Question 1

A common approach to study a certain metabolic process is to isolate organisms defective in that particular process. These organisms are called

Accepted Answer

A)  agents. 
B)  wild type. 
C)  prototrophs. 
D)  mutants. 
E)  vectors. 
A)  agents. 
B)  wild type. 
C)  prototrophs. 
D)  mutants. 
E)  vectors.

Question 2

Observe the figure below and discuss how a single northern blot can reveal differences in size and abundance of the E. coli acid-resistance gene gadA with respect to the gadBC operon and the inducible expression of these genes at low pH.

Accepted Answer

RNA extracted from cells grown at pH 7.7

Question 3

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 4

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 5

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 6

The migration of linear DNA molecules in agarose or polyacrylamide gels occurs at a rate that is

Accepted Answer

A)  independent of their size. 
B)  directly proportional to their size. 
C)  inversely proportional to their size. 
D)  dependent on the AT content. 
E)  dependent on the GC content. 
A)  independent of their size. 
B)  directly proportional to their size. 
C)  inversely proportional to their size. 
D)  dependent on the AT content. 
E)  dependent on the GC content.

Question 7

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 8

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

Accepted Answer

Gene-specific RNAs (riboswitches) have b

Question 9

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 10

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 11

In a DNA protection assay gel, it is necessary to run sequencing ladders of the putative protein-binding DNA region along with DNase I-treated samples in order to

Accepted Answer

A)  establish the position of the binding protein relative to the transcription start site. 
B)  provide molecular weight markers. 
C)  check that the gel running conditions are correct. 
D)  check for nonspecific DNA degradation. 
E)  check for specific DNA degradation. 
A)  establish the position of the binding protein relative to the transcription start site. 
B)  provide molecular weight markers. 
C)  check that the gel running conditions are correct. 
D)  check for nonspecific DNA degradation. 
E)  check for specific DNA degradation.

Question 12

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 13

Discuss possible disadvantages of the yeast two-hybrid system.

Accepted Answer

Because putative interacting proteins ar

Question 14

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.

Question 15

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 16

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 17

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

Accepted Answer

Real-time PCR utilizes a reporter probe

Question 18

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 19

In the first stage of the western blot procedure, a technique known as SDS-PAGE is used to separate proteins according to their

Accepted Answer

A)  isoelectric points. 
B)  quaternary structures. 
C)  molecular weights. 
D)  amino acid sequences. 
E)  secondary structure compositions. 
A)  isoelectric points. 
B)  quaternary structures. 
C)  molecular weights. 
D)  amino acid sequences. 
E)  secondary structure compositions.

Question 20

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

Exam 12: Biotechniques and Synthetic Biology

A common approach to study a certain metabolic process is to isolate organisms defective in that particular process. These organisms are called

Observe the figure below and discuss how a single northern blot can reveal differences in size and abundance of the E. coli acid-resistance gene gadA with respect to the gadBC operon and the inducible expression of these genes at low pH.

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

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

The migration of linear DNA molecules in agarose or polyacrylamide gels occurs at a rate that is

Bacillus thuringiensis stores insecticidal proteins

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

Which answer choice INCORRECTLY labels the figure below?

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

In a DNA protection assay gel, it is necessary to run sequencing ladders of the putative protein-binding DNA region along with DNase I-treated samples in order to

Which answer choice INCORRECTLY labels the figure below?

Discuss possible disadvantages of the yeast two-hybrid system.

Which of the following is correct regarding biological toggle switches?

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

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

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

In the first stage of the western blot procedure, a technique known as SDS-PAGE is used to separate proteins according to their

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

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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