lecture 19 Flashcards
(23 cards)
anabolic pathways build? what are examples? what kind of operons do they have?
larger molecules from smaller ones
–examples are pathways that build amino acids
-repressible operons
when are anabolic pathways shut down, how?
end product is made in sufficient quantities–> end product binds to repressor which then the repressor binds to the operator
–this is negative feedback
-trp is a corepressor –> ‘effector’
how many genes does the trp operon have and what regions does it have?
5 genes—E,D,C,B,A
6th gene–trpR– repressor protein
trpP promoter, trpO operator
trpL leader region that contains the attenuator region
what is the role the trpL plays in attention of trp operon ?
–has 2 back to back trp codon (UGG) that function to sense the availability of trp for attenuation
what does pairing of 3/4 do? 1/2?
1 is comp to 2, 2 comp to 3, 3 comp to 4
-termination stem loop:
3-4 pairing, halts RNA pol, terminating transcription before it reaches the structural genes
–region 4 has poly UUU, which is similar to intrinsic termination in bacteria
termination :
-1/2 paring caused when ribosome does not affiliate with the nascent trp operon leader mRNA–> leads to 3/4 pairing
–translation initiation breaks the 1/2 loop
what does pairing of 2/3 stem loop do and when does it happen?
antermination:
forms when region 1 can’t pair with region 2
–allows for RNA pol to continue transcription thru the leader region and genes of the trp operon
what are 3 features of the leader mRNA?
1) poly peptide coding sequence overlaps the leader region 1 + stop codon is adjacent to region 2
2) codon 10/11 specify trp, making translation dependent on trp availability
3)region 4 followed by poly u, which is associated with intrinsic termination of transcription
what happens if there is good amt of trp made?
ribosome makes steady progress along trpL until it arrives at the stop codon at region 2, then transcribes region 3 +4
since 2 is occupied by ribosome, 3 pairs w/4 , which will make it terminate via intrinsic termination due to the poly uuu at the end of 4
what happens when the cell needs trp ?
ribosome is forced to pause at codons 10 and 11 to wait for more charged trp tRNA to arrive
-ribsome is paused at region 1, so RNA pol transcribes region 3, which finds its complementary partner in region 2, forming 2/3 formation
-since region 3 does not have poly uu, termination is not possible
there is balance between 2/3 loops and 3/4 loops all the time, what happens to the ratio when trp is high and low?
high: more 3/4 loops than 2/3
low: more 2/3 loops than 3/4 loops
what happens if the trp 10 and 11 codon are mutated (missense)?
mutation of just one: affects responsiveness tot tryptophan
both:attenuator no longer senses trp concentration & senses the availability of the aa encoded by the mutated codon
what are 4 amino acids that are attenuated?
his, leu, pheA, thr
what happens to bacteria when they undergo heat shock and what does the new sigma unit bind?
what proteins are now expressed?
–rpoH encodes alternative sigma unit– sigma 32 + sigma 24
–sigma 32 binds different promoter–> -10 region is GC rich
-expression of heat shock proteins + chaperone proteins that help refold OR degrade the proteins at high heat
what happens to sigma 32 at normal growth temperatures + at high temperatures?
chaperon proteins bind it & inhibit it to form a holoenzyme
chaperons proteins release sigma 32 + let it form the holoenzyme
how do sigma factor work in B. Subtilis?
sigma factor is replaced by 2 new ones, which recognize promoters for genes used in sporulation
how do translation repressor proteins work?
how is translation inhibited by activation of the antisense RNA?
-bind near the Shino darlgarno—> interferes with recognition of shine dalgarno by the 16s subunit–> blocks intiation
-antisense prevents ribosome attachment via excessive transposase, which leads to excessive movements of transposable genetic elements
what is a riboswitch? what is the riboswtich in bacteria?
how does thi operon work?
a segment of mRNA that binds small regulatory molecule
-in bacteria, can regulate transcription + translation, alter stability of mRNA
thi operon uses TPP + ribswitch in 5’UTR of mRNA to produce mRNA that are dependent on TPP concentration
low TPP–> TPP can not bind riboswitch, which allows formation of anti termination stem loop to transcribe the thi operon genes
high TPP—>binds riboswitch, termination stem loop followed by pol uu makes intrinsic termination before reaches thi
what is the riboswtich in E coli for TPP synthesis (translation) ?
how does it work when there is low TPP and high TPP?
low TPP– 5 UTR folds into structure that has Shine Dalgarno antisequsetor stem loop, which allows shine dalgarno to bind 16s rRNA sub unit
—AUG is close, so the proteins are produced
high—–TPP bound to switch induces formation of mRNA stem loop–> shine dalgarno does not fold so it is not available to 16RNA subunit, so can’t bind the AUG and start translation
how does riboswitch work to control mRNA stability?
high and low GlcN6P concentration?
B. subtilus has glmS gene that produces glutamine transferase
low Glcn6P: transcription of glmS and translation will occur
high Glcn6p: Glcn6p wil bind to riboswitch in 5’ UTR of glmS mRNA–_> induce cleavage of mRNA
what does SigD do?
what can sigma factors be positively and negatively regulated by?
controls motility genes + toxin production during vegetative state
pos; other sig factors + pos effectors
neg: transcriptinal repressors, anti sigma factors
in C thermocellum, cellulose digesting enzymes are regulated by?
how does it work?
polysaccharide detection by anti sigma factor
polysaccharide biding causes conformation change in anti sigma factor CBM
sigma 24 release + actives transcription of genes required to transport + digest cellulose
sensors in attenuation can be?
riboswitch– bind small molecule
T box—binds tRNA
leader– binds tRNA
in trpR mutation, depletion of trp led to?
higher trp mRNA expression in presence of trp
