Lecture 14 Flashcards
what is the goal of transcription regulation
to maintain internal environment and survive
parts of the lac promoter
cap…rna binding site…lac O…shine dalgaro…start codon
where does positive and negative regulation in response to glucose happen
the lac promoter
why does lactose bind to the repressor
so it cant bind to lac O and prevent RNA pol from binding
types of transcription regulation
2 component system, quorum sensing, attenuation and lamdda phage
2 component pathway
let bacteria respond to external stimuli
-the receptor will get a signla and autophosphorylate on a histidine side chain
-the receptor sends phosphate to response regulator (protein) whihc is a DNA binding protein that will regulate transcription
how do ecoli respond to changes in the osmotic environment?
they use omp c and omp f porin proteins to limit the influx of solutes
porin protein
form pores in the outer membrane allowing molecules/ water to go in and out
omp c
narrower than omp f
-less molecules will flow causing the cell to stop shrinking
EnvZ receptor sensory kinase
change shape and activity to respond to osmotic pressure by increasing osmolarity and kinase activity
increase osmolarity
increase molecules in external environment which will in turn decrease water potential outside bacteria cell
how does EnvZ work with omp c and f
it will phosphorylate omp r and omp r will then regulate osmolarity genes
-the genes are omp c and f
-EnvZ has to activate omp c and f using omp r
-these are genes that alter the cells permeability
increase osmolarity response
use omp c to close gates in membrane so solute doesn’t enter
-very salty
decreasing osmolarity response
omp f will open the gates bc the environment is less salty
How many omp r site do c and f have
many
high affinity
bind tightly
-omp r doesnt need to be phosphorylated to bind
-omp f
omp r gets phosphorylated when?
when it needs to bind to sites of high and low affinity bc it also has to bind downstream (low affinity) to block transcription of omp F and turn on C
what happens to kinase when omp r is unphosphorylated
it doesnt change shape
what else can omp r control
pathogenesis
-only if in proper osmotic conditions and host environment
pathogenesis pathway
phosphorylated omp r goes to Ssra with will phosphorylate SsrB and then phosphorylate the pathogenesis gene
-these genes ARE NOT omp c or f
fusing photosynthetic light sensory to EnvZ
when omp r phosphorylates to omp c it will trigger lac Z (reporter gene) and we will see a black output
-this proves that omp c drives lac Z transgene
-turns bacteria into photographic film
collective bacteria behaviors
virulence factors, biofilm, antibiotic production and bioluminescense
autoinducer
secreted by bacteria, increase bacteria increase autoinducers
-at high concentrations they can enter cells and regulate genes
what binds to autoinducer
lux R
-targets gene activation
lux I
a.i. producing enzyme
lux r
needs autoinducer to binds @ operator and activate trancription
-the ligand must bind
-similar to CAP
prokaryote
simultaneous transcription and translation
where are bacterial structural gene coding regions
all on single polycistronic mRNA
what does ribosome do when it reached stop codon
stops and slides to the next ORF
trp operon
encodes enzyme for making amino acid tryptophan
-the regulation will depend on transcription and translation
what inhibites trp operon
tryptophan the amino acid because once it is made we dont need to keep making more
without tryptophan we cant?
there will be no dna binding and rna pol will not be blocked
-we can transcribe
no lactose present
trp repressor binds to operator while being bound to tryptophan
trpL
first trp operon
-makes short peptide for attenuation
hairpins
control rna pol depending on which regions are touching
1 and 2
pause
2 and 3
antitermination
-rna pol can go faster
-rna pol will be waiting at the 1 to make tryptophan
3 and 4
termination
-when rna pol is @ 2
-too much tryptophan so we kick rna pol off
cells that are close together have similar?
transcription factors
hershman chase
prove DNA is genetic material
attentuation
makes it easy to make amino acid because base pairing with RNA hairpin
-this is easier than proteins binding to specific DNA
lambda phage
goes into e.coli genome between gal and bio genes
-the spot it takes in the genome is determined by integration enzymes
lambda lysis
-determined by lambda repressor (CI gene) and cro binding proteins
-CI and cro will enter the bacterial genome
cro
kill
ci
-repressor
-keeps rna pol more upstream away from cro
-dont kill
ci decrease
cro wins, blocks ci, makes lysis gene
UV damage
-cro responds to threat by activating an enzyme to repair DNA
-this enzyme will accidentally blocks cI and let cro win accidentaly
euakryotes have
3 rna pol
rna 2
transcribes protein coding region
-only binds when general transcription factors bind to DNA bc it can’t make RNA by itself
rna 1
ribosomal rna genes
rna 3
tRNA genes
where does RNA pol 2 bind?
TATA box
what binds at tata box aside from RNA pol 2?
-tata binding proteins (TBP)
-TATA binding complex (TFIID)
what do TBP doa t the box
bend the DNA at the box by intercalating amino acids between base pairs
what complexes recruite RNA pol 2 to core promoter
TFIIB and TFIIA
what determines effectiveness of rna pol
cis regulatory region
-things like CAP and lux R
enhancers
only in eukaryotes
-proteins that enhance RNA recuitment
silencer
inhibit RNA recruitment
-inhibit turning on w out being a physical block
-repressor that does competitive DNA binding
-can happen it the activator would express a gene we dont want
mediator complex
simtulate or inhibit rna pol 2
shapes of transcription factors binding at DNA
helix loop helix, Zn 2+ inger (ions make the finger structures), leucine zipper (protein w zipper)
combinatorial control
allowed by mutliple enhancers and transcription factors
what can an enhancer with the right transcription factor do?
turn on a gene
