Question 1

An advantage of using fluorescent protein technology to track protein movements in cells and tissues is that

Accepted Answer

A)  intracellular GFP-protein fusions can be detected by fluorescence microscopy in vivo. 
B)  a mobile protein can be tracked as it moves through organs or tissues. 
C)  a fusion with a mutant protein might reveal incorrect localization or movement. 
D)  it can identify the gene encoding prey protein. 
E)  it can be used to detect protein-protein interactions. 
A)  intracellular GFP-protein fusions can be detected by fluorescence microscopy in vivo. 
B)  a mobile protein can be tracked as it moves through organs or tissues. 
C)  a fusion with a mutant protein might reveal incorrect localization or movement. 
D)  it can identify the gene encoding prey protein. 
E)  it can be used to detect protein-protein interactions.

Question 2

The phenomenon that allows a quencher dye to reduce the fluorescence of the reporter dye in real-time PCR techniques is called

Accepted Answer

A)  nuclear magnetic resonance. 
B)  fluorescence resonance energy transfer (FRET). 
C)  atomic force tunneling. 
D)  magnetic resonance imaging. 
E)  random nicking. 
A)  nuclear magnetic resonance. 
B)  fluorescence resonance energy transfer (FRET). 
C)  atomic force tunneling. 
D)  magnetic resonance imaging. 
E)  random nicking.

Question 3

Which of the following experimental procedures is NOT used in ChIP-seq?

Accepted Answer

A)  DNA-protein complexes are cross-linked. 
B)  DNA is extracted and sheared. 
C)  Bead-bound antibodies to transcription factors are used to precipitate transcription factors cross-linked with DNA. 
D)  The bead-bound antibodies are precipitated using a secondary antibody. 
E)  Transcription factors are released from DNA, amplified and identified by sequencing. 
A)  DNA-protein complexes are cross-linked. 
B)  DNA is extracted and sheared. 
C)  Bead-bound antibodies to transcription factors are used to precipitate transcription factors cross-linked with DNA. 
D)  The bead-bound antibodies are precipitated using a secondary antibody. 
E)  Transcription factors are released from DNA, amplified and identified by sequencing.

Question 4

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

Question 5

What is the conceptual basis of the primer extension technique?

Accepted Answer

Given a translatable mRNA, the regions o

Question 6

The replacement of the genome of Mycoplasma capricolum with the modified genome of M. mycoides is considered to be a significant accomplishment because it

Accepted Answer

A)  demonstrates that genetic manipulation of recalcitrant organisms is impossible. 
B)  opens the possibility to redesign prokaryotic genomic systems. 
C)  enables gene editing of species. 
D)  merges the genomes into a hybrid. 
E)  creates a riboswitch board. 
A)  demonstrates that genetic manipulation of recalcitrant organisms is impossible. 
B)  opens the possibility to redesign prokaryotic genomic systems. 
C)  enables gene editing of species. 
D)  merges the genomes into a hybrid. 
E)  creates a riboswitch board.

Question 7

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 8

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 9

What are translational fusions used for? How are they constructed?

Accepted Answer

Translational fusions are designed to ex

Question 10

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 11

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 12

In a yeast two-hybrid analysis of several strains containing different prey/bait combinations, the screening of interacting proteins is done by growing cells on a medium containing X-Gal. White and blue colonies are observed after incubation. Which of the following statements is NOT true regarding blue/white selection in the yeast two-hybrid method?

Accepted Answer

A)  Blue colonies result from X-Gal hydrolyzed by the reporter enzyme b-galactosidase. 
B)  White colonies result from cells in which the prey and bait proteins do not interact. 
C)  Galactose released from X-Gal hydrolysis does not contribute to a colony's blue color. 
D)  White colonies indicate that b-galactosidase catalyzed the hydrolysis of X-Gal. 
E)  Blue colonies are an indication that GAL4 activated transcription of GAL1-lacZ. 
A)  Blue colonies result from X-Gal hydrolyzed by the reporter enzyme b-galactosidase. 
B)  White colonies result from cells in which the prey and bait proteins do not interact. 
C)  Galactose released from X-Gal hydrolysis does not contribute to a colony's blue color. 
D)  White colonies indicate that b-galactosidase catalyzed the hydrolysis of X-Gal. 
E)  Blue colonies are an indication that GAL4 activated transcription of GAL1-lacZ.

Question 13

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 14

His₆-fusion-tagged proteins can be recovered from affinity chromatography columns because the histidine tag tightly binds to beads coated with ________ ions. The elution buffer contains ________, which has stronger affinity for these ions.

Accepted Answer

A)  copper; sulfate 
B)  magnesium; EDTA 
C)  iron; citrate 
D)  calcium; EGTA 
E)  nickel; imidazole 
A)  copper; sulfate 
B)  magnesium; EDTA 
C)  iron; citrate 
D)  calcium; EGTA 
E)  nickel; imidazole

Question 15

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

Accepted Answer

The principles of "logic gates" derive f

Question 16

Bacillus thuringiensis stores insecticidal proteins

Accepted Answer

A)  surrounding the spore. 
B)  in the cytoplasm. 
C)  as proteins crystallized in the parasporal body. 
D)  as part of the spore. 
E)  in the plasma membrane. 
A)  surrounding the spore. 
B)  in the cytoplasm. 
C)  as proteins crystallized in the parasporal body. 
D)  as part of the spore. 
E)  in the plasma membrane.

Question 17

Noise in synthetic biology is a result of the

Accepted Answer

A)  ara operon. 
B)  lac operon. 
C)  dual-feedback oscillator. 
D)  fluctuation of gene expression among single-cells in a population. 
E)  oscillatory genetic circuit. 
A)  ara operon. 
B)  lac operon. 
C)  dual-feedback oscillator. 
D)  fluctuation of gene expression among single-cells in a population. 
E)  oscillatory genetic circuit.

Question 18

The purpose of a DNA protection assay is to determine what nucleotide sequences directly interact with which macromolecules?

Accepted Answer

A)  DNA-binding proteins 
B)  rRNA 
C)  endonucleases 
D)  exonucleases 
E)  tRNA 
A)  DNA-binding proteins 
B)  rRNA 
C)  endonucleases 
D)  exonucleases 
E)  tRNA

Question 19

The figure below shows a gel with Escherichia coli DNA fragments separated by size. The marker lanes help to locate the transcription start following the promoter region of a gene encoding for glutamate decarboxylase (GadA). There are five lanes from an experiment in which varying amounts of the protein GadX were added to DNA prior to treatment with DNase I. What do the roman numeral boxes indicate?

Accepted Answer

A)  change RNA to DNA. 
B)  topoisomerases-binding regions 
C)  thus not protected 
D)  translational start 
E)  GADF-binding site 
A)  change RNA to DNA. 
B)  topoisomerases-binding regions 
C)  thus not protected 
D)  translational start 
E)  GADF-binding site

Question 20

CRISPR-Cas9, a prokaryotic defense mechanism, is a powerful emerging tool in biotechnology for all of the following EXCEPT

Accepted Answer

A)  allowing the editing of defective genes in eukaryotic cells. 
B)  introducing insertions, deletions, or sequence modifications into a given genome with CRISPR-Cas9. 
C)  regulating gene expression in bacteria with CRISPRi, in which case Cas9 is no longer active as a nuclease. 
D)  marking a defective gene with antibiotic resistance. 
E)  disrupting latent HIV provirus in infected cells. 
A)  allowing the editing of defective genes in eukaryotic cells. 
B)  introducing insertions, deletions, or sequence modifications into a given genome with CRISPR-Cas9. 
C)  regulating gene expression in bacteria with CRISPRi, in which case Cas9 is no longer active as a nuclease. 
D)  marking a defective gene with antibiotic resistance. 
E)  disrupting latent HIV provirus in infected cells.

Exam 12: Biotechniques and Synthetic Biology

An advantage of using fluorescent protein technology to track protein movements in cells and tissues is that

The phenomenon that allows a quencher dye to reduce the fluorescence of the reporter dye in real-time PCR techniques is called

Which of the following experimental procedures is NOT used in ChIP-seq?

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

What is the conceptual basis of the primer extension technique?

The replacement of the genome of Mycoplasma capricolum with the modified genome of M. mycoides is considered to be a significant accomplishment because it

The uses for phage display include all the following EXCEPT

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

What are translational fusions used for? How are they constructed?

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

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?

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?

His₆-fusion-tagged proteins can be recovered from affinity chromatography columns because the histidine tag tightly binds to beads coated with ________ ions. The elution buffer contains ________, which has stronger affinity for these ions.

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

Bacillus thuringiensis stores insecticidal proteins

Noise in synthetic biology is a result of the

The purpose of a DNA protection assay is to determine what nucleotide sequences directly interact with which macromolecules?

CRISPR-Cas9, a prokaryotic defense mechanism, is a powerful emerging tool in biotechnology for all of the following EXCEPT

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

Energetics and Catabolism

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

Microbial Diseases

Antimicrobial Therapy

Clinical Microbiology and Epidemiology

Filters

His₆-fusion-tagged proteins can be recovered from affinity chromatography columns because the histidine tag tightly binds to beads coated with ions. The elution buffer contains , which has stronger affinity for these ions.