genes exam 3 gene regulation in bacteria

processes regulated at the genetic level

metabolism, environmental stress response, cell division

unregulated genes

genes that are constantly expressed; constitutive genes; housekeeping genes; actin for CYP1A

trans-acting factor

regulatory molecule to regulate genes on different chromosomes (such as transcription factors)

cis-acting factors

regulatory molecule to regulate genes on the same DNA strand/ chromosome as itself (such as promoters, silencers: specific DNA sequences as binding sites for transcription factors, such as activators and repressors)

regulatory proteins

have 2 binding sites: one for the DNA it regulates, and one for the effector molecules to bind to. is a repressor or an activator

effector molecules

bind to a repressor or activator, affecting whether those proteins can bind to DNA

inducer

molecule whose goal is to increase transcription rate of inducible genes. binding to repressor=prevents repressor from binding to DNA. binding to activator=promotes activator binding to DNA

corepressor

molecule whose goal is to decrease transcription rate of repressible genes. binding to repressor= helps protein to bind to DNA

inhibitor

molecule whose goal is to decrease transcription of repressible genes. binds to activator=inhibits activator from binding to DNA

regulation of the lac operon

no lactose=no synthesis of enzymes. each protein in lactose metabolism is coded by a different gene

operon

multiple genes under the transcriptional control of a single promoter. contains one promoter that regulates transcription of all genes needed for lactose metabolism

polycistronic mRNA

contains the sequence of two or more genes

lac promoter

tells where transcription should start for lactose metabolism

operator site (lacO)

binding site for the lac repressor (coded by lac i regulatory gene): upstream from promoter region

CAP site

recognized and bound by activator protein (catabolite activator protein: CAP) to start lactose metabolism

parts of the lac operon

CAP site, Lac promoter (lacP), operator site (lacO), protein-encoding genes (lacZ, lacY, lacA), and terminator

lacZ

encodes B-galactosidase

B-galactosidase

enzyme that cleaves lactose into galactose and glucose, or cleaves lactose into allolactose

allolactose

small effector molecule (inducer) on the lac operon

lacY

codes for lactose permease

lactose permease

membrane protein needed for the active transport of lactose into the cytoplasm of a cell of the bacterium

lacA

codes for galactoside transacetylase

galactoside transacetylase

covalently modifies lactose and lactose analogs

lac i gene

regulatory, not part of lac operon, has its own i promoter. constitutive expression at low levels: always inhibiting expression because lactose is not always present. codes for the lac repressor

lac repressor

binds to lac operator site and represses transcription. is a homotetramer

lac i- mutation

constitutive expression of lac operon when lactose is not present. unable to synthesize repressor proteins (end up with too much lacZ, lacY, and lacA). repressor is unable to bind to lac operator.

lac i s mutation

operon cannot be induced even when lactose is present. no ability to bind to allolactose, so induction does not occur

regulation of lac operon

lactose becomes available. converted to lacZ and lacA. allolactose binds to repressor, causing it to fall off operator site. lac operon proteins are synthesized, promoting metabolism of lactose. lactose is depleted, allolactose levels decrease, it is released from repressor, allowing it to bind to operator site. proteins involved are degraded. no lactose=no synthesis of enzymes. each protein in lactose metabolism is coded by a different gene

repressor protein w/ inducer molecule OR activator protein w/ inducer molecule

transcription proceeds

repressor protein w/ corepressor OR activator protein w/ inhibitor molecule

transcription is inhibited

diauxic growth

when there are two sugars present to metabolize (glucose and lactose), so one is preferentially metabolized first; one at a time b/c glucose is easier to metabolize. the preferred sugar is consumed first

cyclic-AMP (cAMP)

inducer effector molecule produced by adenylyl cyclase. helps bind cap to cap site. cAMP decreases when adenylyl cyclase is blocked when glucose is present. mediates CAP

adenylyl cyclase

production of this is blocked when glucose is present, which leads to decreased levels of cAMP, because this produces cAMP

catabolite activator protein (CAP)

mediated by cAMP. has two subunits that can be bound to cAMP. trans acting factor. regulator transcription factor proteins

lactose, no glucose

high levels of adenylyl cyclase, so CAP can bind to cAMP. allolactose is present, so repressor cannot bind to operon. high expression of lacZ, Y, and A.

no lactose, no glucose

no allolactose present, so repressor binds. presence of adenylyl cyclase, so cAMP binds to CAP. very low transcription because repressor overpowers activator

lactose, glucose

allolactose is present, so repressor cannot bind. adenylyl cyclase is blocked, so cAMP level is low, so CAP cannot bind to CAP site on operon. low transcription rate.

glucose, no lactose

adenylyl cyclase expression is blocked, so cAMP levels are low, so CAP does not bind to CAP site. no allolactose is present, so repressor binds. transcription rate is very low.

trp operon

enzymes involved in the synthesis of the amino acid tryptophan. regulated by a repressor protein and attenuation

tryptophan

amino acid whose synthesis is regulated through the trp operon: trpR and trpL

attenuation

premature termination of transcription before the transcription of all the genes in the operon is complete

genes in the trp operon

trpE, trpD, trpC, trpB, trpA. responsible for the synthesis of tryptophan

trpR

not part of the trp operon; has its own promoter. codes for the repressor of the operon. always turned on. very upstream of the operon.

trpL

part of the trp operon; not involved in synthesis of tryptophan. enhances or inhibits txn. made of 14 amino acids in the mRNA. regulated by the operon; not always turned on

trp repressor does not mind to the trp operon, which increases the transcription of the trp operon. in order to increase tryptophan in the cell

what happens when tryptophan levels are decreased?

trp repressor binds to the trp operon, decreasing rate of transcription of tryptophan. shuts down expression of operon

what happens when tryptophan levels are increased?

attenuator sequence

downstream of the trpL and operator. transcription stops here before it reaches the genes

region 1 of the trp operon

contains 2 trp codons. will bind to region 2 or the ribosome. ribosome could get stuck here or bind to region 2

region 2 of the trp operon

can bind to region 1 (no translation, but there is attenuation), or bind to ribosome (leading to attenuation), or bind to region 3 (no attenuation)

region 3 of the trp operon

forms stem loop with region 4 (attenuation), or binds with region 2 (when ribosome is stuck at region 1; no attenuation).

3-4 stem loop

dependent on translation of the trpL gene (if there is no translation, there will be a stem loop) and the amount of tryptophan in the cell (increased tryptophan)

u-rich attenuator

example of rho-independent termination (intrinsic).

shine dalgarno sequence

9 mRNA nucleotides attached to the 16S portion of the small subunit of the ribosome

peptidyl transferase reaction

catalyzed by the 23S portion of the large subunit of the ribosome

posttranslational modification

covalent modifications of a protein that either inhibit or activate the function of a protein

translational repressor regulatory protein

recognizes sequences in mRNA and inhibits translation. does this by binding to the shine dalgarno sequence and the start codon

osmoregulation

the amount of water in a cell

hypotonic

less solute, more water

hypertonic

more solute, less water

ompF gene

increases the loss of water from the cell

low amount of solute. increased amount of ompF protein (the goal:___).

decreased osmolarity

high amount of solute. decreased amount of ompF protein (the goal:___)

increased osmolarity

micF

inhibits ompF, which decreases the loss of water in a cell, because ompF increases the loss of water in a cell. this can happen because they are complementary. this is a posttranslational regulation

low amount of ompF

high amount of micF

high amount of ompF

low amount of micF

antisense strand of mRNA of micF

the sense strand of ompF is complimentary to

sense strand of mRNA of micF

the sense strand of ompF is the same as

allosteric site bound by regulatory protein

cannot bind to substrate, so protein synthesis is inhibited

post translational regulation by feedback inhibition

the concentration of the final product regulates the pathway

low tpp (thiamin levels) in transcriptional control

formation of antitermination loop. transcription continues

high tpp in transcriptional control

inhibition of antitermination loop. termination loop forms. attenuation proceeds

low tpp in translational control

formation of stem loop. shine dalgarno antisequestor is accessible to ribosome. translation occurs

high tpp in translational control

conformational change in secondary structure. shine dalgarno antisequestor cannot form. ribosome does not have access to RNA. translation is inhibited