BIOL 300 Discussion - Prokaryotic Gene Regulatory Circuits

what is the positive control mechanism?

activator protein binds to the promoter and increases transcription rates

what is the negative control mechanism?

repressor protein binds downstream of promoter called the operator, and stops transcription from occuring

how much of bacteria is controlled?

all of it - ½ is negative, ½ is positive

what is the role of the inducer?

inducer helps turn on transcription by allowing activator to bind onto DNA

what is the role of the corepressor?

helps repress transcription by allowing repressor to bind to operator

what is an operon?

group of genes thats controlled by a regulatory unit through promoters, enhancers, and operators

what is the purpose of the lac operon?

takes lactose and breaks down into sugars the bacteria can use - expressed when lactose is present, and when glucose is absent

what are the lacZYA genes?

3 structural genes that are under one promoter and one terminator - all encode diff products

what does lacZ encode?

beta-galactosidase gene, which breaks lactose into monomers (glucose and galactose)

what does lacY encode?

permease - allows lactose to go into cell

what does lacA encode?

acetylases beta-galactosidase

what is the lacI repressor?

not a part of the operon - turns off the lac operon

when is lacI repressed?

when lactose/IPTG is present, as it will be metabolized into allolactose (a reducer) and pull the repressor off the lac operon, and therefore make the repressor unable to bind to the operator

when is lacI active?

when lactose is absent

what is the CRP?

cAMP receptor protein

what does cAMP do?

amplifies signals in a cell

when is cAMP turned on?

when glucose levels are low (inverse relationship) - will bind to CRP, and the two will make a complex that stabilizes and recruits RNAP

how is the lac operon turned on?

it’s turned off by default through lacI gene is expressed into repressor which is bound to operator. when lactose is present, its metabolized into allolactose (which is an inducer), binds to repressor and pulls it off so repressor protein is bound to it. RNAP will bind to promoter region, but is unstable. because glucose is low, cAMP is high, so it will bind to CRP, and the complex will bind to RNAP to stabilize it, to allow for transcription

what is the purpose of the lac operon, and is it automatic?

this process is autonomous; also when lactose is broken down into glucose, it can then be metabolized and used for energy

what is a phage?

virus that infects bacteria

what does phage lambda infect?

e.coli

what are the two phage lifecycles?

lytic and lysogenic

whats involved in the lytic life cycle?

phage quickly injects itself into the host cell, makes many copies, and lyses the host cell - happens when bacteria is in good environmental condition, because it will take advantage of all the resources

whats involved in the lysogenic life cycle?

phage incorporates itself into the host genome and becomes a prophage - it will be replicated along with the cell. this occurs if environmental conditions are poor, because the immune system of the bacteria will be down

can lifecycles swap?

yes, a phage can switch from lysogenic to lytic

what is the process of the lysogenic pathway?

3 promoters are turned on: promoter left (creates N gene into mRNA transcript > protein, hits A, which can be turned on or off, and stops), promoter right (creates Cro gene > protein and stops at R), and promoter right prime (hits an attenuator immediately so nothings created). N protein turns off promoter left and right terminators, so CIII gene product is made. Cro protein is still made, so C2 protein and Q protein is made. these proteins accumulate, and the CIII protein will bind to CII, and together they’ll travel to PRE (speciically CII turns it on), which will make CII, Cro, and C1 products. However, these are made in the opposite orientation, which means the newly created products are antisense, which will bind to original mRNA and turn off production of any more products. C1 becomes a protein after translated, and will bind to operator left and right and repress them, shutting everything down (so only Prm is still on). this locks the phage into the lysogenic pathway.

what is the process of the lytic pathway?

3 promoters are turned on: promoter left (creates mRNA that contains N gene > N protein), promoter right (creates mRNA that contains Cro gene > Cro protein), and promoter right prime (). N will bind to terminators at promoter left and promoter right for further transcription, so CIII is transcribed > protein products (CIII and N). promoter right can then make an mRNA that has Cro, CII, and Q, all of which will make protein products. THIS IS THE POINT WHERE LYTIC PATHWAY DIVERGES* 
These proteins can’t build up, and CII will eventually be degraded, so PRE won’t get turned on and CI won’t get made. Therefore, Cro proteins bind to operator left and right to stop chance of making CI protein. Protein Q will then turn off terminator at promoter right prime, so it can be active, and create mRNA that has S and R gene products, and make their proteins. these proteins are needed for lysis of cell.