Microbiology Chapter 12 Quiz – Flashcards
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c. infectious dose. Food-borne bacteria, including Escherichia coli, cannot survive the highly acidic environment of the human stomach. An acid-resistant mutant such as E. coli O157:H7 resists environments with pH as low as 2 and therefore even a few cells may be enough to infect the intestinal tract. For more information, see Section 12.1.
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If a person becomes infected after ingesting only a few cells of a pathogen, this organism is said to have a low Select one: a. morbidity. b. penetrance. c. infectious dose. d. antibiotic resistance.
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c. chromatin immunoprecipitation. Chromatin immunoprecipitation, or ChIP, is a method used to isolate DNA-binding proteins. For more information, see Section 12.4.
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A protocol includes the following steps: cross-link putative DNA-binding proteins with DNA, shear the DNA, and use an antibody to pull down the protein along with associated DNA. This is a technique called Select one: a. Southern blotting. b. western blotting. c. chromatin immunoprecipitation. d. cDNA microarray analysis.
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a. amplify the DNA in the presence of fluorescent nucleotides. Prior to exposing the isolated DNA to a DNA microarray, you must first use PCR to amplify the DNA in the presence of fluorescent nucleotides. For more information, see Section 12.4.
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After performing chromatin immunoprecipitation, you want to determine the DNA sequences pulled down. Your first step is to Select one: a. amplify the DNA in the presence of fluorescent nucleotides. b. treat the DNA sequences with DNase. c. pour an agarose gel to run a Southern blot. d. expose the immunoprecipitated DNA to a DNA microarray chip.
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d. design of fail-safe kill mechanisms leading to the timely suicide of genetically modified bacteria. The elimination of genetically modified organisms released outside the laboratory after they have fulfilled their function, but not earlier, can be accomplished by a suicidal mechanism. For example, a crRNA-ccB, which encodes the DNA-damaging protein CcdB, would kill the cell too quickly, unless a modulation mechanism such as an arabinose-induced taRNA, is present. For more information, see Section 12.6.
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An application of engineered genetic switchboards is the Select one: a. production of bacteria capable of catabolizing compounds leached from railroad tracks. b. production of bacteria capable of catabolizing crude-oil-derived compounds. c. design of bacterial genetic circuits to detect toxins. d. design of fail-safe kill mechanisms leading to the timely suicide of genetically modified bacteria.
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c. design of bacterial genetic circuits to detect toxins. The interactions between two feedback genetic loops result in a genetic switch that can be toggled depending on the concentration of the inducers. Toxic chemicals, such as arsenic, can be detected by a gfp-fusion system that is activated in the presence of the offending substance. For more information, see Section 12.6.
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An application of synthetic biology based on bacterial oscillator switches is the Select one: a. production of bacteria capable of performing novel metabolic pathways. b. production of electricity using cytochromes. c. design of bacterial genetic circuits to detect toxins. d. design of fail-safe kill mechanisms leading to the suicide of genetically modified bacteria.
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b. insecticides. The Bt toxin, originally produced by Bacillus thuringiensis, is used to kill the larvae of certain crop pests. For more information, see Section 12.5.
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Certain crystallized proteins of Bacillus thuringiensis are used as Select one: a. herbicides. b. insecticides. c. reporter genes in gene fusions to measure transcription. d. molecules that emit fluorescence in FRET.
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b. reporter gene must use the ribosome-binding site of the target gene. By using the subject gene's ribosome-binding site, we can detect whether any factor may affect translation of the subject gene. For more information, see Section 12.2.
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Gene fusions can provide information about translational control because the Select one: a. reporter gene has its own ribosome-binding site. b. reporter gene must use the ribosome-binding site of the target gene. c. gene fusion must be translated in order to be detected. d. reporter gene is a ribosomal protein.
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b. Specially engineered small RNAs Based on the properties of previously known small RNAs in stabilizing and regulating mRNA translatability, synthetic biologists may design riboswitches (crRNA/taRNA) to control the translation of nearly any target gene. For more information, see Section 12.6.
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Genetic switchboards use cis-repressed and trans-activating RNA (crRNA/taRNA) combinations. What type of RNA molecules are cr- and taRNA? Select one: a. Highly modified tRNAs b. Specially engineered small RNAs c. A subset of previously unknown ribosomal RNAs d. Long noncoding RNAs
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d. Both a and b LacZ fusions can be used to monitor gene expression by determining enzymatic activity of a mixed population of cells containing LacZ fusions and cells without them. GFP-fusion proteins can be observed in individual cells within a population by microscopy. For more information, see Section 12.2.
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GFP fusions are preferred over LacZ fusions in the study of phenomena such as gene expression in individual cells because Select one: a. GFP allows the tracking of gene expression in individual cells. b. the enzymatic activity of LacZ represents the average of a population c. separating cells containing GFP-fusion proteins is easier than separating cells containing LacZ fusions. d. Both a and b
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c. nickel. The His6 tagged proteins can be affinity purified by passing the cell contents through a column containing nickel-coated agarose beads. The tagged protein will stick to the nickel, whereas untagged proteins pass through. A subsequent step can elute the tagged proteins. For more information, see Section 12.3.
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His6 tagged proteins can be separated from other proteins, based on the affinity of the histidine cluster for Select one: a. magnesium. b. manganese. c. nickel. d. zinc.
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a. energy released by the fluorescent dye is absorbed by a second, nearby molecule. For energy transfer to happen, the second molecule must absorb the energy and the two molecules must be in close proximity. For more information, see Section 12.3.
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In fluorescence resonance energy transfer (FRET), a molecule is labeled with a florescent dye and the Select one: a. energy released by the fluorescent dye is absorbed by a second, nearby molecule. b. energy released by the fluorescent dye is reflected by a second, nearby molecule. c. energy released by the fluorescent dye is absorbed by a second, distant molecule. d. energy to excite the fluorescent dye is provided by a second, distant molecule.
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c. His6. His6-tagged proteins can be purified on a nickel column or nickel beads. A fusion with GFP or, β-gal, can elucidate transcriptional activity and is used as a reporter fusion, not to purify a protein. Taq polymerase is a thermostable DNA polymerase used in PCR, not for protein purification. For more information, see Section 12.3.
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In order to purify a protein by affinity tagging, one can create a fusion between the protein and Select one: a. beta-galactosidase. b. green fluorescent protein (GFP). c. His6. d. Taq polymerase.
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a. more slowly through a gel than the DNA without a bound protein. Migration through a gel depends on the molecular weight of the migrating species. The DNA protein complex has a larger molecular weight than the free DNA and thus migrates more slowly. For more information, see Section 12.3.
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In the electrophoretic mobility shift assay, DNA with a bound protein will run Select one: a. more slowly through a gel than the DNA without a bound protein. b. more quickly through a gel than the DNA without a bound protein. c. at the same rate through a gel as the DNA without a bound protein. d. It is impossible to predict how protein binding will affect DNA migration.
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a. logic gates. A promoter and a gene constitute a genetic logic gate. Bayes theorem is a genetic tool to determine conditional probability. Quantum mechanics is not yet widely used in biology and, broadly defined, materials science studies the microscopic and macroscopic properties of matter. For more information, see Section 12.6.
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One of the engineering principles used in synthetic biology is Select one: a. logic gates. b. Bayes theorem. c. quantum mechanics. d. materials science.
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a. transposons. Transposons can insert themselves into genes, thus disrupting them and causing mutations. For more information, see Section 12.2.
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One technique to create random mutations in bacterial genes uses Select one: a. transposons. b. DNA sequence homology computer software. c. Southern blot analysis. d. DNA microarray.
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c. northern blots. Although northern blots can be used to quantify specific RNA molecules present in cell extracts, real-time PCR allows us to measure the relative abundance of different RNA species in a sample. For more information, see Section 12.3.
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Real-time PCR can give information similar to that given by Select one: a. electromobility shift assay. b. primer extension analysis. c. northern blots. d. western blots.
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d. real-time PCR is quantitative. Unlike traditional PCR, real-time PCR includes a reporter probe and analyzes samples throughout the experiment. These changes allow real-time PCR to be quantitative and can be used to determine the amount of starting template. For more information, see Section 12.3.
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Real-time PCR differs from standard PCR in that Select one: a. whereas real-time PCR can be completed in a day, standard PCR takes longer. b. only real-time PCR uses primers. c. only real-time PCR uses thermostable Taq polymerase. d. real-time PCR is quantitative.
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c. synthetic biology. Biotechnology uses living organisms (wild type or genetically modified) in the manufacture of useful products; this includes directed evolution, in which specific molecular phenotypes are selected, and recombinant DNA, in which natural or synthetic pieces of DNA are joined in vitro. Synthetic biology is biology by design. For more information, see Section 12.6.
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The branch of science that is concerned with the development of biological systems that do NOT exist in nature is called Select one: a. directed-evolution. b. biotechnology. c. synthetic biology. d. recombinant DNA.
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d. Fusion proteins The gene for the yeast GAL4 regulator was split in two functional halves that were then cloned separately. A fusion protein is made from one of the proteins of interest and the GAL4 DNA-binding domain (bait). Another fusion protein is constructed with the second protein of interest and the GAL4 transcriptional activation domain (prey). If the proteins fused to the disjointed domains of GAL4 interact, GAL4 reorganizes, binds to the GAL1 promoter, and starts transcription of the reporter gene lacZ. For more information, see Section 12.4, V.B.ii.
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The yeast two-hybrid assay relies on which of the following techniques? Select one: a. DNA footprint protection assay b. Primer extension analysis c. Western blotting d. Fusion proteins
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d. fuse the promoter of the gene to a reporter construct and check reporter activity in the presence and absence of the stimulus. A reporter construct is an appropriate technique to assay transcriptional changes. Both Southern blotting and PCR are methods to detect specific regions of DNA. The DNA for the gene will not change in the presence or absence of the stimulus. Creating a mutant may shed light on the function of the gene but will not give information on transcriptional control. For more information, see Section 12.2.
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To determine whether the transcription of a certain gene varies in response to an environmental stimulus, the best option is to Select one: a. amplify the gene by PCR in the presence and absence of the stimulus. b. perform a Southern blot of the gene in the presence and absence of the stimulus. c. generate a mutation in the gene by introducing an antibiotic resistance gene into the target gene's open reading frame. d. fuse the promoter of the gene to a reporter construct and check reporter activity in the presence and absence of the stimulus.
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a. Connectible DNA pieces that can direct the manufacture of novel compounds DNA segments of known sequence and function have been made publicly available to be used as building materials for engineering new genetic circuits with a wide diversity of applications. For more information, see Section 12.6.
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What are BioBricks and what are their uses? Select one: a. Connectible DNA pieces that can direct the manufacture of novel compounds b. Small nonribosomal peptides that can be modeled into larger, protein-like structures c. A registered trademark of the Lego company; a great educational tool for children d. Another name for directional cloning vectors
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c. To detect the presence of the primary antibody on the blot through fluorescence or a color-producing enzymatic reaction After washing off nonbound antibodies (IgGs), the location of a protein-primary antibody complex is evidenced by the attachment of a secondary IgG that either has a fluorescent tag or is linked to an enzyme that forms a colored product from a colorless substrate. For more information, see Section 12.3.
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What is the purpose of using a fluorescently labeled or enzyme-linked secondary antibody in a western blot experiment? Select one: a. To make sure that the primary antibody was prepared in the appropriate animal b. To specifically detect the regions of the target protein that are responsible for the molecule's activity c. To detect the presence of the primary antibody on the blot through fluorescence or a color-producing enzymatic reaction d. None of the above
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a. Protein-protein The yeast two-hybrid assay can detect protein to protein binding that might be involved in gene expression control, signal transduction, or other phenomena involving in vivo interactions among proteins. For more information, see Section 12.4.
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What type of interactions does the yeast two-hybrid assay detect? Select one: a. Protein-protein b. Protein-DNA c. DNA-RNA d. RNA-RNA
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b. DNase I DNase I is used in DNA protection assays. The region of DNA bound by a protein is protected from DNase I digestion. For more information, see Section 12.3.
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Which enzyme can help determine the DNA sequence directly in contact with a particular DNA-binding protein? Select one: a. Beta-galactosidase b. DNase I c. DNA ligase d. Reverse transcriptase
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d. Reverse transcriptase everse transcriptase is used to extend the primer back to the 5′ end of the mRNA. For more information, see Section 12.3.
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Which enzyme is required for primer extension analysis? Select one: a. Beta-galactosidase b. DNase I c. DNA ligase d. Reverse transcriptase
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c. Western blot Western blots can be probed with antibodies specific to a protein of interest. For more information, see Section 12.3.
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Which of following techniques could be useful in determining if a particular protein is present in a cell extract? Select one: a. Northern blot b. Southern blot c. Western blot d. None of the above
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a. A sequence encoding His6 Nearly all research plasmids contain an origin of replication, an antibiotic resistance gene, and a multiple cloning site. The His6 sequence is unique to plasmids designed for protein purification. For more information, see Section 12.3.
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Which of the following elements would be present in a plasmid used for protein expression and affinity purification, but not present in a simple cloning plasmid? Select one: a. A sequence encoding His6 b. A multiple cloning site c. An antibiotic resistance gene d. An origin of replication
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d. There may be environmental concerns with genetically modified plants. Some people worry about the escape of genetically modified plants into the wild. Lack of refrigeration is an advantage. Vaccine production in plants can be inexpensive, and a variety of edible plants such as corn and potatoes can be used. For more information, see Section 12.5.
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Which of the following is a potential disadvantage to producing vaccines in plants? Select one: a. They do not require refrigeration b. It is more expensive than traditional vaccine production c. Only hard to grow, water-intensive plants can be used. d. There may be environmental concerns with genetically modified plants.
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b. Primer extension analysis In primer extension analysis, reverse transcriptase extends a primer that is complementary to a sequence near the 5 end of the RNA being analyzed. The sequence information produced can lead to the determination of the transcriptional start site. For more information, see Section 12.3.
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Which of the following is a technique to determine the transcriptional start site of a gene? Select one: a. Electrophoretic mobility shift assay (EMSA) b. Primer extension analysis c. Reporter fusion d. Southern blot analysis
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a. Phage display In phage display, DNA sequences encoding random peptides are cloned into capsid protein genes of single-stranded DNA phages. Phages displaying peptides with desired properties can be selected. For more information, see Section 12.5.
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Which of the following laboratory techniques depends on viruses to study directed evolution of peptides? Select one: a. Phage display b. Real-time PCR c. DNA protection assay d. Southern blotting
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a. Operon fusions reflect transcriptional control of the subject gene, whereas gene fusions reflect both transcriptional and translational control. Both types of fusions give information about transcriptional control. Since operon fusions have their own ribosome-binding sites but gene fusions do not, gene fusions also give information about translational control. For more information, see Section 12.2.
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Which of the following statements is correct? Select one: a. Operon fusions reflect transcriptional control of the subject gene, whereas gene fusions reflect both transcriptional and translational control. b. Operon fusions reflect translational control of the subject gene, whereas gene fusions reflect both transcriptional and translational control. c. Both operon fusions and gene fusions reflect transcriptional and translational control of the subject gene. d. Neither operon fusions nor gene fusions reflect transcriptional control of the subject gene.
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c. GFP-fusion proteins Green fluorescent protein fusions can light up a protein of interest so the protein's cellular localization can be observed by microscopy. Western blotting can determine the presence of a protein in an extract, but not its cellular localization. For more information, see Section 12.3.
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Which of the following techniques is best suited to visualize the subcellular localization of a protein? Select one: a. Real-time PCR b. Primer extension analysis c. GFP-fusion proteins d. Western blotting
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b. Real-time PCR Real-time PCR employs FRET to monitor DNA synthesis as it occurs. For more information, see Section 12.3.
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Which of the following techniques is most likely to use fluorescence resonance energy transfer (FRET)? Select one: a. DNA protection assay b. Real-time PCR c. Electrophoretic mobility shift assay (EMSA) d. Northern blotting e. All of the above
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a. Northern blot Northern and Southern blotting use nucleic acid hybridization to detect RNA and DNA, respectively. In western blotting, antibodies are used to detect proteins. In denaturing polyacrylamide gel electrophoresis (SDS-PAGE), proteins are separated based on their molecular weight For more information, see Section 12.3.
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Which of the following techniques relies on nucleic acid hybridization to detect an mRNA of interest? Select one: a. Northern blot b. Southern blot c. Western blot d. SDS-PAGE
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c. DNA co-immunoprecipitated with the protein is amplified and identified on a microarray (ChIP-on-chip). Each spot on the microarray chip contains a small segment of the genome of the bacterium under study, indicating which specific genes may be controlled by the transcription factor For more information, see Section 12.4.
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You have isolated a bacterial transcription factor using ChIP. What is the next step in order to find out all the sites in the genome that can be bound by this particular protein? Select one: a. The co-immunoprecipitated DNA fragment is used as a probe in a whole-genome Southern blot. b. The transcription factor can be identified by western blotting while still bound to the DNA. c. DNA co-immunoprecipitated with the protein is amplified and identified on a microarray (ChIP-on-chip). d. None of the above
