03/13 prokaryotic regulation Flashcards
what does I^S mean
it is a super repressor where the repressor is always on even with an inducer present
allolactose cannot bind to the repressor and allow it to release
what is diauxic growth?
it is the use of two sugars by a bacterium
in this case it is glucose and lactose
What if both lactose and glucose are present? why can the lac operon not be turned on simulataneously?
it is a waste of energy to create the enzymes needed to digest lactose when glucose is present
when is catabolic repression alleviated in the lac operon?
when there is no glucose present, the catabolic repression is alleviated and the lac operon is turned on to digest lactose
what is catabolic repression in the lac operon
it prevents the breakdown of lactose in the presence of glucose
what is the role of the catabolite activator protein?
it is the activator protein that will bind to the CAP site in the lac operon in the absence of glucose
is the CAP protein always active?
no, it is usually inactive until the inducer, cyclic AMP is present and binds to it
what is the role of cAMP?
it is the effector molecule that binds to the CAP protein and activates it
how is cAMP made?
it is made from ATP via the enzyme adenylyl cyclase when there are low levels of glucose
what is the general role of cAMP?
it is a signalling molecule
what is the cAMP-CAP complex?
it is the complex that binds near the lac operon that induces transcription under positive control
in the presence of high levels of glucose, what happens to the enzyme adenylyl cyclase?
it is inhibited and cannot make cAMP
in the presence of high levels of glucose, how is the lac operon affected?
if there is an abundance of glucose, the enzyme required to make cAMP is inhibited and the CAP activator protein cannot bind to the lac operon, thus the rate of transcription decreases
what is the common role of the repressor and activator protein?
they are both induced by effector molecules that increase the rate of transcription
what are the conditions to take the brakes off of the lac operon?
lactose must be present to make allolactose, which will bind to the repressor and cause it to release
what are the conditions to put the gas on in the lac operon
glucose must be absent so the enzyme can make cAMP and the CAP protein can bind to the lac operon to activate it
if there are high levels of glucose, what are the relative amounts of ATP and cAMP?
there are high levels of ATP and low levels of cAMP
if there are low levels of glucose, what are the relative amounts of ATP and cAMP
there are low levels of ATP and high levels of cAMP
what is common of allolactose and cAMP?
they are both inducer effector molecules that increase the rate of transcription
what is bound to the operon in the presence of lactose and absence of glucose
the repressor is off and the activator is on (high amounts of cAMP)
in the presence of lactose and absence of glucose, what is the rate of transcription at the lac operon
the rate is high
what is bound to the operon in the absence of lactose and glucose
the repressor is on (no allolactose) and the activator is on (high amounts of cAMP)
in the absence of lactose and glucose, what is the rate of transcription at the lac operon
the rate is low
in the presence of lactose and glucose, what is bound at the lac operon
the repressor is off and the activator is off (low amounts of cAMP)
in the presence of lactose and glucose, what is the rate of transcription
the transcription is at a low basal rate
in the presence of glucose and absence of lactose what is bound at the operon?
the repressor is on (no allolactose) and the activator is off (low levels of cAMP)
in the presence of glucose and absence of lactose, what is the rate of transcription
very low
what is the purpose of the trp operon
it is involved in the biosynthesis of tryptophan
what is the role of the trpR gene in the trp operon
it codes for the repressor protein
what is the trpL gene
it is involved in the synthesis od a short polypeptide called the leader peptide that is involved in attenuation
what is a catabolic process
it is the breakdown of something, like lactose metabolism
what is an anabolic process
it is a process involved in “building up”
ex) tryptophan biosynthesis
how is the repressor in the trp operon different from the repressor in the lac operon
the repressor is initially inactive and not bound to DNA
when does the repressor bind in the trp operon
it binds when there are high amounts of tryptophan which act as corepressors
what type of effector molecule does the repressor in the trp operon act with?
a corepressor
when there are large amounts of trptohan, the repressor is
bound
when there is a low amount of tryptophan, the repressor is
not bound
what is the effector molecule for the repressor in the trp operon
it is tryptophan
is there an accelerator equivalent in the trp operon?
no, the operon is always on until a threshold amount of tryptophan has been synthesized
what does it mean to attenuate?
it means to cut a process short
how does the word attentuation describe the tryptophan operon?
it describes how transcription begins but stops at the attenuator sequence
why does attenuation occur
it occurs in bacteria due to the coupling of transcription and translation and it stops transcription midway
in the trp-L sequence, what are the critical regions?
1,2,3,4, these regions are complementary and can form stem loops
between what regions do the stem loops form and what is the third alternate loop that forms
regions 1-2 and 3-4 bind
2-3 is the alternate loop
what is the role of the 3-4 stem loop?
it functions as a terminator before the RNA polymerase can reach the structural genes
when a 3-4 stem loop forms, what happens to gene expression
the genes will not be expressed and the mRNA is attenuatd
if the 2-3 alternate stem loop forms, what will happen to gene expression
the genes will be expressed and will not be attenuated
what causes one stem-loop to form over another?
the level of tryptophan
if you have low levels of tryptophan, which stem loop will form?
the alternate 2,3 stem loop, this will allow transcription to occur to make new tryptophan
if you have high levels of tryptophan, which stem loop will form
the 3-4 snd 1-2 stem loop will form, this terminates transcription
why does the amount of tryptophan matter
it matters for determining whether or not transcription should occur based on the amount of charged tRNAs that are presemt
when transcription is not coupled with translation in the trp operon, what occurs?
two stem loops form, the 1-2 and 3-4, which will terminate the RNA polymerase
what is the role of the 3-4 stem loop in the trp operon?
it forms a rho-independent terminator that kicks off RNA polymerase
when there are low levels of trptophan, what loop forms?
an alternative 2-3 loop that allows transcription to occur
why is it important that the co-transcript and translation occur?
without transcription, the system would terminate
why is it important that there are two trp codons?
it regulates the speed at which the ribosome translates it
if there are high levels of tryptophan, how many charged tRNAs are present? why is this important
there are large amounts of charged tRNAs, this allows the ribosome to quickly translate the transcript and the 3-4 loop will form and terminate the RNA polymerase
if there are low levels of tryptophan, how many charged tRNAs are present? why is this important?
there are small amounts of charged tRNAs, this will stall the ribosome and allow the alternative loop to form which allows transcription to occur
if we do not have tRNAs for trptopan translation, what will occur?
the ribosome will stall and lead to the formation of a 2-3 alternate loop
what regions can region 2 hydrogen bond with>
1 and 3
what regions can region 3 hydrogen bond with?
2 and 3
what are the two conditions where attenuation occurs?
when transcription and translation are not coupled and when there are high levels of tryptophan
what is the situation where attenuation does not occur
when there are low levels of tryptophan
