Midterm 4 Flashcards
regulons
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
Catabolite repression
shutdown of several systems that utilize various nutrients when glucose is present
the SOS response
a multigene system for wide scale DNA repair
jean jacques weigle
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
what does the sos response allow cells to do?
recognize and respond to serious dna damage
weigle experiment
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.
once they knew that the sos response existed, they wanted to know _______
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
how to screen to identify genes involved in sos regulation
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
RecA is a ___ for din gene
inducer
LexA is a _____ for the din gene
repressor
blue is ____
constitutively expressed
white is _____
unable to be expressed
RecA binds ____
single stranded DNA.
when it binds it, it is activated. then it cleaves the LexA repressor
heat shock genes are a __
regulon
what do sigma factors do?
in bacteria the use of different sigma factors directs RNA polymerases to certain genes
sigma 54
regulating nitrogen utilization in genes
sigma 32
heat shock protein gene regulator
sigma 38
general stress response gene regulation
post initiation control of gene expression
post transcriptional regulation
Regulatory RNAs
genomes carry regions of DNA coding for non-translated RNA
sRNA
control gene expression at transcription or translation points
quorum sensing
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
lux
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.
how does lux work?
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
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
Lux operon has _____
positive control
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
mechanisms controlled by quorum sensing:
motility
conjugation –> transformation
biofilm formation
pathogenesis
autoinducers may ________
play a role in competition interrupting or inhibiting a control pathway in other organisms in the environment
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
____ and _____ are examples of two component systems
sensor kinase (to detect environmental stimulus) and response regulator (to regulate transcription)
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
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
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
che proteins are ______
two component regulatory systems
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
when attractant is bound
flagella moves in the diredction it was going
when attractant (MCP) isn’t bound
tumble occurs flagella changes direction
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
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
transcriptomes
collection of transcribed mRNA molecules in a cell
northern blots
all Rnas including sRNAs
northern blots
separation of RNA fragments by electrophoresis followed by blot transfer and probing with labeled DNA fragments
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
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
paralogs
= genes that are different from each other yet arose from a single duplication event in the same ancestor
orthologs
-orthologs - genes that have evolved from the same ancestor with the same function in different organisms
to reproduce viruses must:
- get into permissive host
- acquire resources needed for replication
- evade host defenses
- spread to new hosts
acute infections
short duration, signs/symptoms observed, infection is cleared (immunity usually results)
ex. common cold = rhinovirus
or flu
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
herpesviruses latent
maintain circular episome during latency
latency associated transcripts (LATs) help maintain latency
reactivation events ______
typically damage the host cell
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
types of transmission
horizontal
vertical
zoonotic (horizontal)
mechanical (horizontal)
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
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
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
why have hiv rates decline in the us?
antiretroviral drug therapies and c sections
if untreated, roughly ___ infected mothers will infect their infants w hiv
1/3
2% now in US
reservoir
continual source of infective pathogens
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)
direct transmission
reservoir is other mammals
indirect transmission
reservoir is bird populations even tho you get bit by mosquito
there’s a vector bw you and the reservoir
mechanical transmission
intraspecies facilitated transfer of virus from host to host via another vector (e.g myxoma virus, yellow fever)
mosquito vector is NECESSARY
how is zoonotic transmission different from mechanical?
same species = mechanical
different species = zoonotic
ways viruses can cause cells to die:
necrosis –> direct
apoptosis –> indirect
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
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
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
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
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
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
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
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
how do tranducing rna tumor causing viruses possibly work
retrovirus effects by turning proto oncogene into oncogene
seasonality effects of covid
when little to no immunity exists in a population seasonality effects can be diminished
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
most material to least material in genetic library:
genome = DNA transcriptome = RNA Proteome = Proteins Metabolome = sugars, nucleotides amino acids
t or f transcriptomes include all RNAs including sRNAs
yes
SNOW DROP
southern dna
northern rna
western protein
dna and rna have a ____
negative charge to them so they go to the positive side of the electric field in electrophoresis
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
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
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
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
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
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
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
cellulose in gut w cows is _____
mutualism
parasitism
one species does obvious harm to the other
commensalism
one species benefits but nothing happens to other species
mutualism
both species happen
endophytes
plant endosymbionts
rhizobia
endophytes that can infect plant root cells fixing nitrogen and forming root nodules
endosymbionts go ____
into cells
we don’t have true endosymbionts –> mitochondria kinda they are anciently symbiotic
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)
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
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
lichens
a different arrangement
they have microbes/microbe symbionts
