1.3: Prokaryotic Transcriptional Regulation Continued Flashcards
what is the difference between negative and positive regulation
for negative: when bound to dna, repressor protein prevents transcription
positive: when bound to dna, activator protein promotes transcription
determine whether the following description matches the lac repressor or trp repressor: ligand binds to remove regulatory protein from dna. such that during negative regulation the addition of ligand switches gene on by removing repressor, and in positive regulation, the addition of ligand switches gene off by removing activator protein
lac repressor
determine whether the following description matches the lac repressor or trp repressor: the ligand binds to allow regulatory protein to bind to dna. the removal of ligand swithces gene on by removing repressor protein (now in its inactive state) for negative regulation. and for positive, removing the ligand switches gene off by removing activator protein
trp repressor
which binding motif does the tryptophan repressor contain
helix turn helix
describe negative regulation
competition between rnap and repressor protein for promoter binding
describe positive regulation
activator protein recruits rnap to the promoter to activate transcription
cis regulatory elements/gene regulatory elements are typically close to which site of prokaryotic genes
the transcriptional start site
other than the transcriptional start site, where can regulatory elements also be found in prokaryotes and eukaryotes?
- far upstream of the gene
- downstream of gene (eukaryotes)
- within gene (introns; eukaryotes)
what is the NtrC protein
a transcriptional activator
describe the type of mechanism allows the interaction of NtrC to interact w rnap; even if it is a distance away
dna looping allows NtrC to directly interact w rnap to activate transcription from a distance. the process involves the dna to conduct a looped activation intermediate to allow the temporary interaction between rnap and NtrC (called kissing) which turns it on
what is a bacteriophage
virus that effects bacterial cell
is the lifestyle of bacteriophage lambda regulated by positive or negative regulatory mechanisms
trick question, its both
under what conditions are the prophage and lytic pathway favored
prophage: under favorable bacterial growth conditions
lytic: when the host cell is damaged
the two gene regulatory proteins, ______ (cI) and ________ are responsible for initiating the switch between prophage and lytic pathways actually _______ each other’s synthesis
lambda repressor protein (cI), Cro protein, repress
describe how the lambda repressor functions in the prophage state
the lambda repressor occupies the operator which blocks the synthesis of Cro, activates its down synthesis, most bacteriophage DNA is NOT transcribed
describe how the cro protein function in the lytic state
Cro occupies the operator, blocks synthesis of cI/lambda repressor. allows its own synethesis. most bacteriophage DNA is extensively transcribed. dna is replicated, packaged, new bacteriophage released by host cell lysis
t/f can the lambda repressor protein act as an activator
true
t/f can the cro protein act as an activator
false
describe what triggers the switch between prophage and lytic states
its host response to dna damage (induction event) which switches it to lytic state inactivates repressor.
under good growth conditions, lambda repressor protein turns off Cro and activates itself in a positive feedback loop to maintain the prophage state
what type of feedback maintains the prophage state
positive feedback loop
what type of feedback loop can be used to create cell memory
positive feedback loops - through the initial transient signal turning on expression of a gene and the cell will always remember it had that signal and the gene continues to be transcribed the the daughter cells regardless of signal
what can feed forward loops measure and how
it can measure the duration of a signal.
as both a and b are required for the transcription of z. z is only transcribed given the input is accumulated sufficiently.
describe how feed forward loops can decrease the sensitivity
crude example but just to help understand, if a or b is too sensitive to the signal - a splits in half (insufficient a to get both b and z going) so needs more signal to get enough such that z is transcribed
what is synthetic biology
when scientists construct artificial circuits and examine their behaviour in cells
describe the repressilator (tbh idk if we need to know this)
it’s an example of synthetic biology where scientists created a simple gene oscillator using a delayed(!!) negative feedback circuit. introduced the lac repressor, tet repressor (response to antibiotic), lambda repressor - tested out expressing and repressing diff genes. they observed increasing amplitude of fluorescence due to bacterial growth.
define transcription attenuation
premature termination of transcription
how is rna involved in transcription attentuation
rna adopts a structure that interferes with rnap, regulatory proteins can bind to rna and interfere with attenuation
can prokaryotes, eukaryotes, or both be affected by transcription attenuation
both
prokaryotes, plants, and some fungi can use _______ to regulate gene expression
riboswitches - NOT ALL RIBOSWITCHES DO TRANSCRIPTION ATTENUATION
define riboswitches are
short rna seq that change conformation when bound by a small molecule
provide an example of riboswitches and what is it regulated by
example: prokaryotic riboswitch that regulates purine (A,G) biosynthesis. regulated by low guanine levels
describe how high and low guanine levels impact the riboswitch that regulates purine (A,G) biosynthesis
low guanine levels: transcription of purine biosynthetic gene is on.
high guanine levels: guanine binds to riboswitch and the riboswitch undergoes conformational change. causes rnap to terminate transcription by prying it off before it has the chance to get to the coding sequence - the transcription of purine biosynthetic genes is off
t/f the flip flop device easy to draw
false
