Chapter 14 Micro Bio

Check the answers that apply to catabolite repression and the lac operon.

- CAP is active when bound to cAMP - Adenlyl cyclase synthesizes cAMP when glucose levels are low - The lac operon contains a CAP recognition site

Select all the conditions that apply in the cell when tryptophan levels are low.

- 1:2 pause and 3:4 terminator loops do not form - Charged tRNAs are not able to fill both the P site and the A site with the required tryptophan amino acids so translation of the leader peptide stalls - The 2:3 antiterminator loop forms

The E. coli lac operon has ________ operator sequences.

3

The standard or housekeeping sigma factor used most often by E. coli RNA polymerase under normal growth conditions is called sigma _________.

70

An active repressor protein _________.

binds to the DNA molecule and prevents transcription

In general, riboswitches regulate _____________in Gram-negative bacteria such as Escherichia and _______________in Gram-positive bacteria such as Bacillus.

translation; transcription

Select all of the characteristics that apply to a helix-turn-helix DNA-binding domain.

- This DNA-binding domain recognizes and binds to palindromic sequences. - This DNA-binding domain is found in the lac repressor. - The regulatory protein forms a dimer, with each component interacting with a major groove of the DNA. - This DNA-binding domain is found in the trp repressor.

Many bacteria use second messengers for global regulation, such as the use of _________.

- c-di-GMP - cAMP - ppGpp

Check all of the structures associated with archaeal cells.

- cannulae - flagella - Hami - Pili

In attenuation regulation of the trp operon, which stem loop forms when tryptophan is readily available to the cell?

3:4

Which of the following is an example of gene regulation at the posttranslational level?

Alteration of protein structure

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

Attenuation

__________ is used to control transcription of some anabolic pathways involved in amino acid biosynthesis.

Attenuation

Which of the following is not a regulatory mechanism used to control the lactose operon in Escherichia coli?

Attenuation NOT: Catabolite repression

Which of the following events occurs initially when Escherichia coli cells are in a gradient of a chemorepellent?

CheA autophosphorylates

Match the following terms associated with regulation of transcription initiation.

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

__________ activate repressor proteins, thereby decreasing the synthesis of certain enzymes.

Corepressors

An sRNA is isolated from a bacterial cell. What would you do to determine whether it is a cis-encoded or a trans-encoded sequence?

Identify whether or not the sRNA sequence is complementary to the coding strand of mRNA gene target.

If autophosphorylation of CheA protein does not occur, then Escherichia coli cells must be _________.

In a gradient of a chemoattractant NOT: in a gradient of a chemorepellant

In the absence of lactose, the lac repressor is __________.

Inactive and can bind to the operator?????

__________ alter repressor proteins thereby increasing the rate of transcription initiation.

Inducers

What is the function of cyclic dimeric GMP in bacterial global regulation systems?

It acts as a secondary nucleotide messenger

For many years microbial geneticists focused almost exclusively on the regulation of transcription initiation. A likely reason for this is _________.

NOT: examples of translational control had not been discovered in microbes

Which is a false statement regarding riboswitches?

The effector molecules that bind to riboswitches are proteins.

What is the key factor determining whether or not attenuation will occur when transcription of the E. coli trp operon has been initiated?

The level of trp-tRNA that is charged with tryptophan

How do translational riboswitches and transcriptional riboswitches differ?

Translational riboswitches are mainly observed in Gram-negative bacteria while transcriptional riboswitches are associated with Gram-positive bacteria.

The sensor kinase for the OmpF: OmpC two-component regulatory system is _________.

the EnvZ protein

Select all of the characteristics that apply to transcriptional riboswitches.

- An effector molecule binds directly to the mRNA to terminate transcription. - Transcription depends upon the folding pattern of the mRNA mediated by the bound effector. - This type of regulation is used by Gram-positive bacteria to regulate amino acid-related genes.

Most E. coli antisense RNAs work with a protein called __________ to regulate their target mRNAs.

Hfq

In which situation might methylation of membrane proteins in Escherichia coli initiate a phosphorelay system that evokes clockwise rotation of flagella?

Presence of a chemorepellent in the extracellular environment

When does a cell regulate gene expression?

Pretranscription through posttranslation

Evaluate the following statements and classify them according to whether they pertain to restriction-modification or the CRISPR/Cas system in bacteria.

Restriction modification - methyl's enzymes modify DNA bases - discovered in 1950s - restriction enonucleases hydrolyze nonmethylated DNA -analogous to human innate immunity CRISPR/Cas - discovered after analysis of genomes analogous to human adaptive immunity - makes protein/RNA site-specific endonulceases - genome consists of areas of repeats and speakers

Guanine tetraphosphate (ppGpp) is associated with which process?

Stringent response in Escherichia

Bacterial responses to phage infection can be compared to the human immune system. Which of the phrases is true?

TRUE Restriction-modification can be compared to innate immunity and CRISPR/Cas to adaptive immunity.

Drag the terms to their corresponding class in order to review various aspects of gene regulation.

Transcriptional Control - attenuation - regulatory protein binds to DNA - riboswitch causes termination Translational Control - inhibition by small RNA molecules - riboswitch blocks initiation - binding of antisense RNA Posttranslational Control - covalent modification of protein product feedback inhibition by end product

When a repressor binds to the operator site on the DNA it normally _________.

inhibits the initiation of transcription

The lac operon is expressed when glucose is _________.

low and lactose is present

If, however, phosphate levels fall, _____________________sense the drop and their activity is _________________, degrading c-di-GMP.

phosphodiesterase; increased

In two component regulatory systems, the response regulator typically receives a(n) __________ from the sensor kinase when it has been activated.

phosphoryl group

Transcription is turned off by _________.

repression

The activity of adenyl cyclase is influenced by _________.

the phosphotransferase system

Cell-to-cell communication by quorum sensing has been shown to be important in the regulation of genes needed for _________.

- virulence - biofilm production - plasmid transfer

Under normal environmental conditions, Rhizobium synthesizes the σ70 sigma factor. When the only nitrogen available is nitrogen gas, Rhizobium synthesizes the σ60 sigma factor. From this information you can deduce _________. (Check all that apply.)

- σ60 is used for expression of genes involved in nitrogen fixation - σ60 binds to a different promoter than σ70 - σ60 allows for expression of a specific subset of genes

During the stringent response, ppGpp-regulated genes for amino acid biosynthesis have a(n) _________ promoter, thus forming a open ___________initiation complex.

AT-rich; more stable

Which of the following statements best explains why microbial geneticists initially focused on regulation of gene expression at the transcriptional, rather than the translational, level?

By regulating the first step of protein synthesis, cells conserve the greatest amount of energy.

It has been observed that when the sugar source changes in a growth medium, the growth rate of yeast vary widely in response. Some strains of yeast are slow to induce catabolic operons while other strains quickly synthesize proteins to process the new sugar. What might be one explanation for this difference in the growth rate of the strains?

Catabolic repression strategies of operons for using different sugars may vary among strains, thereby favoring initiation of transcription in one strain over another depending on the sugar.

Which of the following is not a regulatory mechanism used to control the tryptophan operon in Escherichia coli?

Catabolite repression

How does E. coli assess whether the level of attractant in the media is increasing or decreasing in order to modulate runs vs. tumbles?

Every few seconds the attractant level is measured by comparing the level of methylation on the cytoplasmic side of the MCPs against the level of bound attractant on the periplasmic side of the MCPs.

TRUE OR FALSE: The sensor kinase is phosphorylated by the response regulator when the extracellular environment changes.

FALSE (The sensor kinase is phosphorylated by the response regulator when the extracellular environment changes.)

Because LapG is bound to LapD, it cannot cleave the adhesion protein ___________, thus the cells remain part of the biofilm.

LapA

c-di-GMP binds to a pocket on the cytoplasmic side of ____________, a trans-membrane protein, which assumes a shape that allows it to bind to the periplasmic effector protein, LapG, a ________________.

LapD; protease

Without c-di-GMP bound, LapD releases _____________ which is free to cleave LapA releasing the cells from the biofilm. This survival mechanism allows the cells to seek ________________ elsewhere.

LapG; phosphate

When E. coli is grown in a high osmotic pressure environment, _________.

MicF RNA is transcribed and base pairs with the OmpF mRNA at the ribosome binding site effectively preventing translation of the OmpF porin protein

What term describes a set of genes that is controlled by a common regulatory protein?

Regulon

Assess the following statements and classify them according to whether they would promote a run or a tumble with reference to bacterial motility.

Run - chemoattractant present - counterclockwise flagellar rotation - CheA inactive - Methylation = attractant Tumble - CheY phosphorylated - clockwise flagellar rotation - Methylation > attractant - CheA autophosphorylates

Serratia marcescens bacteria has a gene that regulates red pigment production by cells. A student inoculates two nutrient agar plates of Serratia and incubates one at 25oC and the other at 37oC. Following incubation, the student observes that colonies on the 25oC plate are red while those on the 37oC plate are nonpigmented. Which of the following statements is a logical conclusion based on these results?

Serratia genes for pigment production are induced at certain temperatures.

Distinguish between transcriptional riboswitches and translational riboswitches by classifying the characteristics of each group.

Transcriptional riboswitch - Interrupted mRNA production - FMN as effector -Gram-positive bacteria - Riboflavin operon Translational riboswitch - Occlusion of Shine-Delgarno site - Ribosome binding inhibition - Gram-negative bacteria - Thiamine biosynthesis operon

Distinguish between the quorum sensing in Vibrio fischeri from that in Vibrio harveyi by classifying the characteristics of each organism.

Vibrio fischeri - single autoinducer - positive autoregulation - luxl gene - simple feedback loop Vibrio harveyi - HAI-1, AI-2, CAI-1 - Phosphorelay system - luxM, luxS genes - Type III protein secretion

In regulation by repression _________.

an amino acid activates the repressor so that the repressor binds to the operator and prevents transcription

The __________ is a factor-independent termination site found in the leader region of certain operons, which, under the influence of ribosome behavior, controls the continued transcription of that operon.

attenuator

Acylhomoserine lactones used in quorum sensing regulate their own synthesis by a(n) _________ system.

autoinduction

Bioluminescence in Vibrio fischeri is dependent on __________.

autoregulation of the luxI gene

In the CRISPR/Cas system __________.

bacteria integrate portions of the viral genome into their own so they have a molecular snapshot of their attacker to prevent future encounters

When the catabolite activator protein binds to its binding site in DNA, it _________.

bends the DNA

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

cAMP; switches on

When a microorganism such as E. coli is grown on glucose it is _________.

capable of amino acid production

Enzymes that are expressed at a constant level all the time are said to be .

constitutive

If flagellar rotation of Escherichia coli cells is ____________, then CheA is ______________.

counterclockwise; unphosphorylated

In some circumstances, when two different carbon sources are available, growth will occur first using one carbon source, then after a short lag period, growth will resume using the second carbon source. This process is called __________ growth.

diauxic

When phosphate levels are high in the environment surrounding a biofilm of Pseudomonas fluorescens, it is detected by the sensory domain on _____________________ and c-di-GMP is _____________

diguanylate cyclase ; formed

With the E. coli trp operon where both repression and attenuation occur, the extent of regulation achieved by repression is _________ the extent of regulation achieved by attenuation.

greater than

The site on the DNA to which a repressor protein binds is the __________.

operator

In terms of global gene regulation, which of the following molecules is most similar to c-di-GMP and cAMP?

ppGpp

When bound to the DNA, the repressor protein usually prevents attachment of the RNA polymerase to the __________.

promoter

While standard two-component regulatory systems typically act to control gene transcription, phosphorelay systems can act either to control gene transcription or to control .

protein activity

Which statement best describes the mechanism(s) of posttranslational regulation of gene expression?

Allosteric regulation following transcription of mRNA occurs in many biosynthetic pathways.

The terminator versus anti-terminator function of the T box-based riboswitch used by Gram-positive bacteria to regulate amino acid-related genes is determined by _________.

the binding of the appropriate uncharged tRNA

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

If Escherichia coli is cultured in broth containing both glucose and lactose, it _________.

uses glucose preferentially until the supply is exhausted, then uses lactose