Chapter 5 Exploring Genes and Genomes
Matching Questions
Use the following to answer questions 1-10:
Choose the correct answer from the list below. Not all of the answers will be used.
a) Haemophilus influenzae
b) restriction enzymes
c) pUC18
d) expression
e) Sanger
f) footprint
g) vector
h) E. coli
i) fingerprint
j) reverse trancriptase
k) fluorescent
l) Kary Mullis
1 Arber, Smith, and Nathans discovered and pioneered the use of
____________.
Ans b
:
Section: 5.1
2 A pattern of DNA fragments can serve as a ____________ of a particular DNA
molecule.
Ans i
:
Section: 5.1
3 The most common type of DNA sequencing is ____________.
Ans e
:
Section: 5.1
4 Instead of radioactivity, current DNA sequencing commonly uses
____________ base analogues.
Ans k
:
Section: 5.1
5 ____________ The first genome to be sequenced of a free-living organism.
Ans a
:
Section: 5.3
6 ____________ Won the Nobel prize for discovery of the polymerase chain
reaction.
Ans l
:
Section: 5.1
7 A plasmid is an example of a common ____________.
Ans g
:
Section: 5.2
8 ____________ A plasmid vector that contains the β-galactosidase gene and is
useful for screening cells with recombined DNA.
Ans c
:
Section: 5.2
9 ____________ The enzyme used to create DNA from RNA.
Ans j
:
Section: 5.4
10 ____________ The type of vector used for synthesis of protein.
Ans d
:
Section: 5.4
Fill in the Blank Questions
11 The enzyme that catalyzes the formation of a phosphodiester linkage at a
break in a DNA strand is __________________.
Ans: DNA ligase Section: 5.1
12 ___________________________ cleave DNA at sites with inverted repeat
sequences referred to as palendromic sequences.
Ans: Restriction endonucleases Section: 5.1
13 Complementary, single-strand overhangs that are produced by some
restriction endonucleases are referred to as ___________________.
Ans: sticky ends or cohesive ends Section: 5.2
14 The Sanger technique for sequencing DNA involves the use of
__________________ nucleotide analogs that terminate chain elongation.
Ans: 2',3'-dideoxy Section: 5.1
15 In solid-phase synthesis of oligonucleotides, the 2'deoxyribonucleotide-3'-
phosphoramidite is added to the _______ end of the growing
oligonucleotide.
Ans: 5' Section: 5.1
16 PCR is the abbreviation for ____________________________, which is an in-
vitro technique used to make multiple copies of a DNA molecule.
Ans: Polymerase Chain Reaction Section: 5.1
17 Bacterial plasmid DNA and bacteriophage DNA are commonly used
______________ to introduce foreign DNA into a bacterium.
Ans: vectors Section: 5.1
18 The enzyme _________________ can be used to add nucleotides to the 3'
end of DNA.
Ans: terminal transferase Section: 5.4
19 Complimentary DNA (cDNA) is formed by the action of reverse transcriptase
on ___________.
Ans: mRNA Section: 5.4
20 DNA fragments can be visualized in polyacrylamide gel electrophoresis by
staining with _______________, which binds to double-stranded DNA and
fluoresces an intense orange when irradiated by UV light.
Ans: ethidium bromide Section: 5.1
Multiple Choice Questions
21 The biological role of restriction enzymes in bacteria is to
A) repair DNA. D) All of the above.
B) induce DNA crossover. E) None of the above.
C) cleave foreign DNA.
Ans: C Section: 5.1
22 Which of the following DNA sequences contains a 48 base palindromic site?
(Note: Only one strand is shown.)
A) CAGTCC D) GAGAGAGA
B) GCATCC E) GCATATGC
C) CGATTAGC
Ans: E Section: 5.1
23 What do Southern, Northern, and Western blots detect, respectively?
A) DNA, RNA, and protein D) protein, DNA, and RNA
B) DNA, protein, and RNA E) RNA, protein, and DNA
C) RNA, DNA, and protein
Ans: A Section: 5.1
24 The specificity or strigency of a PCR reaction can be controlled by altering the
reaction
A) volume. D) all of the above.
B) target sequence. E) None of the above.
C) temperature and salt
concentration.
Ans: C Section: 5.1
25 Reagents necessary for sequencing by chain termination include
A) template DNA, deoxyribonucleoside triphosphates (dNTPs), primer,
dideoxy nucleotide analogs, DNA polymerase, and radioactive probe.
B) template DNA, deoxyribonucleoside triphosphates (dNTPs), primer,
dideoxy nucleotide analogs, and DNA polymerase.
C) template DNA, deoxyribonucleoside triphosphates (dNTPs), primer,
dideoxy nucleotide analogs, RNA polymerase.
D) All of the above.
E) None of the above
Ans: B Section: 5.1
26 The first three bases of the 6-base recognition cleavage site of HindIII are
AAG. What is the complete sequence of this 6 bp site?
A) AAGAAG D) AAGCUU
B) AAGCTT E) None of the above.
C) AAGGAA
Ans: B Section: 5.1
27 Plasmids used in recombinant DNA technology typically
A) possess a gene for antibiotic resistance.
B) replicate independently of the host genome.
C) are circular double stranded molecules.
D) all of the above.
E) a and b.
Ans: D Section: 5.2
28 A polylinker site contains
A) many closely spaced restriction enzyme sites.
B) links for antibiotic resistance.
C) sequences allowing linkage to mRNA.
D) All of the above.
E) None of the above.
Ans: A Section: 5.2
29 Why are met and trp often used to design DNA probes from amino acid
sequences?
A) They are not degenerate and have single codons.
B) Met is the first amino acid in the protein chain.
C) Both are used often in proteins.
D) All of the above.
E) None of the above.
Ans: A Section: 5.2
30 For identification of a gene, against which strand of DNA must the probe
complement: the top or bottom strand?
A) either strand D) only the template strand
B) both strands E) None of the above.
C) only the coding strand
Ans: A Section: 5.2
31 Reverse transcriptase is normally found in
A) plants. D) All of the above.
B) retrovirus. E) None of the above.
C) mitochondria.
Ans: B Section: 5.4
32 The probe used to isolate a gene from a genomic library is often
A) the ligand that binds to the D) All of the above.
protein.
B) its promoter region. E) None of the above.
C) a portion of the mRNA of the
gene.
Ans: C Section: 5.2
33 Genes can be inserted into eukaryotic cells by
A) viruses. D) All of the above.
B) chemical treatment. E) None of the above.
C) microinjection.
Ans: D Section: 5.4
34 Animals that harbor a foreign gene as a result of recombinant gene
manipulation are called
A) transgenic. D) All of the above.
B) mutants. E) None of the above.
C) aliens.
Ans: A Section: 5.4
35 Techniques for engineering new proteins by site-directed gene mutations
include:
A) oligonucleotide directed D) a and b.
mutagenesis.
B) cassette mutagenesis. E) All of the above.
C) chromosome walking
mutagenesis.
Ans: D Section: 5.4
Short-Answer Questions
36 A number of tools are critical to gene exploration. Name at least four.
Ans Tools include restriction enzyme analysis, blotting techniques (Southern
: and Northern), DNA sequencing, solid-phase synthesis of nucleic acid,
PCR, and computer analysis.
Section: 5.1
37 Design a potential DNA-restriction enzyme site. Show both strands.
Ans Any palindromic site of four or more base pairs would be appropriate.
:
Section: 5.1 and Figure 5.1
38 How can DNA fragments of various sizes be separated?
Ans Electrophoresis is used to separate DNA. Fragments migrate according
: to size, with larger fragments migrating more slowly than smaller
fragments. Agarose gels are used for larger fragments. Polyacrylamide is
used for shorter fragments, and can resolve fragments differing by as
little as one base. Several techniques for visualization can be used,
including ethidium bromide staining, or autoradiography.
Section: 5.1
39 What is a DNA probe?
Ans A DNA probe is used to identify specific DNA fragments. The probe
: sequence is complementary to the DNA sequence of interest, thus it can
base pair, or hybridize, with the DNA strand. Probes can be small
oligomers or long fragments. They are labeled for detection using
radioactivity or another tag, such as fluorescent probes.
Section: 5.1
40 What is the basis of the Sanger method?
Ans Sanger sequencing is based upon replication of DNA under conditions in
: which the chain is terminated by controlled interruption, resulting in
various sizes of DNA fragments. By including limited amounts of
radioactive bases, strands differing by one base in length can be
observed. By reading the bands, the sequence can be determined.
(Fluorescent or dye tags can also be used in an automated process.)
Section: 5.1
41 Explain the basis of the polymerase chain reaction.
Ans Using primers that flank the sequence of interest and carrying out
: repetitive replication reactions can make copies of a particular DNA
fragment. Template DNA, DNA polymerase, dNTPs, and other necessary
reagents are added to the reaction mixture. The DNA is heated to
separate the strands, cooled to allow the primers to anneal, and then
replicated. The process is repeated many times, each time doubling the
number of DNA copies present. The enzyme used is thermostable, and
can withstand the repetitive heating and cooling steps.
Section: 5.1 and Figure 5.8
42 Describe two ways PCR can be used in medical diagnosis.
Ans PCR can be used to identify the presence of infecting bacteria or viruses;
: can detect if certain mutations, such as those found in cancer cells, are
present; and can be used as a diagnostic tool to investigate known gene
mutations.
Section: 5.1
43 Briefly outline the steps necessary to create a recombinant DNA molecule.
Ans Both the fragment of interest and the vector DNA are cut with
: restriction enzyme(s), which create complementary sticky ends. The
pieces of DNA are allowed to anneal and DNA ligase is added to join the
ends.
Section: 5.2
44 How is a single gene of interest identified on a plate containing many
different library clones?
Ans By using a probe specific for the DNA of interest, the clone can be
: identified. The probe is designed to hybridize to the DNA of the clone
that has been transferred to the membrane. The probe is labeled with
radioactivity or another tag so that it can be easily detected and the
proper clone identified and selected.
Section: 5.2
45 If a gene is inserted into an antibiotic marker gene in a plasmid such as
ampicilin, will the resulting clone be sensitive or resistant to the antibiotic?
Ans When inserted into a gene, the new DNA interrupts the previous gene.
: Thus, the antibiotic gene is unlikely to be functional, the clone will be
sensitive to the antibiotic, and the clone will not grow.
Section: 5.2
46 Briefly outline how a cDNA library is made.
Ans Reverse transcriptase is used to convert mRNA molecules into DNA, and
: the RNA is then digested away by alkali. Terminal transferase is used to
add several residues to the end of the fragment, such as G. Then, a
complementary primer, such as polyC, can be used to synthesize the
opposite strand. Linkers can be added so the fragment can be inserted
into a vector, and then into a host, such as bacteria.
Section: 5.3 and Figure 5.17
47 Why are foreign genes often inserted with a different promoter, such as the
metallothionein gene promoter?
Ans Promoters are selected that are easy to control, and can be turned on
: or off as desired. Thus, metallothionein, which is induced by the
presence of heavy metals, can be mediated by altering metals
concentrations.
Section: 5.4
48 How is gene disruption used to determine the function of a gene?
Ans If a gene is completely disrupted (also called gene knockout), a
: functioning protein is not made. By examining the knockout organism,
clues to the protein’s function can be made by observation and testing.
Section: 5.4
49 How is a gene gun used?
Ans DNA is coated onto tungsten pellets, and the microprojectiles are shot
: into the tissue at very high velocity.
Section: 5.4
50 What advantage can be gained by splicing together portions of two different
genes?
Ans This technique allows the creation of novel bifunctional genes. Distinct
: functional domains are paired and aligned into one gene, often resulting
in proteins with unique characteristics and activities.
Section: 5.4
