Chapter 9 DNA-Based Information Technologies
Multiple Choice Questions
1. Studying genes and their products
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.
2. Studying genes and their products
The biological role of restriction enzymes is to:
A) aid recombinant DNA research.
B) degrade foreign DNA that enters a bacterium.
C) make bacteria resistant to antibiotics.
D) restrict the damage to DNA by ultraviolet light.
E) restrict the size of DNA in certain bacteria.
3. Studying genes and their products
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.
4. Studying genes and their products
Which of the following statements about type II restriction enzymes is false?
A) Many make staggered (off-center) cuts within their recognition sequences.
B) Some cut DNA to generate blunt ends.
C) They are part of a bacterial defense system in which foreign DNA is cleaved.
D) They cleave and ligate DNA.
E) They cleave DNA only at recognition sequences specific to a given restriction enzyme.
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5. Studying genes and their products
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.
6. Studying genes and their products
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. Studying genes and their products
The E. coli recombinant plasmid pBR322 has been widely utilized in genetic engineering
experiments. pBR322 has all of the following features except:
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.
8. Studying genes and their products
Which of the following statements regarding plasmid-cloning vectors is correct?
A) Circular plasmids do not require an origin of replication to be propagated in E. coli.
B) Foreign DNA fragments up to 45,000 base pairs can be cloned in a typical plasmid.
C) Plasmids do not need to contain genes that confer resistance to antibiotics.
D) Plasmid vectors must carry promoters for inserted gene fragments.
E) The copy number of plasmids may vary from a few to several hundred.
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9. Studying genes and their products
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. Studying genes and their products
Common features found in a cloning plasmid used for protein expression include all except which of
the following?
A) Polylinker
B) Origin of replication.
C) Antibiotic resistance marker(s)
D) Ribosome binding site
E) Telomeric ends
11. Studying genes and their products
Which of the following is not used as a heterologous host for the expression of recombinant proteins?
A) Retroviruses
B) Bacteria such as E. coli
C) Eukaryotes such as S. cerevisiae
D) Insect cells
E) Mammalian cells
12. Studying genes and their products
Which of the following 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
13. Studying genes and their products
The PCR reaction mixture does not include:
A) all four deoxynucleoside triphosphates.
B) DNA containing the sequence to be amplified.
C) DNA ligase.
D) heat-stable DNA polymerase.
E) oligonucleotide primer(s).
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14. Studying genes and their products
Which of the following statements 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. Using DNA-based methods to understand protein function
Which of the following 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.
16. Using DNA-based methods to understand protein function
Which of the following is not needed to build a cDNA library?
A) Genomic DNA
B) mRNA
C) Reverse transcriptase
D) dNTPs
E) DNA polymerase
17. Using DNA-based methods to understand protein function
Which one of the following analytical techniques 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
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18. Using DNA-based methods to understand protein function
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.
19. Using DNA-based methods to understand protein function
Which of the following tags is not used to study protein function?
A) Green fluorescent protein (GFP)
B) Synteny tag
C) Tandem affinity purification (TAP)
D) Gal4p DNA binding domain
E) Gal4p activation domain
20. Genomics and the human story
Which of the following is not needed in 454 pyrosequencing of DNA?
A) dNTPs
B) Sulfurylase
C) Luciferase
D) ddNTPs
E) Apyrase
21. Genomics and the human story
Current estimates indicate that humans have about ________ genes.
A) 3,000
B) 10,000
C) 30,000
D) 100,000
E) 300,000
22. Genomics and the human story
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%
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23. Genomics and the human story
Rank the following 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. Genomics and the human story
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
25. Genomics and the human story
Which of the following methods is not used in linkage analysis?
A) Compare densely spaced polymorphisms.
B) Collect DNA from a family affected by the disease of interest.
C) Sequence selected parts of the genome.
D) Introduce retroviruses at the mutated locus.
E) Look for SNP variants.
Short Answer Questions
26. Studying genes and their products
Pages: 317–319 Difficulty: 2
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?
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27. Studying genes and their products
Pages: 317–322 Difficulty: 3
Explain how each of the following is used in cloning in a plasmid: (a) antibiotic-resistance genes; (b)
origin of replication; (c) polylinker region.
28. Studying genes and their products
Page: 318 Difficulty: 2
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 .
29. Studying genes and their products
Pages: 317–319 Difficulty: 2
Explain briefly the properties of the plasmid pBR322 that make it so convenient as a vector for
cloning fragments of foreign DNA.
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30. Studying genes and their products
Page: 319 Difficulty: 2
When bacterial artificial chromosomes (BACs) are used as cloning vectors, what size of DNA
fragment can be cloned?
31. Studying genes and their products
Pages: 319–320 Difficulty: 2
How does a bacterial artificial chromosome (BAC) differ from a plasmid?
32. Studying genes and their products
Page: 320 Difficulty: 2
What is(are) the distinguishing feature(s) of a shuttle vector?
33. Studying genes and their products
Page: 322 Difficulty: 2
What sequences are required in an expression vector (for use with E. coli) that are not essential in a
cloning plasmid?
34. Studying genes and their products
Page: 322 Difficulty: 3
A scientist wishes to produce a mammalian protein in E. coli. The protein is a glycoprotein with a
molecular weight of 40,000. Approximately 20% of its mass is polysaccharide. The isolated protein
is usually phosphorylated and contains three disulfide bonds. The cloned gene contains no introns.
(a) What sequences or sites will be required in the vector to get this gene regulated, transcribed, and
translated in E. coli? (b) List two problems that might arise in producing a protein identical to that
isolated from mammalian cells and describe each problem in no more than two sentences.
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35. Studying genes and their products
Pages: 322–323 Difficulty: 3
List three different heterologous expression systems and include one advantage and one disadvantage
for each.
36. Studying genes and their products
Page: 328 Difficulty: 2
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.
37. Studying genes and their products
Page: 328 Difficulty: 1
What happens in PCR if you use DNA polymerase derived from E. coli instead of from a
thermostable source?
38. Using DNA-based methods to understand protein function
Page : 332 Difficulty: 2
What is the essential difference between a genomic library and a cDNA library?
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39. Using DNA-based methods to understand protein function
Page: 332 Difficulty: 2
Distinguish between protein function at the molecular, cellular, and phenotypic level.
40. Using DNA-based methods to understand protein function
Page: 332 Difficulty: 2
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.
41. Using DNA-based methods to understand protein function
Pages: 335–337 Difficulty: 2
Name two different methods by which protein-protein interactions can be discovered and probed.
42. Using DNA-based methods to understand protein function
Pages: 337 Difficulty: 2
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.
43. Using DNA-based methods to understand protein function
Pages: 337–338 Difficulty: 2
What is a DNA microarray? How does it resemble and how does it differ from a DNA library?
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44. Genomics and the human story
Pages: 339–341 Difficulty: 2
Briefly explain the procedure used in next-generation pyrosequencing.
45. Genomics and the human story
Pages: 342–343 Difficulty: 2
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?
46. Genomics and the human story
Pages: 346–347 Difficulty: 3
Explain the importance of outgroups for understanding genomic lineages.
47. Genomics and the human story
Pages: 347–349 Difficulty: 3
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.