gene regulation

Question 1

what are control circuits

Answer 1

circuits with the function of conserving energy via feedback inhibition to prevent unnecessary production

Question 2

what are catabolites

Answer 2

external molecules which moderate induction or repression of a reaction

Question 3

what is a negatively controlled inducible reaction

Answer 3

a repressor naturally inhibits the reaction but an inducer can act on the repressor to induce the reaction

Question 4

what is a negatively controlled repressible reaction

Answer 4

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

Question 5

what is a positively controlled inducible reaction

Answer 5

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

Question 6

what is a positively controlled repressible reaction

Answer 6

the reaction is naturally induced by an inducer but a repressor can act on the inducer to inhibit the reaction

Question 7

what does the lac operon encode

Answer 7

beta galactosidase (the lac Z gene, hydrolysed lactose into glucose and galactose) and permease (the lac Y gene, transports lactose into the cell)

Question 8

what does lac I encode

Answer 8

a repressor protein which binds to the lac operator and prevents RNAP binding, inhibiting transcription

Question 9

what does lactose do to the repressor

Answer 9

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

Question 10

what happens in the E. coli operator mutation

Answer 10

the operator is mutated so the repressor can no longer recognise it and transcription always takes place

Question 11

what is the I- mutation

Answer 11

the repressor protein is non functional and can no longer bind to the operator. the mutation is recessive to wild type I+

Question 12

what is the Is mutation

Answer 12

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

Question 13

how does the repressor bind to the operator

Answer 13

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

Question 14

what is the effect of the conformational change lactose causes to the repressor

Answer 14

the spacing between the dimers is changed and they can no longer bind to the minor groove of the operator DNA

Question 15

what is CRP

Answer 15

catabolite repressor protein. it also used helix- turn- helix motif and is an additional control circuit for the lac operon

Question 16

what is diauxic growth

Answer 16

metabolites are used sequentially rather than all at once. glucose is used first (for immediate energy) then lactose which needs to be hydrolysed

Question 17

what is cAMP

Answer 17

cyclic AMP, an allosteric effector. it binds to CRP which binds to the lac promoter and increases affinity for RNAP

Question 18

what happens to cAMP when glucose is high

Answer 18

adenylate cyclase is inactive so no cAMP is produced.

Question 19

why does the repressor prevent RNAP binding

Answer 19

their binding sites significantly overlap

Question 20

why doesn’t cAMP- CRP binding prevent RNAP binding

Answer 20

there is no significant overlap of their binding sites. cAMP- CRP touches the alpha subunit of RNAP which stimulates it

Question 21

what does bistable entail

Answer 21

the operon is either on or off. it can appear gradacious at a [population level (bimodal population)

Question 22

how does the lac repressor bind to the operator

Answer 22

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

Question 23

what is complete dissociation

Answer 23

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

Question 24

what is partial dissociation

Answer 24

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

Question 25

what is transcription attenuation

Answer 25

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

Question 26

how does attenuation work in E.coli

Answer 26

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

Question 27

how does attenuation work in B.subtilis

Answer 27

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