Deck 10: Molecular Regulation

Question 1

________ prevent transcription, whereas ________ stimulate transcription.

A) Activators; repressors
B) Inducers; corepressors
C) Corepressors; inducers
D) Regulators; repressors
E) Repressors; activators

Answer 1

E

Question 2

One benefit of operons in bacteria is that they

A) allow for alterations in DNA sequence by flipping promoters around.
B) allow for coordinated gene expression of related genes on one mRNA controlled by one promoter.
C) do not need ligands and regulatory proteins as single genes would.
D) do not need any modification of the proteins after they are expressed.
E) allow for the bacteria to utilize a wide variety of carbon sources.

Answer 2

B

Question 3

When an inducer is added to a medium containing an organism with a metabolic pathway controlled by a repressor, the inducer then

A) combines with the repressor and activates the repressor.
B) combines with the repressor and inactivates the repressor.
C) combines with the substrate and blocks induction.
D) combines with the substrate and activates induction.
E) does not combine with, but functions as a chaperone molecule for, the enzyme-substrate complex.

Answer 3

B

Question 4

In some, but not all, instances, ________ molecules bind RNA transcripts and help or hinder degradation.

A) tsRNA
B) rRNA
C) tRNA
D) sRNA
E) mRNA

Question 5

A bacterial growth curve is presented below. The curve represents ________ growth, which is caused by the ________.

A) binary; addition of more growth media after the fulture reaches stationary phase
B) diauxic; addition of more growth media after the fulture reaches stationary phase
C) binary; addition of a needed vitamin after it runs out
D) diauxic; addition of a needed vitamin after it runs out
E) diauxic; growth on two carbon sources resulting in a lag after the preferred substrate is depleted; new genes are then induced and growth resumes

Question 6

Which form of control is the LEAST reversible and MOST drastic?

A) posttranslational control
B) control of transcription
C) alterations of DNA sequence
D) translational control
E) mRNA stability

Question 7

Transcriptional attenuation is a common regulatory strategy used to control many operons that code for

A) amino acid degradation.
B) amino acid biosynthesis.
C) carbohydrate degradation.
D) carbohydrate biosynthesis.
E) lipid degradation.

Question 8

As diagrammed below, some amino acid biosynthetic operons have stem loop structures in the mRNA. These structures play a role in the regulation of the operon by which of the following mechanisms?

A) The leader sequence shown contains codons for the amino acid. When these are low, the ribosome stalls, allowing a hairpin between the two middle regions to form so that the rest of the message can be translated.
B) A repressor protein made of that amino acid will bind to the region and prevent translation when large amounts of the amino acid are present.
C) In the presence of large amounts of the amino acid, the hairpin will wind around the amino acid and prevent further translation.
D) The uridine-rich region has codons for that amino acid; when present, this region will be a terminator region. The hairpins allow for an RNA to bind that then allows translation to occur.
E) Catabolite repressor protein can bind and prevent the hairpins from forming, thus allowing translation to occur.

Question 9

Finding an inverted repeated sequence within 100-200 bases of a promoter suggests the presence of a ________ binding site.

A) DNA
B) transcriptional regulator
C) RNA
D) ribosome
E) corepressor

Question 10

When both glucose and lactose are added to the growth medium, Escherichia coli will have a growth curve that

A) does not change.
B) grows slowly and then, halfway through, grows faster.
C) grows, levels off, and then grows again.
D) grows more slowly than with glucose alone.
E) grows more quickly than with glucose alone.

Question 11

Binding of tryptophan to the ________ makes a holorepressor.

A) aporepressor
B) corepressor
C) repressor
D) inducer
E) activator

Question 12

Which of the following is the favored carbon source of Escherichia coli?

A) lactose
B) galactose
C) sucrose
D) glucose
E) fructose

Question 13

The araBAD and araC genes are transcribed in the ________ direction with respect to each other.

A) same
B) opposite
C) forward
D) left
E) right

Question 14

All of the following typically occur in the presence of high glucose and high lactose concentrations EXCEPT

A) enzyme II glucose is unphosphorylated.
B) cAMP concentrations are low.
C) C-reactive protein levels in the cell are low.
D) inhibition of LacY activity.
E) lactose is kept out of the cell.

Question 15

A feature common to all control mechanisms is

A) quorum sensing.
B) phosphorylation cascades.
C) the ability to sense that something inside or around the cell has changed.
D) housekeeping enzymes.
E) increased or decreased gene expression.

Question 16

How many of the gene products of the lactose operon are required for the utilization of lactose to occur?

A) none
B) one
C) two
D) three
E) four

Question 17

In a two-component signal transduction system, a ________ is transferred from a sensor kinase to a ________ in response to an environmental signal.

A) phosphate; sensor domain
B) phosphate; sensor phosphatase
C) phosphate; response regulator
D) magnesium; sensor domain
E) magnesium; response regulator

Question 18

The figure below shows a regulatory being produced on the left. Based on the information in the figure, this protein must function in which of the following ways?

A) When glucose binds to it, the protein binds to the regulatory sequence and prevents transcription of the target gene.
B) This protein must influence a hairpin sequence and thus fine tunes the operon.
C) In the presence of the end product of the operon, this protein will bind to the regulatory region and acts as an activator.
D) When a ligand is or is not bound, this protein may act as either an activator or repressor.
E) This protein would not have an effect on transcription of the target gene.

Question 19

If a cell always needs a gene for housekeeping purposes, it is

A) constitutive.
B) inducible.
C) repressible.
D) derepressible.
E) promotable.

Question 20

A transmembrane sensor kinase protein senses an environmental condition outside ________ bacteria or in the periplasm of a(n) ________ bacteria.

A) Gram-positive; Gram-negative
B) Gram-negative; Gram-positive
C) prokaryotic; eukaryotic
D) prokaryotic; archaean
E) Gram-positive; acid-fast

Question 21

Which of the following is a second messenger that helps to regulate biofilm production?

A) ppGpp
B) ATP
C) cAMP
D) cGMP
E) cdiGMP

Question 22

How does the AraC regulatory protein turn on transcription in the presence of arabinose?

A) With the addition of arabinose, AraC no longer dimerizes and will form a large loop by binding to araO and aria, and thus can interact with RNA polymerase to permit transcription.
B) The dimer will form a large loop by binding to araO and aria, and thus can interact with RNA polymerase to permit transcription.
C) With the addition, AraC no longer dimerizes and thus can interact with RNA polymerase to permit transcription.
D) It becomes less flexible, so that a monomer can bind to araI1 and araI2 and interact with RNA polymerase to permit transcription.
E) It becomes more flexible, so that the dimer can bind to araI1 and araI2 and interact with RNA polymerase to permit transcription.

Question 23

The role of the Hin recombinase is to

A) recombine specific segments of the DNA of Haemophilus influenzae.
B) recombine specific segments of flagellin genes in Neisseria gonorrhoeae.
C) recombine specific segments of MCP genes in Salmonella enterica.
D) recombine specific segments of flagellin genes in Salmonella enterica.
E) repair damage in DNA.

Question 24

The stringent response relies on the production of

A) pG.
B) ppG.
C) pppG.
D) pGp.
E) ppGpp.

Question 25

Which of the following is NOT true of sRNA genes?

A) They have a ribosomal-binding site.
B) They occur between genes.
C) They share homology between related species.
D) They can act as antisense RNAs.
E) They play a role in regulating genes involved in oxidative stress, acid resistance, and quorum sensing.

Question 26

Which genes always occur in intergenic regions?

A) tRNA
B) mRNA
C) sRNA
D) rRNA
E) tsRNA

Question 27

The stringent response involves all EXCEPT

A) downregulation of rRNA synthesis.
B) downregulation of tRNA synthesis.
C) ATP.
D) GTP.
E) a lack of change in gene expression.

Question 28

Phase variation in Salmonella enterica involves

A) gene inversion.
B) chemotaxis.
C) outer membrane proteins.
D) sRNA.
E) slipped-strand mispairing.

Question 29

Some microbes use gene regulation to periodically change their appearance, in a process called

A) sporulation.
B) attenuation.
C) regulation.
D) activation.
E) phase variation.

Question 30

Bacterial systems using an AraC/XylS-type regulator include ________ as regulated by ________.

A) a type III secretion system in Pseudomonas; NitR
B) a type III secretion system in Pseudomonas; ExsA
C) a type III secretion system in Pseudomonas; YbtA
D) virulence genes and cholera toxin in Vibrio; TxtR
E) virulence genes and cholera toxin in Vibrio; ExsA

Question 31

The regulatory activity of sRNA

A) codes for a sigma factor.
B) prevents CRP interaction with RNA polymerase, thereby blocking its access to the promoter.
C) synthesizes ppGpp.
D) targets mRNAs for degradation.
E) creates an attenuator stem loop.

Question 32

The role of a leader sequence is to

A) directly control transcription.
B) determine whether transcription can proceed through the genes in the operon.
C) determine whether RNA polymerase can bind.
D) terminate transcription.
E) direct the looping of the DNA that prevents transcription initiation.

Question 33

The mechanism behind slipped-strand mispairing is that

A) short repeats allow for slippage of the RNA polymerase during transcription of the affected genes.
B) short repeats allow for slippage of DNA polymerase during replication, which leads to an out-of-frame reading sequence.
C) an invertible promoter slips into different reading frames.
D) the genes coding for lipopolysaccharide in Gram-negative bacteria can be slipped in and out of frame.
E) short repeats slip and turn genes off, but they can never be turned back on.

Question 34

The best description of the initial step in the regulatory process shown below is

A) an sRNA is produced that can then be used to turn on genes.
B) an sRNA is produced that can then be used to turn off genes.
C) a sigma factor mRNA is transcribed and forms secondary structures at lower temperatures. When heated, the structures melt and the mRNA for the heat shock sigma factor, rpoH, can be translated.
D) The hairpins contain codons for a needed amino acid. When amino acid is lacking, the ribosome stalls and prevents its formation, thus allowing translation.
E) The hairpins contain codons for needed amino acids. When amino acid is present, the ribosome stalls and prevents the formation of hairpins, thus allowing translation.

Question 35

When the forespore is first produced, about what percentage of the chromosome is actually inside it?

A) 10
B) 20
C) 30
D) 40
E) 50

Question 36

The little amount of sigma H that is made at 30°C is ________ by the DnaK/GrpE/DnaJ chaperones.

A) enhanced
B) activated
C) degraded
D) protected
E) folded

Question 37

If the newly synthesized DNA strand slips back relative to the template strand, one copy of the repeated unit is ________ the growing strand.

A) inserted in
B) deleted from
C) folded over
D) folded under
E) bound to

Question 38

Which of the following statements about riboswitches is true?

A) They are found mainly at the 3' end of a mRNA.
B) They are capable of binding to a ligand and activating transcription but do not repress transcription.
C) They can control transcription but no translation.
D) Ligands that can bind range from vitamins, amino acids, magnesium, and fluoride.
E) They have no secondary structures involved in their control.

Question 39

What type of RNAs bind to complementary sequences of target transcripts and stimulate or prevent translation?

A) ribosomal
B) transfer
C) messenger
D) antisense
E) small

Question 40

In the regulation of chemotaxis, proteins are modified in which of the following ways?

A) phosphorylations
B) methylation
C) feedback inhibition
D) phosphorylation and methylation
E) feedback inhibition, phosphorylation, and methylation

Question 41

Which of the following is a technique used in studying the proteome of an organism?

A) knowing the DNA sequence to predict the amino acid sequence
B) predicting the protein sequence by using the mRNA sequence
C) two-dimensional protein gels followed by mass spec of the proteins
D) obtaining cDNA and then probing a DNA microarray
E) digesting a cell extract with trypsin

Question 42

Glucose transport into the cell brings about a phenomenon known as inducer exclusion.
Describe how this functions with respect to the lac operon.

Question 43

Integrated circuits are involved in all of the following EXCEPT

A) controlling chemotactic activities of a cell.
B) coupling the genetic and biochemical control of a metabolic pathway.
C) timing the events of a developmental cycle.
D) having an influence on nitrogen metabolism.
E) specifically inverting the flagellin genes.

Question 44

The figure below diagrams a process used to study bacterial physiology. Which is the correct description of the steps shown?

A) Cells are lysed, two-dimensional gels are run, and then spots of protein are run through mass spec. Proteins' peaks are identified.
B) Cells are lysed, two-dimensional gels are run, isobaric tags are added to the proteins, and they are run through a mass spec. Proteins' peaks are identified.
C) Cells are lysed, two-dimensional gels are run, and proteins are digested with trypsin and run through a mass spec. Proteins' peaks are identified.
D) Cells are lysed, proteins are digested with trypsin, and column is used followed by mass spec. Proteins' peaks are identified.
E) Cells are lysed, RNA is purified, cDNA is made, and sequencing is carried out.

Question 45

With respect to quorum sensing, all of the following are true EXCEPT that it

A) can be involved in cross-talk between species, including eukaryotes.
B) can be involved in some pathogenesis and biofilm formation.
C) has only one autoinduction system per species.
D) is carried out with an autoinducer such as homoserine lactone.
E) plays a role in some antibiotic production.

Question 46

Many bacteria produce some type of homoserine lactone for quorum sensing, yet some Gram-positive bacteria will produce ________ for this same purpose.

A) antibiotics
B) peptides
C) furanosyl borate diester
D) cyclic di-GMP
E) ppGpp

Question 47

The AraC regulator both activates and represses transcription of the genes involved in arabinose catabolism. How is this system more advantageous to a cell than a simpler repressor system like that used on the lac operon?

Question 48

Describe what happens to the lac operon in the presence of both lactose and glucose.

Question 49

Explain a way that organisms sense and respond to their environment.

Question 50

Which of the following statements is true concerning the use of cyclic di-GMP as a second messenger?

A) It activates the expression of flagellin genes and thus enhances motility.
B) It is found in all microbes: bacteria, archaea, and eukaryotic microbes.
C) The action of diguanylate cyclase produces it.
D) It decreases in level as biofilm is produced.
E) Phosphodiesterase can convert GMP to cyclic di-GMP.

Question 51

The value of studying a transcriptome rather than a genome is that

A) RNA is much easier to work with than DNA.
B) using bacterial RNA eliminates the introns they all have.
C) one can get a snapshot of what genes are expressed under some conditions but not others.
D) a transcriptome is more related to the protein.
E) deep sequencing can only be performed on RNA.

Question 52

Autoinducers regulate gene expression by

A) accumulating inside the cell until enough is present to bind repressor proteins and stop transcription.
B) accumulating inside the cell until enough is present to bind activator proteins and initiate transcription.
C) interacting with small RNAs to either inhibit or enhance transcription.
D) diffusing out of the cell and when a critical cell density is reached, moving back in and binding to a regulatory protein to initiate transcription.
E) being synthesized after glucose is used up, thereby bypassing catabolite repression.

Question 53

In terms of controlling chemotaxis, the proteins involved control chemotaxis in which way?

A) They control which form of flagellin is expressed.
B) They change the direction of the flagella from counterclockwise to clockwise and back.
C) They promote longer "tumbles" when a chemoattractant is present.
D) They increase the phosphorylation of CheY so that there are more counterclockwise flagella.
E) They respond to demethylation of methyl-accepting chemotaxis proteins to bring about longer runs.

Question 54

How is repression of biosynthetic pathways different than repression of a catabolic pathway? Why does repression of these two types of pathways work differently?

Question 55

A quorum-sensing gene system requires the accumulation of a secreted small molecule called a(n)

A) autoinducer.
B) activator.
C) repressor.
D) inducer.
E) corepressor.

Question 56

Which of the following describes the process of obtaining RNA sequence information?

A) Proteins are isolated and mass spec is used. Once the proteins are known, the RNA that coded for them can be determined.
B) RNA from a particular growth condition is isolated and converted to cDNA; DNA adapters are added, allowing high-throughput sequencing to be carried out. The genome position of the sequence obtained is then determined using computer software.
C) A DNA microarray is used to find the RNA sequences expressed at that time.
D) One examines the tRNA and rRNA in a given culture in order to study various physiological conditions.
E) One determines the RNA sequence of every gene in the genome and then determines if it is present in a given culture.

Question 57

What is diauxic growth and why does it occur?

Question 58

Describe the function of prokaryotic activator proteins.

Question 59

Which molecule is used for hybridization to DNA bound on a DNA microarray?

A) DNA
B) RNA
C) mRNA
D) cDNA
E) qDNA

Question 60

All the cell's expressed RNAs are collectively referred to as the cell's

A) genome.
B) transcriptome.
C) proteome.
D) holoenzyme.
E) ORF.

Question 61

How is sigma H degradation controlled by temperature, and why is this important to the cell?

Question 62

During the process of endospore formation, different sigma factors are active in the mother cell and forespore. How is this possible, and why is it important?

Question 63

Explain the process of bioluminescence in Allivibrio fischeri. How is this an example of a mutualistic relationship?

Question 64

What does the gene inversion in Salmonella enterica accomplish with respect to its course of infection? Briefly describe how this mechanism works.

Question 65

Explain what happens to motility when a chemoattractant is added to bacterial cells.

Question 66

Explain how small, untranslated RNAs (sRNAs) regulate iron uptake and iron storage.

Question 67

Briefly explain two-dimensional gel electrophoresis. What is the procedure used to determine, and why are both dimensions necessary?

Question 68

Explain how riboswitches can be compared to activator and repressor proteins. State an example.

Question 69

The stringent response downregulates rRNA synthesis. Does it similarly downregulate ribosomal protein synthesis?

Question 70

Explain the process of attenuation in regulating transcription of the tryptophan operon.

Question 71

Quorum sensing plays a role in interspecies communications. Describe the relationship between green seaweed Enteromorpha and Vibrio anguillarum bacterial cells in biofilms, and explain how Escherichia coli was used to understand this interaction.

Question 72

Explain how a repressor protein works with respect to a biosynthetic operon.

Question 73

What happens when strand slippage occurs on the template or the newly synthesized DNA strand? How does Neisseria gonorrhoeae use slipped-strand mispairing to its advantage?