Midterm 2 Flashcards
3 ways regulation of promotor region by DNA modification
- methylation
- DNA inversion
- local sequence variation
3 mechanisms for sigma factor release from antisigma factor
- proteolytic cleavage
- chemical interaction
- partner swapping
3 sites in ribosome
aminocyl site
peptidyl site
exit site
translation control: growth rate-dependent control of 70S ribosome
ribosomal proteins can bind to their won mRNA and prevent translation.
Higher levels of ATP promote translation. Lower levels inhibit.
translation consensus sequence
AGGAGG- critical for ribosome binding.
two types of M tRNA
initiator tRNA, elongator tRNA
translation - 3 elongation steps
aminoacyl-tRNA binding
transpeptidation
translocation
trigger factors
-ensure proper de novo protein folding
-2-3x more TF than ribosomes in cells
-
DnaK
hydrophobic core
sandwich subdomain, helical lid domain which compose the substrate binding domain.
DnaJ
cystein rich
zn finger domain
DnaK, DnaJ, GrpE - mechanism
DnaK is a holdase
DnaK is bound to ATP. DnaJ brings in protein to be folded. ATP is used to fold protein. DnaJ is released. GrpE facilitates the ADP ATP exchange.
signal sequence
N terminal marks the protein for secretion
tat system
transports proteins out of the cell - usually with cofactor.
powered by the PMF
how does the N terminus affect protein turnover
some AA are unstable (RKFLWY) and have a short half life.
4 reasons for protein degradation
- misfolded/unfolded
- denatured or damage
- missing their partner
- not needed anymore by the cell (process is complete
AAA protease
ATPases Assocated with a number of cellular activites
sspB
modulate kinetics of substrate binding y the protease
RssB
absolutely required for substrate recognition and proteolysis
regulated proteolysis mechanism
- truncated protein
- tagged with SsrA by tmRNA
- SspB binds to substrate to mark for the protease
- Proteolysis in protease with RssB and ATP.
enzyme regulation
activity
amount
allosteric effect
end product acts as an allosteric effector for the enzyme that is catalyzing the reaction, binding and changing the conformation of the enzyme.
covalent modifications of enzymes
methylation, AMP/ADP addition, phosphate group addition
corepressor
a repressor may need a corepressor to bind to it so it cna bind and block transcription.
inducer
bind to repressor and prevent them binding to DNA, allowing transcription
lac operon
-needs lactose present and high cAMP-CRP
-
arabinose operon
AraC is both activator and repressor
can for loop through dimerization
can bind to I and promote transcription of araBADa
Embdem-Meyerhof Pathway
glucose is used as precursor to form precursors for TCA.
gluconeogenesis - formation of glycogen/starch
can produce pyruvate, lactate, glycerol etc.
net yield of glycolysis
2ATP
2 pyruvate
2NADH
2 H2O
Cra and regulatory pathways
when glucose and lactose are present: Cra is off - repression of gluconeogenesis, ED and EM activated
when lactose is present: Cra is off- same as above
when neither is present: Cra is on - gluconeogenesis is activated, ED and EM off.
Cra - where does it bind? how do catabolites affect function
upstream of RNAP activator, downstream = inhibitor.
-catabolites bind and repress gluconeogenic genes and activate glycolytic genes.
CsrA
going to activate anything relating to growth - glyocolysis and pathogenesis
ED Net
1 ATP
1NADH
ED genes
all genes are not essential
ED genes
all genes are not essential
Pentose phosphate NET
ribulose 5-P, CO2, 2NADPH, 1ATP
TCA NET (including the pre step)
2 pyruvvate 6 CO2 8. NADH 2FADH2 2 GTP
FNR
Fumarate and nitrate reductase
TCA regulator
ArcA
aerobic respiration control, member o two component regulatory system responding to oxygen availability.
