Question 1

What is the simplest definition of a genetic "logic gate"?

Accepted Answer

A)  a promoter (which interacts with input signals such as regulatory proteins) and a gene, which produces mRNA and protein (output signal) 
B)  The interaction among proteins and specific DNA sequences modulate gene expression. 
C)  the combination of genetic elements from different organisms to engineer a novel metabolic pathway or reproduce one in vivo 
D)  determine whether a gfp gene is turned on or off 
E)  bind inducer molecules and have an effect on gene expression 
A)  a promoter (which interacts with input signals such as regulatory proteins) and a gene, which produces mRNA and protein (output signal) 
B)  The interaction among proteins and specific DNA sequences modulate gene expression. 
C)  the combination of genetic elements from different organisms to engineer a novel metabolic pathway or reproduce one in vivo 
D)  determine whether a gfp gene is turned on or off 
E)  bind inducer molecules and have an effect on gene expression

Question 2

What is the main indication that the figure below depicts a transcriptional (operon) fusion?

Accepted Answer

A)  A single mRNA is transcribed, from which two proteins are translated. 
B)  The reporter gene keeps its biological properties: in this case, fluorescence. 
C)  Transcription proceeds from a single promoter. 
D)  The target gene maintains its ribosomal binding site. 
E)  The reporter gene is inserted into the target gene in the proper codon-reading frame. 
A)  A single mRNA is transcribed, from which two proteins are translated. 
B)  The reporter gene keeps its biological properties: in this case, fluorescence. 
C)  Transcription proceeds from a single promoter. 
D)  The target gene maintains its ribosomal binding site. 
E)  The reporter gene is inserted into the target gene in the proper codon-reading frame.

Question 3

What is the conceptual basis of the primer extension technique?

Accepted Answer

Given a translatable mRNA, the regions o

Question 4

The uses for phage display include all the following EXCEPT

Accepted Answer

A)  antibody fragments cloned from synthetic sources. 
B)  the identification of high-affinity peptides that bind to attachment proteins of some eukaryotic viruses and effectively block viral infection. 
C)  antibody fragments cloned from natural sources. 
D)  collections of mutant enzymes to be tested for activity. 
E)  directed evolution projects. 
A)  antibody fragments cloned from synthetic sources. 
B)  the identification of high-affinity peptides that bind to attachment proteins of some eukaryotic viruses and effectively block viral infection. 
C)  antibody fragments cloned from natural sources. 
D)  collections of mutant enzymes to be tested for activity. 
E)  directed evolution projects.

Question 5

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 6

Describe the whole-genome DNA-binding analysis using ChIP-on-chip technology.

Accepted Answer

This technique is useful in determining

Question 7

Gene fusions of a protein of interest and GFP, or its derivatives, can be used in all of the following EXCEPT

Accepted Answer

A)  studying protein targeting to organelles in eukaryotic cells. 
B)  monitoring microbial protein movement inside infected eukaryotic cells. 
C)  tracking viral protein movement inside or between infected eukaryotic cells. 
D)  detecting interactions between microbial extracellular proteins and attachment surfaces. 
E)  CRISPR-Cas9. 
A)  studying protein targeting to organelles in eukaryotic cells. 
B)  monitoring microbial protein movement inside infected eukaryotic cells. 
C)  tracking viral protein movement inside or between infected eukaryotic cells. 
D)  detecting interactions between microbial extracellular proteins and attachment surfaces. 
E)  CRISPR-Cas9.

Question 8

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 9

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

Question 10

Real-time PCR can be used to quantify the original amount of RNA in a sample. What additional step must be accomplished in this particular application?

Accepted Answer

A)  the careful design of specific forward and reverse primers 
B)  RNA must first be converted to cDNA. 
C)  RNA must be denatured with formaldehyde to avoid secondary structures. 
D)  the separation of mRNA from other RNA species 
E)  DNA is converted to RNA. 
A)  the careful design of specific forward and reverse primers 
B)  RNA must first be converted to cDNA. 
C)  RNA must be denatured with formaldehyde to avoid secondary structures. 
D)  the separation of mRNA from other RNA species 
E)  DNA is converted to RNA.

Question 11

A "buffer gate" in synthetic biology can best be described as

Accepted Answer

A)  a single repressor molecule (R1) that prevents the production of an output molecule (Pr1). 
B)  alternate input molecules (I1 or I2) that drive the production of alternative proteins (Prn). 
C)  a single input inducer molecule (I1) that leads to the production of a single product (Pr1). 
D)  kill switches. 
E)  a potent DNA-damaging toxin. 
A)  a single repressor molecule (R1) that prevents the production of an output molecule (Pr1). 
B)  alternate input molecules (I1 or I2) that drive the production of alternative proteins (Prn). 
C)  a single input inducer molecule (I1) that leads to the production of a single product (Pr1). 
D)  kill switches. 
E)  a potent DNA-damaging toxin.

Question 12

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 13

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 14

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 15

In the yeast two-hybrid analysis technique, in vivo protein-protein interactions are explored. The "bait" and "prey" proteins are translationally fused to the cleaved activation and DNA-binding domains of the GAL4 transcription factor. What is the target gene of GAL4?

Accepted Answer

A)  lacZ 
B)  gadA/B 
C)  GAL1 
D)  lacY 
E)  lacA 
A)  lacZ 
B)  gadA/B 
C)  GAL1 
D)  lacY 
E)  lacA

Question 16

The genes for proteins such as b-galactosidase (lacZ) or green fluorescent protein (gfp) can be fused to the promoter of a gene of interest. Which of the following statements is NOT correct about gfp and lacZ?

Accepted Answer

A)  They are called reporter genes. 
B)  The enzymatic activity of b-galactosidase can be easily assayed. 
C)  GFP is visualized by fluorescence microscopy. 
D)  Both genes are of viral origin. 
E)  The gfp gene is of eukaryotic origin, whereas lacZ is a bacterial gene. 
A)  They are called reporter genes. 
B)  The enzymatic activity of b-galactosidase can be easily assayed. 
C)  GFP is visualized by fluorescence microscopy. 
D)  Both genes are of viral origin. 
E)  The gfp gene is of eukaryotic origin, whereas lacZ is a bacterial gene.

Question 17

Which of the following is correct regarding operon fusions?

Accepted Answer

A)  They expose both transcriptional and translational controls. 
B)  Both target and reporter genes have their own promoter sequences. 
C)  Both target and reporter genes have ribosome-binding sites. 
D)  Only the reporter gene has a promoter. 
E)  They produce a single transcript and a single hybrid reporter-target polypeptide. 
A)  They expose both transcriptional and translational controls. 
B)  Both target and reporter genes have their own promoter sequences. 
C)  Both target and reporter genes have ribosome-binding sites. 
D)  Only the reporter gene has a promoter. 
E)  They produce a single transcript and a single hybrid reporter-target polypeptide.

Question 18

How is the concept of "logic gates" used in synthetic biology?

Accepted Answer

The principles of "logic gates" derive f

Question 19

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 20

What type of reporter fusions can expose both transcriptional and translational controls?

Accepted Answer

A)  operon fusions 
B)  gene fusions 
C)  either operon fusions or gene fusions 
D)  a fluorescent protein construct such as gfp, yfp, rfp, and so on 
E)  lac operon 
A)  operon fusions 
B)  gene fusions 
C)  either operon fusions or gene fusions 
D)  a fluorescent protein construct such as gfp, yfp, rfp, and so on 
E)  lac operon

Exam 12: Biotechniques and Synthetic Biology

What is the simplest definition of a genetic "logic gate"?

What is the main indication that the figure below depicts a transcriptional (operon) fusion?

What is the conceptual basis of the primer extension technique?

The uses for phage display include all the following EXCEPT

The role of kill switches in genetically engineered microorganisms is to

Describe the whole-genome DNA-binding analysis using ChIP-on-chip technology.

Gene fusions of a protein of interest and GFP, or its derivatives, can be used in all of the following EXCEPT

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

What kind of mutation is produced by transposable elements?

Real-time PCR can be used to quantify the original amount of RNA in a sample. What additional step must be accomplished in this particular application?

A "buffer gate" in synthetic biology can best be described as

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

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

In the yeast two-hybrid analysis technique, in vivo protein-protein interactions are explored. The "bait" and "prey" proteins are translationally fused to the cleaved activation and DNA-binding domains of the GAL4 transcription factor. What is the target gene of GAL4?

The genes for proteins such as b-galactosidase (lacZ) or green fluorescent protein (gfp) can be fused to the promoter of a gene of interest. Which of the following statements is NOT correct about gfp and lacZ?

Which of the following is correct regarding operon fusions?

How is the concept of "logic gates" used in synthetic biology?

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

What type of reporter fusions can expose both transcriptional and translational controls?

Microbial Life: Origin and Discovery

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