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Midterm 2 Flashcards

1
Q

Tool to display localization of protein expression

A

biophotonic images

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2
Q

what is necessary for the analysis of colony forming units

A

the dilution of the sample

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3
Q

uses low energy laser pulse to isolate tissue from infected animals

A

laser capture microdissection

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4
Q

What are the methods to determine bacterial infectivity in animal models

A

clinical observations, pathological analysis, colony forming units, bio photonic images and laser capture microdissection

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5
Q

what does a CI over 1 indicate

A

mutant does better than the wildtype

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6
Q

What are the cons of the CI model

A

growth rate does not always correspond to virulence and the simultaneous inoculation may provide the necessary factors for virulence

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7
Q

What is the difference between in vivo and in vitro

A

in vivo occurs in living animals while in vitro happens with a tissue sample

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8
Q

What are the cons of LD50 ID50 models

A

lowly pathogenic batceria, requires a lot of animals, doesnt show progression, needs clear time measurements, and depends on the animal used

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9
Q

What are in the in vitro methods to measure virulence and infectivity

A

plaque assay and gentamicin protection

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10
Q

what does gentamicin do

A

kills surface bacteria but not invading ones

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11
Q

What does the plaque assay allow us to determine

A

how a bacteria is being spread. Those that spread cell to cell through junctions will survie

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12
Q

What does proteotomic profiling do

A

take a snapshot of all the proteins present in a cell

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12
Q

What are the drawbacks of tissue culture models

A

may not fully encapsulate in vivo environment, immortalized cells may behave differently, and limited number of generations in primary cells

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13
Q

what does transcriptional microarrays tell us

A

the amount of mRNA in a cell

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14
Q

what do we use RNAI screening for

A

to knock down expression of genes in a cell

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15
Q

what is the biochemical approach

A

isolate virulence factors and reintroduce them into the host

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15
Q

What is forward genetics

A

we have the phenotype and we want to deduce the genes responsible

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16
Q

what is a drawback of the biochemical method

A

misses in vivo factors of the bacteria

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17
Q

gene expression in non pathogenic bacteria cons

A

can only catch single- gene mediate phenotypes and the processes may be different inside the original bacteria

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18
Q

How does gene rearrangments in bacteria work

A

phase variation and gene duplication/amplification.

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18
Q

which cell type loses its polarity, expresses an array of surface proteins, and cannot be used to evaluate effects of mucus/secreted fluids

A

immortalized cells

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19
Q

gene duplication

A

increase copies of gene to increase chance of secondary mutation

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20
Q

gene amplification

A

increases diversity by introducing nonrandom repeats into a genome

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21
Q

what does the a’’ subunit do

A

interact with promoter regions

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22
what does the B subunit of rna polymerase do
rna synthesis
23
stabilizes and assembles rnap
W
24
reduces affinity for nospecific dna and increases for specific dna
sigma
25
multiple genes controlled by a single promoter
operon
26
what is the structure and function of the TCS
TCS is composed of histidine kinase and response regulator. The histidine kinase has an extracellular domain to sense and an intracellular domain that autophosphor
26
regulons
multiple genes in dif locations with similar promoters that are controlled by the same regulatory protein
27
how does the tcs stimulate gene expression
phosphorylate the regulators
28
how do anti-sigma factors cause disassociation of the sigma factor
phosphorylate/disulfide bond
28
what does the histidine kinase phosphatase do
remove the phospho group from the regulator and block gene expression
29
How does DNA supercoiling regulate gene expression
change in DNA topology in response to temp and osmolaity changes gene expression
30
How do RNA thermosensors work
low temp MRNA forms hairloops that block translation high temp opens up and allows for translation
31
what the translational forms of regulation
RNA thermosensors and small RNA regulatory systems
32
what are the main transcriptional regulators
sigma, cis acting rna sensors, and TCS
33
what are the nonprotein toxins
endotoxins and mycolactone toxins
34
LPS is what kind of protein and secreted by what
endotoxin and secreted by gram negative
35
bind to target molecules but do not translocate
type 1 super antigens
36
disrupt the membrane
type 2, membrane disrupting
37
type 3 toxins
A-B toxins. B translocates A into the cell
38
which toxin type is known to stimulate t cells and cause cytokine storms
type 1 toxins
38
which class of type 2 exotoxins requires oligomerization
the beta type
39
which domain of the type 3 exotoxins binds to cellular receptors
B domain
40
what kind of bond links the mature A and b domains of type 3 exotoxins
disulfide bond
40
can multiple B subunits interact with one A subunit in the type 3 exotoxin
yes
41
where does the translocation of A subunits (type 3 ) exotoxin occasionally occur
trans-golgi apparatus
42
what are the SEC dependent systems in gram negative bacteria
type 2 and type 5
43
sec system generally has ___ proteins
unfolded
44
what are the SEC independent systems
type 1,3,4, and 6
45
what is the function of secB
to keep proteins unfolded
46
what is the function of secYEG
protein export chanel
47
secA function
serves as the ATPase for the export channel
48
where is the signal peptide located for the sec system and is it cleaved
n terminus and yes
49
TAT transports what kind of proteins
proteins that are already folded
50
is the signal cleaved for TAT proteins
no, they are already folded
51
two step processing for excretion
type 2 and type 5
52
one step process
1,3,4, and 6
53
what are type 2 proteins associated with
adhesion, motility, and type 4 fimbriae
53
which sec type contributes to dna transformation in gram negative bacteria
type 2
54
diverse set of proteins that mediate their own export
type V
55
what is special about the type 1 signal sequence
not cleaved during transport and located at the c terminal
56
what guides proteins in the type 3 secretion system
chaperone proteins, they do not have a signal peptide
57
which secretion system has proteins closely linked to the assembly of the flagella
type 3
58
what kind of signal do type 6 ss proteins have
they have no signal
58
which secretion system has injectosomes that are generally conserved
type 3
59
what is the ATP dependent secretion system
type 6
60
which secretion system type is involved in cell to cell injections
type 6
61
what are the main activites coordinated using auto inducers
expression of virulence factors, sporulation, mating and bioluminescence
62
why are autoinducers beneficial
encourages spreading and allows for better protection against viral defenses
63
what kind of intraspecies auto inducers do gram negative bacteria release
hydrophobic
64
what kind of intraspecies auto inducers do gram pos bacteria release
auto inducing oligopeptides that are processed and then transported across the membrane
64
what kind of interspecies auto inducers do gram neg and gram pos release
Furanosyl borate diester
65
LUXI produces __
AHL
66
binding mechanism for AHL
diffuses into the membrane and then binds to the LUX-R proteins
67
what are the main classes of gram negative intraspecies autoinducers
AHLs, AI-1, and AHKs
68
what is AI2 associated with
interspecies gram neg and gram pos autoinducer
69
what enzyme produces AI2
LuxS
70
how is redifussion of AI2 prevented
phosphorylation of AI2
71
What are the methods of detection for AI2
cell surface TCS and direct import
72
which method incorporates radiolabeled/fluorescent bases to terminate polymerase reaction
Sanger
73
What are the advantages of 16s rna gene analysis
rapid information, cheaper, and gives reliable readout on the identity of an organism
74
what are the cons of 16sRNA gene analysis
not quant, species may be missed if they are not amplified well, limited to 1 gene: 1clone and rarely gives physiological information about the organisms
75
what does DNA hybridize with in the phylo chip process
probes on the coated chip
76
what are the advantages of phylochips
cheaper than large scale sequencing and allow a large number of samples to be analyzed
77
what are the disadvantages of phylochip
cross hybridization, not quantitative, and may miss uncommon bacteria
78
what is illumina sequencing associated with
sequencing by synthesis
79
how does pacific biosciences compare to illumina
lower throughput, higher cost, lower error, and longer reads
80
does illumina or pacific biosciences have a higher per read error rate
pacific biosciences
81
what kind of sequencing is illumina known for
very high throughput with very short reads
82
what is shotgun analysis
all dna in a sample, little PCR selection, and high throughout
83
what are the advantages of metagenomic analysis
extensive genetic info and preliminary functional analysis
84
what are the cons of metagenomic analysis
very expensive, difficult to associate a gene with a particular microbe, and does not tell us about the gene expression profile
85
what are the two dimensions of protetomic profiling
isoelectric focusing and protein expression pattern
86
what is the purpose of the type 7 secretion system
for gram positive bacteria that have a mycomembrane

Medical Microbiology (3 decks)

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