Chapter 9 - DNA-Based Information Technologies
Chapter 9 - DNA-Based Information Technologies
Chapter 9 - DNA-Based Information Technologies
Restriction enzymes:
A) act at the membrane to restrict the passage of certain molecules into the cell.
B) are highly specialized ribonucleases that degrade mRNA soon after its synthesis.
C) are sequence-specific DNA endonucleases.
D) are very specific proteases that cleave peptides at only certain sequences.
E) catalyze the addition of a certain amino acid to a specific tRNA.
3. The size of the DNA region specifically recognized by Type II restriction enzymes is
typically:
A) 4 to 6 base pairs.
B) 10 to 15 base pairs.
C) 50 to 60 base pairs.
D) 200 to 300 base pairs.
E) about the size of an average gene.
5. Certain restriction enzymes produce cohesive (sticky) ends. This means that they:
A) cut both DNA strands at the same base pair.
B) cut in regions of high GC content, leaving ends that can form more hydrogen bonds
than ends of high AT content.
C) make a staggered double-strand cut, leaving ends with a few nucleotides of
single-stranded DNA protruding.
D) make ends that can anneal to cohesive ends generated by any other restriction
enzyme.
E) stick tightly to the ends of the DNA they have cut.
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6. In the laboratory, recombinant plasmids are commonly introduced into bacterial cells
by:
A) electrophoresis—a gentle low-voltage gradient draws the DNA into the cell.
B) infection with a bacteriophage that carries the plasmid.
C) microinjection.
D) mixing plasmids with an extract of broken cells.
E) transformation—heat shock of the cells incubated with plasmid DNA in the
presence of CaCl2.
7. The E. coli recombinant plasmid pBR322 has been widely utilized in genetic
engineering experiments. Which feature does pBR322 NOT have?
A) a number of conveniently located recognition sites for restriction enzymes
B) a number of palindromic sequences near the EcoRI site, which permit the plasmid
to assume a conformation that protects newly inserted DNA from nuclease
degradation
C) a replication origin, which permits it to replicate autonomously
D) resistance to two different antibiotics, which permits rapid screening for
recombinant plasmids containing foreign DNA
E) small overall size, which facilitates entry of the plasmid into host cells
9. A convenient cloning vector with which to introduce foreign DNA into E. coli is a(n):
A) E. coli chromosome.
B) messenger RNA.
C) plasmid.
D) yeast “ARS” sequence.
E) yeast transposable element.
10. Common features found in a cloning plasmid used for protein do NOT include:
A) a polylinker.
B) an origin of replication.
C) an antibiotic resistance marker(s).
D) a ribosome binding site.
E) telomeric ends.
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11. A(n) _____ would NOT used as a heterologous host for the expression of recombinant
proteins/
A) retrovirus
B) bacterium such as E. coli
C) eukaryote such as S. cerevisiae
D) insect cell
E) mammalian cell
12. _____ is NOT a commonly used tag for affinity purification of cloned proteins.
A) Glutathione-S-transferase
B) Maltose binding protein
C) Nickel
D) Protein A
E) Chitin-binding domain
14. Which statement about the polymerase chain reaction (PCR) is FALSE?
A) DNA amplified by PCR can be cloned.
B) DNA amplification is linear in magnitude.
C) Newly synthesized DNA must be heat-denatured before the next round of DNA
synthesis begins.
D) The boundaries of the amplified DNA segment are determined by the synthetic
oligonucleotides used to prime DNA synthesis.
E) The technique is sufficiently sensitive that DNA sequences can be amplified from a
single animal or human hair.
15. Which statement does NOT apply to the construction or use of a DNA library?
A) Determining the location of a particular DNA sequence in a DNA library requires a
suitable hybridization probe.
B) Genomic libraries are better for expressing gene products than cDNA libraries.
C) Many segments of DNA from a cellular genome are cloned.
D) Specialized DNA libraries can be made by cloning DNA copies of mRNAs.
E) The DNA copies of mRNA found in a cDNA library are made by reverse
transcriptase.
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16. Which compound is NOT needed to build a cDNA library?
A) genomic DNA
B) mRNA
C) reverse transcriptase
D) dNTPs
E) DNA polymerase
17. Which analytical technique does NOT help illuminate a gene's cellular function?
A) DNA microarray analysis
B) protein chip analysis
C) Southern blotting
D) two-dimensional gel electrophoresis
E) two-hybrid analysis
18. The technique known as two hybrid analysis for detecting interacting gene products
depend on:
A) activation of DNA polymerase by the nearby binding of hybridizing protein
complexes.
B) direct binding of a Gal4p activation domain to a DNA sequence in the promoter
region.
C) having a promoter that responds directly to one of the two proteins whose
interactions is being measured.
D) hybridization of DNA segments corresponding to the two genes being examined.
E) stimulation of transcription by interaction of two Gal4p domains via fused protein
sequences.
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21. Current estimates indicate that humans have about _____ genes.
A) 3,000
B) 10,000
C) 30,000
D) 100,000
E) 300,000
22. Current estimates indicate that _____% of the human genome is translated into protein.
A) less than 0.5
B) roughly 1.5
C) roughly 10
D) roughly 25
E) more than 50
23. Which list ranks the organisms in order from smallest genome (number of base pairs of
DNA) to largest genome?
A) Human, fruit fly, E. coli bacterium
B) E. coli bacterium, human, fruit fly
C) E. coli bacterium, fruit fly, human
D) fruit fly, E. coli bacterium, human
E) fruit fly, human, E. coli bacterium
24. Which type of DNA sequence is NOT found in the human genome?
A) long repetitive repeats
B) introns
C) retro-palindromes
D) simple sequence repeats
E) transposons
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26. Which DNA sequence is a palindrome?
A) AATGCC
B) GGATCC
C) GATATG
D) CCCGCG
E) AGTAGT
27. Which restriction endonuclease cuts DNA in a way that leaves blunt ends?
A) EcoRI
B) HindIII
C) BamHI
D) EcoRV
E) PstI
28. Which statement regarding Type I and Type II restriction endonucleases is NOT
accurate?
A) Type I endonucleases cleave DNA at random sites.
B) Type II endonucleases recognize small (4–6 bp) palindromic sequences.
C) Type II endonucleases always make staggered cuts in DNA strands.
D) Type I endonucleases require ATP.
E) Type I endonucleases are generally large, multisubunit complexes.
29. When cloning a gene into a plasmid, which enzyme would you use to covalently attach
the gene to the plasmid DNA?
A) DNA polymerase
B) exonuclease III
C) DNA Ligase
D) alkaline phosphatase
E) a restriction endonuclease
30. If you want to clone a gene by using E. coli and then transfer that cloned gene into yeast
to express the protein the gene encodes, what type of self-replicating DNA should you
use for your cloning process?
A) a bacmid
B) a plasmid
C) a yeast artificial chromosome
D) a shuttle vector
E) a bacterial artificial chromosome
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31. A good cloning vector should NOT have:
A) an origin of replication.
B) an antibiotic resistance gene.
C) several unique restriction sites.
D) a small size.
E) genes allowing its insertion into the host chromosome.
32. Which amino acid when repeated six to ten times at the N- or C-terminal ends of a
protein allows that protein to bind to Ni2+ ions?
A) Glu
B) His
C) Ala
D) Tyr
E) Asp
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36. A good expression vector for protein expression in E. coli should have which feature(s)?
A) an origin of replication
B) a selectable marker
C) a promoter, operator, and ribosome-binding site
D) All of the answers are correct.
E) None of the answers is correct.
37. Common problems with expression of eukaryotic proteins in bacteria may include
proteins:
A) aggregating into inclusion bodies.
B) not folding correctly due to absence of chaperones.
C) not undergoing posttranslational modification.
D) All of the answers are correct.
E) None of the answers is correct.
38. If you wanted to clone a large fragment of DNA into a unicellular eukaryotic host, what
would you use?
A) a bacmid
B) a plasmid
C) a bacterial artificial chromosome
D) a yeast artificial chromosome
E) a virus
39. If you wanted to create specific DNA sequence changes to a plasmid in the coding
sequence for a protein you are researching, but there are no suitably located restriction
sites nearby, which technique would you use?
A) error-prone PCR
B) site-directed mutagenesis
C) oligonucleotide-directed mutagenesis
D) exposing the plasmid DNA to UV light
E) exposing the cells containing the plasmid DNA to chemical mutagens
40. Which technique can be used to estimate the relative copy numbers of particular DNA
sequences in a sample?
A) reverse transcriptase PCR
B) quantitative PCR
C) some gel based analysis such as with the Bioanalyzer and Fragment Analyzer gel
band density are used in calculating concentration in a lot of labs.
D) normal PCR
E) in vitro transcription
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41. To make an DNA copy of a RNA sequence, you need the reverse transcriptase enzyme
and an oligonucleotide primer made of which nucleotide?
A) deoxyadenosine
B) deoxythymine
C) deoxycytosine
D) deoxyuridine
E) deoxyguanosine
42. If you want to express two different genes on different plasmids in a bacterial host,
which procedure will NOT be successful?
A) using plasmids that have the same promoter sequence
B) using EcoRI and BamHI restriction endonucleases to clone the genes into their
respective plasmids
C) placing different fusion tags on each of the genes when cloning them
D) using plasmids with the same origin of replication
E) using plasmids that have different selectable markers
43. Which factor is required to accurately determine the relative amount of gene expression
of two or more genes in an organism using qPCR?
A) a “no template” control
B) an oligonucleotide probe labeled with a fluorophore and a quenching molecule at
its ends
C) use of reverse transcriptase to copy the RNA products into DNA
D) All of the answers are correct.
E) None of the answers is correct.
45. The biochemical activity of a protein, such as its enzymatic activity, is called its _____
function.
A) phenotypic
B) genotypic
C) cellular
D) molecular
E) organismal
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46. Genes that have sequence and functional relationships to each other within a single
species are called:
A) orthologs.
B) paralogs.
C) analogs.
D) homologs.
E) lincolnlogs.
47. The gene for green fluorescent protein was originally isolated from which species?
A) a panda
B) a firefly
C) a mushroom
D) a jellyfish
E) a glowworm
48. What common protein tertiary structure does green fluorescent protein contain?
A) an helix
B) a barrel
C) a coiled coil
D) a Greek key
E) a four-helix bundle
49. Which method of visualizing a protein's location should you use if you want to
determine its location in a living cell?
A) a GFP fusion tag
B) immunofluorescence
C) qPCR
D) Gram stain
E) affinity purification
50. If you want to determine what other proteins might be interacting with the protein you
have been studying, what type of fusion tag would you add to your protein to aid in
purification of both the protein you have been studying and the proteins interacting with
it?
A) a green fluorescent protein fusion tag
B) a tandem affinity purification tag
C) a maltose-binding protein tag
D) an epitope tag
E) a -galactosidase tag
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51. A method of determining if proteins are interacting in vivo that makes use of a
transcription factor involved in regulating galactose metabolism genes is:
A) a DNA microarray.
B) yeast two-hybrid analysis.
C) tandem affinity purification.
D) immunofluorescence.
E) quantitiative PCR.
52. A method of comparing the relative gene expression of all the genes in an organism at
two different stages of its development is:
A) a DNA microarray.
B) yeast two-hybrid analysis.
C) tandem affinity purification.
D) immunofluorescence.
E) quantitiative PCR.
53. If you are comparing the total gene expression of a black panther during its early
development and later adult life and have labeled the cDNA you obtained from its early
development stages with a green fluorophore and the cDNA you obtained from its adult
life stages with a red fluorophore, what color would you expect to see on your DNA
microarray for genes that are equally expressed in both the early development and adult
life stages?
A) green
B) red
C) yellow
D) brown
E) magenta
54. Which protein forms a complex with a guide RNA to target DNA for cleavage and
destruction?
A) RecA
B) Cas9
C) EcoRI
D) Gal4p
E) GST
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55. If you wanted to study the effects of inactivating a specific gene on development of a
mouse, which technique or system would you use to inactivate that gene?
A) transfection
B) CRISPR/Cas9
C) tandem affinity purification
D) yeast two-hybrid
E) oligonucleotide-directed mutagenesis
56. Conserved gene order observed in the chromosomes of two distantly related organisms
provides evidence of a(n) _____ relationship between genes.
A) orthologous
B) homologous
C) paralogous
D) analogous
E) genologous
57. The fluorophore in GFP is derived from covalent modifications of which structures
located at the interior of the protein?
A) coenzymes
B) amino acids
C) prosthetic groups
D) metal ions
E) nucleotides
58. What is a significant problem with regard to making cDNA libraries to analyze overall
gene function in an eukaryotic organism?
A) A cDNA library will only contain genes that are actively transcribed in the
organism.
B) Reverse transcriptase cannot be used to make cDNA libraries.
C) cDNA cannot be amplified by PCR.
D) cDNA libraries do not contain intron sequences.
E) cDNA libraries may contain several alternatively spliced forms of the same gene.
59. Which type of organism do you NOT expect to express functionally fluorescent GFP?
A) an obligate aerobe
B) a multicellular eukarotic organism
C) a facultative anaerobe
D) an obligate anaerobe
E) a unicellular eukaryotic organism
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60. If you want to determine which proteins might be interacting in a cell, which technique
would you use to examine the interaction in a living cell?
A) yeast two-hybrid analysis
B) immunoprecipitation
C) a DNA microarray
D) immunofluorescence
E) comparative genomics
62. Approximately how much of the human genome encodes the exons of protein-coding
sequences?
A) 1.5%
B) 5%
C) 30%
D) 100%
E) 80%
63. Groups of single nucleotide polymorphisms that are usually inherited together from one
parent are called:
A) genotypes.
B) haplotypes.
C) phenotypes.
D) karyotypes.
E) cytotypes.
64. Due primarily to single nucleotide polymorphisms, each human differs from every other
human, on average, by what percentage of the human genome?
A) 6%
B) 15%
C) 0.1%
D) 98%
E) 1.5%
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65. Which repeating sequences in the human genome are the targets of technologies used in
forensic DNA analysis?
A) simple-sequence repeats
B) single nucleotide polymorphisms
C) introns
D) short tandem repeats
E) long repetitive sequences
66. Chimpanzees and humans differ by approximately how much due to transposons,
base-pair changes, and chromosome segment duplications and rearrangements across
their entire genomic sequences?
A) 1.5%
B) 4%
C) 95%
D) 10%
E) 0.1%
68. Especially stable haplotypes exist in which portions of the human genome due to their
relative lack of meiotic recombination?
A) the Y chromosome
B) the X chromosome
C) the mitochondrial genome
D) both the Y chromosome and the mitochondrial genome
E) both the X chromosome and the mitochondrial genome
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69. The process of linkage analysis does NOT rely on which technique to determine the
genetic causes of diseases?
A) analysis of family pedigrees
B) identification of SNPs that are most often inherited with the disease-causing gene
C) the sequence of the entire chromosome where the disease-causing gene is located
to directly identify it
D) comparing the DNA of people who have the disease with the DNA of people who
don't have the disease
E) obtaining many sequences of a region of the chromosome that is associated with
the disease
70. During their multiple migrations from Africa to the rest of the world, gene flow likely
occurred between which populations of early humanoids?
A) between Neanderthals and modern humans
B) between Denisovans and modern humans
C) between Neanderthals and Denisovans
D) All of the answers are correct.
E) None of the answers is correct.
72. If you wanted to compare the sequence of a gene you isolated in the laboratory with a
database of other genetic sequences, which tool would you use?
A) linkage analysis
B) BLAST
C) forensic DNA analysis
D) haplotype identification
E) quantitative PCR
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73. You are comparing the DNA sequences of several species with a shared evolutionary
ancestry. Species 1 has a sequence of ATGCCA, species 2 has a sequence of ATACCA,
species 3 has a sequence of ATACTA, species 4 has a sequence of ACACTG, and
species 5 has a sequence of ATGCCA. Which species is an outgroup compared with all
the others?
A) species 1
B) species 2
C) species 3
D) species 4
E) species 5
74. Mutations in which genetic sequences are NOT likely to have a phenotypic effect?
A) noncoding RNAs
B) exons
C) interspersed nuclear elements
D) All of the answers are correct.
E) None of the answers is correct.
75. For what reason is the mitochondrial genome and the Y chromosome the easiest
portions of human DNA to use to trace human evolutionary lineages?
A) All human cells have mitochondria and Y chromosomes.
B) Mitochondrial DNA and the Y chromosome do not undergo significant meiotic
recombination.
C) The size of the mitochondrial genome and the Y chromosome is small.
D) Mitochondrial DNA and the Y chromosome exhibit very unstable haplotypes.
E) Mitochondrial DNA is inherited along both the male and female human
evolutionary. lineages
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77. A plasmid that encodes resistance to ampicillin and tetracycline is digested with the
restriction enzyme PstI, which cuts the plasmid at a single site in the
ampicillin-resistance gene. The DNA is then annealed with a PstI digest of human
DNA, ligated, and used to transform E. coli cells. (a) What antibiotic would you put in
an agar plate to ensure that the cells of a bacterial colony contain the plasmid? (b)
What antibiotic-resistance phenotypes will be found on the plate? (c) Which phenotype
will indicate the presence of plasmids that contain human DNA fragments?
78. Explain how each of the following is used in cloning in a plasmid: (a)
antibiotic-resistance genes; (b) origin of replication; (c) polylinker region.
79. Match each feature of the plasmid pBR322 (at left) with one appropriate description
presented (at right) (see illustration of pBR322 below). Descriptions may be used more
than once.
____ ampR sequence (a) Permits selection of bacteria containing the plasmid.
____ ori sequence (b) A sequence required for packaging recombinant plasmids
____ tetR into bacteriophage.
____ BamHI sequence (c) Origin of replication.
____ PstI sequence (d) Cleavage of the plasmid here does not affect antibiotic
sequence resistance genes.
(e) Insertion of foreign DNA here permits identification of
bacteria containing recombinant plasmids .
80. Explain briefly the properties of the plasmid pBR322 that make it so convenient as a
vector for cloning fragments of foreign DNA.
81. When bacterial artificial chromosomes (BACs) are used as cloning vectors, what size of
DNA fragment can be cloned?
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82. How does a bacterial artificial chromosome (BAC) differ from a plasmid?
84. What sequences are required in an expression vector (for use with E. coli) that are NOT
essential in a cloning plasmid?
86. List three different heterologous expression systems and include one advantage and one
disadvantage for each.
87. A DNA sequence that may be present as only a single copy in a large mammalian
genome can be amplified and cloned using the polymerase chain reaction (PCR).
Describe the steps and reaction components required in a PCR experiment. Illustrate
the steps in just one round.
88. What happens in PCR if you use DNA polymerase derived from E. coli instead of from
a thermostable source?
89. What is the essential difference between a genomic library and a cDNA library?
90. Distinguish between protein function at the molecular, cellular, and phenotypic level.
91. Name one enzyme that is always used to make a cDNA library but is generally not used
to make a genomic DNA library. Describe its function briefly.
92. Name two different methods by which protein-protein interactions can be discovered
and probed.
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93. Explain why a probe designed to detect a gene encoding a particular amino acid
sequence must usually consist of a mixture of different DNA sequences rather than only
one sequence.
94. What is a DNA microarray? How does it resemble and how does it differ from a DNA
library?
96. Which would you expect to be larger, the percentage of the human genome that is
translated into protein or the percentage of the genome of a bacterium that is translated
into protein? Why?
98. As the cost of sequencing your personal human genome rapidly approaches $1,000,
consider the benefits and risks of having every fetus' DNA sequenced before birth.
99. Describe the difference between selectable markers and screenable markers and their
use in cloning experiments.
100. Describe how the CRISPR/Cas9 system is used to inactivate a gene during the process
of genomic engineering.
102. Diagram a phylogenetic tree to show the relationship between several sequences from
the same gene in different organisms. The sequences are GAACTA, GGATTA,
AGATCA, GGACTA, and AGATTA.
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Answer Key
1. C
2. B
3. A
4. D
5. C
6. E
7. B
8. E
9. C
10. E
11. A
12. C
13. C
14. B
15. B
16. A
17. C
18. E
19. B
20. D
21. C
22. B
23. C
24. C
25. D
26. B
27. D
28. C
29. C
30. D
31. E
32. B
33. D
34. B
35. E
36. D
37. D
38. D
39. C
40. B
41. B
42. D
43. D
44. A
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45. D
46. B
47. D
48. B
49. A
50. B
51. B
52. A
53. C
54. B
55. B
56. A
57. B
58. A
59. D
60. A
61. D
62. A
63. B
64. C
65. D
66. B
67. D
68. D
69. C
70. D
71. C
72. B
73. D
74. C
75. B
76. B
77.
78.
79.
80.
81.
82.
83.
84.
85.
86.
87.
88.
89.
90.
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91.
92.
93.
94.
95.
96.
97.
98.
99.
100.
101.
102.
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