Flashcards in Regulation I Deck (54):
how many ATP are used for protein synthesis?
2 million ATP per second
levels of regulation
- level of activity of enzyme
best to regulate at
make if you need it
- all use same promotor
- group of genes grouped together that are all part of the same transcriptional unit.
- multiple open reading frames
H2 = 2 H+ to 2 e-
hydrogenase operon of B. japonicum
- 4 operons
- 4 promotters
- each promotor slightly different.
- hupUV regulate hydrogenase synthesis - on all the time
- transfers signal to hoxXA and turns on genes
- encoded by hupSL
- hydrogenase typically turned off
- only expressed when
- hydrogen to eat
- nickel to make active site
- O2 to accept electron.
- hup SLCDF contains hydrogenase and needs to be on when condition are right
- proteins to put hydrogenase together
- always on
- keep the gene from being transcribed
- do at the promoter
- usually done by either helping (positive control) or preventing (negative control) the RNA polymerase from binding to the promotor
DNA binding proteins
- can bind to DNA backbone or either major or minor groove.
- to interfere with RNA pol binding
- the helices fit into the major groove of B-DNA
- they usually bind as dimers to dual half sites on the DNA centered 10 bp apart
bind to DNA and have region that contact RNA pol to make more active, get more RNA
- 2 phase growth
- depletes all glucose first then goes to lactose
Adaptation and Lactose
- if lactose is absent, none of the gene products are present
- if lactose is present as the sole sugar source, the gene products appear in near equimolar amounts
- if lactose is removed as the sole sugar source, new gene products are no longer made and previously made enzymes decay.
- a permease
- lactose transporter
- regulatory protein
operon for LacZ, LacY, and LacA
regulatory proteins bind
uninduced lac operon
repressor can bind
induced lac operon
lacI always made and binds to operator to repress
LacI binds to allolactose and won't bind to operator
How does glucose repress lac?
- lac operon regulated by levels of cAMP
when glucose present,
- level of cAMP low
when glucose levels decline
- adenylate cyclase is activated and catalyzes formation of cAMP from ATP
- now higher levels of lactose
Catabolite activating protein
- CAP binds to cAMP and the complex activates lac operon to break down lactose
- CAP is a DNA binding protein that activates many different (100) promoters
- global regulator
- E. Coli can grow on arabinose when glucose is depleted, but in order to do so, needs to turn on an operon to use the substrate
- turn on araA, arak, and araD
- convert to xylulose-5-phosphate and shuttled to pentose phosphate pathway
- can be activate ( in presence of arabinose) or repress (in absence of arabinose) the ara operon
binding sites for AraC
- 4 of them
- araO2, araO1, araI1, and araI2
- araC binds to 2 operators (one far away from promotor and one near) and loops out DNA
- araC monomers dimerize and transcription inhibited
- binds to O2 and I1
- arabinose fills in binding sites
- AraC changes conformation and loses affinity for O2
- binds to two adjacent operator sequences near promotor and allows for transcription.
- binds to I2 and I1 now
- encodes the enzymes for tryptophan biosynthesis
- only make when you don't have product
1st level of regulation of trp
- the trp repressor, when bound to tryptophan, will bind to the trp operator, repressing transcription.
- If trpR loses bound tryptophan, it falls off operator and transcription resumes.
2nd level of transcription
- at high trp levels, transcription of the structural genes will be terminated at attenuator sequence
- as mRNA is transcribed, the attenuator stem loop forms
- ribosome not stalled because tryptophan still there.
- sequence 1 and 2 form a loop and allow sequences 3 and 4 to form a transcriptional terminator.
- regions 3 and 4 will form a G-C rich stem loop with a oligo-U sequence.
- stops transcription before the rest of the operon is transcribed.
tryptophan starved condition
- sequence 3 is unavailable to make the transcriptional terminator, so transcription continues
- there is no tryptophan so the ribosome stalls at the tryptophan codons
- sequence 1 can't bind to sequence 2
- sequence 2 now binds to sequence 3 and transcriptional terminator does not form.
anti sigma factors
- if an alternate sigma factor of RNA polymerase is needed for transcription, some negative regulators act to bind the sigma factor and keep it rom recruiting RNAP
- obscuring DNA recognition domain.
- anti sigma 28
- represses transcription of flagellin (structural subunit) until motor and hook have been made.
- only want flagellin when assembling flagella
- flagella assembled outside of cell, so flagellin needs to be transported through hole made up of motor and hook.
assembly of the basal body - hook protein, and FlgM
assembly of the filament, sigma 28 regulated
When FlagM drops
sigma 28 recognizes promoter and RNA polymerase transcribes flagellin.
Two component regulatory system
- not convenient to bring compound being sensed into close contact with promotor
- composed of a sensor and a response regulator
- the sensor is a kinase (transfers a phosphate form ATP)
- most sensors are an autokinase
- sensor transfers phosphate onto regulator (aspartic acid residue), which becomes activated and allows transcription to occur
- meaning they transfer the phosphate to themselves upon sensing the environmental signal on a histidine residue.
- cell to cell signaling in bacterial communities
- autoinducers made at low levels and exported into medium.
- cells measure levels of AI to determine how many other cells are present
- few cells - low amount of AI
- many cells - high amounts of AI
Vibrio fischeri quorum sensing
- produce light when large concentration of cells
- AI is a homoserine lactone
- autoinducer synthase and the LuxR are always
- If enough AI sense LuxR will bind to AI allowing to dimerize and turn on luciferase
- make acyl-HSL
- At high enough levels will bind to LuxR and turn on transcription of luciferase