Question 1

Both southern and northern blots involve the use of agarose gels. How do the types of agarose gels differ and why?

Accepted Answer

A typical, nondenaturing agarose gel is

Question 2

The applications of the yeast two-hybrid method include all of the following EXCEPT

Accepted Answer

A)  mapping protein-protein interactions in E. coli. 
B)  identifying of physiologically significant protein-protein interactions as potential antibiotic targets. 
C)  finding unknown proteins ("prey") that interact with proteins of known functions ("bait"). 
D)  mapping protein-protein interactions in M. tuberculosis. 
E)  the ability to probe interactions in vivo. 
A)  mapping protein-protein interactions in E. coli. 
B)  identifying of physiologically significant protein-protein interactions as potential antibiotic targets. 
C)  finding unknown proteins ("prey") that interact with proteins of known functions ("bait"). 
D)  mapping protein-protein interactions in M. tuberculosis. 
E)  the ability to probe interactions in vivo.

Question 3

Existing biocontainment strategies employ natural auxotrophies that are not easily met in natural, or conditional suicide switches introduced into the organism's genome. However, these mechanisms can be compromised through

Accepted Answer

A)  genetic mutation. 
B)  synthetic auxotrophy. 
C)  synthetic biology. 
D)  logic gates. 
E)  genetic circuit. 
A)  genetic mutation. 
B)  synthetic auxotrophy. 
C)  synthetic biology. 
D)  logic gates. 
E)  genetic circuit.

Question 4

The colorless molecule o-nitrophenyl galactoside (ONPG) can be used as an artificial substrate to assay b-galactosidase in cell extracts of Escherichia coli in which lacZ is used as a reporter gene. Which of the following statements is NOT true with respect to the use of ONPG?

Accepted Answer

A)  Hydrolysis of ONPG by b-galactosidase produces yellow o-nitrophenol. 
B)  o-nitrophenol can be measured with a spectrophotometer. 
C)  Hydrolysis of ONPG by b-galactosidase also releases colorless galactose. 
D)  The o-nitrophenol moiety is blue and more suitable for use in solid media. 
E)  The o-nitrophenol moiety is green and less suitable for use in solid media. 
A)  Hydrolysis of ONPG by b-galactosidase produces yellow o-nitrophenol. 
B)  o-nitrophenol can be measured with a spectrophotometer. 
C)  Hydrolysis of ONPG by b-galactosidase also releases colorless galactose. 
D)  The o-nitrophenol moiety is blue and more suitable for use in solid media. 
E)  The o-nitrophenol moiety is green and less suitable for use in solid media.

Question 5

Which probing technique detects DNA immobilized on a membrane using labeled DNA fragments?

Accepted Answer

A)  northern blot 
B)  southern blot 
C)  western blot 
D)  polyacrylamide gel electrophoresis in SDS 
E)  isoelectrofocusing 
A)  northern blot 
B)  southern blot 
C)  western blot 
D)  polyacrylamide gel electrophoresis in SDS 
E)  isoelectrofocusing

Question 6

In the figure below, the labels for the genetic logic gates are missing. Which answer choice locates them correctly?

Accepted Answer

A)  i) Buffer, ii) NOT, iii) OR 
B)  i) NOT, ii) Buffer, iii) OR 
C)  i) Buffer, ii) OR, iii) NOT 
D)  i) OR, ii) Buffer, iii) NOT 
E)  i) NOT, ii) OR, iii) Buffer 
A)  i) Buffer, ii) NOT, iii) OR 
B)  i) NOT, ii) Buffer, iii) OR 
C)  i) Buffer, ii) OR, iii) NOT 
D)  i) OR, ii) Buffer, iii) NOT 
E)  i) NOT, ii) OR, iii) Buffer

Question 7

Use the figure below to describe how the CRISPR-Cas9 editing tool is used in eukaryotic cells.

Accepted Answer

[1] The Streptococcus pyogenes Cas9 endo

Question 8

The figure below depicts a "kill switch" or suicide module designed to eliminate an organism at a predetermined point, namely once the microorganism's function is accomplished. Explain how this kill switch can be regulated to prevent the untimely death of a microorganism harboring it.

Accepted Answer

CcdB is a powerful DNA damaging toxin. T

Question 9

Acid-resistant Escherichia coli cells counteract H⁺ in their cytoplasm through the combined action of two proteins: a decarboxylase enzyme and

Accepted Answer

A)  H+ channel. 
B)  [H+]-ATPase. 
C)  GABA/glutamate antiporter. 
D)  putative DNA-binding protein. 
E)  putative antiporter. 
A)  H+ channel. 
B)  [H+]-ATPase. 
C)  GABA/glutamate antiporter. 
D)  putative DNA-binding protein. 
E)  putative antiporter.

Question 10

Which technique is used to select novel enzymes or peptides produced through directed evolution?

Accepted Answer

A)  mutagenesis with transposons 
B)  enzyme phage display 
C)  multiplex PCR 
D)  ethane methyl sulfonate mutagenesis 
E)  directional cloning 
A)  mutagenesis with transposons 
B)  enzyme phage display 
C)  multiplex PCR 
D)  ethane methyl sulfonate mutagenesis 
E)  directional cloning

Question 11

What is the principle of the electrophoretic mobility shift assay (EMSA)? What is its main application? Mention a possible limitation.

Accepted Answer

Migration rate of linear DNA molecules i

Question 12

Use the figure below to describe the model of acid resistance in Escherichia coli O157:H7. Make sure to identify the molecules involved using the letters on the figure.

Accepted Answer

[1] Internal pH falls when E. coli cells

Question 13

A protein of interest can be specifically detected on western blots; this technique requires all of the following EXCEPT

Accepted Answer

A)  primary antibodies produced against the protein under study. 
B)  an enzyme-tagged secondary antibody, directed against the primary antibody. 
C)  an easily detectable product formed by the enzyme in the tagged secondary antibody. 
D)  labeled DNA. 
E)  antibodies to detect quantity and size of specific proteins in cell extracts. 
A)  primary antibodies produced against the protein under study. 
B)  an enzyme-tagged secondary antibody, directed against the primary antibody. 
C)  an easily detectable product formed by the enzyme in the tagged secondary antibody. 
D)  labeled DNA. 
E)  antibodies to detect quantity and size of specific proteins in cell extracts.

Question 14

How is bacterial DNA cross-linked to putative binding proteins for chromatin immunoprecipitation (ChIP)?

Accepted Answer

A)  exposure to UV light 
B)  treatment with formaldehyde 
C)  treatment with heat 
D)  reduction with dithiothreitol 
E)  reduction with b-mercaptoethanol 
A)  exposure to UV light 
B)  treatment with formaldehyde 
C)  treatment with heat 
D)  reduction with dithiothreitol 
E)  reduction with b-mercaptoethanol

Question 15

In isolating acid-sensitive Escherichia coli using tetracycline-resistant transposons, why is it necessary to screen first for tetracycline resistance and then for acid sensitivity?

Accepted Answer

One screens first for tetracycline resis

Question 16

The role of kill switches in genetically engineered microorganisms is to

Accepted Answer

A)  serve as a fail-safe mechanism to timely kill the organisms after they have fulfilled their purpose. 
B)  induce proliferation of reproduction to kill a host cell. 
C)  destroy organisms that have a risk of biological contamination or invasion. 
D)  block the translation of CcdB. 
E)  elimiate toxins within the cell. 
A)  serve as a fail-safe mechanism to timely kill the organisms after they have fulfilled their purpose. 
B)  induce proliferation of reproduction to kill a host cell. 
C)  destroy organisms that have a risk of biological contamination or invasion. 
D)  block the translation of CcdB. 
E)  elimiate toxins within the cell.

Question 17

The type of genes that encode proteins whose activity is easily assayed are

Accepted Answer

A)  deep sequencing genes. 
B)  transcriptional fusions. 
C)  operons. 
D)  reporter genes. 
E)  translational fusions. 
A)  deep sequencing genes. 
B)  transcriptional fusions. 
C)  operons. 
D)  reporter genes. 
E)  translational fusions.

Question 18

Potential applications of bacterial oscillator switches include all of the following EXCEPT the

Accepted Answer

A)  study of controlled interactions between two feedback genetic loops. 
B)  design of bacterial genetic circuits to detect toxins. 
C)  design of bacterial clocks. 
D)  reduction of noise in biological circuits. 
E)  reactivity to concentrations of specific molecules such as arabinose. 
A)  study of controlled interactions between two feedback genetic loops. 
B)  design of bacterial genetic circuits to detect toxins. 
C)  design of bacterial clocks. 
D)  reduction of noise in biological circuits. 
E)  reactivity to concentrations of specific molecules such as arabinose.

Question 19

Which answer choice INCORRECTLY labels the figure below?

Accepted Answer

A)  A-DNA primer 
B)  B-transposon 
C)  C-amplification of gene-transposon junction 
D)  D-interface gene-transposon 
E)  There is no incorrect label. 
A)  A-DNA primer 
B)  B-transposon 
C)  C-amplification of gene-transposon junction 
D)  D-interface gene-transposon 
E)  There is no incorrect label.

Question 20

What kind of mutation is produced by transposable elements?

Accepted Answer

A)  inversion 
B)  point 
C)  insertion 
D)  substitution 
E)  transposition 
A)  inversion 
B)  point 
C)  insertion 
D)  substitution 
E)  transposition

Exam 12: Biotechniques and Synthetic Biology

Both southern and northern blots involve the use of agarose gels. How do the types of agarose gels differ and why?

The applications of the yeast two-hybrid method include all of the following EXCEPT

Existing biocontainment strategies employ natural auxotrophies that are not easily met in natural, or conditional suicide switches introduced into the organism's genome. However, these mechanisms can be compromised through

The colorless molecule o-nitrophenyl galactoside (ONPG) can be used as an artificial substrate to assay b-galactosidase in cell extracts of Escherichia coli in which lacZ is used as a reporter gene. Which of the following statements is NOT true with respect to the use of ONPG?

Which probing technique detects DNA immobilized on a membrane using labeled DNA fragments?

In the figure below, the labels for the genetic logic gates are missing. Which answer choice locates them correctly?

Use the figure below to describe how the CRISPR-Cas9 editing tool is used in eukaryotic cells.

The figure below depicts a "kill switch" or suicide module designed to eliminate an organism at a predetermined point, namely once the microorganism's function is accomplished. Explain how this kill switch can be regulated to prevent the untimely death of a microorganism harboring it.

Acid-resistant Escherichia coli cells counteract H⁺ in their cytoplasm through the combined action of two proteins: a decarboxylase enzyme and

Which technique is used to select novel enzymes or peptides produced through directed evolution?

What is the principle of the electrophoretic mobility shift assay (EMSA)? What is its main application? Mention a possible limitation.

Use the figure below to describe the model of acid resistance in Escherichia coli O157:H7. Make sure to identify the molecules involved using the letters on the figure.

A protein of interest can be specifically detected on western blots; this technique requires all of the following EXCEPT

How is bacterial DNA cross-linked to putative binding proteins for chromatin immunoprecipitation (ChIP)?

In isolating acid-sensitive Escherichia coli using tetracycline-resistant transposons, why is it necessary to screen first for tetracycline resistance and then for acid sensitivity?

The role of kill switches in genetically engineered microorganisms is to

The type of genes that encode proteins whose activity is easily assayed are

Potential applications of bacterial oscillator switches include all of the following EXCEPT the

Which answer choice INCORRECTLY labels the figure below?

What kind of mutation is produced by transposable elements?

Microbial Life: Origin and Discovery

Observing the Microbial Cell

Cell Structure and Function

Bacterial Culture, Growth, and Development

Environmental Influences and Control of Microbial Growth

Viruses

Genomes and Chromosomes

Transcription, Translation, and Bioinformatics

Gene Transfer, Mutations, and Genome Evolution

Molecular Regulation

Viral Molecular Biology

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Electron Flow in Organotrophy, Lithotrophy, and Phototrophy

Biosynthesis

Food and Industrial Microbiology

Origins and Evolution

Bacterial Diversity

Archaeal Diversity

Eukaryotic Diversity

Microbial Ecology

Microbes in Global Elemental Cycles

Human Microbiota and Innate Immunity

The Adaptive Immune Response

Microbial Pathogenesis

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