Microbiology Chapter 14

1. Small RNAs that regulate translation by binding to the leader region of mRNAs are called antisense RNAs.

2. How do translational riboswitches and transcriptional riboswitches differ? A. Translational riboswitches are mainly observed in Gram-negative bacteria while transcriptional riboswitches are associated with Gram-positive bacteria. B. Translational riboswitches are located in the mRNA trailer while transcriptional riboswitches are in mRNA leader sequence. C. Translational riboswitch effectors bind to ribosomes while transcriptional riboswitch effectors bind to mRNA. D. All of these are differences between translational and transcriptional riboswitches.

3. The THI-element is part of the operon that controls synthesis of thymine in mRNA.

4. Most E. coli antisense RNAs work with a protein called ______ to regulate their target mRNAs. A. CAP B. MicF C. Hfq D. None of the choices are correct.

5. 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? A. Identify whether or not the sRNA sequence is complementary to the coding strand of mRNA gene target. B. Analyze the molecular position of hydrogen atoms in the sRNA nucleotides. C. Determine whether the sRNA binds to mRNA or to tRNA. D. Find out if the sRNA acts as a transcriptional or as a translational inhibitor.

6. What is the key factor determining whether or not attenuation will occur when transcription of the E. coli trp operon has been initiated? A. The activity level of adenyl cyclase B. The trp operon repressor C. The level of tryptophan in the environment D. The level of trp-tRNA that is charged with tryptophan

7. 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. A. modulator B. operator C. attenuator D. terminator

8. ______________ is used to control transcription of some anabolic pathways involved in amino acid biosynthesis. A. Attenuation B. Catabolite repression C. Induction D. All of the choices are correct.

9. Which is a false statement regarding riboswitches? A. Riboswitches are regions in the 5' untranslated leader of an mRNA. B. The effector molecules that bind to riboswitches are proteins. C. When the effector binds the riboswitch, it may serve to terminate transcription of its target mRNA. D. When the effector binds the riboswitch, it may serve to continue transcription of its target mRNA.

10. 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. A. the same as B. less than C. greater than D. Repression is not used in the regulation of the E. coli trp operon.

11. Riboswitches regulate transcription, rather than translation, in cells.

12. 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 A. the binding of the appropriate uncharged tRNA. B. the rate of leader peptide synthesis. C. the binding of the T box binding protein. D. the utilization of the appropriate sigma factor by RNA polymerase.

13. In general, riboswitches regulate in Gram-negative bacteria such as Escherichia and in Gram-positive bacteria such as Bacillus. A. transcription; translation B. translation; transcription C. replication; translation D. transcription; replication

14. In attenuation regulation of the trp operon, which stem loop forms when tryptophan is readily available to the cell? A. 3:4 B. 1:3 C. 2:3 D. 2:4

15. During tryptophan synthesis in Escherichia coli, the 1:2 attenuator sequence of mRNA is called the pause loop.

16. During regulation by attenuation in the trp operon, if the pause and terminator loops form in mRNA, transcription is uncoupled to translation and protein synthesis is not occurring.

17. Which of the following is not a regulatory mechanism used to control the tryptophan operon in Escherichia coli? A. Repression B. Catabolite repression C. Attenuation D. All of the choices are correct.

18. When tryptophan levels in a cell are low, a cell will stall transcription but continue translation of the tryptophan operon.

19. When arabinose is present in the environment, the AraC protein acts as a(n) ______________ for the E. coli ara operon.

20. 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? A. Serratia genes for pigment production are induced at certain temperatures. B. This is an example of constitutive gene expression. C. Low temperatures cause repression of certain housekeeping genes. D. Serratia cells undergo a genotypic change that is proportional to changes in temperature.

21. Helix-turn-helix and zinc fingers are secondary structural motifs in DNA and RNA, respectively.

22. In terms of transcription regulation, the role of a helix-turn-helix is most similar to that of a(n) . A. zinc finger B. sigma factor C. poly-A tail D. guanine cap

23. When there is no arabinose available in the environment, the AraC protein acts as a(n) ______________ for the E. coli ara operon.

24. If a set of genes is repressed in the presence of the controlling substance, it is referred to as __________ control.

25. If a set of genes is induced in the presence of the controlling substance, it is referred to as __________ control.

26. The binding of arabinose to the AraC protein allows it to form a loop in the DNA upstream of the ara operon promoter.

27. __________ activate repressor proteins, thereby decreasing the synthesis of certain enzymes. A. Inducers B. Corepressors C. Effectors D. Modulators

28. __________ alter repressor proteins thereby increasing the rate of transcription initiation. A. Inducers B. Corepressors C. Effectors D. Modulators

29. When a repressor binds to the operator site on the DNA it normally A. inhibits the initiation of transcription. B. reduces the rate of transcription. C. terminates transcription that has already been initiated. D. has no effect on transcription.

30. Which of the following is not a regulatory mechanism used to control the lactose operon in Escherichia coli? A. Induction B. Catabolite repression C. Attenuation D. All of the choices are correct.

31. Enzymes that are expressed at a constant level all the time are said to be . A. inducible B. repressible C. constitutive D. attenuated

32. The site on the DNA to which a repressor protein binds is the __________. A. operon B. operator C. promoter D. regulator

33. When bound to the DNA, the repressor protein usually prevents attachment of the RNA polymerase to the __________. A. operon B. operator C. promoter D. regulator

34. Which statement best describes the mechanism(s) of posttranslational regulation of gene expression? A. Allosteric regulation following transcription of mRNA occurs in many biosynthetic pathways. B. Protein synthesis is often repressed by feedback or noncompetitive inhibition. C. Covalent modification of newly synthesized proteins generally has no marked effect on protein function. D. Once a protein is synthesized, there is little to no postranslational modification.

35. 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? A. By regulating the first step of protein synthesis, cells conserve the greatest amount of energy. B. The process of transcription was best understood by researchers at the time. C. Cellular regulation of transcription is common to all prokaryotic cells. D. The process of synthesizing an mRNA transcript is much less complex than translation of mRNA into protein.

36. Which of the following is an example of gene regulation at the posttranslational level? A. Alteration of protein structure B. Early termination of an mRNA transcript C. Initiation of protein synthesis D. Prevention of RNA synthesis

37. Scientists first focused on gene regulation at the level of translation, rather than transcription, because more was known about protein than nucleic acids at the time.

38. When does a cell regulate gene expression? A. Pretranscription through postranslation B. Posttranscription through postranslation C. Pretranscription through pretranslation D. Posttranscription through pretranslation

39. The inducer for the E. coli lac operon is allolactose produced by the action of permease on lactose.

40. In the presence of both glucose and lactose, the lactose repressor is not bound to the operator and the genes of the lactose operon are expressed.

41. ____________ is used to measure the amount of a chemoattractant encountered over time.

42. One way to regulate gene expression is through the production of different sigma factors. These cause RNA polymerase to bind to different sets of promoters, thereby altering the pattern of gene expression.

43. Gene regulation during sporulation in Bacillus subtilis involves BOTH temporal and spatial control.

44. A collection of genes or operons controlled by a common regulatory protein is called a(n) ___________ .

45. In two component regulatory systems, the response regulator typically receives a ____________ from the sensor kinase when it has been activated. A. pyruvate group B. phosphoryl group C. acetyl group D. methyl group

46. While standard two-component regulatory systems typically act to control gene transcription, phosphorelay systems can act either to control gene transcription or to control . A. translation B. protein activity C. DNA replication D. All of the choices are correct.

47. The sensor kinase for the OmpF: OmpC two-component regulatory system is A. the OmpK protein. B. the EnvZ protein. C. the MicF RNA. D. None of the choices are correct.

48. The E. coli lac operon has ________ operator sequences. A. one B. two C. three D. four

49. Which is false regarding the two-component regulatory system in bacteria? A. The system involves a sensor kinase and a response regulator. B. The sensor kinase is phosphorylated by the response regulator when the extracellular environment changes. C. Regulation of OmpF and OmpC porin proteins in E. coli is modulated by this type of system. D. One part of the system is exposed to the external cellular environment while another part is exposed to the cytoplasm.

50. If Escherichia coli is cultured in broth containing both glucose and lactose, it A. uses glucose preferentially until the supply is exhausted, then uses lactose. B. uses lactose preferentially until the supply is exhausted, then uses glucose. C. uses glucose and lactose simultaneously. D. uses only the glucose (it cannot use lactose as a source of carbon).

51. What term describes a set of genes that is controlled by a common regulatory protein? A. Codon B. Regulon C. Transcription D. Kinase

52. 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. A. alternating B. bimorphic C. diauxic D. dimorphic

53. The activity of adenyl cyclase is influenced by A. the phosphotransferase system. B. the presence of lactose in the environment. C. homoserine lactones. D. None of the choices are correct.

54. The standard or housekeeping sigma factor used most often by E. coli RNA polymerase under normal growth conditions is called sigma ___. A. 70 B. 32 C. S D. E

55. Acylhomoserine lactones used in quorum sensing regulate their own synthesis by a(n) ____________ system. A. riboswitch B. antisense C. catabolite repression D. autoinduction

56. During sporulation in Bacillus subtilis, the response regulator that positively controls many genes needed for sporulation and negatively controls genes not needed during sporulation is A. SpoOB. B. SpoOA. C. SpoOF. D. SpoOC.

57. During the early stages of sporulation in Bacillus subtilis, ________ is active in the forespore and ________ is active in the mother cell. A. σE; σF B. σK; σF C. σF; σK D. σF; σE

58. During sporulation in Bacillus subtilis, inactive precursor forms of new sigma factors are activated at the appropriate time by which mechanism? A. Proteolysis B. Phosphorylation C. RNA-binding D. Chaperone refolding

59. The sensing of starvation that leads to sporulation in Bacillus subtilis is accomplished by a . A. small RNA B. sensor kinase C. response regulator D. quorum regulatory effector

60. Cell-to-cell communication by quorum sensing has been shown to be important in the regulation of genes needed for A. virulence. B. biofilm production. C. plasmid transfer. D. All of the choices are correct.

61. When the Catabolite Activator Protein binds to its binding site in DNA, it A. displaces repressors. B. bends the DNA. C. promotes the assembly of other transcription factors at the promoter. D. eliminates the need for a sigma factor on the part of RNA polymerase.

62. In order for high level expression of the E. coli lac operon to occur, a complex of catabolite activator protein and __________ must be bound to the DNA near the promoter.

63. Two-component signal transduction systems are found in the Bacteria, but not in Archaea.

64. Guanine tetraphosphate (ppGpp) is particularly associated with which process? A. Spore formation in Bacillus B. Chemiosmosis in Paracoccus C. Stringent response in Escherichia D. Quorum sensing in Vibrio

65. During the stringent response, ppGpp-regulated genes for amino acid biosynthesis have a(n) -rich promoter, thus forming a open initiation complex. A. GC-rich; more stable B. GC-rich; less stable C. AT-rich; more stable D. AT-rich; less stable

66. Bioluminescence in Vibrio harveyi is due to an alternate sigma factor that prevents from binding to Lux mRNA, thus allowing translation of bioluminescent genes. A. antisense B. phosphate C. ribosomes D. autoinducing proteins

67. Which of the following is not a mechanism of quorum sensing in Vibrio? A. Phosphorelay B. Stringent response C. Autoinduction D. Antisense RNAs

68. In which situation might methylation of membrane proteins in Escherichia coli initiate a phosphorelay system that evokes clockwise rotation of flagella? A. Presence of a chemorepellent in the extracellular environment. B. Change in environmental osmotic pressure. C. Utilization of lactose due during diauxic growth. D. Cellular population reaches a quorum.

69. If autophosphorylation of CheA protein does not occur, then Escherichia coli cells must be A. in a gradient of a chemoattractant. B. in a gradient of a chemorepellant. C. tumbling. D. rotating flagella clockwise.

70. If flagellar rotation of Escherichia coli cells is , then CheA is . A. counterclockwise; unphosphorylated B. counterclockwise; autophosphorylated C. clockwise; autophosphorylated D. clockwise; unphosphorylated

71. Which of the following events occurs initially when Escherichia coli cells are in a gradient of a chemorepellent? A. CheA autophosphorylates B. Flagella rotate clockwise C. Cells tumble D. CheY is phorphorylated

72. In terms of global gene regulation, which of the following molecules is most similar to c-di-GMP and cAMP? A. ppGpp B. rRNA C. ATP D. EnvZ

73. During regulation of biofilm formation in Pseudomonas, cells leave the biofilm when levels of cyclic dimeric GMP are high.

74. What is the function of cyclic dimeric GMP in bacterial global regulation systems? A. It acts as a secondary nucleotide messenger. B. It is a sensor kinase. C. It converts GTP to cGTP. D. It is an autoinducer.

75. In catabolite repression systems of some Gram-positive bacteria, such as Bacillus subtilis, transcription of catabolic operons is regulated by CcpaA (catabolite control protein A) rather than cAMP. Propose a hypothesis to explain the preferential use of glucose in the presence of a second sugar such as sucrose by Bacillus subtilis. A. CcpaA acts as a repressor of sucrose operon genes in Bacillus subtilis when both sugars are present. B. CcpaA acts as an inducer of sucrose operon genes in Bacillus subtilis when both sugars are present. C. CcpaA acts as a repressor of sucrose operon genes in Bacillus subtilis when lactose, but not glucose, is present. D. CcpaA acts as an inducer of sucrose operon genes in Bacillus subtilis when glucose, but not lactose, is present.

76. 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? A. Different sugars can act as effector or repressor molecules in various strains, promoting or inhibiting transcription of genes depending on the type of sugar present. B. Operons for anabolic pathways are controlled by many global regulatory mechanisms, and different sugars can favor initiation of different pathways depending on the strain of yeast. C. All of the choices are correct. D. 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.