Deck 12: Biotechnology and Synthetic Biology

Question 1

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

Answer 1

A

Question 2

Cells that have "insertional inactivation" of the lacZ gene are

A) blue.
B) white.
C) yellow.
D) fluorescent green.

Answer 2

B

Question 3

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.

Answer 3

A

Question 4

What is the most important advantage of Pfu polymerase over Taq polymerase?

A) Unlike Taq polymerase, Pfu polymerase functions well at relatively high temperatures.
B) It is from a bacterium, not an archaean, so it is more effective for replicating eukaryotic DNA.
C) Pfu polymerase removes the need for primers during PCR.
D) Unlike Taq polymerase, Pfu polymerase has proofreading activity.

Question 5

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

Question 6

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 polymeraseʹs proofreading
C) nucleotide substitution when one is depleted
D) transposase-induced base pair changes

Question 7

One of the more formidable obstacles to mammalian gene cloning is the presence of

A) introns.
B) exons.
C) repressors.
D) integrators.

Question 8

What is the difference between PCR and RT-PCR?

A) Only PCR makes many copies of DNA rapidly.
B) RT-PCR uses an RNA template whereas PCR uses a DNA template.
C) Only PCR produces cDNA.
D) PCR uses a single stranded template whereas RT-PCR uses a double-stranded template.

Question 9

Cosmids are a type of

A) bacterial artificial chromosomes (BACs).
B) cloning vector.
C) heat stable polymerase.
D) RNA/DNA hybrid.

Question 10

Which of the following is NOT a common step in molecular cloning using plasmids?

A) Fragment DNA into small segments.
B) Hybridize DNA sequences with slightly mismatched oligonucleotides.
C) Ligate DNA into vectors.
D) Insert the vectors into a host.

Question 11

Expression vectors are designed to ensure that ________ can be efficiently ________.

A) mRNA / transcribed
B) DNA / transcribed
C) mRNA / translated
D) DNA / translated

Question 12

Which of those listed below is LEAST similar in what is being studied and concluded?

A) fluorescence in situ hybridization
B) GFP fusion protein
C) Northern blot
D) RT-PCR

Question 13

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.

Question 14

Which of the following sequences is a palindrome, characteristic of many recognition sequences for restriction endonucleases?

A) TTGCCGA AACGGCT
B) GGGGGGG CCCCCCCC
C) GTAATG CATTAC
D) GAATTC CTTAAG

Question 15

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

Question 16

The genes encoding 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.

Question 17

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.

Question 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.

Question 19

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

Question 20

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.

Question 21

What is the first step in constructing a metagenomic library from RNA?

A) The RNA must be converted to cDNA.
B) The RNA must be amplified through PCR, producing many RNA copies.
C) The RNA must be screened to identify the genes of interest.
D) The RNA must be inserted into plasmid vectors.

Question 22

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

Question 23

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.

Question 24

If a protein that could be toxic to the expression host needs to be expressed in large quantities, then it is best to select an expression vector that

A) is not able to be replicated.
B) is inducible.
C) is attached to a normal cell promoter.
D) allows continual expression of the protein.

Question 25

One challenge in cloning human somatotropin is that

A) it consists of multiple polypeptides, making synthesis complex.
B) its gene cannot be cloned as cDNA.
C) it can only be expressed by eukaryotic cells.
D) it is susceptible to digestion by bacterial proteases because it is a small protein hormone.

Question 26

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

Question 27

The principle behind 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.

Question 28

Some proteins expressed at high levels form inclusions that are relatively insoluble. What is the most effective way to facilitate purification of these proteins?

A) Use a reporter gene to locate the inclusion.
B) Decrease the number of insertions in the vector.
C) Produce the protein as a fusion protein.
D) Switch to an expression host with a larger intracellular volume.

Question 29

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.

Question 30

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.

Question 31

It is possible to rapidly screen for mutations in regulatory genes using

A) gene fusions.
B) defective proteases.
C) microinjection.
D) Southern blotting.

Question 32

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.

Question 33

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.

Question 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 otherʹs 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.

Question 35

Using a host defective in proteases is likely to be necessary when

A) engineering a complete metabolic pathway requiring several different enzymes.
B) overproducing proteins.
C) producing a small protein.
D) engineering transgenic animals with immune systems.

Question 36

The Ti plasmid is best suited for genetically manipulating

A) Agrobacterium spp.
B) fish.
C) plants.
D) viruses.

Question 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 photographic

Question 38

Which of the following is NOT a limitation to using auxotrophs to prevent the spread of genetically modified genes to wild populations?

A) Auxotrophs may mutate in ways that allow them to synthesize the limiting nutrient.
B) Auxotrophs self-destruct using self-toxins when this method is applied.
C) Auxotrophs often cross-feed from the metabolites of other organisms in the environment.
D) Back mutation to the wild type may occur.

Question 39

Which process results in the production of a hybrid polypeptide?

A) vector fusion
B) operon fusion
C) protein fusion
D) translational fusion

Question 40

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.

Question 41

Strong promoters used for genetic manipulation are usually regulated by specific molecules.

Question 42

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.

Question 43

A common reporter protein is green fluorescent protein (GFP).

Question 44

Modification enzymes typically methylate specific bases within the recognition sequence to prevent digestion of the nucleotide sequence by restriction endonucleases.

Question 45

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

Question 46

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.

Question 47

An operon fusion has a transcriptional signal from one gene fused with the translational start and coding sequence from another.

Question 48

DNA polymerases from Escherichia coli cannot be used to artificially copy gene sequences with a thermocycler.

Question 49

What makes eukaryotic transcripts easier to isolate than bacterial transcripts?

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.

Question 50

One problem with both BACs and YACs is that genetic regions of these chromosomes cannot be subcloned.

Question 51

Developing vaccines for humans relies heavily on manipulating and engineering vectors.

Question 52

An effective way to introduce DNA into plant cells is using the Ti plasmid, which comes from a plant pathogen.

Question 53

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.

Question 54

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.

Question 55

One fundamental technique of genetic engineering includes the ability to cut DNA into random fragments.

Question 56

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

Question 57

Engineering a metabolic pathway enables a researcher to use different genes from unrelated organisms.

Question 58

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 host.

Question 59

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

Question 60

Genetically modified plants resistant to the herbicide glyphosphate contain a gene from Bacillus thuringiensis.

Question 61

Scientists produced a synthetic bacterium in 2010, but no one has yet produced an entire cell from scratch. How did the synthetic bacterium from 2010 compare with an entirely de novo cell, and what could be reasons that scientists might want to accomplish the latter?

Question 62

Describe the steps of gene cloning using a vector.

Question 63

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

Question 64

When trying to make a mammalian protein in a bacterium, expression vectors are often used.
Using your knowledge of prokaryotic and eukaryotic genetics, explain why expression vectors are so important.

Question 65

Describe a method developed by molecular biologists to easily observe the success of a genetic engineering procedure involving the ligating of a gene of interest into a plasmid.

Question 66

Explain how T7 promoters regulate transcription and why cloning vectors contain them.

Question 67

Defend why codon usage must be considered when cloning a gene into another organism.

Question 68

Describe three characteristics of an ideal cloning host for genetic engineering.

Question 69

PCR rapidly produces many copies of entire DNA molecules.

Question 70

What is necessary for a YAC to function as a normal eukaryotic chromosome?

Question 71

Describe the three main steps to clone a gene into an organism.

Question 72

What are some advantages and limitations of using biofuels, and why are genetically engineered microbes more useful for their production than naturally occurring microbes?

Question 73

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.

Question 74

Explain how eukaryotic genes can be used to produce proteins in a bacterial host. What steps are required?

Question 75

Explain how a metagenomic DNA library is created and what type of vector is needed.

Question 76

When is it appropriate to use an artificial chromosome vector? Describe a specific example.

Question 77

Explain why DNA fragments migrate toward the positive electrode and why some fragments migrate more rapidly than others during gel electrophoresis. How does this electronegativity influence observations and conclusions drawn from DNA migrated through an agarose gel?

Question 78

One method to circumvent issues with introns when expressing a eukaryotic gene in a bacterium is to simply clone the mature transcript.

Question 79

Compare how the process of cloning differs when a vector with sticky ends is used and when a vector with blunt ends is used.

Question 80

Create an experiment where you would use both a Southern blot and a Northern blot to determine if a newly isolated bacterium contains and actively uses the same catabolic pathway as previously demonstrated. What is the value in doing the Southern blot first? With results from these experiments, how would you conclude if the same pathway is active or not?