Chapter 11

20) Which of those listed below is LEAST similar in what is measured and concluded? A) fluorescence in situ hybridization B) GFP fusion protein C) Northern blot D) RT-PCR

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22) Which of those below is NOT an important consideration when designing a fusion protein construct? A) Avoid hybridization of the fusion gene in the artificial construct. B) Reading frame is the same for both the fusion gene and reporter gene. C) Transcriptional start and stop signals are shared. D) Translational start and stop signals are shared.

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36) A poorly immunogenic vaccine often suggests the foreign proteins were not properly recognized by the immune system due to a lack of ________ necessary, which can also be engineered to occur with additional molecular manipulations. A) complex folding B) methylation C) glucosylation D) glycosylation

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37) Which of the following is NOT an example of synthetic biology? A) assembling gene sequences together into genome and creating a living organism from it B) creating a new metabolic pathway that produces a previously unidentified compound C) developing a novel polyvalent vaccine D) making Escherichia coli phototrophic

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T/F: Artificially synthesizing DNA strands (e.g., oligonucleotide primers) involves the careful attachment of one nucleotide at a time to an immobilized sequence

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T/F: Due to well developed molecular tools and careful screening designs, functional genes can be isolated directly by isolation from the environment rather than cultivating the diverse species in a microbial community

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T/F: Engineering a metabolic pathway enables a researcher to use different genes from unrelated organisms

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T/F: Genomic libraries enable the discovery of individual gene(s) involved in a particular function of interest with cloning vectors in an expression host, such as Escherichia coli

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T/F: Green fluorescent protein (GFP) is used for detecting translational activity of a fused protein, whereas lacZ reporters are used to detect transcriptional activity of a fused gene

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T/F: One method to circumvent issues with introns when expression eukaryotic gene is a bacterium is to simply clone the mature transcript

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T/F: The lacZ gene is commonly used as a reporter gene, because its substrate lactose is well known and easily measured.

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T/F: Developing vaccines for humans relies heavily on manipulating and engineering vectors

? True ?

31) If a protein to be overexpressed is toxic to the expression host, it is best to select an expression vector that A) is compatible with a binary vector able to be regulated. B) is inducible. C) has a relatively low copy number per cell. D) prevents folding of the overexpressed protein into its toxic form.

??

39) Using a host defective in proteases is likely to be necessary when engineering A) a complete metabolic pathway requiring several different enzymes. B) overproducing proteins. C) production of a small protein. D) transgenic animals with immune systems.

??

29) Which of the following terms is used to describe a synthetic DNA fragment? A) DNA cassette B) DNA hybrid C) recombinant DNA D) artificial chromosome

A) DNA cassette

26) The enzyme that covalently links both strands of a vector and inserted DNA in molecular cloning is A) DNA ligase. B) DNA phosphatase. C) DNA hydrolase. D) DNA transferase.

A) DNA ligase.

11) Which objective would be best to use a Southern blot rather than a Northern blot? A) Determine if a gene is present in a genome. B) Discover gene function. C) Identify regulatory gene-protein interactions. D) Quantify expression profiles of a gene.

A) Determine if a gene is present in a genome.

19) Which statement is TRUE? A) YACs are more likely than BACs to undergo recombination and rearrangement. B) BACs are more likely than YACs to undergo recombination and rearrangement. C) YACs and BACs undergo recombination and rearrangement at about the same rate. D) It is impossible to state with any certainty whether YACs or BACs are more likely to undergo recombination and rearrangement, because environmental factors play a major role in the probability of one or the other occurring.

A) YACs are more likely than BACs to undergo recombination and rearrangement.

21) The principle behind a nucleic acid probe design is that the probe itself must contain A) a key complementary part of the target gene sequence of interest. B) all of the nucleotide sequence of the gene of interest to conclusively identify the gene. C) an antibody to specifically bind to the gene of interest. D) at least three separate complementary regions of the gene of interest.

A) a key complementary part of the target gene sequence of interest.

18) Inserting a kanamycin resistance cassette into a catabolic operon to confirm the gene is essential in degradation of a particular compound would involve all of the following EXCEPT A) a reporter gene. B) ligation. C) recombination. D) transformation.

A) a reporter gene.

10) To verify a gene was cloned into a vector successfully, sequencing the vector as well as ________ are commonly performed. A) agarose gel electrophoresis B) fluorescence in situ hybridization C) protein purification D) northern blots

A) agarose gel electrophoresis

3) To discover a catabolic gene cluster, cloning large sequences of approximately 40 kbp requires the utility of A) bacterial artificial chromosomes (BACs). B) cosmids or fosmids. C) a eukaryotic host to house the large foreign DNA. D) multiple gene fusions.

A) bacterial artificial chromosomes (BACs). ??

14) At which time period(s) during PCR thermocycling is/are hottest in temperature? A) during DNA denaturation B) during primer annealing C) during primer extension/elongation D) Both the first and last cycles are hotter in temperature than all other cycles.

A) during DNA denaturation

17) What molecular mechanism/feature does site-directed mutagenesis exploit to introduce a mutation at a specific site? A) flanking complementary bound nucleotides permit non-complementary base pairing B) methylated nucleotides disrupt DNA polymerase's proofreading C) nucleotide substitution when one is depleted D) transposase-induced base pair changes

A) flanking complementary bound nucleotides permit non-complementary base pairing

6) One of the more formidable obstacles to mammalian gene cloning is the presence of A) introns. B) exons. C) repressors. D) integrators.

A) introns.

4) Expression vectors are designed to ensure that ________ can be efficiently ________. A) mRNA / transcribed B) DNA / transcribed C) mRNA / translated D) DNA / translated

A) mRNA / transcribed

1) If a foreign gene is cloned into an expression host, it is important that the host itself A) not produce the protein being studied. B) produce the protein in larger amounts than the vector. C) repress the genetic expression being studied. D) produce signal proteins to tag the host protein.

A) not produce the protein being studied.

16) Which of the following is NOT a common step in creating a genomic library? A) Fragment DNA into small segments. B) Hybridize DNA sequences to form inserts of a target size range. C) Ligate DNA into vectors. D) Transform the vectors into a host.

B) Hybridize DNA sequences to form inserts of a target size range.

34) Polyvalent vaccines using vaccinia virus are highly favored by doctors and physicians but are especially challenging for those who develop them, because A) coat proteins form a relatively rigid structure and do not allow much space for additional proteins to be expressed. B) multiple foreign proteins simultaneously synthesized often disrupts each other's activity. C) vaccinia and most other viruses engineered for vaccines contain only one restriction site for cloning in their genome. D) virus genetic manipulation uses transfection, which is an inherently inefficient process.

B) multiple foreign proteins simultaneously synthesized often disrupts each other's activity.

15) To estimate the total concentration of a beneficial bacterial species in yogurt, ________ would provide the quickest results. A) fluorescence in situ hybridization B) qPCR C) RT-PCR D) a Southern blot

B) qPCR

33) The principle underlying how salmon were genetically engineered to grow faster is the A) removal of a gene responsible for feeling full after eating. B) replacement of inducible to constitutive hormone production. C) resistance to bacterial infections which waste metabolic energy in the salmon to fight off. D) addition of genes to enhance blood circulation and tissue development.

B) replacement of inducible to constitutive hormone production.

2) Detecting a specific protein with an antibody is considered a(n) ________ method. A) selection B) screening C) isolation D) duplication

B) screening

13) Which of the following sequences would be cleaved by a type II restriction endonuclease? A) TTGCCGA AACGGCT B) GGGGGGG CCCCCCCC C) GTAATG CATTAC D) GAATTC CTTAAG

C) GTAATG CATTAC

32) Some proteins overexpressed at high levels resulting in the formation of inclusion bodies can abolish the goal of producing large quantities of active protein. What could be done to minimize this issue? A) Codon optimize the gene. B) Decrease the number of biobricks in the vector. C) Simultaneously produce intracellular chaperonins. D) Switch to an expression host with a larger intracellular volume.

C) Simultaneously produce intracellular chaperonins.

25) What makes eukaryotic transcripts easier to isolate than transcripts in bacteria? A) Eukaryotic transcripts are not methylated but their genes are often methylated. B) Larger transcript size in eukaryotes enables easy size-selection methods. C) mRNA is polyadenylated in eukaryotes. D) Transcripts are the most abundant RNAs in eukaryotes

C) mRNA is polyadenylated in eukaryotes.

28) The Ti plasmid is best suited for genetically manipulating A) Agrobacterium spp. B) fish. C) plants. D) viruses.

C) plants.

30) Which construct would be MOST useful in studying translational control? A) gene fusion B) operon fusion C) protein fusion D) shuttle vector

C) protein fusion

27) Type II restriction endonucleases A) are heterodimers. B) natively function to methylate specific nucleotides and prevent foreign DNA from being incorporated into the genome. C) recognize nucleotide sequences that are palindromic. D) require ATP energy to cleave dsDNA.

C) recognize nucleotide sequences that are palindromic.

5) A(n) ________ gene is a gene that encodes a protein that is easy to detect and assay. A) encoder B) translational C) reporter D) recorder

C) reporter

8) What type of vector can replicate and be maintained stably in two (or more) unrelated host organisms? A) virus B) expression C) shuttle D) integrating

C) shuttle

35) Recognizing pathogens that contain multiple unique proteins which enable the human immune system to recognize just one and mount an effective response has opened the door on development of some vaccines only being A) attenuated carrier viruses. B) monovalent. C) subunit vaccines. D) purified protein administered.

C) subunit vaccines.

24) After digesting a DNA sequence, a restriction endonuclease can generate A) blunt ends. B) overhangs. C) sticky ends. D) blunt ends, overhangs, or sticky ends.

D) blunt ends, overhangs, or sticky ends.

38) Cloning vectors can be distinguished from expression vectors by A) carrying ori genes for replication of the cloned sequence. B) having a multiple cloning site (MCS). C) having a high copy number per cell. D) lacking a promoter site upstream of the insertion site.

D) lacking a promoter site upstream of the insertion site.

23) A shuttle vector is most useful for A) engineering a complete metabolic pathway. B) identifying the localization of a protein. C) knocking out a gene by cassette displacement. D) making a foreign protein in a mammalian cell.

D) making a foreign protein in a mammalian cell.

12) A polymerase chain reaction (PCR) copies an individual gene segment in vitro with a(n) ________ primer(s). A) individual RNA B) individual DNA C) pair of RNA D) pair of DNA

D) pair of DNA

9) The genes encoding luciferase, green fluorescent protein (GFP), and β-galactosidase are typically used in cloning as A) transcription regulators. B) global control genes. C) promoter sequences. D) reporter genes.

D) reporter genes.

7) Which of the following is NOT a characteristic of a type II restriction endonuclease? A) cleavage product can be either blunt or sticky ended but is always the same for an individual enzyme B) recognizes a specific palindromic site for cleavage C) recognition site length varies among enzymes but is always the same for an individual enzyme D) unable to cleave methylated DNA

D) unable to cleave methylated DNA

T/F: High expression levels of a eukaryotic gene in a bacterium such as Escherichia coli cannot be accomplished due to the presence of introns

False

T/F: One problem with both BACs and YACs is that genetic regions of these chromosomes cannot be subcloned

False

T/F: Although various codons often code for the same amino acid, it is important to choose the codon preferred by the expression host itself

True

T/F: DNA ligase mediates the insertion of foreign DNA into a vector, but it will only be able to do so if the inserts and vector have matching sticky or blunt ends

True

T/F: DNA polymerases from Escherichia coli cannot be used to artificially copy gene sequences with a thermocycler

True

T/F: If vaccinia viruses were not both immunogenic and relatively benign, they would likely not be a favored vehicle for vaccinations.

True

T/F: In principle, a type II restriction endonuclease with an 8-nucleotide recognition sequence should cut 1 in every 48 nucleotide positions

True

T/F: Modification enzymes typically methylate specific bases within the recognition sequence to prevent digestion of the nucleotide sequence by restriction endonucleases

True

T/F: One fundamental technique of genetic engineering includes the ability to cut DNA into random fragments

True

T/F: One important advantage of eukaryotic cells as hosts for cloning vectors is that they already possess the complex RNA and posttranslational processing systems required for the production of eukaryotic proteins

True

T/F: Strong promoters used for genetic manipulation are usually regulated by specific molecules

True

T/F: The key steps in cloning a foreign gene into a vector, regardless of the application, involve isolating the insert fragment, ligating the insert into a vector, and transforming it into a hos

True

T/F: While other types exist, Type II restriction endonucleases are by far the most commonly used enzymes for genetic engineering.

True

T/F: Regardless of the DNA polymerase used in PCR, such as Taq or Pfu, they all have an inherent inability to perfectly copy the template strand, which means the polymerases themselves occasionally make mutations in the sequences they copy

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