most other soil bacteria lack these genes)
opine catabolism
108
what is the purpose for tra region?
is needed for the transfer of the entire pTi between different agrobacterium
109
what encodes genes necessary for transfer to the plant?
vir genes
110
shi and roi are for what synthesis?
hormone
111
nos and ocs are for what synthesis?
opine
112
the plasmid also carries genes for synthesizing and _______ ________ ( _____ derivatives)
metabolizing opines. arginine
113
what carries genes required for infection?
TDNA
114
what is the transferred region that integrates into the plant chromosome?
T-DNA
115
the vir genes of the Ti plasmid are located _____ the re transferred region and is required for ____________.
outside. transfer process
116
the vir genes are induced by ______ compounds released by plants in response to ______
phenolic, wounding
117
responsible for the transfer of T-DNA to the plant wounded plant cell.
vir region
118
what is the sensor? and receptor for actosyringone?
vir A
119
what is the positive regulator for other vir genes?
virG
120
membrane protein vir A is autophosphorylated on _____ when it binds an ______.
histidine, inducer
121
VirA activates ____ by transferring the ________.
virG, phosphate group
122
what is an example of several bacterial two component systems that uses a phopshohistidine relay?
virA-virG
123
what is the effector?
virG
124
T-DNA is generated when a nick at the________ boundary creates a primer for synthesis of a new DNA strand.
right
125
The preexisting single strand that is displaced by the new synthesis is transferred to the______________________.
plant cell nucleus
126
Transfer is terminated when DNA synthesis reaches a nick at the_______ boundary.
left
127
what nicks and binds to 5' end in TDNA process?
virD2
128
The T-DNA is transferred as a complex of single-stranded DNA with the_________________________________
VirE2 single strand-binding protein.
129
T DNA is converted into_______ and is integrated into the __________.
double stranded DNA, plant genome
130
vir proteins that are transported to the nucleus (3)
vir D2, vir D1, virE2
131
transfer of T-DNA resembles what?
bacterial conjugation
