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12.E: Modern Applications of Microbial Genetics (Exercises)

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    12.1: Microbes and the Tools of Genetic Engineering

    The science of using living systems to benefit humankind is called biotechnology. Technically speaking, the domestication of plants and animals through farming and breeding practices is a type of biotechnology. However, in a contemporary sense, we associate biotechnology with the direct alteration of an organism’s genetics to achieve desirable traits through the process of genetic engineering.

    Multiple Choice

    Which of the following is required for repairing the phosphodiester backbone of DNA during molecular cloning?

    1. cDNA
    2. reverse transcriptase
    3. restriction enzymes
    4. DNA ligase
    Answer

    D

    All of the following are processes used to introduce DNA molecules into bacterial cells except:

    1. transformation
    2. transduction
    3. transcription
    4. conjugation
    Answer

    C

    The enzyme that uses RNA as a template to produce a DNA copy is called:

    1. a restriction enzyme
    2. DNA ligase
    3. reverse transcriptase
    4. DNA polymerase
    Answer

    C

    In blue-white screening, what do blue colonies represent?

    1. cells that have not taken up the plasmid vector
    2. cells with recombinant plasmids containing a new insert
    3. cells containing empty plasmid vectors
    4. cells with a non-functional lacZ gene
    Answer

    C

    The Ti plasmid is used for introducing genes into:

    1. animal cells
    2. plant cells
    3. bacteriophages
    4. E. coli cells
    Answer

    B

    True/False

    Recombination is a process not usually observed in nature.

    Answer

    false

    It is generally easier to introduce recombinant DNA into prokaryotic cells than into eukaryotic cells.

    Answer

    true

    Fill in the Blank

    The process of introducing DNA molecules into eukaryotic cells is called ________.

    Answer

    transfection

    Short answer

    Name three elements incorporated into a plasmid vector for efficient cloning.

    When would a scientist want to generate a cDNA library instead of a genomic library?

    What is one advantage of generating a genomic library using phages instead of plasmids?

    Critical Thinking

    Is biotechnology always associated with genetic engineering? Explain your answer.

    Which is more efficient: blunt-end cloning or sticky-end cloning? Why?

    12.2: Visualizing and Characterizing DNA

    Finding a gene of interest within a sample requires the use of a single-stranded DNA probe labeled with a molecular beacon (typically radioactivity or fluorescence) that can hybridize with a complementary single-stranded nucleic acid in the sample. Agarose gel electrophoresis allows for the separation of DNA molecules based on size. Restriction fragment length polymorphism (RFLP) analysis allows for the visualization by agarose gel electrophoresis of distinct variants of a DNA sequence.

    Multiple Choice

    Which technique is used to separate protein fragments based on size?

    1. polyacrylamide gel electrophoresis
    2. Southern blot
    3. agarose gel electrophoresis
    4. polymerase chain reaction
    Answer

    A

    Which technique uses restriction enzyme digestion followed by agarose gel electrophoresis to generate a banding pattern for comparison to another sample processed in the same way?

    1. qPCR
    2. RT-PCR
    3. RFLP
    4. 454 sequencing
    Answer

    C

    All of the following techniques involve hybridization between single-stranded nucleic acid molecules except:

    1. Southern blot analysis
    2. RFLP analysis
    3. northern blot analysis
    4. microarray analysis
    Answer

    B

    Fill in the Blank

    The __________ blot technique is used to find an RNA fragment within a sample that is complementary to a DNA probe.

    Answer

    northern

    The PCR step during which the double-stranded template molecule becomes single-stranded is called _____________.

    Answer

    denaturation

    The sequencing method involving the incorporation of ddNTPs is called __________.

    Answer

    Sanger sequencing, dideoxy method, or chain termination method

    True/False

    In agarose gel electrophoresis, DNA will be attracted to the negative electrode.

    Answer

    false

    Short answer

    Why is it important that a DNA probe be labeled with a molecular beacon?

    When separating proteins strictly by size, why is exposure to SDS first required?

    Why must the DNA polymerase used during PCR be heat-stable?

    Critical Thinking

    Suppose you are working in a molecular biology laboratory and are having difficulty performing the PCR successfully. You decide to double-check the PCR protocol programmed into the thermal cycler and discover that the annealing temperature was programmed to be 65 °C instead of 50 °C, as you had intended. What effects would this mistake have on the PCR reaction? Refer to Figure 12.2.8.

    What is the advantage of microarray analysis over northern blot analysis in monitoring changes in gene expression?

    What is the difference between reverse transcriptase PCR (RT-PCR) and real-time quantitative PCR (qPCR)?

    12.3: Whole Genome Methods and Industrial Applications

    Advances in molecular biology have led to the creation of entirely new fields of science. Among these are fields that study aspects of whole genomes, collectively referred to as whole-genome methods. In this section, we provide a brief overview of the whole-genome fields of genomics, transcriptomics, and proteomics.

    Multiple Choice

    The science of studying the entire collection of mRNA molecules produced by cells, allowing scientists to monitor differences in gene expression patterns between cells, is called:

    1. genomics
    2. transcriptomics
    3. proteomics
    4. pharmacogenomics
    Answer

    B

    The science of studying genomic fragments from microbial communities, allowing researchers to study genes from a collection of multiple species, is called:

    1. pharmacogenomics
    2. transcriptomics
    3. metagenomics
    4. proteomics
    Answer

    C

    The insulin produced by recombinant DNA technology is

    1. a combination of E. coli and human insulin.
    2. identical to human insulin produced in the pancreas.
    3. cheaper but less effective than pig insulin for treating diabetes.
    4. engineered to be more effective than human insulin.
    Answer

    B

    Fill in the Blank

    The application of genomics to evaluate the effectiveness and safety of drugs on the basis of information from an individual’s genomic sequence is called ____________.

    Answer

    pharmacogenomics or toxicogenomics

    A gene whose expression can be easily visualized and monitored is called a ________.

    Answer

    reporter gene

    True/False

    RNA interference does not influence the sequence of genomic DNA.

    Answer

    true

    Short answer

    If all cellular proteins are encoded by the cell’s genes, what information does proteomics provide that genomics cannot?

    Critical Thinking

    What are some advantages of cloning human genes into bacteria to treat human diseases caused by specific protein deficiencies?

    12.4: Genetic Engineering - Risks, Benefits, and Perceptions

    Many types of genetic engineering have yielded clear benefits with few apparent risks. However, many emerging applications of genetic engineering are much more controversial, often because their potential benefits are pitted against significant risks, real or perceived. This is certainly the case for gene therapy, a clinical application of genetic engineering that may one day provide a cure for many diseases but is still largely an experimental approach to treatment.

    Multiple Choice

    At what point can the FDA halt the development or use of gene therapy?

    1. on submission of an IND application
    2. during clinical trials
    3. after manufacturing and marketing of the approved therapy
    4. all of the answers are correct
    Answer

    D

    Fill in the Blank

    _____________ is a common viral vector used in gene therapy for introducing a new gene into a specifically targeted cell type.

    Answer

    Adenovirus

    Short Answer

    Briefly describe the risks associated with somatic cell gene therapy.

    Critical Thinking

    Compare the ethical issues involved in the use of somatic cell gene therapy and germ-line gene therapy.

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