gene regulation Flashcards
what are control circuits
circuits with the function of conserving energy via feedback inhibition to prevent unnecessary production
what are catabolites
external molecules which moderate induction or repression of a reaction
what is a negatively controlled inducible reaction
a repressor naturally inhibits the reaction but an inducer can act on the repressor to induce the reaction
what is a negatively controlled repressible reaction
an apo repressor alone can’t inhibit the reaction so naturally the reaction takes place. a co- repressor binds to the apo repressor which allows it to inhibit the reaction
what is a positively controlled inducible reaction
an apo activator can’t induce the reaction alone so naturally the reaction doesn’t take place. a co- activator binds to the apo activator and the reaction is induced
what is a positively controlled repressible reaction
the reaction is naturally induced by an inducer but a repressor can act on the inducer to inhibit the reaction
what does the lac operon encode
beta galactosidase (the lac Z gene, hydrolysed lactose into glucose and galactose) and permease (the lac Y gene, transports lactose into the cell)
what does lac I encode
a repressor protein which binds to the lac operator and prevents RNAP binding, inhibiting transcription
what does lactose do to the repressor
it binds to it allosterically, changing it conformationally and prevents it from binding to the operator. its problematic because it is also the substrate. IPTG can also bind to the repressor with the same result
what happens in the E. coli operator mutation
the operator is mutated so the repressor can no longer recognise it and transcription always takes place
what is the I- mutation
the repressor protein is non functional and can no longer bind to the operator. the mutation is recessive to wild type I+
what is the Is mutation
mutation of the repressor allosteric site where lactose cannot bind. this means the repressor always binds to the operator and transcription never occurs. the mutation is dominant to the wild type I+ mutation
how does the repressor bind to the operator
it used a helix- turn- helix motif and binds to the major groove of the operator DNA. the operator sequence is an inverted repeat which matches the repressor which is a mirror- image dimer
what is the effect of the conformational change lactose causes to the repressor
the spacing between the dimers is changed and they can no longer bind to the minor groove of the operator DNA
what is CRP
catabolite repressor protein. it also used helix- turn- helix motif and is an additional control circuit for the lac operon
what is diauxic growth
metabolites are used sequentially rather than all at once. glucose is used first (for immediate energy) then lactose which needs to be hydrolysed
what is cAMP
cyclic AMP, an allosteric effector. it binds to CRP which binds to the lac promoter and increases affinity for RNAP
what happens to cAMP when glucose is high
adenylate cyclase is inactive so no cAMP is produced.
why does the repressor prevent RNAP binding
their binding sites significantly overlap
why doesn’t cAMP- CRP binding prevent RNAP binding
there is no significant overlap of their binding sites. cAMP- CRP touches the alpha subunit of RNAP which stimulates it
what does bistable entail
the operon is either on or off. it can appear gradacious at a [population level (bimodal population)
how does the lac repressor bind to the operator
there are three binding sites. the repressor forms a tetramer (two dimers), one binding to the O1 site and the other either to O2 or O3. this loops the DNA and represses it
what is complete dissociation
at high levels of inducer, inducer molecules will bind at each of the four monomers. the tetramer will completely dissociate from the operator and the DNA will unloop, allowing induction
what is partial dissociation
at medium levels of inducer, inducer molecules will bind at some of the monomers. there will be partial dissociation then rapid rebinding. there is a small amount of transcription, including that of permease, which can eventually increase the inducer levels enough for complete dissociation
what is transcription attenuation
an additional regulatory circuit which can prevent translation past the attenuator sequence in certain conditions eg if Trp levels are high it will stop Trp biosynthesis
how does attenuation work in E.coli
by forming stem loops. if Trp is high then regions 3 and 4 will bind in a stem loop and cause ejection of RNAP. if Trp is low then regions 2 and 3 will bind, preventing 3 and 4 stem loop and therefore preventing RNAP ejection. this is positive repressible
how does attenuation work in B.subtilis
via TRAP. if Trp levels are low then mRNA will form an anti-terminator sequence. if Trp is high then mRNA will bind to trp then TRAP to promote a terminator. this is negative repressible where TRAP is apo and trp is co
