CH.12 Flashcards
plasmids are self replicating circular genomes that maintain a relatively _______ copy number
constant
explain what low copy of plasmids are?
1-10 copies per cell. have a segregation mechanism
explain high copy in plasmids
more than 10 copies, sometimes up to 100 or more. are distributed between the daughter cells randomly
episome
a plasmid that can integrate into the host chromosome
phages are self replicating entities that produce _________________. may be ______ or ______, _____ or ______.
infectious particles. circular, linear, DNA OR RNA
lysogenic
phages that can integrate into the host genome
immunity
ability of a phage or plasmid to exclude reinfection by similar entity
the transfer of phages occurs through _______
infectious particles
the transfer of plasmids occurs through _______
conjugation
plasmids are always ________, but phages may exist as either _______ or _______.
circular. linear or circular
DNA pol usually binds region
that _______ origin
surrounds
what is the linear template called?
adenovirus
bottom strand is used as _______ and the top strand is _______
template, displaced
top strand forms ______ before initiating DNA synthesis..
terminal duplex
duplex origin formed by _________
base pairing
what is an example of a small protein that intervenes with the problem of linear replication?
adenovirus DNA
protein intervenes are often used by ____________ that have proteins linked to the 5’ terminal base
viral nucleic acids
during strand displacement for linear DNA replication, the first synthesis uses a _______________.
normal double- stranded linear template
the displaced strand mimics a____________ by forming what?
linear double strand, hairpin structure
terminal protein ______ binds to the 5’ end of the ______ of adenovirus DNA between ____ and _____ nucleotides
dCTP, top strand, 9-18
host protein ______ is essential for the _______. it binds between ___ and ____ nucleotides
nuclear factor 1, initiation. 17-48
initiation complex forms between positions __ and ___= ___________ from the actual DNA end
9 and 48. a fixed distance
what serves as a primer for DNA synthesis in strand displacement?
3, OH of dCTP
new strand is _________ to the initiating dCTP
covalently
old TP is _______ by the new TO fir each new replication cycle
displaced
does TP remain attached during elongation?
yes
name two of the solutions
hairpins, and telomere( repetitive sequences)
another solution used is converting ______ to _______ or multimeric molecules.
linear to circular
lambda phage is an example of what?
T4 phage is an example of what?
circular, multimeric
rolling circle generate what?
single stranded multimers of the original sequence
rolling circle is an example of what?
each strand being replicated independently
what does the nicking in rolling circle?
protein A which is a endonuclease (cuts in the middle)
what does an exonuclease do
cuts on the ends
ϕX A protein is a cis acting _______. what does it do?
relaxase. generates single stranded circles from the tail produced by rolling circle replication
A protein has multiple functions, what are the three?
origin recognition, endonuclease, and ligas
rolling circle replication is a model for what?
leading strand synthesis
plus strand is what? when it replicates it becomes what?
single stranded, minus strand
is the replicative form double stranded or single ?
double
rolling circle is used by ______ to do what?
plasmids to transfer themselves and host chromosome sequences to other bacteria during conjugation
F factor replication system is ________
surpressed
F plasmid is an example of a ______ in E.coli
episome
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
three methods of replication?
oriV, oriC, oriT
____ as free plasmid (one copy/bacterial chromosome)
oriV
uses e.coli chromosomal origin when integrated is called what? ____ is surpressed
oriC,OriV
______ during conjugation
oriT
discrete regions that has transfer genes?
TRA
simple transposons- encode transposase. used to insert into host chromosomes (integration)
IS
used to initiate plasmid replication- vegetative
oriV
where are tra and trb loci?
40 genes
used to initiate replication for transfer ( in conjugation- rolling circle model)
OriT
which bacteria is F +
the one that has F factpr
outer membrane protein that blocks mating pair formation?
T
blocks DNA transfer?
S
covalently attaches to 5’ end of DNA and unwinds (relaxase)
I
recruits TraI to 5’ end of DNA
Y
what proteins are involved with immunity?
s AND t
DNA nicking and unwinding?
Y and I
pilin-
A
SENSES THAT MATING PAIR FORMED
m
transfer of an F factor is initiated when rolling circle replication begins at _______
oriT
the free 5’ end initiates what? what is bound to the 5’ end?
transfer into the recipient bacterium. traI
transferred DNA is converted into __________ in the recipient bacterium?
double stranded
when F factor is ____, conjugation “infects” the recipient bacterium with a copy of the F factor
free
when F factor is _________, conjugation causes transfer of the bacterial chomosome
integrated
pilus is composed of what?
pilin subunits
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
transfer begins from _____ which is nicked by ______ complex at a ____ site. ( what usually does the nicking)
OriT. traY/traI. traI
how many unit lengths are transferred in conjugation?
one
plasmids can be either mobilizable or self transmissible. a mob plasmid only contains an _______. a self transmissible plasmid contains a ____ region
oriT. tra
tra systems are linked to their what?
incompatibility group
plasmids that allow transfer ofr DNA to unrelated species are known as what? and they recognize a range of oriT?
promiscuous
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
name this process: another plasmid is needed for this process. (helper plasmid must contain tra functions)
mobilization
binds near oriT and recruits TraI (relaxase),
traY
has nuclease & helicase (ATP) activity. Function enhanced by TraY & IHF (integration host factor);
traI
is a transferase covalent attachment of the 5’ end of the DNA to the protein (serves as the pilot protein)
traI
active transport, binds DNA, ATP/GTP binding sites, inner membrane protein, necessary for DNA transfer, directs 5’ end to the T4SS channel.
traD
protein A has the combined activities of _____ and _____. it recognized the ____ like traY and does nicking like traI
traY and traI, ori
blocks DNA transfer, inner membrane
TraS
outer membrane protein that blocks mating-pair formation
traT
name the two mechanisms of DNA integration in bacteria
homologous recombination and transposisiton
what does the Hfr cell contain?
an integrated F plasmid
F+ cell contains what?
episomal F plasmid
after integration, F plasmid ______________________________________________________. and _____ is suppressed
replicates as part of the host replicon. oriV
the donor chromosome is transferred as what?
single stranded DNA starting at the origin of transfer oriT
which gene is transferred first between bacteria?
the one closest to the origin
the integrated F plasmid is found when transferring into another bacteria?
both at the beginning and at the end of the DNA being transferred
does the F- strand stay -
yes it does
the transfer process using Hfr uses the _____ method or replication.
rolling circle
how long does it take to transfer entire chromosome of E.coli?
100 min
the double stranded transferred DNA is _____ into the recipient chromosome by __________.
integrated, double recombintation
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
the transfer of the host chromosome is ____ from the tra region and F- plasmid. except for a small part around _____.
away, oriT
in host chromosome transfer, donor DNA integrates into the host genome by _______ and _______.
recombination and transposition
most transfers are near the site of _____, which causes what to be formed?
insertion. gradient of transfer frequencies
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
A. timefaciens can transform plant cells into tumors. the infectious agent is a ______ carried by the ______.
plasmid, bacterium
is produced by wounded plant cells (phenolic compound).
Acetosyringone
Agrobacterium infection succeeds only on
wounded plants
what uses opines as nutrients in the soil?
agrobacterium
what transfers T DNA to the plant cell?
agrobacterium in tumor at wound sitt
opines are made up of what?
basic amino acids and alpha ketogluterate
encodes all of the functions required for the transfer of the T-strand to the plant
Virulence region( Vir)
23 kb region that is transferred to the plant (only the T-strand actually transferred)
T-DNA
T DNA is involved with the synthesis of what two things?
opine synthesis and plant hormone synthesis
allows the bacterium to use octopine and nopaline nutrient (most other soil bacteria lack these genes)
opine catabolism
what is the purpose for tra region?
is needed for the transfer of the entire pTi between different agrobacterium
what encodes genes necessary for transfer to the plant?
vir genes
shi and roi are for what synthesis?
hormone
nos and ocs are for what synthesis?
opine
the plasmid also carries genes for synthesizing and _______ ________ ( _____ derivatives)
metabolizing opines. arginine
what carries genes required for infection?
TDNA
what is the transferred region that integrates into the plant chromosome?
T-DNA
the vir genes of the Ti plasmid are located _____ the re transferred region and is required for ____________.
outside. transfer process
the vir genes are induced by ______ compounds released by plants in response to ______
phenolic, wounding
responsible for the transfer of T-DNA to the plant wounded plant cell.
vir region
what is the sensor? and receptor for actosyringone?
vir A
what is the positive regulator for other vir genes?
virG
membrane protein vir A is autophosphorylated on _____ when it binds an ______.
histidine, inducer
VirA activates ____ by transferring the ________.
virG, phosphate group
what is an example of several bacterial two component systems that uses a phopshohistidine relay?
virA-virG
what is the effector?
virG
T-DNA is generated when a nick at the________ boundary creates a primer for synthesis of a new DNA strand.
right
The preexisting single strand that is displaced by the new synthesis is transferred to the______________________.
plant cell nucleus
Transfer is terminated when DNA synthesis reaches a nick at the_______ boundary.
left
what nicks and binds to 5’ end in TDNA process?
virD2
The T-DNA is transferred as a complex of single-stranded DNA with the_________________________________
VirE2 single strand-binding protein.
T DNA is converted into_______ and is integrated into the __________.
double stranded DNA, plant genome
vir proteins that are transported to the nucleus (3)
vir D2, vir D1, virE2
transfer of T-DNA resembles what?
bacterial conjugation
