Question 1

How do operon fusions reveal transcriptional control of a target gene?

Accepted Answer

Operon (transcriptional) fusions have a target gene that carries its own promoter and ribosome-binding site (RBS). The target gene has a promoterless reporter gene that also has an RBS. Transcription solely depends on the target gene's promoter; hence, a single mRNA is produced. However, two peptides are independently produced, as a result of having two RBSs. Gene expression from this artificial single-promoter operon only reflects transcriptional control.

Question 2

Which of the following is correct regarding biological toggle switches?

Accepted Answer

A)  They can be thought of as two back-to-back OR gates. 
B)  They can be described as straightforward "buffer gates." 
C)  They consist of a single NOT gate. 
D)  Two inducer signals are necessary to toggle the switch. 
E)  They have two repressor genes whose products can repress each other's transcription. 
A)  They can be thought of as two back-to-back OR gates. 
B)  They can be described as straightforward "buffer gates." 
C)  They consist of a single NOT gate. 
D)  Two inducer signals are necessary to toggle the switch. 
E)  They have two repressor genes whose products can repress each other's transcription. E

Question 3

Explain the principle of riboswitches and switchboards, and provide examples of their application.

Accepted Answer

Gene-specific RNAs (riboswitches) have been engineered to control translation at will. The concept of riboswitches is based on the phenomenon of mRNA stability and translation regulated by small RNAs. Initially, a cis-repressed mRNA (crRNA) is made by linking a crRNA sequence to an output gene; the crRNA transcript displays a 5'-hairpin structure that covers the ribosome-binding site (RBS). A matching trans-activating (taRNA) is added to the system to allow base-pairing with the crRNA and exposing the RBS, thus leading to ribosome binding and translation. Applications of this technique include simultaneous regulation of several metabolic pathways via a set of linked riboswitches (a metabolic switchboard). Another important potential application is the development of kill switches, or fail-safe mechanisms, leading to the suicide of genetically modified organisms after they have fulfilled their function.

Question 4

Advantages in real-time PCR over regular, end-time PCR include all of the following EXCEPT

Accepted Answer

A)  initial amounts of template DNA can be quantified by the length of time it takes to detect PCR products. 
B)  amplified DNA is quantified while the PCR is still taking place. 
C)  earlier increments in fluorescence indicate larger amounts of template DNA in the original sample. 
D)  real-time PCR uses GadX. 
E)  real-time PCR can be used to quantify DNA or RNA in a sample. 
A)  initial amounts of template DNA can be quantified by the length of time it takes to detect PCR products. 
B)  amplified DNA is quantified while the PCR is still taking place. 
C)  earlier increments in fluorescence indicate larger amounts of template DNA in the original sample. 
D)  real-time PCR uses GadX. 
E)  real-time PCR can be used to quantify DNA or RNA in a sample.

Question 5

What is synthetic biology? Provide an example of its potential applications.

Accepted Answer

Synthetic biology is the conception and

Question 6

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 7

What kind of gene expression controls are revealed by operon fusions?

Accepted Answer

A)  transcriptional 
B)  translational 
C)  both transcriptional and translational 
D)  posttranslational 
E)  pretranscriptional 
A)  transcriptional 
B)  translational 
C)  both transcriptional and translational 
D)  posttranslational 
E)  pretranscriptional

Question 8

Double-stranded DNA probes must be denatured when used in northern blot experiments to ensure that

Accepted Answer

A)  they are properly radioactively labeled or tagged with a dye. 
B)  the DNA coding strand hybridizes to RNA on the membrane. 
C)  both DNA strands bind the single-stranded RNA on the membrane. 
D)  the RNA coding strand hybridizes to DNA on the membrane. 
E)  an RNA strand binds to another RNA strand on the membrane. 
A)  they are properly radioactively labeled or tagged with a dye. 
B)  the DNA coding strand hybridizes to RNA on the membrane. 
C)  both DNA strands bind the single-stranded RNA on the membrane. 
D)  the RNA coding strand hybridizes to DNA on the membrane. 
E)  an RNA strand binds to another RNA strand on the membrane.

Question 9

Which kind of phage vectors are most frequently used in phage display technology?

Accepted Answer

A)  double-stranded DNA T-odd 
B)  double-stranded DNA T-even 
C)  filamentous single-stranded DNA phages 
D)  lambda-based vectors 
E)  alpha-based vectors 
A)  double-stranded DNA T-odd 
B)  double-stranded DNA T-even 
C)  filamentous single-stranded DNA phages 
D)  lambda-based vectors 
E)  alpha-based vectors

Question 10

Which answer choice INCORRECTLY labels the figure below?

Accepted Answer

A)  D indicates the CO₂ entering the cell. 
B)  C points to GABA. 
C)  A marks the GABA/glutamate antiporter. 
D)  D is the label for H+ entering the cell. 
E)  B points to glutamate. 
A)  D indicates the CO₂ entering the cell. 
B)  C points to GABA. 
C)  A marks the GABA/glutamate antiporter. 
D)  D is the label for H+ entering the cell. 
E)  B points to glutamate.

Question 11

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 12

Describe the difference between autoradiography and phosphor imaging.

Accepted Answer

In autoradiography, emissions from a rad

Question 13

How can a protein be detected on a western blot?

Accepted Answer

A sample of the protein of interest is i

Question 14

Sigma B is a stress-induced transcription factor in Bacillus subtilis. Bacteria producing a sigma B-YFP fusion protein were exposed to constant energy stress, and fluorescence pulses emitted by individual cells were detected by time-lapse microscopy. Could this result have been obtained using a sigma B-b-gal fusion protein?

Accepted Answer

A)  Yes. Hydrolysis of X-Gal by b-galactosidase produces a blue product detectable by eye. 
B)  Yes. Hydrolysis of ONPG by b-galactosidase in liquid medium produces an orange compound measurable by spectrophotometry. 
C)  Yes. It depends on how well the reporter gene is inserted into the vector with respect to the position of the ribosome-binding site. 
D)  No. Whereas YFP fluorescence can be carefully observed and measured by time-lapse microscopy, b-gal activity is measured as an average of the population as a whole. 
E)  No; the product would not be detectable by eye. 
A)  Yes. Hydrolysis of X-Gal by b-galactosidase produces a blue product detectable by eye. 
B)  Yes. Hydrolysis of ONPG by b-galactosidase in liquid medium produces an orange compound measurable by spectrophotometry. 
C)  Yes. It depends on how well the reporter gene is inserted into the vector with respect to the position of the ribosome-binding site. 
D)  No. Whereas YFP fluorescence can be carefully observed and measured by time-lapse microscopy, b-gal activity is measured as an average of the population as a whole. 
E)  No; the product would not be detectable by eye.

Question 15

Briefly explain how real-time polymerase chain reaction (PCR) works.

Accepted Answer

Real-time PCR utilizes a reporter probe

Question 16

For a reporter protein to be synthesized, its gene must be fused in the proper codon reading frame with respect to the

Accepted Answer

A)  ribosome binding site. 
B)  promoter of the gene of interest. 
C)  vector origin of replication. 
D)  target gene. 
E)  vector's antibiotic marker sequence. 
A)  ribosome binding site. 
B)  promoter of the gene of interest. 
C)  vector origin of replication. 
D)  target gene. 
E)  vector's antibiotic marker sequence.

Question 17

How were GadE and GadX demonstrated to be transcription factors for the gadA gene?

Accepted Answer

Footprint analysis can be used to find o

Question 18

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 19

DNA protection assays identify specific nucleotide-protein contacts. What is the role of deoxyribonuclease (DNase) I treatment in footprint analysis?

Accepted Answer

A)  DNase I is used to break DNA previously bound to protein. 
B)  Protein-bound DNA is protected from DNase I and it can be isolated and characterized. 
C)  DNase I prepares protein-bound DNA for sequencing. 
D)  DNase I is used to cleave Taq polymerase. 
E)  DNase I synthesizes DNA from the upstream primer. 
A)  DNase I is used to break DNA previously bound to protein. 
B)  Protein-bound DNA is protected from DNase I and it can be isolated and characterized. 
C)  DNase I prepares protein-bound DNA for sequencing. 
D)  DNase I is used to cleave Taq polymerase. 
E)  DNase I synthesizes DNA from the upstream primer.

Question 20

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.

Exam 12: Biotechniques and Synthetic Biology

How do operon fusions reveal transcriptional control of a target gene?

Which of the following is correct regarding biological toggle switches?

Explain the principle of riboswitches and switchboards, and provide examples of their application.

Advantages in real-time PCR over regular, end-time PCR include all of the following EXCEPT

What is synthetic biology? Provide an example of its potential applications.

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?

What kind of gene expression controls are revealed by operon fusions?

Double-stranded DNA probes must be denatured when used in northern blot experiments to ensure that

Which kind of phage vectors are most frequently used in phage display technology?

Which answer choice INCORRECTLY labels the figure below?

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

Describe the difference between autoradiography and phosphor imaging.

How can a protein be detected on a western blot?

Briefly explain how real-time polymerase chain reaction (PCR) works.

For a reporter protein to be synthesized, its gene must be fused in the proper codon reading frame with respect to the

How were GadE and GadX demonstrated to be transcription factors for the gadA gene?

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

DNA protection assays identify specific nucleotide-protein contacts. What is the role of deoxyribonuclease (DNase) I treatment in footprint analysis?

Which of the following is correct regarding operon fusions?

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