Microbiology [14]: Regulation of Bacterial Cellular Processes

Which two of the following are characteristics of transcriptional regulatory proteins?

- Bind to DNA - Bind to palindromes

The transcription of all catabolite operons are regulated by which two of the following?

- Catabolite activator protein - Regulatory protein specific to the operon

Match each mRNA-targeting sRNA with its location in the genome. - Cis-encoded sRNA - Trans-encoded sRNA

- Cis-encoded sRNA: synthesized from the non-template strand of their target - Trans-encoded sRNA: synthesized from genes at sites distinct from their target

Match the following types of genes: - Constitutive genes - Regulated genes

- Constitutive genes: genes that are continuously expressed - Regulated genes: genes that are only expressed when needed

Match each of the following types of enzymes with its description. - Constitutive - Inducible - Repressible

- Constitutive: play a critical and indispensable role in central metabolic pathways - Inducible: often used in the transport and breakdown of specific energy sources - Repressible: generally used in anabolic (biosynthetic) pathways

Bacteria can regulate transcription at the levels of ___.

- Elongation - Initiation

Which four of the following are characteristics of the attenuator antiterminator?

- Formed by the pairing of regions 2 and 3 - Prevents the generation of the terminator loop - Located in the leader region - Prevents the generation of the pause loop

Match each bacterial group with their most common use of riboswitches. - Gram-positive bacteria - Gram-negative bacteria

- Gram-positive bacteria: control of transcription - Gram-negative bacteria: control of translation

Which two of the following are common motifs of the DNA-binding domains of regulatory proteins?

- Helix-turn-helix - Zinc fingers

Which two of the following statements about the interaction between the lac repressor and inducer are true?

- Inducer binding changes the repressor shape - Inducer binding causes repressor to lost ability to bind to the operator sites

Which of the following are steps where gene expression is commonly regulated in bacteria?

- Initiation of transcription - Transcription elongation - Initiation of translation

Match each type of regulated gene with the correct statement about its regulatory protein. - Negatively controlled repressible gene - Positively regulated repressible gene

- Negatively controlled repressible gene: Repressor protein is inactive; activated by a corepressor - Positively regulated repressible gene: Activator protein is active; inactivated by an inhibitor

Match the nutrient conditions with the appropriate cellular regulation response. - Neither lactose nor glucose present - Lactose present but no glucose - Glucose present but no lactose - Both lactose and glucose present

- Neither lactose nor glucose present: CAP binds, repressor binds - Lactose present but no glucose: CAP binds, repressor is inactive - Glucose present but no lactose: CAP is inactive, repressor binds - Both lactose and glucose present: Repressor and CAP are inactive

DNA-bound repressor proteins inhibit the initiation of transcription by either ___.

- Preventing the movement of RNA polymerase - Blocking the binding of RNA polymerase

Match the following terms associated with regulation of transcription initiation. - Repressible genes - Constitutive genes - Housekeeping genes - Inducible genes

- Repressible genes: genes that encode proteins serving an anabolic function - Constitutive genes: genes expressed continuously by the cell - Housekeeping genes: genes that encode for proteins that are frequently needed by the cell - Inducible genes: genes that encode proteins serving a catabolic function

Transcription of the trp operon is controlled by which two of the following mechanisms?

- Repressor protein inhibits initiation - Premature termination through attenuation

Two types of flagellar movement in E. coli are:

- Run - Tumble

Which of the following conditions must exist to fully induce the lac operon?

- Shortage of preferred carbon and energy source - Lactose present in the medium

Which three of the following are components of a bacterial operon?

- Structural genes - Operator - Promoter

Which two of the following are examples of second messengers?

- cAMP - ppGpp

Match each sigma factor with its correct timing and location during sporulation. - σF - σE - σG - σK

- σF: Genes involved in flagellum assembly - σE: Genes needed to restore membrane integrity and the proper folding of membrane proteins - σG: - σK:

Order the following events in the regulation of the trp operon of E. coli when there is little charged tRNA-Trp present in the cell.

1. RNA polymerase initiates transcription at the promoter 2. A ribosome initiates translation of the trpL gene 3. The ribosome stalls, in need of charged tRNA-Trp 4. The anti terminator loop forms in the transcript 5. RNA polymerase transcribes the structural genes of the trp operon

Riboswitches contain effector-binding elements at the ___ of the mRNA.

5' end

The signaling molecule used in quorum sensing by Vibrio fischeri and many other Gram-negative bacteria is ___.

AHL: N-acylhomoserine lactone (AHL)

A(n) ___ protein is a DNA-binding protein that promotes the initiation of transcription.

Activator

If transcription and translation were not coupled in bacteria, what type of regulation would be affected?

Attenuation

___ is a regulatory process that results in the termination of transcription within a leader sequence that precedes the structural genes.

Attenuation

Which statement best describes the ara operon?

Both negative and positive transcriptional control

If E.coli is grown in a medium containing glucose and maltose in equal amounts, the gluose is broken down immediately followed by the maltose at a slower rate. This diauxic growth is an example of the use of ___.

Catabolite repression

The trp operon is ___ expressed under normal conditions i.e. the trp repressor is ___.

Constitutively; Inactive

Which of the following is NOT a characteristic of regulatory proteins? A. Responsible for processes such as induction and repression B. Individual subunits associate to form dimers C. Binds to palindromic sequences on DNA D. Controls which molecules can be transported across a biological membrane

Controls which molecules can be transported across a biological membrane

T/F: Most enzymes in biosynthetic pathways are inducible enzymes.

False (repressible)

What is the name given to the collection of genes that encode protein products that must be expressed all the time?

Housekeeping genes (constitutive genes)

If lactose is present in the media, the lac repressor is inactivated by binding the ___ allolactose.

Inducer

The lactose (lac) operon is an example of negative regulation of an ___ operon.

Inducible

At which level do riboswitches block translation?

Initiation

___ occurs when the initiation of transcription is inhibited by the binding of a protein to DNA.

Negative transcriptional control

Which statement best describes the lac operon in E. coli?

Negative transcriptional control of inducible genes (i.e., turned "off" until turned "on")

DNA in cells can encode thousands of different proteins. Why do cells require mechanisms to regulate expression of the genes that code for these proteins?

Not all proteins are needed at all times, or in equal amounts. Regulating their expression saves energy and time.

___ occurs when the initiation of transcription is promoted by the binding of a protein to DNA.

Positive transcriptional control

Which statement best describes the regulation of transcription elongation (not initiation)?

Premature termination of transcription

This occurs due to the fact that the formed complex blocks the action of ___.

RNA polymerase

This in turn bends the DNA and inhibits ___ action, preventing ___.

RNA polymerase; Transcription

Which of the following is NOT a mechanism by which bacteria regulate gene expression? A. Regulation of transcription elongation B. Regulation of transcription initiation C. Regulation of transition initiation D. Regulation of mRNA processing

Regulation of mRNA processing

The tryptophan (trp) operon is an example of negative regulation of a ___ operon.

Repressible

___ encode enzymes that have their expression levels decreased by the presence of pathway products.

Repressible genes

However, if the trp ___ binds its ___, tryptophan, transcription stops.

Repressor; Corepressor

In the absence of lactose, the active lac ___ binds to the lac ___.

Repressor; Operator

T/F: Most enzymes in biosynthetic pathways are repressible enzymes.

True

The sugar ___ is the inducer of the lac operon.

allolactose

The stringent response is induced when bacterial cells are starved for ___.

amino acids

Regulation of transcription by attenuation vs. riboswitches differs in that ___.

attenuation contributes to transcriptional regulation by directing alternative folding of the leader mRNA depending on levels of tryptophan in the cell, whereas riboswitches are nontranslated areas in the leader mRNA that are bound by non protein molecules.

In the trp operon, the sequence of nucleotides referred to as trpL, encode the leader peptide and ___.

attenuator sequences

The AHL signaling molecule is termed a(n) ___ to reflect the autoregulatory nature of the system.

autoinducer (AI)

An active repressor protein ___.

binds to the DNA molecule and prevents transcription.

When in a complex with ________, the CAP protein binds to the CAP site and ________ the expression of the lac operon.

cAMP; switches on

A(n) ___ is a protein that is used to sense the presence of specific chemicals in the environment.

chemoreceptor

In the E. coli chemotactic response pathway that controls the direction of flagellar rotation, MPC functions as the ___.

chemoreceptor

A pattern of bacterial growth in two phases caused by the presence of two sugars in the media is called ___.

diauxic growth

In Pseudomonas fluorescens, when phosphate levels are high, the activity of the enzyme ____________________ is also high and c-di-GMP is formed. Conversely, when phosphate levels are low, ____________________ activity is low and c-di-GMP is destroyed.

diguanylate cyclase; phophodiesterase

The term "regulation of ___ expression" refers to the process of controlling transcription and/or translation.

gene

Regulatory systems that simultaneously control the expression of multiple operons or pathways are referred to as ___.

global regulatory pathways

A protein that activates or represses multiple operons or genes is referred to as a(n) ___.

global regulatory protein

In the absence of tryptophan, the trp repressor is ___.

inactive and cannot bind to the operator.

The level of some enzymes, such as B-galactosidase, increase significantly in the presence of a small effector molecule called a(n) ___.

inducer

Enzymes whose level increases in the presence of small effector molecules are encoded by ___.

inducible genes

The lac operon is expressed when glucose is ___.

low and lactose is present.

Short, inverted sequences of bases in DNA are called ___.

palindromes

A second messenger that regulated the stringent response in many species of bacteria is ___.

ppGpp: guanosine tetraphosphate

Each sigma factor has its own set of ___ to which it binds.

promoter consensus sequences

Autoinduction can also be called ___.

quorum sensing

The exchange of signaling molecules to coordinate gene expression between members of a bacterial population is called ___.

quorum sensing

Proteins that are responsible for the induction or repression of enzyme encoding genes are referred to as ___.

regulatory proteins

Proteins that inhibit the initiation of transcription by binding to DNA are called ___.

repressor proteins

In riboswitches that control translation, the binding of an effector molecule alters the shape of the mRNA leader sequence and inhibits ___ binding at the Shine-Dalgarno sequence.

ribosome

A specialized form of attenuation that involves alternate folding of the leader sequence of a mRNA, but not ribosome behavior, is called ___.

riboswitch control

Sigma factor O^F is encoded by the gene ___.

sigF

Producing alternative versions of ___ can immediately change the expression of many bacterial genes.

sigma factors

RNA molecules that do not function as mRNA, tRNA, or rRNA are referred to as ___ or ___ RNAs.

small; noncoding

Genes that encode the non-regulatory proteins in an operon are referred to as ___.

structural genes

Coordinated regulation of large sets of genes by alternate sigma factors occurs at the level of ___.

transcription

The steps of gene expression, in the correct order, are ___.

transcription, translation

The term used to describe the metabolic pathway that uses DNA as a template for the manufacture mRNA is called ___, and the pathway that uses mRNA as the template for the manufacture of protein is called ___.

transcription; translation

When E.coli is in the presence of a chemical gradient, the frequency of movements called ___ decreases as long as the cell moves towards the chemical attractant.

tumbles

Comparing two-component signal transduction systems and phosphorelay systems, ___.

two-component signal transduction systems mediate the transfer of a single phosphoryl group from a sensor kinase to a response regulator, whereas phosphorelay systems transfer multiple phosphoryl groups between a series of proteins.