chapter 5- transcriptional regulation

why regulate transcription and not the others?

transcription is the first step in protein synthesis
the most energetically efficient way to control which proteins are made

if the decision was during translation, it would be energetically wasteful if the mRNA will not end up being used

regulation of gene expression at the lvl of transcription

genes are expressed when their encoded proteins are needed, rather than all of the time
regulating mRNA production and protein synthesis conserves energy

regulation of gene expression can be influenced by the condition of the bacterial cell (change in type and lvl of nutrients available in environment)

tryptophan

amino acid required for the translation of some proteins

can be acquired from the environment or be synthesized by the bacterial cell if none are available

what happens if theres low tryptophan available

transcription of the trp operon

what happens if theres high tryptophan

transcription of the trp operon is repressed

promoter

dna sequence that is recognized by the sigma factor of rna polymerase that binds to dna at the promoter

what are the five co-transribed genes in the trp operon

trpEDCBA encodes enzymes that can produce tryptophan for the cell when it is scarce

preceded by a promoter and an operator

trp operon regulation

it is costly to the bacterial cell to make these enzymes and to produce tryptophan, so the trp operon is turned off when the cell can obtain sufficient tryptophan from its environment

the actions of the corepressor tryptophan on the trp operon

tryptophan acts as a corepressor, which is a small molecule that binds to the repressor, changing its shape so it can attach to DNA and block a gene

mechanism for repressors: when tryptophan is present in high concentrations

tryptophan binds directly to the inactive repressor protein

this binding switches the repressor into its active DNA-binding shape

the active repressor-tryptophan complex binds to the operator sequence

because the operator overlaps/ sits next to the promoter, the bound repressor physically blocks the promoter

the rna polymerase (sigma factor) cannot bind to the promoter, completely stopping transcription and preventing mRNA production

mechanisms for repressors: when tryptophan is present in low concentrations

without tryptophan to bind to it, the repressor cant change into its active shape. it just exists as an inactive protein

the inactive repressor is unable to attach to the DNA operator sequence

the promoter allows the RNA polymerase (sigma factor) to bind freely and transcribe trpEDCBA, allowing the cell to manufacture the tryptophan it needs

what is the operator

specific dna sequence in an operon that acts as a regulatory switch by serving as a binding site for a repressor protein

what is lactose

disaccharide composed of two monosaccharides (glucose and galactose) linked together by a glycosidic bond- could be used as carbon and energy source

genes involved in lactose catabolism are located within what?

lac operon
lacZYA

lacZ functions

encodes the enzyme B-galactosidase- cleaves lactose into glucose and galactose

lacY

encodes the protein B-galactoside permease- transports lactose into the cell

what is the expression of lacZYA regulated by

lacI repressor protein
encoded by the lacI (always expressed) gene located upstream of the lac operon

what is located between the lacI gene and lacZYA

promoter and an operator
a binding site for proteins to bind to DNA and influence transcription

own its own, the lacI repressor binds to ___ and inhibits ___

lac operator
transcription of lacZYA

what is the ability of the LacI repressor to bind to the lac operator is impacted by

effector molecule —> allolactose (small molecule that binds and regulates activity of a protein)

what is allolactose

isomer of lactose and produced from lactose by the enzyme B-galactosidase

what does it mean for b-galactosidase to be bifunctional

it breaks down lactose into the simple sugars glucose and galactose, which the cell uses for energy

it rearranges lactose into its isomer, allolactose- inducer molecule that binds to the lacI repressor to turn the operon on

deletion of lacI gene

lactose absent and present: lacZYA on

no repressor is produced, so RNA polymerase can always transcribe the operon

deletion of the lacZYA operator

lactose absent and present: lacZYA on

repressor cant bind- binding site is missing
operon is always transcribed

deletion of the lacZYA promoter

lactose absent and present: lacZYA off

RNA polymerase cant bind- transcription never occurs

deletion of lacZ gene (B-galactosidase)

lactose absent and present: lacZYA is off

B-galactosidase can’t be encoded to convert lactose to allolactose, which is an inducer that binds to the lacI repressor protein to remove it from the operator

therefore, repressor protein is still bound to the operator

deletion of lacY gene (B-galactoside permease)

lactose present and absent: lacZYA off

B-galactoside permease can’t be encoded, so lactose cant efficiently enter the cell- repressor remains bound and the operon is not efficiently induced

the presence of glucose represses the expression of genes needed for the metabolism of __?

lactose —> catabolite repression

low glucose = ?

high cAMP- binds to CAP

CAP-cAMP complex is able to bind to the intergenic region between lacZYA and lacI- acts as an activator for the expression of lacZYA from its promoter

high glucose = ?

low cAMP

glucose is efficiently processed to produce ATP

what is cAMP

form of adenosine monophosphate where the phosphate is bound to both 5’ and 3’ carbons

explain two-component regulators and how they sense change and alter transcription

the membrane bound sensor kinase senses a signal from outside the cell and autophosphorylates, using a phosphate from ATP

this phosphoryl group is then passed on to a response regulator

the phosphorylated RR undergoes a conformational change, allowing it to bind DNA and regulate gene expression in response to the external signal

explain ONE programmed change to DNA that alters transcription locally

bacteria can use phase variation to alter transcription lvls using sequence repeats in the promoter

changes in the length of these repeats can increase/ decrease the ability for the sigma factor to bind to its consensus, recruit RNAP, and initiate transcription at the start point

explains ANOTHER programmed change to DNA that alters transcription locally

some genes are driven by promoters that are affected by inversion events

Inversion of a region of DNA, where the sequence is turned around in the opposite orientation, can impact upon expression.

Promoters in the invertible region are switched in their orientation relative to the gene.

The inversion has switched the expression of the gene, with mRNA being produced when the promoter is in one orientation and not when it is in the other.