Regulation I Flashcards
1
Q
how many ATP are used for protein synthesis?
A
2 million ATP per second
2
Q
levels of regulation
A
- transcriptional
- translational
- level of activity of enzyme
3
Q
best to regulate at
A
transcriptional level.
4
Q
anabolic pathways
A
make if you need it
5
Q
catabolic pathways
A
break down
6
Q
operon
A
- all use same promotor
- group of genes grouped together that are all part of the same transcriptional unit.
- multiple open reading frames
7
Q
hydrogenase formula
A
H2 = 2 H+ to 2 e-
8
Q
hydrogenase operon of B. japonicum
A
- 4 operons
- 4 promotters
- each promotor slightly different.
9
Q
1st operon
A
- 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.
10
Q
2nd operon
A
- hup SLCDF contains hydrogenase and needs to be on when condition are right
- chaparones
11
Q
3rd operon
A
- proteins to put hydrogenase together
- structural
12
Q
4th operon
A
- always on
- sensors
13
Q
transcriptional control
A
- 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
14
Q
DNA binding proteins
A
- can bind to DNA backbone or either major or minor groove.
- to interfere with RNA pol binding
15
Q
helix-turn-helix
A
- 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
16
Q
activators
A
bind to DNA and have region that contact RNA pol to make more active, get more RNA
17
Q
dioxic growth
A
- 2 phase growth
- depletes all glucose first then goes to lactose
18
Q
Adaptation and Lactose
A
- 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.
19
Q
LacZ
A
encodes B-galactosidase
20
Q
LacY
A
- a permease
- lactose transporter
21
Q
LacA
A
a transacetylase
22
Q
LacI
A
- regulatory protein
- repressor
23
Q
Plac
A
operon for LacZ, LacY, and LacA
24
Q
Operator
A
regulatory proteins bind
25
uninduced lac operon
repressor can bind
26
induced lac operon
no repression
27
no lactose
lacI always made and binds to operator to repress
28
with lactose
LacI binds to allolactose and won't bind to operator
29
How does glucose repress lac?
- lac operon regulated by levels of cAMP
30
when glucose present,
- level of cAMP low
31
when glucose levels decline
- adenylate cyclase is activated and catalyzes formation of cAMP from ATP
- now higher levels of lactose
32
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
33
Arabinose operon
- 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
34
AraC
- regulator
| - can be activate ( in presence of arabinose) or repress (in absence of arabinose) the ara operon
35
binding sites for AraC
- operators
- 4 of them
- araO2, araO1, araI1, and araI2
36
no arabinose
- 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
37
with arabinose
- 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
38
trp operon
- encodes the enzymes for tryptophan biosynthesis
| - only make when you don't have product
39
1st level of regulation of trp
- transcriptional
- 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.
40
2nd level of transcription
- at high trp levels, transcription of the structural genes will be terminated at attenuator sequence
41
excess tryptophan
- 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.
42
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.
43
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.
44
FlgM
- 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.
45
Class I
master regulator
46
Class II
assembly of the basal body - hook protein, and FlgM
47
Class III
assembly of the filament, sigma 28 regulated
48
When FlagM drops
sigma 28 recognizes promoter and RNA polymerase transcribes flagellin.
49
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
50
auto-kinase
- meaning they transfer the phosphate to themselves upon sensing the environmental signal on a histidine residue.
51
Quorum sensing
- 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
52
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
53
Actyl-HSL mechanism
- make acyl-HSL
| - At high enough levels will bind to LuxR and turn on transcription of luciferase
54
biofilm formation
- regulate toxin production when a lot of bacteria around
- don't waste resources
- controlled by LuxR type regulators
- if attach to surface, produce alginate when a lot of other bacteria are around to form biofilm.
