Deck 14: Molecular Genetic Analysis and Biotechnology

Question 1

All of the following are requirements of a bacterial cloning vector EXCEPT:

A)origin of replication.
B)unique restriction enzyme sites.
C)Ti plasmid.
D)selectable markers.
E)All of these are requirements of a bacterial cloning vector.

Answer 1

C

Question 2

The restriction enzyme Pst1 cleaves phosphodiester bonds between the G and the A nucleotides in its recognition sequence which is 5' CTGCAG 3' for one of the two DNA strands.After cutting by Pst1, the resulting DNA fragments will have:

A)3' single-stranded overhanging ends (end in a 3' group).
B)5' single-stranded overhanging ends.
C)blunt ends.
D)3' P groups.
E)both 5'single-stranded overhanging ends and 3' P groups.

Answer 2

3' single-stranded overhanging ends (end in a 3' group).

Question 3

Which of the following is a set of molecular techniques for locating, isolating, altering, and studying DNA segments?

A)DNA libraries
B)Gel electrophoresis
C)Gene cloning
D)Southern blotting
E)Recombinant DNA technology

Answer 3

E

Question 4

Antibodies are to Western blots as _____ are to Southern blots.

A)RNA
B)proteins
C)DNA
D)amino acids
E)both RNA and DNA

Question 5

How do bacteria that produce restriction enzymes protect their own DNA from the nuclease activity of these restriction enzymes?

A)They add methyl groups to their DNA.
B)They quickly ligate the sites that have been cut by the restriction enzymes.
C)They have extra DNA so the activity of the restriction enzymes does not matter.
D)They have long proteins that bind to their DNA, which protects it from being cut by the restriction enzymes.
E)They produce proteins that degrade their restriction enzymes.

Question 6

Which of the following is NOT true regarding the basic components required for a bacterial cloning vector?

A)Selectable markers provide a means for preferentially allowing growth of only those bacterial cells that have been transformed with the cloning vector.
B)Unique restriction enzyme sites allow for pieces of foreign DNA to be inserted into the bacterial plasmid cloning vector that range in size from 20 kb to 50 kb.
C)Unique restriction enzyme sites provide a means for inserting the foreign DNA into the cloning vector at a specific, known, sequence site.
D)A bacterial origin of replication ensures that the plasmid is replicated while present within the bacterial cell.
E)Selectable markers provide a means for selecting cells that have been transformed with a recombinant plasmid.

Question 7

Which of the following is a TRUE statement?

A)DNA ligase forms hydrogen bonds between nucleotide bases.
B)DNA ligase can seal nicks between amino acids.
C)DNA ligase recognizes and cuts at specific sequences.
D)DNA ligase can be used for creating recombinant plasmids.
E)DNA ligase is a requirement of a sequencing reaction.

Question 8

Southern blotting is a technique used to transfer _____ to a solid medium.

A)DNA
B)RNA
C)protein
D)Two of the answers are correct.
E)All of the answers are correct.

Question 9

Which of the following can be used for genetic engineering in plants?

A)Ti plasmid
B)Restriction enzymes
C)Selectable markers
D)Ti plasmid and restriction enzymes are both correct.
E)All of the answers are correct.

Question 10

Which of the following is NOT a challenge of working at the molecular level?

A)Cells contain thousands of genes.
B)Individual genes cannot be seen.
C)It is not possible to transfer DNA in a stable form.
D)A genome can consist of billions of base pairs.
E)No physical features mark the beginning or end of a gene.

Question 11

Which of the following is NOT usually used as a cloning vector in bacteria?

A)Plasmid
B)Bacteriophage l
C)Agrobacterium Ti plasmid
D)Bacterial artificial chromosome
E)Cosmid

Question 12

A new restriction enzyme has been discovered in a bacterium.When a sample of DNA is cleaved with this restriction enzyme, it is found that the resulting DNA fragments average about 256 nucleotides in length.What is the likely size of the DNA sequence recognized by this restriction enzyme?

A)Three nucleotides
B)Four nucleotides
C)Five nucleotides
D)Six nucleotides
E)At least 10 nucleotides

Question 13

Which of the following is NOT a step in the Southern blotting procedure?

A)Digestion of the DNA with a restriction enzyme
B)Ligation of the DNA into a vector
C)Separation of the DNA fragments on a gel
D)Transfer of the DNA fragments to a nitrocellulose membrane
E)Hybridization of the membrane-bound DNA with a labeled probe

Question 14

Which of the following would be MOST appropriate for cloning a gene that is 225 kb in size?

A)Plasmid
B)Cosmid
C)Phage lambda
D)BAC
E)Yeast phage

Question 15

Which of the following is NOT correct regarding the restriction enzymes that are used in biotechnology?

A)They can create blunt ends.
B)They make double-stranded cuts in DNA.
C)They recognize specific sequences and make cuts farther away from the recognition sequence.
D)They are named based on their bacterial origin.
E)They often recognize target sequences of four or six nucleotides

Question 16

Gel electrophoresis can be used to separate DNAs on the basis of:

A)size.
B)sulfur groups.
C)nucleotide content.
D)the probe used.
E)both size and sulfur group.

Question 17

Which of the following represents an appropriate cloning vector for cloning a gene into a bacterial cell?

A)YAC
B)Ti plasmid
C)Plasmid
D)Agrobacterium tumefaciens
E)lacZ

Question 18

You are interested in a particular segment of rhinoceros DNA and would like to clone it into a cloning plasmid.You have the following restriction map of the region that includes the DNA of interest and the plasmid (E = EcoRI, H = HindIII, X = XbaI, S = SphI, N = NotI). Which restriction enzymes would you choose to clone the DNA of interest into the cloning vector?

A)E and H
B)S
C)X and N
D)S and N
E)S and X

Question 19

During gel electrophoresis, large DNA fragments will _____ small DNA fragments.

A)migrate more rapidly than
B)migrate at the same speed as
C)migrate more slowly than
D)cause degradation of
E)separate into

Question 20

What is the purpose of Taq polymerase in a PCR reaction?

A)DNA denaturation
B)Primer annealing
C)DNA synthesis
D)Heating of the reaction
E)All of these are associated with Taq polymerase.

Question 21

Which of the following is NOT true regarding the differences between a genomic and cDNA library?

A)Genomic libraries contain fewer restriction enzyme sites, whereas cDNA libraries contain many more.
B)A genomic library is prepared from total genomic DNA, whereas a cDNA library is prepared from mRNA.
C)Genomic libraries contain much more sequence information and are much larger than cDNA libraries.
D)Genomic libraries contain coding and noncoding (regulatory, intron, etc.)sequences, whereas cDNA libraries contain only coding sequences along with their associated 5' and 3' untranslated regions.
E)cDNA libraries are generated from mRNAs, whereas genomic libraries are not.

Question 22

Restriction site sequences for six restriction enzymes are shown below.The "|" symbol shows the site at which the sequence is cut."N" is any nucleotide, "Pu" is any purine, and "Py" is any pyrimidine.Which of these enzymes would create blunt ends rather than "sticky" single-stranded ends?

A)BstEII G|GTNACC
B)DraI TTT|AAA
C)HaeII PuGCGC|Py
D)HhaI GCG|C
E)EcoRI G|AATTC

Question 23

The lungfish Protopterus aethiopicus has a genome 38 times larger than that of humans.Most of the DNA in this species is noncoding repetitive DNA.What type of library would be more efficient to use if you wish to compare the expressed regions of genes in the lungfish to those in humans?

A)cDNA library
B)PCR library
C)Genomic library
D)Knockout library
E)Transgenic library

Question 24

What is the function of dideoxynucleotides in Sanger DNA sequencing?

A)They act as primers for DNA polymerase.
B)They act as primers for reverse transcriptase.
C)They cut the sequenced DNA at specific sites.
D)They allow only the specific sequencing of the RNAs of a genome.
E)They stop synthesis at a specific site, so the base at that site can be determined.

Question 25

Which of the following statements is NOT correct?

A)Coding sequences for gene products can be isolated from cDNA libraries.
B)Antibodies are used for Northern blot analysis.
C)The number of STR copies is variable throughout human populations.
D)PCR amplification generates large numbers of linear DNA fragments.
E)RNA molecules can be used as hybridization probes in Southern blot analysis.

Question 26

A scientist mutates a gene in yeast and then looks to see what effect the mutation has on the phenotype in yeast.This is an example of:

A)DNA fingerprinting.
B)next-generation sequencing.
C)transgenic research.
D)reverse genetics.
E)positional cloning.

Question 27

You identify an RFLP in mice by digesting genomic DNA with HindIII enzyme and radiolabeling a piece of probe DNA.Southern blot analysis shows that the probe detects a 2-kb fragment in one strain of mice and a 4-kb fragment in another strain of mice.The two mice strains are crossed to produce an F₁ generation.Two F₁ siblings are mated to produce a dozen F₂ progeny.You isolate genomic DNA from several F₁ and F₂ individuals, digest with HindIII, and perform a Southern blot with the same probe. How many bands would be seen in the Southern blot of an F₂ individual?

A)1
B)2
C)3
D)4
E)Two of the answers are possible.

Question 28

Which of the following is NOT part of the normal process of cloning recombinant DNA in bacteria?

A)Restriction digestion of cellular and plasmid DNA
B)Production of recombinant DNA using DNA ligase and a mixture of digested cellular and plasmid DNAs
C)Separation of recombinant DNAs by electrophoresis using Southern blotting to determine where the desired recombinant molecule migrates
D)Transformation of bacteria by the recombinant DNA plasmids using a selective medium
E)Probing recombinant clones with a labeled DNA probe to find the desired clone

Question 29

Arabidopsis thaliana has one of the smallest genomes among higher plants with a haploid genome size of about 100 million base pairs.If this genome is completely digested with the restriction enzyme NotI that has an eight-base recognition sequence, approximately how many DNA fragments per genome will be produced?

A)22, 540
B)65, 535
C)4, 096
D)1526
E)125

Question 30

Before sequencing, the DNA fragment was cloned into a plasmid.On the strand that acted as the template in the sequencing reaction, what base of the cloned fragment was CLOSEST to the primer?

A)G
B)A
C)C
D)T
E)G or T

Question 31

Dideoxy nucleotides that are used in DNA sequencing experiments terminate DNA synthesis because they:

A)cannot be recognized by DNA polymerases and therefore not incorporated during synthesis.
B)have methyl groups attached to the 5'position of the sugar and can't be incorporated during synthesis.
C)are only recognized by reverse transcriptases.
D)have no 3'-OH group and so no additional nucleotides can be added to them after they are incorporated.
E)have no phosphate groups.

Question 32

Which of the following is NOT used in DNA sequencing by the dideoxy method?

A)DNA polymerase
B)Nucleoside triphosphates (NTPs)
C)Dideoxynucleoside triphosphates
D)Ligase
E)Single-stranded DNA template

Question 33

In using a cloning vector with a multiple cloning site spliced into the front part of the lacZ gene, production of beta-galactosidase, as shown by the blue color when grown on Xgal, indicates that:

A)an insert has been placed into the multiple cloning site.
B)the cells are antibiotic sensitive.
C)the cells lack plasmids.
D)the cells have not been successfully transformed.
E)there is no insert in the multiple cloning site.

Question 34

From what cellular molecules are cDNAs for cDNA libraries derived?

A)mRNAs
B)Proteins
C)Antibodies
D)Nucleases
E)Microsatellites

Question 35

The DNA strand 3'0-GACTATTCCGACCC-5' is being sequenced using the dideoxy method.One reaction mixture contains all four deoxynucleoside triphosphates (dATP, dTTP, dCTP, dGTP)and a small amount (10%)of dideoxythymidine (ddTTP).After synthesis is completed, what sized bands will appear in the gel? (Assume that the primer is present but not counted in the size of any of the bands.)

A)2-bp, 5-bp, and 11-bp bands
B)2-bp, 11-bp, 12-bp, 13-bp, and 14-bp bands
C)4-bp band only
D)4-bp, 6-bp, and 7-bp bands
E)1-bp, 2-bp, 3-bp, and 4-bp bands

Question 36

You identify an RFLP in mice by digesting genomic DNA with HindIII enzyme and radiolabeling a piece of probe DNA.Southern blot analysis shows that the probe detects a 2000 bp fragment in one strain of mice and a 4-kb fragment in another strain of mice.The two mice strains are crossed to produce an F₁ generation.Two F₁ siblings are mated to produce a dozen F₂ progeny.You isolate genomic DNA from several F₁ and F₂ individuals, digest with HindIII, and perform a Southern blot with the same probe. How many bands would be seen in the Southern blot of an F₁ individual?

A)1
B)2
C)3
D)4
E)Two of the answers are possible.

Question 37

One technique for finding a gene of interest involves first generating a genetic map to find the general location of the gene, and then identifying the specific location of the gene.What is this technique called?

A)Next-generation sequencing
B)DNA fingerprinting
C)Positional cloning
D)In silico gene discovery
E)Site-directed mutagenesis

Question 38

Which of the following BEST describes knockout mice?

A)They have a gene of interest that has been fully disabled.
B)They have lower expression levels of a gene of interest.
C)They have higher expression levels of a gene of interest.
D)They have a point mutation in the gene of interest.
E)They have a gene removed which results in lowered fertility.

Question 39

A fragment of DNA is cloned into a plasmid with a sequencing primer-binding site.After dideoxy sequencing, the gel pattern shown in this diagram is obtained.What was the sequence of the DNA strand that acted as the template in the sequencing reaction?

A)5' GCTAGCA 3'
B)5' ACGATCG 3'
C)5' TGCTAGC 3'
D)5' CGATCGT 3'
E)None of the answers is correct.

Question 40

Which of the following is false of DNA sequences within a cDNA library?

A)They do not contain exons.
B)They do not contain introns.
C)They do not contain promoters.
D)They do not contain enhancers.
E)They are produced from mRNAs.

Question 41

What are CRISPR RNAs?

A)Small RNAs associated with nucleases that cut DNA at defined sites
B)Large RNAs found in eukaryotes that inhibit gene expression at specific locations
C)Small RNAs that are often used as primers in PCR experiments
D)Large RNAs found in eukaryotes that prevent infection by certain viruses that have a RNA genome
E)Small RNAs found in eukaryotes that are complementary to highly repeated DNA sequences

Question 42

Which of the following remains a problem of gene therapy?

A)To date, there has not been a case of gene therapy curing a disease.
B)We have yet to develop a vector for delivering the gene.
C)Patients mount immune responses to the transferred gene and vectors.
D)We do not have the ability to use somatic gene therapy at this time.
E)We can only alter germ-line cells at this time.

Question 43

A cDNA encoding a protein that is specific for a particular strain (strain Q)of bacteria has been cloned.How would you determine whether an infection contains this particular bacterial strain?

Question 44

Cronin et al.(Science, 2009, 325: 340-343)used RNA interference to study the immune response of the fruit fly, Drosophila melanogaster, to the bacterial pathogen, Serratia marcescens.They identified several members of the JAK-STAT cell-cell signaling pathway in their analysis.
a.The PIAS gene is a negative regulator of JAK-STAT signaling (that is, it inhibits the signaling pathway).RNAi to block PIAS activity causes flies to die significantly earlier than control flies when exposed to bacteria.Does JAK-STAT signaling appear to protect the flies from the bacteria? Explain.
b.The upd gene encodes a ligand that activates JAK-STAT signaling.RNAi that blocks upd function causes flies to survive longer than control flies when exposed to bacteria.Explain how this is or is not consistent with your answer from part a.

Question 45

You are trying to determine whether a certain RFLP marker is linked to a specific disease gene in dogs.A cross between a diseased male and a healthy female produces nine offspring.You isolate genomic DNA from parents and offspring, digest with EcoRI, radiolabel a portion of RFLP marker to use as a probe, and perform a Southern analysis.The pedigree and autoradiogram results are shown in the following figure.Assume that the disease is an autosomal dominant. a.Explain the relationship between the crossing results (i.e., diseased versus healthy)and the RFLP patterns.
b.How would you explain the results seen for the second male puppy?

Question 46

You are given a plasmid containing a part of a gene of Drosophila melanogaster.The gene fragment is 303 base-pairs long.You would like to amplify it using PCR.You design oligonucleotide primers 19 nucleotides in length that are complementary to the plasmid sequences immediately adjacent to both ends of the cloning site.What would be the exact length of most of the resulting PCR product in base pairs?

A)303
B)38
C)341
D)322
E)265

Question 47

What is the technique that can be used to determine the size of a particular protein and its pattern of expression?

A)PCR
B)Forward genetics
C)Northern blotting
D)Autoradiography
E)Western blotting

Question 48

The haploid human genome contains about 3 × 10⁹ nucleotides.On average, how many DNA fragments would be produced if this DNA was digested with restriction enzyme PstI (a 6-base cutter)? RsaI (a 4-base cutter)? How often would an 8-base cutter cleave?

Question 49

Which of the following is NOT a potential benefit of using transgenic plants?

A)They can reduce the use of harmful chemical pesticides in the United States, and thus provide an ecological benefit.
B)They can generate restriction enzyme sites on a foreign gene of interest to be cloned.
C)They often increase yields, providing more food per acre and reducing the amount of land needed for agricultural use.
D)They can allow crops to be grown on land previously unavailable for productive agricultural use.
E)They can be used to express large quantities of specific biological products more cheaply and quickly than by expression in animal systems.

Question 50

How might RNAi be used to treat diseases in humans?

A)siRNAs could be generated that would silence elevated levels of a harmful gene.
B)An RNAi library could be generated for harmful genes that are expressed.
C)RNAi probes could bind to good genes, and thus increase their expression.
D)RNAi is a process that has the ability to amplify large amounts of therapeutic proteins.
E)RNAi is not a process that could work in humans, as it is a process found only in plants.

Question 51

You are attempting to determine whether a plant-derived processed food sample (for example, a corn chip)contains material from a transgenic organism.First, you crush the sample and attempt to extract DNA from it.Next, you perform PCR using two different sets of primers.One primer set will amplify a DNA sequence present in all plants.The second primer set will amplify a DNA sequence only found in transgenic plants.
a.Why must you use both sets of primers for this experiment?
b.You obtain the results shown in the panel below.What conclusions can you draw from these reaction results? Does this test sample contain genetically modified components? Why or why not? [Lanes 1-6 are the same as listed above.]

Question 52

A pedigree and Southern blot results in humans are shown in the following figure.Filled-in figures represent individuals expressing a dominant trait (hypothetical)for blue tongue.What can you say about the location of the allele responsible for the trait? Shaded regions within the homologs of an autosomal chromosome represent sequences that hybridize to the probe used for the Southern analysis.Arrows indicate cleavage sites used for the Southern analysis.

Question 53

Cloned eukaryotic genes are not always able to be expressed in bacterial cells.What is a possible reason for this?

Question 54

Explain what an RFLP is.Why do RFLPs behave like "codominant" markers?

Question 55

The full-length (i.e., containing the entire protein coding region)cDNA for a specific eukaryotic gene in humans is 1500 nucleotides long.You screen a pig genomic library with this cDNA and isolate two genomic clones of different lengths.Both clones are sequenced and found to be 1900 and 2100 nucleotides long, from start codon to stop codon.How would you explain the presence of two genomic clones in pigs, and the discrepancies in their length compared to the cDNA probe?

Question 56

Briefly define and compare knock-in mice and knockout mice.

Question 57

Which of the following is an example of reverse genetics?

A)A geneticist maps the location of mutations associated with strains of mice found to have heart defects.
B)A geneticist searches for naturally occurring mutations that affect the sleep cycle in breeds of dogs.
C)A geneticist runs a Southern blot to map the location of a mutant gene in a species of bacterium growing in a hot spring and then clones that mutant gene.
D)A geneticist experimentally creates a mutation in a gene of unknown function in Drosophila and then observes the mutant phenotype.
E)None of these is an example of reverse genetics.

Question 58

Figure A below shows a restriction map of a rare prokaryotic gene with its direction of transcription indicated by the arrow.Figure B shows the unique restriction sites contained within a plasmid-cloning vector.The blackened region in Figure A represents the amino acid coding sequence of a protein that can be used in humans as a vaccine.The stippled region in Figure B is a highly active, constitutive (unregulated)prokaryotic promoter region.Letters indicate the cleavage sites for different restriction enzymes.Known DNA sequences are indicated by short thick lines.Explain how you would isolate and then insert the coding region (Figure A)under the control of the indicated promoter in the cloning vector (FigureB)to produce large amounts of the protein in bacterial cells.Assume that the cloning vector carries the gene for tetracycline (an antibiotic)resistance.Letters represent different restriction enzymes.

Question 59

What is an expression vector, and what characteristics should it possess?

Question 60

What are some of the advantages in using the mouse as a model organism in genetic research?

Question 61

Which of the following statements about gene therapy in humans is FALSE?

A)A major problem with treatment can be an adverse immune response.
B)The vector may insert into a cancer-causing gene.
C)Genes have been inserted into reproductive tissue so that the children of the patient will also be helped.
D)Gene therapy has been used successfully to treat several children with X-linked adrenoleukodystrophy, a fatal disorder of the central nervous system.
E)Viruses are often used as vectors in gene therapy.

Question 62

Which of the following DNA sequences is NOT normally part of a bacterial expression vector?

A)A selectable genetic marker
B)A gene for a DNA polymerase
C)Transcriptional initiation sequences
D)An origin for DNA replication
E)Transcriptional termination sequences

Question 63

The restriction enzyme AcyI cuts duplex DNA at the sequence 5' GPuCGPyC 3'
3' CPyGCPuG 5'
Where Pu = either purine and Py = either pyrimidine.On average, what is the length of DNA fragments in base pairs created by this enzyme? (Assume that the four bases are found in equal frequencies in this DNA sample.)

A)48
B)512
C)4096
D)256
E)1024

Question 64

A geneticist wishes to study the genetic basis of proline biosynthesis in yeast.She first collects as many spontaneous and induced mutations that results, as much as possible, in the inability to synthesize proline.She then investigates the molecular basis for this inability in these mutants.What type of genetic analysis is the geneticist doing?

A)Reverse genetics
B)Positional cloning
C)Gene cloning
D)Forward genetics
E)Structural genomics

Question 65

What is the process by which MOST plasmid vectors carrying a cloned piece of DNA are taken up by host bacteria?

A)Transformation
B)Phage infection
C)Electroporation
D)Ligation
E)Restriction

Question 66

Which of the following statements about finding a particular gene in a gene library is TRUE?

A)Unless the DNA sequence of the desired gene is known, using an antibody specific for the gene product will not be useful.
B)A DNA probe for the desired gene does not need to be perfectly complementary to the gene of interest so DNA of an homologous gene from another species can sometimes be used as a probe.
C)Generally it is not possible to find a particular gene in a gene library unless it has been expressed; and, therefore, both mRNA and a protein product of the gene must be available to be analyzed.
D)It is almost impossible to find a desired gene in a gene library unless the library was made using a BAC vector.
E)If the gene is not expressed, it will not be possible to find a gene library using a nucleic acid probe.

Question 67

mRNA can be transferred from a gel to a solid support and then a probe can be utilized to determine the size and relative abundance of this mRNA.This procedure is called:

A)reverse genetics.
B)next-generation sequencing.
C)Northern blotting.
D)RNA fingerprinting.
E)autoradiography.

Question 68

The genome of Mycobacterium tuberculosis consists of a single circular chromosome that is 4, 410, 000 nucleotides in length and has a 66% (2/3)GC content.The MseI restriction enzyme cuts at a 5' TTAA 3' sequence (one DNA strand given).How many MseI sites should be present in this genome?

A)3403
B)17, 227
C)4307
D)256
E)12, 586

Question 69

The Federal Bureau of Investigation has developed the Combined DNA Index System (CODIS), which is 13 loci that are used to develop DNA fingerprints for crime solving.Which of the following characteristics is FALSE concerning these 13 loci?

A)They are unlinked so that variation at each locus can assort independently.
B)Alleles at each locus are analyzed with Southern blotting.
C)Each locus has multiple alleles.
D)When all 13 loci are used together, the probability that two randomly selected people will have the same DNA fingerprint is less than one in 10 billion.
E)The 13 loci are short tandem repeats (STRs).