Q&A Hero

Q: Explain why one cell of a pathogenic bacterium by itself typically does not secrete a toxin, despite the species as a whole being characterized as toxin producing. To help in your explanation, predict what would happen to an individual pathogen that secreted a toxin inside a human.

Q: Defend why is it unsurprising that two-component regulatory systems are all but absent in bacteria that live at the expense of a host?

Q: Explain the sequence of events that would follow the transfer of an organism from a complex medium to a minimal medium.

Q: Illustrate and explain an operon that is subject to both positive and negative control containing the operator region, the operon, the promoter, the activator binding site, and the functional genes in a DNA sequence. Also compare and contrast the roles activators and repressors have in regulating the illustrated operon.

Q: Explain why regulation of enzyme synthesis is more time consuming than regulation of enzymatic activity.

Q: Compare and contrast chemical, spatial, and temporal gradients as found in bacterial regulatory systems.

Q: Describe the basic two-component regulatory system, and compare the function of each component.

Q: Explain the phenomenon known as diauxic growth. Hypothesize why this type of regulation might be important for survival of a microbe in a community as well as a situation where lacking it might be advantageous.

Q: Explain the translational attenuation mechanism.

Q: Using the tryptophan operon as a model, explain a transcription pause site and the formation of a stem-loop.

Q: Describe the function and the functional components of the maltose regulon system.

Q: How is the leucine zipper formed, and what is its function?

Q: What is the difference between an operator and a promoter?

Q: Multiple mechanisms for small RNA (sRNA)-mediated translational regulation exist but all are unified by inactivating protein synthesis of the target mRNA.

Q: Heat shock proteins are produced at high numbers to minimize damaging effects during high heat conditions as well as other stress signals unrelated to heat such as ultraviolet radiation.

Q: Multiple sigma factors are essential to induce the biosynthesis of endospores, all of which are encoded by genes, so a complex regulatory mechanism such as this likely has a higher chance of mutations leading to incorrect functioning compared to a simple repression mechanism.

Q: During chemotaxis, attractants increase the rate of autophosphorylation whereas repellants decrease this rate.

Q: Quorum sensing requires a strong gradient to be reached before the signaling molecules are transported into the cytoplasm.

Q: In catabolic repression, cells use the least abundant carbon source first.

Q: In most cases, the first product of a particular biosynthetic pathway represses the enzymes of the pathway.

Q: Once cytoplasmic sensor proteins involved in chemotaxis regulation are phosphorylated, a cascade of other phosphate-transferring mechanisms provide ATP energy to rotate flagella.

Q: Cyclic AMP (cAMP) is involved in the global regulation of catabolic pathways in Escherichia coli, including the lac operon, and a low activity of adenylate cyclase that makes cAMP is suggestive of catabolite repression.

Q: DNA-binding proteins typically affect translation of a protein.

Q: A two-component regulatory system usually involves both the sensor and response proteins being subject to phosphorylation.

Q: Studying the transcriptional activity of flagellar genes would not likely reveal differential changes when the cells are actively motile compared to nonmotile activity, because a two-component regulatory system is sufficient to control flagellar activity.

Q: Proteins and RNA molecules that are needed in the cell, at about the same level under all growth conditions, require constitutive expression.

Q: The preferential use of glucose over other available carbon substrates for growth is mechanistically explained by catabolite repression.

Q: Transcriptional regulation is considered negative when an inducer binds to and deactivates a repressor.

Q: A regulon always includes at least two operons.

Q: Depending on the type of regulatory mechanism, activators and repressors can bind to operator regions which control transcription.

Q: Once the regulatory proteins and effector molecules are made, the actual mechanisms for regulation rarely require net energy input.

Q: A repressor is a molecule that represses biosynthesis of an mRNA transcript.

Q: The biodegradation pathway for benzoate is likely to be subject to induction rather than repression.

Q: Some proteins that bind to DNA block transcription, whereas other proteins can activate transcription.

Q: The actual residues in a DNA-binding protein that interacts with DNA usually correspond to each other according to the amino acids encoded by the DNA. For example, a DNA sequencing containing AGC-AGA-CAG which encodes for Ser-Arg-Gln would likely have a DNA-binding protein with Ser-Arg-Gln bind to it.

Q: A common structure for proteins that bind DNA is helix-turn-helix.

Q: Small molecules usually act directly (rather than indirectly) in regulating transcription.

Q: Short regions at the beginning and end of gene sequences are not translated into proteins.

Q: Proteins required at approximately the same level throughout a cell's growth cycle are often not subject to regulatory mechanisms and are constitutively synthesized.

Q: Transcriptomics is a common approach to infer which metabolic pathways are actively functioning, but which regulation process can MOST significantly complicate or even abolish conclusions from this approach? A) activity of a catabolite repressor protein on multiple pathways B) antisense RNA silencing C) feedback inhibition with allosteric proteins D) presence of corepressors and inducers which are molecules undetected by transcriptomics

Q: How is the activity of a riboswitch controlled? A) by other riboswitches B) metabolite binding can change its structure C) sigma factor binding alters its structure D) small RNA complementary binding disrupts its function

Q: Which organism would likely harbor the MOST two-component regulatory systems? A) an archaeon living in an extreme environment B) a bacterium occupying a heterogeneous niche will high nutrient mixing C) an organism capable of quorum sensing D) a parasitic bacterium living inside another organism

Q: What type of sRNA often requires a chaperon protein for strong regulation activity? A) antisense RNA B) riboswitches C) siRNA D) trans-sRNA

Q: Quorum sensing generally follows the mechanism of which type of regulation? A) feedback inhibition B) negative transcriptional regulation C) positive transcriptional regulation D) two-component regulation system

Q: During the biotransformation of a large molecular weight compound, two major products are formed. While one of the products is catabolized, the other compounds accumulation represses the biotransformation of the large compound. Which approach is MOST likely to artificially enhance the biotransformation beyond this point in a batch culture? A) addition of an isoenzyme for the biotransformation route to increase its transcription B) addition of inducer molecules into the medium to increase transcriptional repression C) inclusion of more of an intermediate compound in the catabolic pathway D) spike in additional activator proteins that control the transcription of this pathway

Q: What are the primary regulator units that control endospore formation? A) allosteric proteins B) antisense RNAs C) riboswitches D) sigma factors

Q: Phosphorylation of ________ regulates which direction a flagellum rotates, thus controlling whether an organism runs or tumbles. A) CheAW B) CheB C) CheY D) CheZ

Q: A bacterium that either partially or fully catabolizes an acyl-homoserine lactone will likely disrupt A) attenuation. B) chemotaxis. C) endospore formation. D) quorum sensing.

Q: An organism grown in a high nutrient liquid broth to high turbidity always appears to produce a blue pigment and even when a large inoculum is transferred to a nutrient rich agar plate it appears blue. When the researcher noticed it never appears blue when very small colonies were grown in low nutrient agar plates. What is the most plausible conclusion? A) Large populations enabled the differentiation of a subpopulation of cells that created the blue pigment. B) Only high nutrient conditions provide enough energy for cells to produce this secondary metabolite that appears blue. C) The blue pigment production is linked to quorum sensing. D) The strong gradient from very high to low nutrient bioavailability induces production of the blue metabolite.

Q: Which regulatory mechanism does NOT depend on a conformational change in protein/enzyme structure to change activity? A) attenuation B) catabolite repression C) feedback inhibition D) negative control

Q: Which of the following IS a characteristic of an isoenzyme? A) More than one enzyme is regulated by the same mechanism. B) The same reaction can be catalyzed by multiple enzyme variants. C) Multiple binding sites on the same enzyme enable multiple regulation mechanisms. D) More than one gene makes the same enzyme.

Q: Post-translational regulation of an enzyme's activity, such as glutamine synthetase, can be finely controlled at varied levels due to A) the varied strengths metabolite-regulating compounds can have with the enzyme such as hydrogen bonding, covalent bonding, and van der Waals attractions. B) having multiple independently functional subunits. C) the structural strength enzymes have once properly folded compared to short-lived and easily degradable transcripts during translational regulation. D) weak chemical modifications of the enzyme rather than harsh protein-protein or protein-DNA interactions.

Q: Attenuation is a type of regulation that can control A) allosteric enzyme activity. B) transcriptional activity exclusively. C) translational activity exclusively. D) both transcriptional and translational activity.

Q: Based on our understanding of the early stages of life, ________ is/are thought to be one of the earliest forms of metabolic regulation that evolved. A) attenuation B) feedback inhibition C) riboswitches D) transcription factors

Q: How could you identify potential riboswitches with bioinformatics tools? A) Advanced 3D modeling techniques of mRNA folding would be necessary because complementary nucleotide binding predictions would not be useful. B) Locate short regions of an individual transcript with several complementary sites. C) Identify homologous sRNAs in other organisms. D) Identify several complementary mRNAs encoded in the genome.

Q: When the nontemplate strand of a gene is transcribed into RNA, what is likely to result? A) A complementary sRNA will bind to it and form a functional ribozyme with secondary structure. B) It will complementary bind to the gene sequence, form a hairpin loop, and transcriptionally repress the gene. C) The complementary mRNA also transcribed from the template strand will bind to it and halt its translation. D) A global regulator will identify this as a stress, respond by inducing ribonuclease production, and it will degraded.

Q: Which of the following mechanisms leads to INCREASED transcriptional activity? A) An sRNA binds to the ribosome binding site. B) Ribonuclease activity is blocked by sRNA complementary binding to the end of a transcript. C) The ribosome binding site is made available from sRNA binding to part of it. D) Recruitment of RNA polymerase is enhanced when sRNA binds to and removes a repressor.

Q: How would you design an sRNA to bind to a sequence? A) select six continuous nucleotides from the sequence B) take the complementary sequence of six continuous nucleotides C) select 200 continuous nucleotides from the sequence D) take the complementary sequence of 200 continuous nucleotides

Q: Which statement is TRUE of two separate regulators controlling one individual operon? A) The two regulators themselves must respond to different signals, which enables both to control the operon differently. B) One regulator will likely control the transcription of one section of the operon, whereas the other regulator will control the other component. C) One regulator will bind to the operator region whereas the other will bind to the promoter region so they can co-occur and co-regulate the operon. D) Two regulators trying to control the same operon will likely result in only one being maintained after several generations.

Q: Bacteria from the genus Caulobacter are used to model cellular differentiation in eukaryotes. The abundance of CtrA, DnaA, and GcrA separately control activity of other genes necessary for differentiation in Caulobacter. Thus, these three proteins can be classified as A) activating sensors. B) heterologous regulators. C) differentiating regulons. D) transcriptional regulators.

Q: Which enzyme would be BEST to include in a protein extract to refold and denature improperly folded proteins? A) DnaK B) RepA C) RpoH D) Spo0A

Q: In Bacteria, sensor kinases that respond to extracellular signals transfer this signal to the cytoplasmic machinery by typically phosphorylating the ________ residues. A) histidine B) serine C) threonine D) tyrosine

Q: Based on their abundance and location in bacterial genomes, deduce which is LEAST likely to horizontally transfer into another bacterium while maintaining its identical function and regulatory roles. A) heat shock protein-encoding gene B) lac operon C) catabolic regulon D) quorum sensing operon

Q: Interpret the results to the following experiment. Transcriptional activity of chemotactic genes showed a high expression level during the following conditions: repelling away from compound 1, moving towards compound 2, and remaining sessile when presented compounds 3 and 4. A) Activity during movement in any direction led to high measurements observed, and the sessile population responded equally to both a chemoattractant and a chemorepellant but remained in the same location for their net movement. B) Gene expression by itself cannot distinguish between cells responding to both an attractant and repellent, so this ambiguity makes transcriptomics unfavorable but nonetheless indicates activity. C) The activity observed during a sessile existence suggests the molecular probe was targeting a chemotactic gene that is also involved in other non-chemotactic functions due to the activity observed. D) Transcriptomics as a whole cannot be used for chemotaxis genes because they are not regulated at the transcriptional level (i.e., they are constitutive), which is why activity is observed on all three conditions.

Q: When a Bacillus anthracis population suddenly must form spores to survive a harsh nutrient poor environment, how do the cells obtain energy? A) Cells in a growth phase that have not used up all of their energy will be the only ones to make endospores, which is why relatively few endospores are often made from a large population. B) Intracellular energy reserves are quickly made available to produce endospores. C) Slow responding cells are cannibalized by others that already began spore formation. D) Global regulation is initiated to minimize energy waste in biosynthetic pathways and catabolic pathways are increased to consume remaining usable substrates to fuel spore formation.

Q: The most frequent way in which regulatory RNA molecules exert their effects is by A) base pairing with other RNA molecules that have regions of complementary sequence. B) binding to a repressor and repressing enzyme transcription. C) acting as an inducer that then binds to an activator protein to allow transcription to proceed. D) signal transduction.

Q: To be most sensitive to a repellant, a methyl-accepting chemotaxis protein must be ________ methylated to initiate a ________. A) fully / run B) fully / tumble C) not / run D) not / tumble

Q: The promoters of positively controlled operons require activator proteins, because A) RNA polymerase easily recognizes the consensus sequence. B) they are required to inactivate the repressor proteins. C) the promoters have nucleotide sequences that bind RNA polymerase weakly, which are not close matches to the consensus sequence. D) they are needed to bind to the allosteric site of RNA polymerase.

Q: The function of a kinase is A) methylation. B) response regulation. C) phosphorylation. D) glycosylation.

Q: Which type of regulatory protein(s) is/are present in Archaea? A) Activators that stimulate RNA polymerase activity are present in Archaea. B) Repressors that block RNA polymerase activity are present in Archaea. C) Both activators and repressors are present in Archaea. D) Similar to regulation in Eukarya, Archaea lack bacterial-like regulators such as activators and repressors and use transcription factors instead.

Q: In negative control of transcription, how does the presence of an inducer affect transcription? A) The inducer binds to the operator. B) The inducer does not bind to the operator. C) The inducer causes the repressor to bind to the operator. D) The inducer prevents the repressor from binding to the operator.

Q: Cyclic AMP is synthesized from ATP by an enzyme called ________ which is involved in ________. A) adenylate cyclase / catabolite repression B) adenylate cyclase / transcriptional activation C) cAMP receptor protein (CRP) synthase / catabolite repression D) cAMP receptor protein (CRP) synthase / transcriptional activation

Q: Which of the following do NOT bind to the promoter sequence during regulation? A) activators B) inducers C) repressors D) activators, inducers, and repressors

Q: What occurs when an inducer is added to an environment containing an organism with a metabolic pathway controlled by a repressor? A) The inducer combines with the repressor and activates the pathway. B) The inducer combines with the repressor and inactivates the pathway. C) The inducer combines with the substrate and blocks induction. D) The inducer does not combine with, but functions as a chaperone molecule for, the enzyme-substrate complex.

Q: During a growth curve of Aliivibrio fischeri, when would you expect to see the strongest bioluminescence? A) lag phase B) early to middle log phase C) late log to early stationary phase D) middle to late stationary phase

Q: Considering the catabolite repression mechanism, which observation would make you suspect it is NOT occurring? A) CRP bound to promoter sites B) elevated levels of transcripts for maltose and sucrose catabolism C) relatively low intracellular cyclic AMP levels D) RNA polymerase bound to biosynthetic promoter sequences

Q: Enzyme induction occurs A) when the substrate is present. B) when the organism is environmentally stressed. C) continuously. D) when the substrate is depleted.

Q: The lac operon is an example of ________ control in which the presence of an ________ is required for transcription to occur. A) negative / activator B) negative / inducer C) positive / activator D) positive / inducer

Q: Which type of regulator(s) specifically bind to operator regions of DNA? A) activators B) activators and inducers C) repressors D) repressors and corepressors

Q: Summarize the evolution of sequencing technology beginning with the Sanger method.