Microbiology Module 4a 2

lac repressor protein characteristics

-Composed of four identical subunits -Each monomer has a helix-turn-helix domain

Place the events in the Pseudomonas motile to sessile transition in order,

1. the Pseudomonas flagellum hits a solid object 2. a membrane sensor activates its DGC domain 3. c-di-GMP concentration rises in the cell 4. genes encoding adhesins are activated 5. the cell adheres to the substrate

How many structural genes are in the lac operon?

3

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

5' end

The adenyl cyclase enzyme converts ______ to cAMP and PPi.

ATP

Which three of the following mechanisms control sporulation in Bacillus subtilis?

Alternate sigma factors, Post translational modification, Phosphorelay

The catabolite activator protein binds to a specific DNA sequence called the ____ recognition site.

CAP

Which statement best describes the result of CAP binding to the CAP recognition site?

CAP binds DNA through a helix-turn-helix motif.

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

Catabolite activator protein Regulatory protein specific to the operon

A cell moving away from an attractant will tumble because

CheA autophosphorylates and then transfers the phosphate to CheY

Transcription factors act to regulate gene expression by binding to

DNA in the promoter region

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

Lactose present in the medium & Lack of preferred carbon and energy source

Under which condition is adenyl cyclase active?

Little or no glucose is available

Which of the following terms indicates that the binding of a repressor protein to DNA inhibits transcription initiation?

Negative transcriptional control

Which statement best describes the lac operon in E. coli? Positive transcriptional control of repressible genes (i.e.,"on" until turned "off") Negative transcriptional control of inducible genes (i.e., turned "off" until turned "on") Constitutively expressed genes (i.e., always "on")

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

At which of the following operator sites must the lac repressor bind to ensure transcription inhibition?

O1

In the complex genetic regulation of the E. coli response to changes in osmolarity, which effects are observed?

Phosphorylated OmpR activates expression of certain small RNAs. Phosphorylated OmpR activates expression of certain structural genes.

Which three of the following are characteristics of the trp repressor protein?

Synthesized in an inactive form, Tryptophan acts as a corepressor, Active form binds operator

ara operon regulation - pos or neg?

The ara operon is regulated by both negative and positive transcriptional control. depends on the presence/absence of arabinose

Which of the following statements is false regarding the motile to sessile transition of Pseudomonas? The sensor of mechanical signals can start the process of adhesion by activating its DGC domain. The release of the LapG protease promotes adhesion to a substrate. Increasing c-di-GMP levels promote adhesion by inducing expression of the genes encoding adhesins. LapD proteins restrain the LapG protease only in the presence of c-di-GMP.

The release of the LapG protease promotes adhesion to a substrate.

The binding of _____to the catabolite activator protein causes it to change to the active form.

cAMP

examples of second messengers

cAMP, ppGpp, cyclic dimeric

Diguanylate cyclases (DGCs) and phosphodiesterases (PDEs) are found in the cell as

cytoplasmic domains of membrane sensors

Which two enzymatic activities determine the level of c-di-GMP in a cell?

diguanylate cyclase & phosphodiesterase

A portion of a protein with a specific function is termed a(n)

domain

The trp operon leader is unusual in that it

encodes a small peptide called the leader peptide

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

global regulatory systems

Adenyl cyclase activity is inversely proportional to the level of ____in the cell.

glucose

The "restriction" component of a restriction-modification system involves ______ in DNA.

hydrolysis of the phosphodiester bond

Match the genes of the lac operon with the enzymes that they encode.

lacZ -> β-galactosidase lacY -> lactose permease lacA -> β-galactoside tranacetylase

In conditions when a gene is said to be "turned off," it is

likely expressed at a very low level

The "modification" component of a restriction-modification system involves ______ in DNA.

methylation of nitrogenous bases

Bacillus subtilis has five different sensor kinases associated with the transition to endospore formation. The reason for this multiplicity of sensor kinases is

multiple environmental conditions are surveyed before committing to endospore formation

In translational riboswitches, the binding of an effector molecule alters the shape of the mRNA leader sequence and inhibits ____ binding at the Shine-Dalgarno sequence.

ribosome

The CRISPR/Cas system "remembers" prior interaction with viruses by

storing a sequence of viral DNA in its CRISPR

Regulation of gene expression at the level of RNA polymerase binding to the promoter occurs through the action of proteins termed

transcription factors

The trp operon is regulated by the

trp repressor (TrpR)

True or false: Some bacteria communicate via chemical messengers.

true

True or false: The CRISPR/Cas system "remembers" previous bacteriophage attacks.

true

Of the several mechanisms used by B. subtilis for control of gene expression during endospore formation, the most important is the use of multiple ____ factors

sigma

Global regulatory systems are not likely to involve the regulation of ______. multiple genes multiple operons single operons multiple pathways

single operons

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

small RNAs/sRNAs

Second messengers are ______ in response to an external signal.

small molecules produced

The _____ response is observed in many bacteria like E. coli when they are starved for amino acids.

stringent

One of the ways the trp operon is regulated is that it is

synthesized in an inactive form

RNA thermometers are located in the leader sequence of mRNAs. The basis for their ability to measure temperature is

the difference in thermal stability of GC and AU base pairs

For operons regulated by transcriptional riboswitches, in one configuration, a transcriptional terminator forms. The alternate configuration results in expression of the operon and occurs when

the effector is not present in the cell

Because of its ability to "remember" prior exposure to viruses, the bacterial and archaeal CRISPR system has been compared with

the human immune system

The intracellular concentration of c-di-GMP is important in regulating cellular responses. This is evidenced by

the number of c-di-GMP molecules required for an effector response

To determine whether the genes of the trp operon should be transcribed, the process of attenutation measures

the speed of translation in the leader peptide

In regulation by attenuation, transcription proceeds through which of the following elements?

transcript leader

In transcriptional riboswitches, one folding pattern forms

a transcriptional terminator

ATP is converted to cAMP by the enzyme

adenyl cyclase

The bacterial RNA polymerase core enzyme needs the assistance of a(n) _____ factor to bind to the promoter and initiate transcription. By producing alternate versions of this factor, the expression of gene sets can be rapidly switched.

alternate sigma

A mechanism to express a gene with a weak promoter generally features

an activator binding site to attract sigma factors

A strong promoter generally feature

an extended upstream region that contacts RNA polymerase

Once formed, c-di-GMP encounters effector molecules

as it moves through the cytoplasm by diffusion

Termination of transcription elongation before RNA polymerase enters the first structural gene of an operon is called

attenuation

Transcription factors are proteins with at least two domains. These domains act to ______ and ______.

bind to DNA at the promoter region & interact with an effector molecule

In E. coli, the proteins necessary to utilize lactose as an energy and carbon source will not be expressed, even when lactose is present, unless the _____ ______ protein is activated by the absence of glucose in the cell.

catabolite activator

The global control of operons encoding enzymes for the catabolism of carbohydrates that must be modified prior to entering glycolysis is referred to as

catabolite repression

The positive regulatory system called ____ ______ prevents the expression of genes encoding proteins necessary for the utilization of sugars other than glucose when adequate supplies of glucose are present.

catabolite repression

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

chemoreceptor/MCP

E. coli detects the presence of specific molecular attractants with

chemoreceptors

Enzymes that catalyze reactions that are in constant demand in a cell are encoded by genes referred to as; What is the name given to genes whose protein products must be present all the time?

constitutive/housekeeping genes

When an MCP binds an attractant, CheA autophosphorylation is inhibited and the cell

continues to run

An E. coli cell is most likely to exhibit a biased random walk when

in a concentration gradient of attractant

Catabolite operons are not transcribed efficiently unless the catabolite activator protein is bound to the CAP recognition site, located

in the promoter region of the operon

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

inducer

At which level do riboswitches usually block translation?

initiation

Translational riboswitches usually regulate translation at the ____ step.

initiation

The lac operon is expressed at high levels when the sugar ____ is available and a preferred source of carbon and energy is lacking.

lactose/allolactose

During endospore formation in B. subtilis, gene expression is restricted to the appropriate compartment by

localizing expression of sigma factors to either the mother cell or the forespore

The stringent response is induced when bacterial cells are under ______ stress

nutritional

A helix-turn-helix domain of a transcription factor recognizes a specific DNA sequence in a promoter region by

placing its recognition helix in the major groove to contact the bases

The phenomenon known as _____ sensing is believed to be a chemical conversation between bacteria.

quorum

Proteins that inhibit transcription initiation by binding to operator DNA are called

repressor proteins

Which two of the following are bacterial defense mechanisms against viruses?

restriction/modification & CRISPR/Cas

In attenuation, a fast-moving ribosome in the leader peptide

results in transcription termination

______ are small molecules produced inside of cells in response to an external signaling event.

second messengers

When an effector binds in the effector binding domain of a helix-turn-helix transcription factor, the DNA binding domain

shifts the position of recognition helices to fit into the major groove

Complex gene regulatory circuits often involve multiple types of regulation. For example, in E. coli, the response to osmolarity uses both ______ and ______.

two component signal transduction small RNAs (sRNAs)

True or false: The lac operon is an example of a positive control system, implying that it is turned "on" until turned "off" by its regulatory protein.

false

When moving in a random walk, E. coli cells

exhibit short runs and frequent tumbles

The trp operon leader extends from ______ to ______.

the transcription start site / the start codon of the first structural gene

Expression of many genes is termed "leaky," meaning that

there is always a low level of transcription

The trp operon consists of five structural genes that encode enzymes needed for

tryptophan biosynthesis