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BIO 315 > Midterm 4 > Flashcards

Midterm 4 Flashcards

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1
Q

regulons

A

genes that are coordinated to respond to the same regulatory systems

(this means multiple sets of operons)

bigger than an operon has more than one promoter

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2
Q

Catabolite repression

A

shutdown of several systems that utilize various nutrients when glucose is present

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3
Q

the SOS response

A

a multigene system for wide scale DNA repair

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4
Q

jean jacques weigle

A

showed uv exposure induces nonspecific repair mechanisms in bacteria

bacteria were pre-exposed to uv light, then infected with damaged phages, repaired the phage DNA but also introduced more mutations

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5
Q

what does the sos response allow cells to do?

A

recognize and respond to serious dna damage

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6
Q

weigle experiment

A

uv light to damage phage. infect e coli with it and infect e coli that was exposed to uv light with it.

you see that a lot of phages are made from the ecoli that were exposed to the uv light because uv induces the repair response and it extends to the phages.

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7
Q

once they knew that the sos response existed, they wanted to know _______

A

which genes were involved in it. they used a promoter probe reporter lacZ gene transposon to figure it out.

When it was inserted next to a gene that was expressed in response to DNA damage, it was also expressed

this showed which genes were required for DNA damage repair

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8
Q

how to screen to identify genes involved in sos regulation

A

screen for mutant e coli cells in the presence pof DNA damging mitomycin C. made containing ampicillin, C-gal and mitomycin C.

pick all the blue e coli that are expressing b galactosidase indicate a high level of expression of genes that respond to dna damage and isolate them.

replica plate colonies on media without mitomycin C. white colonies confirm gene expression is in response to DNA damage (these are din genes that belong to the SOS regulon)

white are on when dna damage and off when not

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9
Q

RecA is a ___ for din gene

A

inducer

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10
Q

LexA is a _____ for the din gene

A

repressor

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11
Q

blue is ____

A

constitutively expressed

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12
Q

white is _____

A

unable to be expressed

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13
Q

RecA binds ____

A

single stranded DNA.

when it binds it, it is activated. then it cleaves the LexA repressor

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14
Q

heat shock genes are a __

A

regulon

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15
Q

what do sigma factors do?

A

in bacteria the use of different sigma factors directs RNA polymerases to certain genes

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16
Q

sigma 54

A

regulating nitrogen utilization in genes

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17
Q

sigma 32

A

heat shock protein gene regulator

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18
Q

sigma 38

A

general stress response gene regulation

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19
Q

post initiation control of gene expression

A

post transcriptional regulation

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20
Q

Regulatory RNAs

A

genomes carry regions of DNA coding for non-translated RNA

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21
Q

sRNA

A

control gene expression at transcription or translation points

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22
Q

quorum sensing

A

gene regulation process that allows bacteria to talk to one another

a number of members of a group that must be present in order to conduct business

cells release autoinducer molecules into the environment as the population density increases

detecting changes in autoinducer levels causes regulation of gene expression

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23
Q

lux

A

example of quroum sensing system

can live freely in symbiosis with the hawaiian bobtail squid. the cells only emit light (via enzyme luciferase) when in the light organ of the squid– this helps the squid evade prey.

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24
Q

how does lux work?

A

tldr AHL has to hit a threshold to induce light emission

when grown to high density, the cells produce N-acyl-homoserine lactose (AHL)

this autoinducer stimulates luminescence

the luxI protein catalyzes AHL synthesis

at low density the cells don’t produce enough AHL to induce light emission

examination of how cells detect levels of AHL has been an area of active research

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25
LuxR
regulator/transcriptional activator interacts with AHL when it reaches a high enough concentration. AHL is like a coactivator. It bins to the lux box, DNA regulatory site and this leads to the transcription of luxA/luxB
26
Lux operon has _____
positive control
27
LuxI
always on at a basal level but when LuxR binds to the lux box in the presence of high AHL it really ramps up production -- this makes the luminscence
28
mechanisms controlled by quorum sensing:
motility conjugation --> transformation biofilm formation pathogenesis
29
autoinducers may ________
play a role in competition interrupting or inhibiting a control pathway in other organisms in the environment
30
two component regulatory systems
use one protein as a sensor and another to control transcription - this allows for response to changes in the environment - signal transduction induced inside the cell alters it to repsond appropriately
31
____ and _____ are examples of two component systems
sensor kinase (to detect environmental stimulus) and response regulator (to regulate transcription)
32
A tumefacians
example of two component reg system vir genes found on the Ti plasmid - only expressed under conditions similar to a plant wound site - virA/virG are required for expression of the other virulence genes - virA is a transmembrane protein HPK - vir G is a transcription activator RR protein
33
chemotaxis
move toward things we want away from things we dont controlled at the level of protein activity rather than via changes in gene expression chemotactic bacteria sense changes in chemical gradients over time changes induce altered direction and duration of flagellar rotation leading to directed movement over time
34
chemotaxis experiment
mutants outside of cap tube regular ones go into the cap tube cap tube is filled with nutrients. so that makes sense normal functioning ones go in and mutants dont
35
che proteins are ______
two component regulatory systems
36
CheA & CheY
works as a sensor kinase becoming phosphorylated phosphorylates CheY the RR protein -the phosporylated RR proteins do not bind DNA they bind to the flagellar motor and change its activity
37
when attractant is bound
flagella moves in the diredction it was going
38
when attractant (MCP) isn't bound
tumble occurs flagella changes direction
39
genomic library
collection of cloned dna fragments that represents the entire genome of an organism the number of cloned fragments needed to encompass an entire genome can be determined by the formula
40
genetic libraries
the method of obtaining the library varies depending on the desired outcome -a true genomic library is generated by shearing the genome and cloning the fragments a library of expressed mRNA molecules of a cell can be formed as a complementary DNA library using reverse transcriptase
41
transcriptomes
collection of transcribed mRNA molecules in a cell northern blots all Rnas including sRNAs
42
northern blots
separation of RNA fragments by electrophoresis followed by blot transfer and probing with labeled DNA fragments
43
microarrays
method of examining transcriptional activity of all genes in a cell simultaneously the technique is miniatured, automated reverse of northern blots - probe DNA fragments are amplified by PCR and placed on glass slide in a known pattern - total cell mRNA is converted to cDNA by reverse transcriptase, labeled with a fluorescent molecule and passed over the microarray slide - the more intensely a spot on the microarray lights up the more cDNA ergo, the more mRNA is present
44
comparative genomics
the study of evolutionary processes using the tools of genomics - genetic variability - different genes may have arisen from duplication events - paralogs = genes that are different from each other yet arose from a duplication vent -orthologs - genes that have evolved from the same ancestor with the same function in different organisms
45
paralogs
= genes that are different from each other yet arose from a single duplication event in the same ancestor
46
orthologs
-orthologs - genes that have evolved from the same ancestor with the same function in different organisms
47
to reproduce viruses must:
- get into permissive host - acquire resources needed for replication - evade host defenses - spread to new hosts
48
acute infections
short duration, signs/symptoms observed, infection is cleared (immunity usually results) ex. common cold = rhinovirus or flu
49
latent infections
period of acute infection followed by latency -virus is still present but replication is shutdown reactivation may occur leading to recurrence of acute infection signs and symptoms ex. include lambda phage and herpesviruses
50
herpesviruses latent
maintain circular episome during latency latency associated transcripts (LATs) help maintain latency
51
reactivation events ______
typically damage the host cell
52
is hiv latent chronic or acute?
technically chronic but after its short acute phase however it must be making a certain amount of infectious virions to be able to be transmitted as we have discussed
53
types of transmission
horizontal vertical zoonotic (horizontal) mechanical (horizontal)
54
horizontal transmission
transfer individual to individual within the same species requires a mode of exit and a mode of entry this is what people commonly think of when they think of catching something from someone
55
vertical transmission
still transmission within the same species from mother to fetus or newborn virus may be transmitted by placenta or during birth (rubella, hepatitis B and C, HIV) viruses can be transmitted via breast milk (HIV MMTV) a few viruses can even be transmitted via germ cells infection. these are endogenous retroviruses
56
endogenous retroviruses
have confluence of interest with the host. dont want to harm host best thing they can do would be silent most germ cell transmitted mmtv do not cause active infection in offspring as would be expected those that do represent recent integration events that have not yet been silence silent endogenous retroviruses make up at least 8% of the human genome
57
why have hiv rates decline in the us?
antiretroviral drug therapies and c sections
58
if untreated, roughly ___ infected mothers will infect their infants w hiv
1/3 2% now in US
59
reservoir
continual source of infective pathogens
60
zoonosis
disease that can be transmitted from non human animals to humans usually humans are the dead end in the transmission cycle still horizontal event ex rabies (direct transmission) and west nile (indirect transmission)
61
direct transmission
reservoir is other mammals
62
indirect transmission
reservoir is bird populations even tho you get bit by mosquito there's a vector bw you and the reservoir
63
mechanical transmission
intraspecies facilitated transfer of virus from host to host via another vector (e.g myxoma virus, yellow fever) mosquito vector is NECESSARY
64
how is zoonotic transmission different from mechanical?
same species = mechanical different species = zoonotic
65
ways viruses can cause cells to die:
necrosis --> direct | apoptosis --> indirect
66
necrosis
viral-induced cellular destruction the cell bursts sometimes due to overfilling the cell with new viruses other times due to viral impairment of normal cell functions
67
apoptosis
viral-induced cellular destruction the cell commits suicide (usually to stop the spread of the virus). often, the virus provokes the host cell to produce interferons which trigger apoptosis in surrounding cells
68
how do some viruses cause cancer?
transformation events produce changes in a cell that make it cancer like some viruses possess oncogenes, genetic material capable of inducing transforming events in host cells tumorigenesis may result from viral protein inducing a normally quiescent (not dividing) cell to enter the cell cycle
69
DNA tumor causing viruses =
papillomaviruses noneveloped icosahedral dsDNA viruses infects epithelial cells, causing warts may also induce transformation through e6/e7 viral proteins (leads most commonly to cervical cancer) not all strains possess genes for transformation vaccine exists against most common e6/e7 carrying strains
70
how do e6/e7 cause cancer?
Rb and p53 normally keep the cell cycle under control. they are tumor suppressor genes/proteins Rb and p53 inhibit progression of the cell cycle in different ways E6 and E7 block their action and encourage cells to enter S phase and reproduce
71
RNA tumor causing viruses
very few RNA viruses seem to cause cancer. MAINLY RETROVIRUSES DO THO WHY? retroviruses may act indirectly to induce cancer via altering proto-oncogenes (genes that code for regulation of the cell cycle) cis-acting retroviruses integrate genomes, activating a cellular proto-oncogene transducing retroviruses acquire a cellular gene and bring it with them into a newly infected cell
72
cis acting retroviruses
– Cis-acting retroviruses integrate their genomes, activating a cellular proto-oncogene. after conversion of rna to cDNa occurs the point of integration may alter expression of a proto-oncogene
73
transducing retroviruses
may have acquired a cellular proto oncogene during previous infections if that proto oncogene is overexpressed cancer results if that proto oncogene becomes altered it may alter the normal function within a cell usually then called an oncogene
74
how do tranducing rna tumor causing viruses possibly work
retrovirus effects by turning proto oncogene into oncogene
75
seasonality effects of covid
when little to no immunity exists in a population seasonality effects can be diminished
76
if you were interested in expressed mRNAs -- how would you gather them to put them into a genetic library?
make a poly U rich area and the poly As will come to it
77
most material to least material in genetic library:
``` genome = DNA transcriptome = RNA Proteome = Proteins Metabolome = sugars, nucleotides amino acids ```
78
t or f transcriptomes include all RNAs including sRNAs
yes
79
SNOW DROP
southern dna northern rna western protein
80
dna and rna have a ____
negative charge to them so they go to the positive side of the electric field in electrophoresis
81
proteomes
collection of expressed proteins in a cell can be studied by multiple methods including - 2D polyacrylamide gel electrophoresis (PAGE) - mass spec - xray crystallography - NMR
82
comparative genomics
is the study of evolutionary processes using the tools of genomics can show genetic variability, and how/when different genes may have arisen from duplication events paralog families can become very large
83
genomes have characteristics G+C nucleotide content
E coli = 50% G+C Streptomyces coelicolor = 72% saccharomyces cerevisiae = 38% areas of genome with significantly lower or higher G+C content than the rest of the genome are likely areas where horizontal transfer has occurred identifying and studying these areas can lend further insight into comparative genomic studies
84
genomic islands
DNA segments of 10-200kB associated with tRNA genes, transposable elements, plasmids, or bacteriophages endogenous prophages are those that are considered a stable part of bacterial genome some do conjugation some do transformation acts like a parasite of the virus interfering with the normal biology of phages to promote their own spread
85
core genome vs accessory gemone
transposable elements can go between taxa, orders, phyla and even kingdoms THEY DONT KNOW HOW accessory is the genes not present in all of strains of a species core genomes are genes present in all genomes
86
metagenomics
involves construction and analysis of gene libraries from DNA extracted directly from complex microbial communities this field is changing our understanding of life on earth, finding evidence for newly discovered organisms in very diverse and challenging locations
87
e coli shiga toxin example
e coli acquire shiga toxin prob through transduction shiga toxins are expressed by genes considered to be something of the genome of lambdoid prophages shigella and e coli are closely related
88
cellulose in gut w cows is _____
mutualism
89
parasitism
one species does obvious harm to the other
90
commensalism
one species benefits but nothing happens to other species
91
mutualism
both species happen
92
endophytes
plant endosymbionts
93
rhizobia
endophytes that can infect plant root cells fixing nitrogen and forming root nodules
94
endosymbionts go ____
into cells we don't have true endosymbionts --> mitochondria kinda they are anciently symbiotic
95
mutualism in plant bacteria example
plant provides leghemoglobin binds oxygen similar to hemoglobin in red blood cells prevents it from damaging nitrogen in a form the plant cells can use the bacteria provide valuable nitrogen in a form the plant cells can use (often ammonium ion)
96
root nodule formation
bacterial nod genes are expressed in presence of plants an infection thread is formed to invade the root the nodule forms providing a low O2 environment the root cells form leghemoglobin to assist the plant provides carbon compounds to the bacteria while bacteria provide ammonium in return
97
nodule metabolism
is it just sugar that the plants provide to the bacteria no it turns out that C4 dicarboxylic acids are provided by the plant, not sucrose these compounds are then inserted into the TCA cycle to produce ATP for the bacteria
98
lichens
a different arrangement they have microbes/microbe symbionts

BIO 315 (4 decks)

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