Deck 12: Molecular Techniques and Biotechnology

Question 1

Hybridization of a DNA probe with an RNA transcript bound to a membrane after transfer from a denaturing agarose gel is the basis for the method known as:

A) Northern blot
B) Southern blot
C) Western blot
D) SDS-PAGE
E) isoelectrofocusing

Answer 1

A

Question 2

When using luminol as part of the detection system in a Western blot, released photons may be revealed by:

A) UV-illumination
B) phosphorimaging
C) colorimetry
D) spectrophotometry
E) none of the above

Answer 2

B

Question 3

DNA fragments with specific sequences are detected by a technique known as __________.

A) Northern blot
B) Southern blot
C) Western blot
D) isoelectrofocusing
E) agarose gel electrophoresis

Answer 3

B

Question 4

The genes for proteins such as $\beta$ -galactosidase (lacZ) or green fluorescent protein (gfp) can be inserted into the promoter of a gene of interest. Which of the following statements is correct about gfp and lacZ?

A) They are called reporter genes.
B) The activity of their products can be easily assayed.
C) Any factor inducing the expression of the gene of interest will also induce the expression of reporter genes.
D) All of the above.
E) None of the above.

Question 5

The first stage of the Western blot procedure involves separating proteins using a technique known as:

A) Northern blot
B) Southern blot
C) HPLC
D) SDS-PAGE
E) TLC

Question 6

A screening of a GadA- $\beta$ -gal fusion protein in E. coli is performed on medium containing X-Gal. White and blue colonies are observed after incubation. Which of the following statements is NOT true regarding blue/white selection?

A) Blue colonies result from X-Gal hydrolyzed by the fusion protein's $\beta$ -galactosidase moiety.
B) White colonies result from cells with a disrupted gene encoding a positive regulator of GadA.
C) Galactose released from X-Gal hydrolysis does not contribute to a colony's blue color.
D) White colonies indicate hydrolysis of X-Gal catalyzed by $\beta$ -galactosidase.
E) All of the above.

Question 7

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

A) transcriptional
B) translational
C) both transcriptional and translational
D) post-translational
E) none of the above

Question 8

Microbes that grow at neutral pH but can survive at pH 2 for short periods are called:

A) acid-fast
B) neutrophiles
C) acid resistant
D) extremophiles
E) none of the above

Question 9

A protein of interest can be specifically detected on Western blots; this technique requires:

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) all of the above
E) none of the above

Question 10

The colorless molecule o-nitrophenyl galactoside (ONPG) can be used as an artificial substrate in assays of $\beta$ -gal in E. coli extracts. Which of the following statements is NOT true with respect to the use of ONPG?

A) Hydrolysis of ONPG by $\beta$ -gal produces yellow o-nitrophenol.
B) o-nitrophenol can be measured with a spectrophotometer.
C) Hydrolysis of ONPG by $\beta$ -gal also releases colorless galactose.
D) The o-nitrophenol moiety is blue and more suitable for use in solid media.
E) None of the above.

Question 11

What kind of mutation is produced by transposable elements?

A) inversion
B) deletion
C) insertion
D) substitution
E) none of the above

Question 12

If a person needs to ingest only a few cells of an organism to become colonized or infected, the organism is said to have a low __________.

A) infectious dose
B) penetrance
C) morbidity
D) antibiotic resistance
E) none of the above

Question 13

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

A) operon fusions
B) gene fusions
C) either operon fusions or gene fusions
D) any GFP construct
E) none of the above

Question 14

Infection of potato crops by the fungus Phytophthora infestans is a constant menace to farmers. A biotechnological approach to prevent the recurrence of such an infestation is:

A) cloning of a wild potato gene that conveys resistance to P. infestans into commercial potato breeds
B) frequently spraying potato plants with fungicide throughout the growing season
C) watering plants with a trickling mechanism to avoid excessive dampness
D) all of the above
E) none of the above

Question 15

What hybridization technique can be used to confirm if two genes are components of an operon by estimating transcript size?

A) Northern blot
B) Southern blot
C) formaldehyde cross-linking
D) agarose gel electrophoresis
E) isoelectrofocusing

Question 16

Nucleic acids are easily transferred from agarose gels onto a membrane using the physical principle of __________.

A) capillarity
B) reverse osmosis
C) ionic strength
D) hydrostatic pressure
E) none of the above

Question 17

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

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

Question 18

Why must double-stranded DNA probes be denatured when used in Northern blot experiments?

A) To ensure that they are properly radioactively labeled or tagged with a dye.
B) To ensure that the DNA coding strand hybridizes to RNA on the membrane.
C) To ensure that both DNA strands bind the single-stranded RNA on the membrane.
D) All of the above.
E) None of the above.

Question 19

Acid-resistant Escherichia coli cells extrude H⁺ through the combined action of two proteins: a decarboxylase enzyme and the transporter:

A) H⁺ channel
B) [H⁺]-ATPase
C) GABA/glutamate antiporter
D) all of the above
E) none of the above

Question 20

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

A) the ribosome binding site
B) the promoter
C) the vector origin of replication
D) the target gene
E) none of the above

Question 21

A major advantage of real-time PCR is that it can be used to quantify the original amount of RNA in a sample. What additional step must be accomplished in this particular application?

A) 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) separation of mRNA from other RNA species
E) none of the above

Question 22

Genes coding for insecticidal peptides have been engineered into the genomes of some crops. These peptides are naturally produced by the bacterium:

A) Bacillus thuringiensis
B) Agrobacterium thumefaciens
C) Anabaena variabilis
D) Erwinia carotovora
E) Escherichia coli

Question 23

Traditionally, vaccines used to prevent microbial diseases have consisted of:

A) incapacitated microorganisms
B) inactivated proteins
C) attenuated viruses
D) all of the above
E) none of the above

Question 24

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

A) independent of their size
B) directly proportional to their size
C) inversely proportional to their size
D) dependent on the AT content
E) none of the above

Question 25

A significant advantage in real-time PCR is that:

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) all of the above
E) none of the above

Question 26

What end of the reporter DNA probe is bound to the reporter dye in real-time PCR?

A) 5'
B) 3'
C) amino terminal
D) carboxy terminal
E) none of the above

Question 27

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

A) nuclear magnetic resonance
B) fluorescence resonance energy transfer (FRET)
C) atomic force tunneling
D) magnetic resonance imaging
E) none of the above

Question 28

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?

A) lacZ
B) gadA/B
C) gal1
D) all of the above
E) none of the above

Question 29

His₆-fusion-tagged proteins can be isolated by affinity chromatography because the histidine tag tightly binds to:

A) copper
B) magnesium
C) iron
D) calcium
E) nickel

Question 30

The most common crops expressing insecticidal peptides are:

A) wheat and rice
B) tomato and potato
C) cotton and corn
D) all of the above
E) none of the above

Question 31

The fluorescent proteins YFP and CFP emit yellow and blue (cyan) light, respectively. These and other variations of GFP have been obtained through:

A) the chemical addition of yellow or blue fluorescent dyes to GFP
B) mutation of the gfp gene in specific sites
C) post-translational modifications of recombinant GFP
D) cloning gfp in different vectors
E) none of the above

Question 32

Among the applications of the yeast two-hybrid method, one can find which of the following?

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) all of the above
E) none of the above

Question 33

Screening food products for more than one pathogen at a time can be achieved by using:

A) real-time PCR with a forward and reverse primer pair
B) multiplex PCR with carefully designed primer pairs targeting species-specific genes
C) multiplex PCR with random hexamers as primers
D) quantitative PCR with a universal forward/reverse primer pair
E) none of the above

Question 34

Gene fusions of a protein of interest and GFP, or its derivatives, can be used in:

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) all of the above

Question 35

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

A) DNA-binding proteins
B) rRNA
C) endonucleases
D) exonucleases
E) none of the above

Question 36

Which field of science involves the use of living organisms or their products to improve human health and the human environment?

A) bacteriology
B) systematics
C) genomics
D) proteomics
E) biotechnology

Question 37

The electromobility shift assay (EMSA) is utilized to monitor molecular interactions between:

A) two proteins
B) RNA and protein
C) DNA and protein
D) DNA and RNA
E) none of the above

Question 38

The amplified product of a PCR reaction is called:

A) replicon
B) operon
C) amplicon
D) cistron
E) none of the above

Question 39

The field of biotechnology changed little over the millennia until 1928, when Alexander Fleming discovered:

A) streptomicyn
B) penicillin
C) chloramphenicol
D) bacitracin
E) none of the above

Question 40

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

A) Cells are exposed to UV light.
B) Cells are treated with formaldehyde.
C) Cells are treated with heat.
D) All of the above.
E) None of the above.

Question 41

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

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

Question 42

Describe the difference between autoradiography and phosphorimaging.

Question 43

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

Question 44

Describe the use of a primary and secondary antibody in a Western blot.

Question 45

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

Question 46

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

Question 47

Edible vaccine proteins made by transgenic plants currently include:

A) hepatitis B antigen
B) E. coli labile toxin
C) human papillomavirus
D) all of the above
E) none of the above

Question 48

Which of the following can be used as vectors in human gene therapy?

A) bacteriophages
B) modified HIV and adenoviruses
C) filamentous phages
D) cosmids
E) modified mosaic tobacco virus

Question 49

Which of the following is an example of an alternative vaccine developed through biotechnology that does NOT involve the use of attenuated pathogens?

A) injection of DNA that encodes bacterial or viral antigenic proteins into humans
B) bananas as an edible vaccine delivery system
C) production of vaccines in plants with further extraction and purification
D) all of the above
E) none of the above

Question 50

What is the purpose of directed evolution?

A) To produce enzymes with an increased ability to catalyze particular reactions.
B) To obtain enzymes with higher affinity for their substrate(s).
C) To produce novel enzymes suitable for harsh biotechnological applications.
D) All of the above.
E) None of the above.

Question 51

Why must secondary antibodies be elicited in an animal of a different species from that in which the primary antibodies were obtained?

Question 52

Among the uses for phage display one can find:

A) the identification of high-affinity peptides that bind to attachment proteins of some eukaryotic viruses and effectively block viral infection
B) antibody fragments cloned from natural sources
C) collections of mutant enzymes to be tested for activity
D) all of the above
E) none of the above

Question 53

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

A) T-odd
B) T-even
C) filamentous single-stranded DNA phages
D) lambda-based vectors
E) none of the above

Question 54

How are libraries of phage enzyme mutants generated?

A) Phage DNA is mutated with X-ray.
B) Phage DNA is subjected to error-prone PCR.
C) Phage particles are treated with formaldehyde.
D) All of the above.
E) None of the above.

Question 55

What is the biochemical mechanism of acid resistance in E. coli O157:H7?

Question 56

What variation of PCR methods can be used in directed evolution?

A) quantitative PCR
B) error-prone PCR
C) real-time PCR
D) multiplex PCR
E) none of the above

Question 57

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

Question 58

You are planning to do some Northern blots and would like to use a nonradioactive label. You decide to use biotinylated DNA. What detection method would you use?

Question 59

Once a gene encoding a putative transcriptional regulatory protein is identified by sequence annotation, what needs to be done to demonstrate this activity?

Question 60

After each round of selection by biopanning in phage display, phages containing the peptides of interest are enriched through:

A) PCR
B) repropagation in E. coli
C) affinity chromatography
D) agarose gel electrophoresis
E) none of the above

Question 61

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

Question 62

Discuss possible disadvantages of the yeast two-hybrid system.

Question 63

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

Question 64

Describe advantages and disadvantages of using adenoviruses and adeno-associated viruses as vectors in gene therapy.

Question 65

When designing the primer sets for multiplex PCR, what are some concerns?

Question 66

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

Question 67

Why would a DNA vaccine be more beneficial than a live-attenuated vaccine?

Question 68

List some of the beneficial aspects of the insecticidal activity produced by the bacterium Bacillus thuringiensis.

Question 69

Briefly explain how real-time PCR works.

Question 70

What is the conceptual basis of the primer extension technique?