Chapter 10 Flashcards
Control of mRNA stability
mRNAs levels regulated by RNase activity (degradation)
posttranslational control
when proteins are made, their activity is controlled by modifying protein structure
• Cleavage, phosphorylation, methylation, acetylation
regulatory proteins
help a cell sense internal changes and alter its gene expression to match
• Bind ligands (specific, low- MW compounds)
repressors
repress transcription of target genes. blocks part of promoter; prevents sigma factor from binding.
repressor scenario 1
repressor binds dna, inducer causes repressor to release.
repressor scenario 2
repressor-corepressor complex binds dna, ligand concentration decreases and releases from repressor
• Known as derepression
Activators (transcriptional control)
bind DNA; activates transcription by interacting w/ RNAP
•activators bind poorly unless inducer is present
• Removal of inducer–>stops transcription
lactose
- Used as C and energy source
* LacY imports lactose from extracellular environment
lac operon
lacZ, lacY, lacA –1 promoter (lacZYA)
• Role of lacA is unclear
lacI
repressor upstream of lacZYA. has diff promoter
•Operator sites (binding sites) – lacO
cAMP
cyclic AMP. AMP–>adenosine monophosphate
Cyclic AMP (cAMP) accumulates
when a cell is starved for carbon
• cAMP-CRP complex binds to specific DNA sequences near bacterial genes (CRP= cAMP receptor protein)
cAMP activation
• cAMP-CRP binds to DNA (as activator)
• RNAP can get stuck even in absence of LacI
• cAMP-CRP causes DNA to bend
• CRP interacts w/alpha subunit of RNAP
-Helps initiate open complex formation
• cAMP-CRP can only bind when LacI is not bound
glucose
represses the lac operon by keeping lactose out of cell. FAVORABLE C source.
•glycolysis enzymes always being produced
• If there is glucose, no need to use lactose
other operons
AraC
both activation and repression
• Arabinose is absent-AraC represses production of genes for catabolism
• Arabinose is present-AraC activates same set of genes
other operons
Tryptophan operon
repression and attenuation
• Example of derepression
Tryptophan binds to
REPRESSION
TrpR (repressor protein)-converts it to active repressor (holorepressor) that binds to operator sequence (blocks RNAP)
• Low tryptophan – derepression of repressor and transcription of genes for trp biosynthesis
Attenuator RNA base pairing options
• 1:2 and 3:4
2:3
• 1:2 and 3:4
-3:4 = intrinsic terminator hairpin
• 2:3 called anti-terminator (more stable)
-Prevents terminator from forming–>transcription of trpE
What controls which hairpins form?
- High trp – ribosome translates, but stops at the stop codon (sequesters region 2) –>3:4 forms
- Low trp – ribosome stalls at double trp codons
- Region 2 binds to region 3
rnas can also bind
metabolites (riboswitches)
-Amino acids, vitamins, SAM, Mg, etc.
• Found in 5’-untranslated region of gene
• Conformational changes in RNA structure when metabolite is bound
regulatory circuits
analagous to electrical circuits
-multiple switches
How does cell know its reached an attractant?
- Methyl-accepting chemotaxis proteins (MCP)
- Cytoplasmic domains bind to CheA w/ protein CheW
- Binding of attractant to MCP causes conformational change that inhibits CheA activity (less tumbling)
of tumbles are supressed by
lower conce–> higher conc.
Quorum sensing
Aliivibrio fischeri – a marine microbe that colonizes a squid
•is bioluminescent but only at high cell densities
Which one gets expressed? cro or cii
High nutrients
low nutrients
dna damage
- High nutrients –cleave CII leaving Cro to start lytic cycle
- Low nutrients – CII
- DNA damage – lysis
Phage enters cell; transcription from PL and PR
Lysis vs Lysogeny depends on which regulation happens first
laz z
also cleaves X-gal–>color change–>blue colonies
If E. coli are treated with ATC
colonies are blue
another name for B galactosidase
lac Z
Lac Operon – no lactose
lac operon is transcribed at low levels (<10 molecules LacZ)
• Repressed by LacI
-Tetramer of LacI binds to two lacO, causes DNA to loop and prevents RNAP access
Lac Operon – high lactose
100-fold higher expression
• LacY to be expressed and let in lactose
• Low concentration of LacZ doesnt cleave the glycosidic bond of lactose; rearranges to allolactose
• Allolactose binds LacI and unlocks protein (removes repressor)
Trp operon ATTENUATION
- transc/translation happen at same time
- ribosome-sensor of amino acid levels
- dna bw operator and trpE
small rnas
- typically post-transcriptional control
- Repress and activate translation
- controls mrna degration
- require chaperone Hfq
How does cell know if concentrations of attractant are increasing?
CheR methylates MCP, reactivate cheA. cell tumbles until higher conc of attractant is encountered. then, no attractant. reset by CheB-P.
