Chapter 14: Gene Regulation in Bacteria

gene regulation

the phenomenon in which the level of gene expression can vary under different conditions

constant

unregulated genes have essentially _____ levels of expression in all conditions over time

constitutive

unregulated gene are also called _____ genes

constitutive genes

a gene that is not regulated and has essentially constant levels of expression over time

constitutive

_____ genes encode proteins that are continuously needed for the survival of the bacterium

times, amounts

the majority of genes are regulated so that the proteins they encode can be produced at the proper _____ and in the proper _____

required

a key benefit of gene regulation is that the encoded proteins are produced only when they are _____

metabolism, response to environmental stress, cell division

few common processes regulated at the genetic level

repressor, activator

two types of regulatory proteins

repressor

a regulatory protein that binds to DNA and inhibits transcription

activator

a regulatory protein that binds to DNA and increases the rate of transcription

negative control

transcriptional regulation by a repressor protein

positive control

transcriptional regulation by an activator protein

negative control

default is doing transcription (have to add repressor to stop)

positive control

default is no transcription (have to add activator to start)

inducer

a small effector molecule that binds to a repressor or activator and cause the rate of transcription to increase

increase

inducers is a small effector molecule that causes the rate of transcription to _____

prevent

inducers can bind to a repressor protein and _____ it from binding to the DNA

cause

inducers can bind to an activator protein and _____ it to bind to the DNA

reduce

corepressors and inhibitors _____ the rate of transcription

corepressor

a small effector molecule that binds to a repressor protein, thereby causing the repressor protein to bind to DNA and inhibit transcription

inhibitor

a small effector molecule that binds to an activator protein, preventing the protein from binding to the DNA and thereby inhibiting transcription

Jacob, Monod

the research of _____ and _____ into genes and gene regulation stemmed from an interest in the phenomenon known as enzyme adaptation

enzyme adaptation

the phenomenon in which a particular enzyme appears within a living cell only after the cell has been exposed to the substrate for that enzyme

lactose metabolism, E. coli

Jacob and Monod focused their attention on the _____ _____ in _____

operon

an arrangement in DNA in which two or more genes are found within a regulatory unit that is under the transcriptional control of a single promoter

polycistronic mRNA

an mRNA that is transcribed from an operon and encodes two or more proteins

promoter, terminator

to facilitate transcription, an person is flanked by a _____ that signals the beginning of transcription and a _____ that signals the end of transcription

lacP (lac promoter)

binds RNA polymerase

lacO (lac operator)

binds the lac repressor protein

CAP site

binds the Catabolite Activator Protein (CAP)

lacZ

encodes b-galactosidase

b-galactosidase

An enzyme that cleaves lactose into galactose and glucose. As a side reaction, also converts a small percentage of lactose into allolactose.

lacY

encodes lactose permease

lactose permease

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

lacA

encodes galactoside transacetylase

galactoside transacetylase

an enzyme that covalently modifies lactose and lactose analogs by the attachment of hydrophobic acetyl groups

lacI

not part of lac operon, encodes lac repressor

lac repressor

a protein that binds to the operator site of the lac operon and inhibits transcription

negative

one way the lac operon is transcriptionally regulated (based on lactose/allolactose and this form of regulation involves lac repressor)

inducer

allolactose is a small effector molecule (_____)

absence, tightly, operator, inhibits

no lactose in the environment → _____ of the inducer allolactose → lac repressor is _____ bound to the _____ site → _____ the ability of RNA polymerase to transcribe the operon

available, repressor, prevents, can

lactose present → allolactose is _____ → allolactose binds to the lac _____ → conformational change of lac repressor _____ its from binding to the operator site → RNA polymerase _____ transcribe the operon

allolactose

the ability of the lac repressor to bind to the operator site depends on whether or not _____ is bound to it

allolactose, prevents, operator

when _____ binds to the lac repressor, a conformational change occurs that _____ the lac repressor from binding to the _____ site and RNA is free to transcribe the operon

inducer

in negative lac person regulation, allolactose works as an _____ (binds to lac repressor, preventing the lac repressor from binding to the operator site, and allows for transcription)

allolactose, operator, inhibits

1. in the absence of lactose, no inducer (_____) is available to bind to lac repressor
2. lac repressor binds to the _____ site and _____ transcription

lactose permease, b-galactosidase, lac repressor, operator, allowing

1. when the bacterium is exposed to lactose, a small amount can be transported into the cytoplasm via _____ _____, and _____ converts some of that lactose to allolactose
2. allolactose binds to _____ _____
3. the binding of allolactose promotes a conformational change that prevents the repressor from binding to the lac _____ site, thereby _____ transcription of the lacZ, lacY, and lacA genes to occur

positive

one way the lac operon is transcriptionally regulated (based on glucose and this form of regulation involves CAP and cAMP)

repression

the presence of glucose ultimately leads to the _____ of the lac operon

glucose, lactose

when exposed to both glucose and lactose, E. coli cells first use _____ and catabolite repression prevents the use of _____

alleviated, lac operon

if the glucose is used up, catabolite repression is _____, and the bacterium then expresses the _____ _____

diauxic growth

the sequential use of two sugars by a bacterium

False

True or False: Glucose is the small effector molecule that binds directly to a genetic regulatory protein

cyclic-AMP (cAMP)

in bacteria, a small effector molecule that binds to CAP (catabolite activator protein)

inducer

cAMP is a small effector molecule (_____)

catabolite activator protein (CAP)

binds to promoters and facilitates transcription

adenylyl cyclase

cAMP is produced from ATP via an enzyme known as _____ _____

decreases, inhibited

when a bacterium is exposed to glucose, the intracellular concentration of cAMP _____ because adenylyl cyclase is _____

low

glucose concentrations are high: cAMP concentrations are _____

high

glucose concentrations are low: cAMP concentrations are _____

inactive, low, does not, infrequent

high glucose → _____ adenyl cyclase → _____ cAMP → CAP _____ bind to DNA → _____ transcription of lac operon

active, high, does, frequent

low glucose → _____ adenyl cyclase → _____ cAMP → CAP _____ bind to DNA → _____ transcription of lac operon

high, prevents, cAMP, promoter, high

When only lactose is present, allolactose and cAMP levels are _____. Allolactose binds to lac repressor and _____ its from binding to the DNA. The effector molecule _____ binds to CAP, and then CAP binds to the CAP site. A domain in CAP interacts with RNA polymerase, which facilitates the binding of RNA polymerase to the _____. Under these conditions, transcription proceeds at a _____ rate.

high, bound, low

In the absence of both lactose and glucose, cAMP levels are _____, so CAP is _____ to the DNA. However, the binding of the lac repressor is a very strong inhibitor of transcription. For this reason, the transcription rate is very _____.

inactive, prevents, decreases, prevents, low

Both lactose and glucose are present. The presence of lactose causes lac repressor to be _____, which _____ it from binding to the operator site. Even so, the presence of glucose _____ cAMP levels, and so cAMP is released from CAP, which _____ CAP from binding to the CAP site. The lack of CAP binding does not completely inhibit transcription. Therefore, the transcription of the lac operon is _____ in the presence of both sugars.

low, inhibits

When only glucose is present, the transcription of the lac operon is very _____ because lac repressor is bound to the operator site and strongly _____ transcription.

three

lac operon has _____ operator sites for lac repressor

O1, O2, O3

three operator sites of lac operon for lac repressor

more, less

when all three operator sites are present → _____ repression & _____ transcription

no, more

when all three operator sites are absent → _____ repression & _____ transcription

O1, O2, O3

When _____ is missing, even in the presence of the other operator sites, repression is nearly abolished because lac repressor cannot bind to _____ and _____.

loop, loop, repressor, loop, inhibits

The binding of lac repressor to two operator sites requires the DNA to form a _____. A _____ in the DNA brings the operator sites closer together, thereby facilitating the binding of the _____ protein. The formation of this _____ dramatically _____ the ability of RNA polymerase to slide past the O1 site and transcribe the operon.

five

how many genes does the trp operon contain?

trpE, trpD, trpC, trpB, trpA

the five genes of the trp operon

tryptophan

trpE, trpD, trpC, trpB, and trpA encode enzymes involved in _____ biosynthesis

trpR, trpL

_____ and _____ (two additional genes of the trp operon) play a role in the regulation of the trp operon

trpL

the _____ gene is part of the trp operon

trpR, promoter

the _____ gene has its own _____ and is not part of the trp operon

trp repressor

the trp operon is regulated by _____ _____

trpR

trp repressor is encoded by the _____ gene

inactive

trp is _____ when tryptophan is not bonded to it

corepressor

tryptophan acts as a _____ that binds to trp repressor

cannot, transcribes, on

low tryptophan levels → trp repressor _____ bind to the operator site → RNA polymerase _____ the trp operon → trp operon is _____

corepressor, binds, inhibits, off

high tryptophan levels →tryptophan acts as a _____ that binds to trp repressor → trp repressor _____ to the trp operator site → _____ RNA polymerase to transcribe the operon → trp operon is turned _____

attenuation

a mechanism of genetic regulation, seen in the trp operon, in which a short RNA is made but its synthesis is terminated before RNA polymerase can transcribe the rest of the operon

attenuator sequence

a sequence found in certain operons in bacteria that stops transcription soon after it has begun

terminates, tryptophan, inhibits

When attenuation occurs, the mRNA from the trp operon is made as a short piece that _____ at the attenuator sequence, which is just downstream from the trpL gene. Because this short mRNA has been terminated before RNA polymerase has transcribed the trpE, trpD, trpC, trpB, and trpA genes, it will not encode the proteins required for _____ biosynthesis. In this way, attenuation _____ the further production of tryptophan in the cell.

two

one key feature of attenuation is that _____ trp codons are found within the mRNA of trpL

rho independent

u-rich attenuator sequence of trpL mRNA resembles _____ termination

1, 2, 3, 4, 3-4, U-rich

When translation is not coupled with transcription, region _____ hydrogen bonds to region _____ and region _____ hydrogen bonds to region _____. Because a _____ terminator stem-loop forms, transcription will be terminated at the _____ attenuator.

trp codons, 1, 2, 3, 2-3, 3-4, not, transcribes

coupled transcription and translation + LOW tryptophan concentration → ribosome pauses at the _____ _____ in the trpL gene → region _____ of the mRNA is blocked → region _____ can hydrogen bond only with region _____ → _____ stem-loop structure forms → _____ stem-loop structure cannot form → transcriptional termination does _____ occur → RNA polymerase _____ the rest of the operon

stop codon, 2, 3, 4, terminated

coupled transcription and translation + HIGH tryptophan concentration → ribosome pauses at _____ _____ → blocks region _____ from hydrogen bonding with any region → region _____ hydrogen bonds with region _____ → transcription is _____ at the U-rich attenuator

antitermination

2-3 stem loop

termination

3-4 stem loop

catabolism

break down of a substance

anabolism

synthesis of small molecules

inducible

operons involved in catabolism are typically _____

catabolism, inducible

operon trend of lactose

repressible

operons involved in anabolism are typically _____