OpenStax Microbiology Test Bank Chapter 12: Modern Applications of Microbial Genetics | LATEST UPDATE

OpenStax Microbiology Test Bank Chapter 12: Modern Applications of Microbial Genetics Chapter 12: Modern Applications of Microbial Genetics * = Correct answer Multiple Choice 1. Which of the following is the definition of biotechnology? A. The alteration of DNA in a cell B. The use of living systems to benefit humankind* C. Using computers to synthesize biomolecules D. Using DNA for solving mathematical problems Difficulty: Easy ASM Standard: 26 2. Which of the following is the definition of genetic engineering? A. The alteration of DNA in a cell* B. The use of living systems to benefit humankind C. Using computers to synthesize biomolecules D. Using DNA for solving mathematical problems Difficulty: Easy ASM Standard: 15, 19, 26, 31 3. The first set of genes to be introduced into E. coli came from which of the following? A. Arabidopsis B. Haemophilus C. Mycobacterium D. Xenopus* Difficulty: Easy ASM Standard: 15, 19 4. Which of the following is a palindrome sequence that could be recognized by a restriction enzyme? A. 5′ – GAAAAG – 3′ 3′ – CTTTTC – 5′ B. 5′ – GAATTC – 3′ * 3′ – CTTAAG – 5′ C. 5′ – GACT – 3′ 3′ – CTGA – 5′ D. 5′ – GCCCC – 3′ 3′ – CGGGG – 5′ Difficulty: Moderate ASM Standard: 26, 36 Page 1 of 17 OpenStax Microbiology Test Bank Chapter 12: Modern Applications of Microbial Genetics 5. Restriction enzymes (endonucleases) are produced by bacteria as a means of protection against which infectious agent? A. antibiotics B. antibodies C. bacteriophages* D. prions Difficulty: Easy ASM Standard: 18, 26 6. Which of the following enzymes rejoins two sugar-phosphate backbones of DNA? A. helicase B. ligase* C. restriction enzyme D. reverse transcriptase Difficulty: Easy ASM Standard: 26, 36 7. Genes to be cloned into a plasmid are typically inserted in which location? A. in a location disrupting the antibiotic selective marker B. oriC (origin of replication) C. polylinker site* D. randomly Difficulty: Easy ASM Standard: 19, 26, 36 8. Which genus of bacterium is naturally competent? A. Bacillus* B. Escherichia C. Listeria D. Yersinia Difficulty: Moderate ASM Standard: 11, 19 9. Which of the following regarding pUC19 and blue/white screening is NOT true? A. Colonies that appear white have the gene of interest inserted into the plasmid pUC19. B. pUC19 confers antibiotic resistance. C. The gene of interest being cloned disrupts the lacI gene.* D. X-gal is a chromogenic agent used in blue/white screening to test for -galactosidase activity. Difficulty: Moderate ASM Standard: 19, 26, 36 Page 2 of 17 OpenStax Microbiology Test Bank Chapter 12: Modern Applications of Microbial Genetics 10. You are in the process of cloning a gene of interest into pUC19 using blue/white screening. You complete your cloning and transform E. coli with your cloned plasmid. You plate your transformation on two media. One medium agar plate contains X-gal only. The second medium agar plate contains X-gal and ampicillin (an antibiotic), in the hope of using blue/white screening. You examine your plates and see a mixture of blue and white colonies. Which of the following colonies should be picked? A. the blue colonies that are resistant to ampicillin B. the blue colonies that are sensitive to ampicillin C. the white colonies that are resistant to ampicillin* D. the white colonies that are sensitive to ampicillin Difficulty: Moderate ASM Standard: 15, 19, 26, 28b, 36, 38 11. Which plasmid encodes the genes for its own conjugation? A. an F-plasmid* B. any plasmid C. Plasmids cannot be transferred by conjugation. D. pUC19 only Difficulty: Easy ASM Standard: 2, 19, 26, 36 12. Which of the following methods can be used to transfect protoplast plant cells? A. Agrobacterium tumefaciens B. electroporation C. gene gun D. All these options can be used.* Difficulty: Easy ASM Standard: 19, 26, 36 13. Which virus is typically used as mechanism to transfect eukaryotic cells? A. adenovirus* B. bacteriophage C. influenza virus D. retrovirus Difficulty: Easy ASM Standard: 2, 19, 26, 36 14. For gel electrophoresis, the matrix used for separation of DNA fragments is ________, whereas the matrix used for separation of proteins is ________. A. agarose; polyacrylamide* B. arabinose; sodium dodecyl sulfate C. polyacrylamide; agarose Page 3 of 17 OpenStax Microbiology Test Bank Chapter 12: Modern Applications of Microbial Genetics D. sodium dodecyl sulfate; arabinose Difficulty: Easy ASM Standard: 36 15. Which charge does a molecule of DNA have? A. positive B. neutral C. negative* D. depends on what the sequence of DNA is Difficulty: Easy ASM Standard: 36 16. A ________ blot is used to identify specific sequences of DNA on a membrane, whereas a ________ blot is used to identify specific sequences of RNA on a membrane. A. Northern; Southern B. Northern; Western C. Southern; Northern* D. Western; Eastern Difficulty: Easy ASM Standard: 36 17. A two-dimensional PAGE separates molecules according to which two properties? A. charge at various pHs and hydrophobicity B. charge at various pHs and size* C. hydrophobicity and presence of disulfide bonds D. size and hydrophobicity Difficulty: Moderate ASM Standard: 36 18. For protein electrophoresis to function, which of the following can be added to the protein to impart a uniform negative charge? A. ammonium persulfate B. phosphate C. polyacrylamide D. sodium dodecyl sulfate* Difficulty: Easy ASM Standard: 36 19. You are interested in determining which genes are upregulated in HeLa cells during intracellular infection with a newly discovered pathogen. You prepare a microarray Page 4 of 17 OpenStax Microbiology Test Bank Chapter 12: Modern Applications of Microbial Genetics experiment as shown in the diagram below and examine the gene expression of three genes (labeled A through C). Which gene’s expression is not altered during intracellular infection? A. gene A* B. gene B C. gene C D. cannot conclude from this experiment; more information is needed Difficulty: Difficult ASM Standard: 28b, 36, 38 20. Which technique can be used to amplify DNA? A. Genomic libraries B. PCR* C. Sanger method D. Southern blot Difficulty: Easy ASM Standard: 26, 36 21. Which of the following are the three steps (in order) of PCR? A. annealing, denaturation, extension B. denaturation, annealing, extension* C. denaturation, extension, annealing Page 5 of 17 OpenStax Microbiology Test Bank Chapter 12: Modern Applications of Microbial Genetics D. extension, annealing, denaturation Difficulty: Moderate ASM Standard: 36 22. Which of the following correctly explains why primers are used in PCR? A. DNA replication requires a free 3′ hydroxyl group.* B. DNA replication requires a free 3′ phosphate group. C. DNA replication requires a free 5′ hydroxyl group. D. DNA replication requires a free 5′ phosphate group. Difficulty: Easy ASM Standard: 36 23. The Sanger method/chain termination reaction relies upon using which unique nucleotide? A. a nucleotide that is missing a 5-carbon sugar B. a nucleotide that is missing a hydroxyl group* C. a nucleotide that is missing a nitrogenous base D. a nucleotide that is missing a phosphate group Difficulty: Moderate ASM Standard: 36 24. Which of the following is a next-generation sequencing technique in which fragmented DNA has DNA adapters attached, is amplified by PCR, is attached to a bead, and then is placed into a well with sequencing reagents. The flash of light produced by the release of pyrophosphate on addition of a nucleotide is monitored. A. pyrosequencing* B. Sanger method C. Southern blot D. transformation Difficulty: Moderate ASM Standard: 36 25. The study of all the DNA of an entire microbial community is known as which of the following? A. genomics B. metagenomics* C. metatranscriptomics D. toxicogenomics Difficulty: Moderate ASM Standard: 20, 21, 36 Page 6 of 17 OpenStax Microbiology Test Bank Chapter 12: Modern Applications of Microbial Genetics 26. In RNAi technology, the dsRNA molecule first combines with which endonuclease that then cleaves it into smaller fragments? A. DICER* B. Ligase C. RecA D. RISC Difficulty: Hard ASM Standard: 17, 36 27. Which of the following is/are completely complementary to the target mRNA in RNAi technology? A. miRNA B. siRNA* C. both miRNA and siRNA D. Neither method cleaves mRNA. Difficulty: Easy ASM Standard: 17, 36 28. Which disease has been effectively controlled by gene therapy? A. bacterial meningitis B. cystic fibrosis* C. ornithine transcarbamylase D. sickle cell anemia Difficulty: Moderate ASM Standard: 19, 26, 31, 36 29. Which agency does not oversee gene therapy? A. FDA B. NIH C. OHRP D. WHO* Difficulty: Moderate ASM Standard: 31 30. Genomics would not be an effective method to detect which type of pathogen? A. bacteria B. helminths C. prions* D. viruses Difficulty: Moderate ASM Standard: 27 Page 7 of 17 OpenStax Microbiology Test Bank Chapter 12: Modern Applications of Microbial Genetics True/False 31. DNA that has been cut with a restriction enzyme, resulting in sticky ends, can be more easily ligated than DNA that has been cut with a restriction enzyme resulting in blunt ends. Answer: True Difficulty: Easy ASM Standard: 19, 26, 36 32. For cloning purposes using transduction, lytic bacteriophages are used. Answer: False Difficulty: Easy ASM Standard: 10, 26 33. Lambda () bacteriophages can be used to make genomic libraries. Answer: True Difficulty: Moderate ASM Standard: 10, 26 34. The uptake of a plasmid by a prokaryotic cell is known as transfection. Answer: False Difficulty: Moderate ASM Standard: 2, 19, 26, 36 35. DNA probes can be used to locate any gene within a cell. Answer: False Difficulty: Moderate ASM Standard: 32, 36 36. Blue/white screening works on the basis of disrupting the lacZ gene in cloning. Answer: True Difficulty: Moderate ASM Standard: 15, 19, 26, 34, 36 37. Reverse transcriptase-PCR amplifies molecules of RNA. Answer: False Difficulty: Easy ASM Standard: 10, 26, 36 Page 8 of 17 OpenStax Microbiology Test Bank Chapter 12: Modern Applications of Microbial Genetics 38. cDNA is made by reverse transcriptase, which is found in all viruses. Answer: False Difficulty: Moderate ASM Standard: 10, 26, 36 39. Due to concerns about gene transfer, genetically engineered microbes cannot be used to manufacture vaccines. Answer: False Difficulty: Easy ASM Standard: 15, 19, 31 40. RNAi is a natural process used by cells as a means of gene regulation. Answer: True Difficulty: Easy ASM Standard: 17 Matching 41. Match the different steps of molecular cloning to their function. A. DNA ligase i. cuts both DNA containing gene of interest and vector DNA B. PCR ii. amplifies gene of interest C. plasmid iii. chromogenic substrate used for blue/white screening D. restriction endonuclease iv. joins together sugar-phosphate backbone of DNA E. X-gal v. small circular DNA used for cloning Answers: A. iv., B. ii., C. v., D. i., E. iii. Difficulty: Easy ASM Standard: 19, 26, 36 Page 9 of 17 OpenStax Microbiology Test Bank Chapter 12: Modern Applications of Microbial Genetics 42. Match the technique to its primary function. A. microarray i. used to detect sequences of DNA B. Northern blot ii. used to compare gene expression between different cells C. PCR iii. used to amplify DNA D. Southern blot used to detect sequences of RNA Answers: A. ii., B. iv., C. iii., D. i. Difficulty: Easy ASM Standard: 36 43. Match the genetically engineered pharmaceutical to what it can treat. A. DNase i. cancers and viral infections B. factor VIII ii. hemophilia C. interferons iii. cystic fibrosis D. plasminogen activator iv. myocardial infarctions Answers: A. iii., B. ii., C. i., D. iv. Difficulty: Moderate ASM Standard: 26, 31 44. Match the mechanism of horizontal gene transfer to its appropriate description. A. conjugation i. uptake of DNA by a eukaryotic cell B. transduction ii. uptake of free DNA by a prokaryotic cell C. transfection iii. transfer of DNA using pili D. transformation iv. transfer of DNA using bacteriophage Answers: A. iii., B. iv., C. i., D. ii. Difficulty: Easy ASM Standard: 2, 26, 36 Fill in the Blank 45. ________ is DNA composed from different organisms. Answer: Recombinant Difficulty: Easy ASM Standard: 19, 26, 36 46. ________ are enzymes produced by bacteria that are used in molecular cloning to cut DNA. Answer: Restriction enzymes (endonucleases) Difficulty: Easy ASM Standard: 26, 36 Page 10 of 17 OpenStax Microbiology Test Bank Chapter 12: Modern Applications of Microbial Genetics 47. ________ are plasmids that have phage sequences so they can be packaged into bacteriophages. Answer: Phagemids Difficulty: Moderate ASM Standard: 10, 18, 26, 36 48. ________ is the technique of using radioactive phosphorous to identify and track sequences of DNA in gel electrophoresis. Answer: Autoradiography Difficulty: Moderate ASM Standard: 36 49. ________ compares DNA banding patterns of different DNA samples after being incubated with restriction enzymes and subjected to agarose gel electrophoresis. Answer: Restriction fragment length polymorphism (RFLP) Difficulty: Easy ASM Standard: 26, 36 50. ________ is a bacterium that causes crown-gall disease and can be used as a molecular biology tool. Answer: Agrobacterium tumefaciens Difficulty: Moderate ASM Standard: 23, 26, 36 51. ________ is the DNA polymerase that is most commonly used in PCR. Answer: Taq polymerase Difficulty: Easy ASM Standard: 26 52. In proteomics, a ________ is the name given to a protein whose expression is affected by disease. Answer: biomarker Difficulty: Easy Page 11 of 17 OpenStax Microbiology Test Bank Chapter 12: Modern Applications of Microbial Genetics ASM Standard: 17, 23, 31, 36 53. A noncoding RNA sequence that is complementary to mRNA is known as ________. Answer: antisense Difficulty: Easy ASM Standard: 16, 17 54. In gene therapy, genes need to be introduced into ________ to ensure they will be passed on to the next generation. Answer: germ-line cells Difficulty: Easy ASM Standard: 19, 31, 36 Short Answer 55. Why is it possible for bacteria to produce human proteins such as insulin? Sample Answer: The genetic code is universal and DNA and RNA can be transcribed and translated in any organism. Difficulty: Difficult ASM Standard: 16, 19, 26, 56. Why do bacteria produce restriction enzymes (endonucleases)? Sample Answer: to protect against bacteriophages Difficulty: Easy ASM Standard: 7, 18, 26 57. How can a molecular biologist tell the difference between a chromosome and a commercial plasmid? Sample Answer: Various answers are correct. Chromosomes are typically larger than plasmids. Chromosomes are essential for the survival of the cell (i.e., they contain housekeeping genes), whereas commercial plasmids are not essential. Commercial plasmids will contain a polylinker or multiple cloning site with restriction enzyme recognition sites in the same region, whereas chromosomes lack this site. Difficulty: Difficult ASM Standard: 2, 8, 19, 36 58. What is a reporter gene? Give an example of one. Page 12 of 17 OpenStax Microbiology Test Bank Chapter 12: Modern Applications of Microbial Genetics Sample Answer: Reporter genes encode an easily observable characteristic used to track gene expression. Examples of reporter genes include lacZ (which would require a chromogenic agent in the medium) and gfp. Difficulty: Easy ASM Standard: 17, 19, 26, 36 59. How can bacterial cells become chemically competent? Sample Answer: Chemical treatment can increase the permeability of the cell membrane by neutralizing charges on the cell membrane. Difficulty: Moderate ASM Standard: 36 60. How does electroporation make bacterial cells competent to receive foreign molecules of DNA? Sample Answer: A brief electric pulse results in the formation of transient pores in the phospholipid bilayers of cells. The electric pulse generates a short-lived positive charge on one side of the cell’s interior to attract the negatively charged DNA molecule (plasmid) into the cell. Difficulty: Moderate ASM Standard: 19, 36 61. Why are phages preferred in making a genomic library? Sample Answer: Phages can hold a larger insert of foreign DNA, as compared with a plasmid. Difficulty: Moderate ASM Standard: 26, 36 62. What is the difference between a genomic library and a cDNA library? Sample Answer: A genomic library contains a copy of all the DNA of an organism. A cDNA library contains a copy of all the genes that are actively being expressed (i.e., genes being currently transcribed into mRNA). Difficulty: Moderate ASM Standard: 26, 36 63. Name two molecular techniques one can use to examine gene expression in a bacterial cell. Sample Answer: Reverse transcriptase-PCR (RT-PCR), DNA microarrays, or Northern blotting Difficulty: Easy ASM Standard: 17, 26, 36 Page 13 of 17 OpenStax Microbiology Test Bank Chapter 12: Modern Applications of Microbial Genetics 64. Why is Taq polymerase used in PCR and not E. coli DNA polymerase? Sample Answer: Taq polymerase is heat stable, which is important because, during PCR, the temperature is raised to 95 °C to denature the DNA template. Difficulty: Easy ASM Standard: 26, 36 65. Explain how qPCR is quantitative. What is it measuring? Sample Answer: qPCR uses a fluorescence probe to monitor the increase in double-stranded template over time. Based upon the kinetics of this, one can determine the amount of original template. Difficulty: Moderate ASM Standard: 36 66. Why is GFP used in the field of proteomics? Sample Answer: The gene encoding GFP is a common reporter gene that can be fused to a gene of interest. In this way, the scientist can track the location and timing of the expression of the gene of interest. Difficulty: Easy ASM Standard: 36 67. Which type of disease could be a candidate for treatment using gene therapy? Sample Answer: Human diseases that result from genetic mutations due to abnormalities in a patient’s genome. Difficulty: Moderate ASM Standard: 17, 19, 31 68. What are the three steps to PCR? Sample Answer: denaturation, primer annealing, and primer extension Difficulty: Easy ASM Standard: 26, 36 69. What are the ways transfection can occur? Sample Answer: Electroporation, gene guns, microinjection, shuttle vectors, and viral vectors Difficulty: Easy ASM Standard: 19, 36 Brief Essay Essay Question Rubric RATING Failing Below Average Competent Advanced Page 14 of 17 OpenStax Microbiology Test Bank Chapter 12: Modern Applications of Microbial Genetics Criteria for evaluati on Answer does not provide an argument. Answer contains inaccuracies. Writing is poor and contains numerous grammatical mistakes and misspellings. Answer fails to provide examples to support an argument. Writing is poor and grammatical errors are common. Answer is somewhat incoherent. Answer provides an argument with one or two examples that support it. Writing is acceptable for the college level but may contain one or two grammatical mistakes or misspellings. Answer clearly provides an argument with two or more excellent examples that support it; student makes the argument clearly and eloquently. Answer is well organized and free of grammatical errors and misspellings. POINT VALUE 0 1 2 3 Assume rating/grading scale for the question ranges from 0 to 3 points. 70. Discuss how you can genetically engineer an E. coli cell to produce human insulin. Be sure to include in your answer the use of restriction enzymes, ligase, pUC19, X-gal, selective media, and a method for determining that your transgenic E. coli contains the insulin gene and that it is producing insulin. Answer: Student answers may vary but should include components of the following. You begin by taking the gene for insulin and the pUC19 plasmid (vector) and digest them both with the same restriction enzymes (choosing a restriction enzyme site in the polylinker or multiple cloning site). After digestion, the insulin gene is inserted into the digested pUC19 using DNA ligase. The plasmid is then introduced into E. coli that is competent. The most common method would be to use chemical transformation or electroporation. The E. coli is then plated on selective media containing X-gal. The selective media should contain an antibiotic to which the plasmid confers resistance. Since X-gal is used in blue/white screening, one would allow the E. coli to grow. E. coli that appear white on the media contain the plasmid with the PCR product inserted into it. You can verify the presence of ins in E. coli using either PCR or using DNA probes (i.e., Southern blot). To verify the transgenic E. coli is producing insulin, grow the bacterium, collect the supernatant, perform polyacrylamide gel electrophoresis, and compare with the supernatant of E. coli that has not been genetically altered. The insulin protein band should be seen only in the proteome of the transgenic E. coli. Difficulty: Moderate ASM Standard: 15, 16, 19, 26, 31, 33, 36 Page 15 of 17 OpenStax Microbiology Test Bank Chapter 12: Modern Applications of Microbial Genetics 71. An outbreak has occurred at a local banquet. You determine that the causative agent was Listeria monocytogenes, which was found in the cold cut meats. You have been asked to further determine from which ribotype the identified L. monocytogenes is. The results of your experiment are shown in the gel diagram below. Answer the questions below the image. a. What is ribotyping and how is it performed? b. Which ribotype was found in the cold cut meats? c. Why do the DNA molecules appear as they do on the gel? Identify where large molecules and small molecules of DNA would be found on this gel. Answer: Student answers may vary but should include components of the following. (a) Ribotyping is a technique in which a short sequence of DNA between the 16S and 23S rRNA gene sequences is used for restriction fragment length polymorphism (RFLP). In RFLP, a segment of DNA is digested using restriction enzymes (endonucleases). The fragments are then resolved using agarose gel electrophoresis. Because restriction enzymes recognize specific DNA sequences, differences in DNA sequences between bacterial strains will lead to different banding patterns after agarose gel electrophoresis. (b) In this ribotyping, we see that the bands from the cold cut meats match L. monocytogenes ribotype R-2. (c) DNA is negatively charged and is pulled toward the positive electrode in agarose gel electrophoresis. The DNA bands you see are located in the gel according to their size. Large molecules of DNA cannot move quickly through the agarose gel matrix, so they would be found at the top of the gel. Small molecules of DNA can move more quickly through the agarose gel matrix, so they would be found toward the bottom of the gel. Difficulty: Moderate ASM Standard: 5, 26, 28b, 31, 34, 36, 38 Page 16 of 17 OpenStax Microbiology Test Bank Chapter 12: Modern Applications of Microbial Genetics 72. You wish to amplify a segment of DNA from the genome of the bacterium Haemophilus influenzae. You decide to use PCR. You prepare your PCR using the following reagents and temperatures. What will be the result of each of these? Be sure to explain why these reactions will work or will not work. (a) You add DNA template, DNA primers (forward and reverse), nucleotides, and E. coli DNA polymerase. You set the denaturing temperature for 95 C, annealing temperature for 50 C, and the extension temperature for 72 C. You repeat this for 30 cycles. (b) You add DNA template, nucleotides, and Taq polymerase. You set the denaturing temperature for 95 C, annealing temperature for 50 C, and the extension temperature for 72 C. You repeat this for 30 cycles. (c) You add DNA template, DNA primers (forward and reverse), nucleotides, and Taq polymerase. You set the denaturing temperature for 95 C, annealing temperature for 70 C, and the extension temperature for 72 C. You repeat this for 30 cycles. Answer: Student answers may vary but should include components of the following. In all cases, the PCR would not work. In (a), you are using E. coli DNA polymerase. This is not a heat-stable polymerase. Therefore, when you heat the reaction to 95 °C for the denaturation reaction, the polymerase will no longer be functional and will be unable to synthesize the complementary strand of DNA. In (b), there are no DNA primers added. DNA synthesis requires a primer to synthesize the complementary strand of DNA (i.e., it cannot perform de novo synthesis). In (c), the annealing temperature is too high, so the DNA primer will not attach. Since the primer doesn’t attach, then the complementary strand of DNA cannot be synthesized. Difficulty: Difficult ASM Standard: 26, 28b, 36 73. Discuss the similarities and differences between miRNA and siRNA. Sample Answer: Student answers may vary but should include components of the following. Both are methods of gene silencing using RNA (RNAi). Both these RNA molecules are double stranded. siRNAs are completely complementary to the mRNA transcript of a specific gene of interest, whereas miRNAs are mostly complementary. They both bind to the endonuclease DICER forming RISC. The siRNA-RISC complex binds to mRNA and cleaves it. In miRNA, only one of the two strands binds to RISC; the miRNA-RISC complex then binds to mRNA, inhibiting translation. Difficulty: Difficult ASM Standard: 17, 26, 36 This file is copyright 2017, Rice University. All rights reserved. Page 17 of 17