biol101 ch14

Genes that are expressed at essentially constant levels because they are continuously necessary for survival are termed _____.

Constitutive

What is the primary physiological benefit of regulating gene expression rather than using constitutive expression for all genes?

Proteins are produced only when required, conserving cellular energy and resources.

At which level of gene expression does the binding of genetic regulatory proteins to DNA primarily occur in bacteria?

Initiation of transcription.

In the context of bacterial transcription, how is 'attenuation' defined?

Transcription terminates prematurely shortly after initiation due to the formation of a transcriptional terminator.

Concept: Translational Repressor Proteins

Definition: Proteins that bind to mRNA to prevent the initiation of translation. Example: Proteins blocking the Shine-Dalgarno sequence.

How do riboswitches regulate gene expression at the translational level?

They produce an mRNA conformation that prevents translation from starting.

In posttranslational regulation, what is the mechanism of 'feedback inhibition'?

The final product of a metabolic pathway inhibits the first enzyme in that pathway.

Transcriptional regulatory proteins that bind to DNA and inhibit transcription are called _____.

Repressors

In transcriptional regulation, 'positive control' refers to regulation mediated by _____ proteins.

Activator

Small effector molecules called 'inducers' increase transcription by binding to activators to cause DNA binding or by binding to _____ to prevent DNA binding.

Repressors

What is the function of a 'corepressor' in a repressible gene system?

It binds to a repressor protein, enabling the repressor to bind to DNA and inhibit transcription.

How does an 'inhibitor' molecule function in a system regulated by an activator protein?

It binds to the activator and causes a conformational change that prevents the activator from binding to DNA.

An _____ is a regulatory unit in bacteria consisting of structural genes under the control of a single promoter.

Operon

What type of mRNA is encoded by an operon, containing the sequences for two or more structural genes?

Polycistronic mRNA

In the $lac$ operon, which DNA element is the specific binding site for the RNA polymerase?

The promoter ($lacP$).

The _____ site in the $lac$ operon is the DNA sequence where the $lac$ repressor protein binds.

Operator

What enzyme is encoded by the $lacZ$ gene, and what are its two primary reactions?

$\beta$-galactosidase; it cleaves lactose into glucose and galactose and converts lactose into allolactose.

The $lacY$ gene encodes _____ _____, a membrane protein required for the active transport of lactose into the cytoplasm.

Lactose permease

Why is the $lacI$ gene considered a regulatory gene rather than part of the $lac$ operon itself?

It has its own promoter and is not transcribed as part of the polycistronic mRNA of the operon.

Which small effector molecule acts as the actual inducer for the $lac$ operon?

Allolactose

When lactose is absent from the environment, why is the $lac$ operon not transcribed?

The $lac$ repressor remains active and bound to the operator site, physically blocking RNA polymerase.

In the $lac$ operon, 'enzyme adaptation' refers to the phenomenon where an enzyme appears in a cell only after exposure to its _____.

Substrate

What specific conformational change occurs in the $lac$ repressor when allolactose binds to it?

A change that prevents the repressor from binding to the operator DNA sequence.

In $lacI^-$ mutant bacterial strains, the $lac$ operon is expressed _____.

Constitutively

Merozygotes, or partial diploids, were used by Jacob and Monod to demonstrate that the $lacI$ gene produces a _____ protein.

Diffusible

If a merozygote has a $lacI^-$ mutation on the chromosome and a wild-type $lacI^+$ gene on the $F'$ factor, what is the resulting phenotype for lactose metabolism?

Inducible (normal) expression.

The 'trans-effect' refers to genetic regulation that can occur even when DNA segments are not physically adjacent because it is mediated by _____ _____.

Regulatory proteins

Contrast the $trans$-effect of the $lacI$ gene with the $cis$-effect of the $lac$ operator ($lacO$).

The $lacI$ gene produces a diffusible protein, whereas the operator is a DNA sequence that only affects the adjacent operon.

If a merozygote contains a $lacO^-$ (constitutive) operator on the chromosome and a wild-type $lacO^+$ on the $F'$ factor, how will the chromosomal genes be expressed?

Constitutively, because the $lacO$ sequence is a $cis$-acting element.

What happens to the level of $lac$ operon expression when $E. coli$ is exposed to both glucose and lactose simultaneously?

The operon is repressed until glucose is depleted, a process known as catabolite repression.

The sequential use of glucose first, followed by lactose, results in a growth pattern termed _____ _____.

Diauxic growth

Which small effector molecule is used by the cell to sense the presence of glucose in catabolite repression?

Cyclic AMP ($cAMP$)

How does the concentration of glucose in the environment affect the internal levels of $cAMP$?

Glucose inhibits adenylyl cyclase, leading to a decrease in $cAMP$ levels.

The $cAMP$-$CAP$ complex binds to the $CAP$ site to enhance the binding of _____ _____ to the promoter.

RNA polymerase

Under what specific environmental conditions (lactose/glucose) is $lac$ operon transcription maximal?

Lactose is present and glucose is absent.

The $lac$ repressor must bind to two of three operator sites ($O_1$, $O_2$, $O_3$) to achieve maximal repression, which requires the DNA to form a _____.

Loop

Where is the $O_2$ operator site located relative to the $lac$ promoter?

Downstream within the $lacZ$ coding region.

What is the metabolic role of the structural genes ($trpE$, $trpD$, $trpC$, $trpB$, $trpA$) in the $trp$ operon?

They encode enzymes required for the biosynthesis of the amino acid tryptophan.

In the $trp$ operon, the $trpR$ gene encodes the $trp$ repressor protein, which functions as part of a _____ system.

Repressible

When tryptophan levels in the cell are high, tryptophan acts as a _____ to activate the $trp$ repressor.

Corepressor

Attenuation in the $trp$ operon is possible in bacteria but not eukaryotes because transcription and translation are _____.

Coupled

The $trpL$ gene encodes a short sequence called the _____ _____, which is central to the mechanism of attenuation.

Leader peptide

In the $trpL$ mRNA, which stem-loop structure acts as the intrinsic (rho-independent) terminator?

The $3-4$ stem-loop.

During attenuation, what happens if the ribosome stalls at the tryptophan codons in the $trpL$ sequence due to low tryptophan?

The $2-3$ stem-loop (antiterminator) forms, and transcription continues into the structural genes.

Why does the formation of a $2-3$ stem-loop in the $trp$ leader sequence prevent transcriptional termination?

It prevents region $3$ from pairing with region $4$, thus precluding the formation of the terminator loop.

When tryptophan levels are high, the ribosome completes translation of the leader peptide and pauses at the _____ _____, which allows the $3-4$ loop to form.

Stop codon

If $trpL$ mRNA is produced but translation does not occur at all, what is the fate of transcription?

It terminates at the $U$-rich attenuator because the $1-2$ and $3-4$ loops form.

Operons involved in _____ (the breakdown of a substance) are typically inducible.

Catabolism

How do translational repressors inhibit translation by binding adjacent to the Shine-Dalgarno sequence?

They sterically hinder the ribosome from initiating translation.

In $E. coli$, antisense RNA is used to regulate the production of the _____ protein during osmoregulation.

$ompF$

What is 'antisense RNA'?

An RNA strand that is complementary to a specific mRNA, preventing its translation.

Why does the presence of antisense RNA for $ompF$ lead to decreased OmpF protein levels?

The antisense RNA binds to the $ompF$ mRNA, creating a double-stranded structure that prevents the ribosome from binding.

Covalent modifications to the structure of a protein, such as phosphorylation, are examples of _____ regulation.

Posttranslational

In the $lac$ operon, what is the effect of a mutation that deletes the $CAP$ site?

The rate of transcription will be low even in the absence of glucose and presence of lactose.

Dr. Weiser's Lab: A strain has a mutation in the $lacI$ gene that prevents allolactose from binding to the repressor. What is the operon expression phenotype?

Super-repressed (the operon is never induced, even when lactose is present).

The Data Decoder: Jacob and Monod used $\beta$-ONPG in their assays because its cleavage results in _____, which is a yellow-colored compound.

$o$-nitrophenol ($O-NP$)

Prove It Protocol: How can you distinguish between a $lacI^-$ mutation and a $lacO^-$ mutation using a wild-type $F'$ factor?

In a merozygote, $lacI^-$ is complemented (expression becomes inducible), but $lacO^-$ is not (expression remains constitutive).

In the $trp$ operon, region $1$ of the leader sequence contains two codons for the amino acid _____.

Tryptophan

What structural feature of the mRNA immediately following the $3-4$ stem-loop promotes rho-independent termination?

A sequence of uracil ($U$) residues.

What is the primary role of the $lacA$ gene in the $lac$ operon?

It encodes galactoside transacetylase, which covalently modifies lactose analogues.

Merozygote Logic: Predict the level of $\beta$-galactosidase in a merozygote ($lacI^- / lacI^+$) without lactose present.

Low (less than $1\%$), because the $lacI^+$ gene provides enough repressor for both operators.

Why is the $lac$ repressor protein considered a tetramer?

It is composed of four subunits that function together as a single unit.

How does the $lac$ repressor increase its binding affinity for the DNA operator sites?

By causing the DNA to loop, which brings separate operator sites into close proximity.

The $trp$ repressor protein is encoded by the _____ gene, which is located outside the $trp$ operon.

$trpR$

What happens to transcriptional regulation of the $trp$ operon if the two $Trp$ codons in $trpL$ are mutated to $Ala$ codons?

Attenuation will occur based on alanine levels rather than tryptophan levels.

If a cell is at low osmolarity, is the $ompF$ gene more likely to be expressed or repressed?

Expressed (preferentially produced at low osmolarity).

Genetic regulation that involves the stabilization of an mRNA secondary structure to prevent initiation is a form of _____ regulation.

Translational

How does the presence of an inhibitor molecule affect a repressible gene under positive control?

It prevents the activator from binding DNA, thereby inhibiting transcription.

In the $trp$ operon, what is the role of the $trpL$ gene product?

The leader peptide's translation determines whether transcriptional attenuation occurs.

The Data Decoder: Why did a merozygote with both chromosomal and $F'$ copies of the $lac$ operon show $220\%$ enzyme activity with lactose?

Both the chromosomal $lac$ operon and the $F'$ $lac$ operon were induced, roughly doubling the output compared to a single wild-type cell.

What is the consequence of region $1$ hydrogen bonding to region $2$ in the $trpL$ leader mRNA?

Region $2$ is unavailable to bond with region $3$, facilitating the formation of the $3-4$ terminator loop.

Concept: Diauxic growth

Definition: The sequential use of two different sugars for growth, typically characterized by two distinct growth phases separated by a lag period.

How does the cAMP-CAP complex physically influence transcription initiation?

It binds to the $CAP$ site and creates a bend in the DNA that enhances RNA polymerase binding to the promoter.

Which regulatory unit allows a bacterium to coordinate the expression of multiple genes with a common functional goal?

The operon.

In the $trp$ operon, does the $trp$ repressor bind to DNA when tryptophan levels are low?

No, it remains in an inactive conformation and cannot bind the operator.

Draw-It-Out Mandate: In the $lac$ operon, which operator ($O_1$, $O_2$, or $O_3$) is located slightly upstream of the promoter?

$O_3$

Why is the $lac$ operon expression not completely zero in the absence of lactose?

A very small, 'basal' amount of expression occurs, allowing for the initial presence of lactose permease and $\beta$-galactosidase.

How does the term 'inducible' differ from 'constitutive' in gene regulation?

Inducible genes are expressed only under specific conditions (usually the presence of a substrate), while constitutive genes are expressed continuously.

A mutation that prevents region $2$ and region $3$ of the $trp$ leader mRNA from base-pairing would result in _____ _____.

Permanent attenuation (termination would always occur).

Under which glucose/lactose condition is the $lac$ repressor inactive and the $CAP$ protein inactive?

Lactose is present and glucose is present.