Deck 10: Analyzing the Structure and Function of Genes
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Deck 10: Analyzing the Structure and Function of Genes
1
Figure 10-13 depicts a strategy by which a DNA fragment produced by cutting with the EcoRI restriction nuclease can be joined to a DNA fragment produced by cutting DNA with the HaeIII restriction nuclease.
Figure 10-13
Note that cutting DNA with EcoRI produces a staggered end, whereas cutting DNA with HaeIII produces a blunt end.Why must polymerase be added in this reaction?
A)Polymerase will fill in the staggered end to create a blunt end.
B)Polymerase is needed to seal nicks in the DNA backbone.
C)Polymerase will add nucleotides to the end produced by the HaeIII restriction nuclease.
D)Without polymerase, there will not be enough energy for the reaction to proceed.

Note that cutting DNA with EcoRI produces a staggered end, whereas cutting DNA with HaeIII produces a blunt end.Why must polymerase be added in this reaction?
A)Polymerase will fill in the staggered end to create a blunt end.
B)Polymerase is needed to seal nicks in the DNA backbone.
C)Polymerase will add nucleotides to the end produced by the HaeIII restriction nuclease.
D)Without polymerase, there will not be enough energy for the reaction to proceed.
A
2
You have a piece of circular DNA that can be cut by the restriction nucleases EcoRI, HindIII, and NotI, as indicated in Figure 10-6.
Figure 10-6
Which of the following statements is FALSE?
A)One piece of DNA will be obtained when this DNA is cut by NotI.
B)A piece of DNA that cannot be cut by EcoRI will be obtained by cutting this DNA with both NotI and HindIII.
C)Two DNA fragments that cannot be cut by HindIII will be obtained when this DNA is cut by EcoRI and NotI.
D)Two DNA fragments of unequal size will be created when this DNA is cut by both HindIII and EcoRI.

Which of the following statements is FALSE?
A)One piece of DNA will be obtained when this DNA is cut by NotI.
B)A piece of DNA that cannot be cut by EcoRI will be obtained by cutting this DNA with both NotI and HindIII.
C)Two DNA fragments that cannot be cut by HindIII will be obtained when this DNA is cut by EcoRI and NotI.
D)Two DNA fragments of unequal size will be created when this DNA is cut by both HindIII and EcoRI.
D
3
Figure 10-12 shows the cleavage sites of several restriction nucleases.
Figure 10-12
You cut a vector using the PciI restriction nuclease.Which of the following restriction nucleases will generate a fragment that can be ligated into this cut vector with the addition of only ligase and ATP?
A)HindIII
B)NcoI
C)MmeI
D)NspV

You cut a vector using the PciI restriction nuclease.Which of the following restriction nucleases will generate a fragment that can be ligated into this cut vector with the addition of only ligase and ATP?
A)HindIII
B)NcoI
C)MmeI
D)NspV
B
4
You have a circular plasmid that can be cut by the restriction nuclease HindIII, as diagrammed in Figure 10-4.
Figure 10-4
If you were to cut this circular piece of DNA with HindIII, which of the answers below best predicts what you would get?
A)one linear piece of DNA
B)two circular pieces of DNA
C)two semicircular pieces of DNA
D)two linear pieces of DNA

If you were to cut this circular piece of DNA with HindIII, which of the answers below best predicts what you would get?
A)one linear piece of DNA
B)two circular pieces of DNA
C)two semicircular pieces of DNA
D)two linear pieces of DNA
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5
DNA can be introduced into bacteria by a mechanism called
A)transcription.
B)ligation.
C)replication.
D)transformation.
A)transcription.
B)ligation.
C)replication.
D)transformation.
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6
During gel electrophoresis, DNA fragments
A)travel through a matrix containing a microscopic network of pores.
B)migrate toward a negatively charged electrode.
C)can be visualized without stains or labels.
D)are separated on the basis of their sequence.
A)travel through a matrix containing a microscopic network of pores.
B)migrate toward a negatively charged electrode.
C)can be visualized without stains or labels.
D)are separated on the basis of their sequence.
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7
DNA ligase is an enzyme used when making recombinant DNA molecules in the lab.In what normal cellular process is DNA ligase involved?
A)none; it is only found in virally infected cells
B)transcription
C)transformation
D)DNA replication
A)none; it is only found in virally infected cells
B)transcription
C)transformation
D)DNA replication
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8
Which of the following statements about genomic DNA libraries is FALSE?
A)The larger the size of the fragments used to make the library, the fewer colonies you will have to examine to find a plasmid that contains the gene you are interested in studying.
B)The larger the size of the fragments used to make the library, the more DNA you will need to examine to find your gene of interest once you have identified a plasmid that contains the gene you are interested in studying.
C)The larger the genome of the organism from which a library is derived, the larger the fragments inserted into the vector will tend to be.
D)The smaller the gene you are seeking, the more likely it is that the gene will be found on a single plasmid.
A)The larger the size of the fragments used to make the library, the fewer colonies you will have to examine to find a plasmid that contains the gene you are interested in studying.
B)The larger the size of the fragments used to make the library, the more DNA you will need to examine to find your gene of interest once you have identified a plasmid that contains the gene you are interested in studying.
C)The larger the genome of the organism from which a library is derived, the larger the fragments inserted into the vector will tend to be.
D)The smaller the gene you are seeking, the more likely it is that the gene will be found on a single plasmid.
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9
You are interested in a single-stranded DNA molecule that contains the following sequence:
5′- .....GATTGCAT....-3′
Which molecule will hybridize to your sequence of interest?
A)5′-GATTGCAT-3′
B)5′-TACGTTAG-3′
C)5′-CTAACGTA-3′
D)5′-ATGCAATC-3′
5′- .....GATTGCAT....-3′
Which molecule will hybridize to your sequence of interest?
A)5′-GATTGCAT-3′
B)5′-TACGTTAG-3′
C)5′-CTAACGTA-3′
D)5′-ATGCAATC-3′
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10
During DNA renaturation, two DNA strands will
A)break the covalent bonds that hold the nucleotides together while maintaining the hydrogen bonds that hold the two strands together.
B)break the hydrogen bonds that hold the two strands together with no effect on the covalent bonds that hold the nucleotides together.
C)re-form a double helix if the two strands have complementary sequences.
D)re-form a double helix if the two strands are identical in sequence.
A)break the covalent bonds that hold the nucleotides together while maintaining the hydrogen bonds that hold the two strands together.
B)break the hydrogen bonds that hold the two strands together with no effect on the covalent bonds that hold the nucleotides together.
C)re-form a double helix if the two strands have complementary sequences.
D)re-form a double helix if the two strands are identical in sequence.
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11
You have a linear piece of DNA that can be cut by the restriction nucleases HindIII and EcoRI, as diagrammed in Figure 10-7.
Figure 10-7
If you were to cut this linear DNA with HindIII, what type of DNA fragments do you predict you would obtain?
A)three linear pieces of DNA
B)two linear pieces of DNA, only one of which can be cut by EcoRI
C)two linear pieces of DNA, both of which can be cut by EcoRI
D)two linear pieces of DNA, only one of which can be cut by HindIII

If you were to cut this linear DNA with HindIII, what type of DNA fragments do you predict you would obtain?
A)three linear pieces of DNA
B)two linear pieces of DNA, only one of which can be cut by EcoRI
C)two linear pieces of DNA, both of which can be cut by EcoRI
D)two linear pieces of DNA, only one of which can be cut by HindIII
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12
You have purified DNA from your recently deceased goldfish.Which of the following restriction nucleases would you use if you wanted to end up with DNA fragments with an average size of 70 kilobase pairs (kb) after complete digestion of the DNA? The recognition sequence for each enzyme is indicated in the right-hand column.
A)Sau3AI GATC
B)BamHI GGATCC
C)XzaI GAAGGATCCTTC
D)NotI GCGGCCGC
A)Sau3AI GATC
B)BamHI GGATCC
C)XzaI GAAGGATCCTTC
D)NotI GCGGCCGC
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13
Which of the following statements about restriction nucleases is FALSE?
A)A reproducible set of DNA fragments will be produced every time a restriction nuclease digests a known piece of DNA.
B)Restriction nucleases recognize specific sequences on single-stranded DNA.
C)Some bacteria use restriction nucleases as protection from foreign DNA.
D)Some restriction nucleases cut in a staggered fashion, leaving short, single-stranded regions of DNA at the ends of the cut molecule.
A)A reproducible set of DNA fragments will be produced every time a restriction nuclease digests a known piece of DNA.
B)Restriction nucleases recognize specific sequences on single-stranded DNA.
C)Some bacteria use restriction nucleases as protection from foreign DNA.
D)Some restriction nucleases cut in a staggered fashion, leaving short, single-stranded regions of DNA at the ends of the cut molecule.
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14
Recombinant DNA technologies involve techniques that permit the creation of custom-made DNA molecules that can be introduced back into living organisms.These technologies were first developed in the
A)1800s.
B)1950s.
C)1970s.
D)2000s.
A)1800s.
B)1950s.
C)1970s.
D)2000s.
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15
Starting with one double-stranded DNA molecule, how many cycles of PCR would you have to perform to produce about 100 double-stranded copies (assuming 100% efficiency per cycle)?
A)2
B)7
C)25
D)100
A)2
B)7
C)25
D)100
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16
PCR was invented in
A)the 1800s.
B)the 1950s.
C)the 1980s.
D)2009.
A)the 1800s.
B)the 1950s.
C)the 1980s.
D)2009.
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17
You have a piece of circular DNA that can be cut by the restriction nucleases XhoI and SmaI, as indicated in Figure 10-5.
Figure 10-5
If you were to cut this circular piece of DNA with both XhoI and SmaI, how many fragments of DNA would you end up with?
A)1
B)2
C)3
D)4

If you were to cut this circular piece of DNA with both XhoI and SmaI, how many fragments of DNA would you end up with?
A)1
B)2
C)3
D)4
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18
A plasmid
A)can confer antibiotic resistance to a bacterium.
B)is a single-stranded circular DNA molecule that can undergo horizontal transfer among bacteria.
C)is a tool designed in the lab and never found in naturally occurring bacteria.
D)always becomes part of the bacterial chromosome during transformation.
A)can confer antibiotic resistance to a bacterium.
B)is a single-stranded circular DNA molecule that can undergo horizontal transfer among bacteria.
C)is a tool designed in the lab and never found in naturally occurring bacteria.
D)always becomes part of the bacterial chromosome during transformation.
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19
Which of the following statements about DNA libraries is TRUE?
A)Production of a DNA library involves the direct insertion of short DNA fragments into bacteria through transformation.
B)By placing the library DNA into bacteria, the bacteria can be used to amplify the desired DNA fragments from the DNA library.
C)Individual bacteria that have taken up most of the library DNA are selected for during the construction of a DNA library.
D)The library DNA within the bacteria will only be replicated when it contains the plasmid with the gene of interest.
A)Production of a DNA library involves the direct insertion of short DNA fragments into bacteria through transformation.
B)By placing the library DNA into bacteria, the bacteria can be used to amplify the desired DNA fragments from the DNA library.
C)Individual bacteria that have taken up most of the library DNA are selected for during the construction of a DNA library.
D)The library DNA within the bacteria will only be replicated when it contains the plasmid with the gene of interest.
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20
A DNA library has been constructed by purifying chromosomal DNA from mice, cutting the DNA with the restriction enzyme NotI, and inserting the fragments into the NotI site of a plasmid vector.What information CANNOT be retrieved from this library?
A)gene regulatory sequences
B)intron sequences
C)sequences of the telomeres (the ends of the chromosomes)
D)amino acid sequences of proteins
A)gene regulatory sequences
B)intron sequences
C)sequences of the telomeres (the ends of the chromosomes)
D)amino acid sequences of proteins
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21
You create a recombinant DNA molecule that fuses the coding sequence of green fluorescent protein to the regulatory DNA sequences that control the expression of your favorite genes.Which of the following pieces of information can you NOT gain by examining the expression of this reporter gene?
A)the tissue where the protein encoded by this gene is expressed
B)the cell in which the protein encoded by this gene is expressed
C)the specific location within the cell of the protein encoded by this gene
D)when, during an organism's development, this gene is expressed
A)the tissue where the protein encoded by this gene is expressed
B)the cell in which the protein encoded by this gene is expressed
C)the specific location within the cell of the protein encoded by this gene
D)when, during an organism's development, this gene is expressed
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22
Why are dideoxyribonucleoside triphosphates used during DNA sequencing?
A)They cannot be incorporated into DNA by DNA polymerase.
B)They are incorporated into DNA particularly well by DNA polymerases from thermophilic bacteria.
C)Incorporation of a dideoxyribonucleoside triphosphate leads to the termination of replication for that strand.
D)Dideoxyribonucleoside triphosphates are more stable than deoxyribonucleoside triphosphates.
A)They cannot be incorporated into DNA by DNA polymerase.
B)They are incorporated into DNA particularly well by DNA polymerases from thermophilic bacteria.
C)Incorporation of a dideoxyribonucleoside triphosphate leads to the termination of replication for that strand.
D)Dideoxyribonucleoside triphosphates are more stable than deoxyribonucleoside triphosphates.
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23
Which portion of an organism's genome is most likely to diverge most rapidly over evolutionary time?
A)the noncoding gene regulatory regions.
B)the noncoding telomeric sequences.
C)the exons.
D)the sequences at the intron/exon border.
A)the noncoding gene regulatory regions.
B)the noncoding telomeric sequences.
C)the exons.
D)the sequences at the intron/exon border.
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24
With fully automated Sanger sequencing, all four chain-terminating ddNTPs are added into a single reaction and loaded onto a capillary gel.The sequence can be determined even though all ddNTPs are mixed together because
A)the Sanger sequencing reactions do not contain dNTPs and use the ddNTPS to synthesize the DNA.
B)the Sanger sequencing reactions utilize ddNTPs, each labeled with a different fluorescent tag, which allows all four ddNTPs to be incorporated into a single molecule of DNA.
C)the Sanger sequencing reactions generate a set of products, each of which carries a single fluorescent tag whose color reveals the identity of the base that is at the end of the product.
D)the fully automated Sanger sequencing reactions do not require DNA polymerase because the bases are read as the DNA is pulled through a tiny pore at the end of the capillary gel.
A)the Sanger sequencing reactions do not contain dNTPs and use the ddNTPS to synthesize the DNA.
B)the Sanger sequencing reactions utilize ddNTPs, each labeled with a different fluorescent tag, which allows all four ddNTPs to be incorporated into a single molecule of DNA.
C)the Sanger sequencing reactions generate a set of products, each of which carries a single fluorescent tag whose color reveals the identity of the base that is at the end of the product.
D)the fully automated Sanger sequencing reactions do not require DNA polymerase because the bases are read as the DNA is pulled through a tiny pore at the end of the capillary gel.
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25
Insulin is a small protein that regulates blood sugar level and is given to patients who suffer from diabetes.Many years ago, diabetics were given insulin that had been purified from pig pancreas.Once recombinant DNA techniques became available, the DNA encoding insulin could be placed into an expression vector and insulin could be produced in bacteria.Which of the following is NOT a reason why purifying insulin from bacteria is a better way to produce insulin for diabetics than using insulin purified from a pig pancreas?
A)Insulin can be easily produced in large quantities from cells carrying the cloned DNA sequence.
B)The creation of transgenic pigs that expressed insulin was very expensive compared to the cost of creating bacteria that expressed insulin.
C)Insulin made from a bacterial culture and then purified will be free of any possible contaminating viruses that pigs (and any other animals) harbor.Since pigs are more closely related to people than bacteria are, their viruses are more likely to be harmful to people than are viruses that might infect bacteria.
D)The pig protein has slight amino acid differences compared to the human protein, so human insulin produced by bacteria will work better in people.
A)Insulin can be easily produced in large quantities from cells carrying the cloned DNA sequence.
B)The creation of transgenic pigs that expressed insulin was very expensive compared to the cost of creating bacteria that expressed insulin.
C)Insulin made from a bacterial culture and then purified will be free of any possible contaminating viruses that pigs (and any other animals) harbor.Since pigs are more closely related to people than bacteria are, their viruses are more likely to be harmful to people than are viruses that might infect bacteria.
D)The pig protein has slight amino acid differences compared to the human protein, so human insulin produced by bacteria will work better in people.
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26
You want to design a set of PCR primers to specifically amplify a portion of a gene from genomic DNA.Which of the following statements about this set of primers is TRUE?
A)One of the primers should contain sequences complementary to common repetitive sequences in the genome, to ensure that it will hybridize to the genomic DNA.
B)Each primer should span the junction of two adjacent exons and leave out intron sequences, to ensure that a portion of the coding portion of the gene is amplified and not noncoding regulatory sequence.
C)If the primers include sequence from both an exon and the adjacent intron, this will help ensure that the amplified product is made from genomic DNA and not any contaminating mRNA.
D)The primers should use "U"s instead of "T"s to ensure that the coding portion of the gene is amplified.
A)One of the primers should contain sequences complementary to common repetitive sequences in the genome, to ensure that it will hybridize to the genomic DNA.
B)Each primer should span the junction of two adjacent exons and leave out intron sequences, to ensure that a portion of the coding portion of the gene is amplified and not noncoding regulatory sequence.
C)If the primers include sequence from both an exon and the adjacent intron, this will help ensure that the amplified product is made from genomic DNA and not any contaminating mRNA.
D)The primers should use "U"s instead of "T"s to ensure that the coding portion of the gene is amplified.
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27
You want to design a set of PCR primers to amplify a portion of a gene from a cDNA library.Which of the following concerns about PCR primer design is the most legitimate?
A)You must be careful when designing your primers to take into account which DNA strand was transcribed in mRNA and make sure both primers are complementary to the mRNA.
B)You must be certain not to include any DNA sequences in your primer that are upstream (5′) of the AUG start codon.
C)You must make sure that all the DNA sequences in your primer lie within an exon, and do not span two exons.
D)You must be certain that all the DNA sequences in your primer are not located downstream (3′) of the polyadenylation signal.
A)You must be careful when designing your primers to take into account which DNA strand was transcribed in mRNA and make sure both primers are complementary to the mRNA.
B)You must be certain not to include any DNA sequences in your primer that are upstream (5′) of the AUG start codon.
C)You must make sure that all the DNA sequences in your primer lie within an exon, and do not span two exons.
D)You must be certain that all the DNA sequences in your primer are not located downstream (3′) of the polyadenylation signal.
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28
Which of the following describes a feature found in bacterial expression vectors but not in cloning vectors?
A)origin of replication
B)cleavage sites for restriction nucleases
C)promoter DNA sequences
D)a polyadenylation signal
A)origin of replication
B)cleavage sites for restriction nucleases
C)promoter DNA sequences
D)a polyadenylation signal
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29
Which of the following limits the use of PCR to detect and isolate genes?
A)The sequence at the beginning and end of the DNA to be amplified must be known.
B)It also produces large numbers of copies of sequences beyond the 5′ or 3′ end of the desired sequence.
C)It cannot be used to amplify cDNAs or mRNAs.
D)It will amplify only sequences present in multiple copies in the DNA sample.
A)The sequence at the beginning and end of the DNA to be amplified must be known.
B)It also produces large numbers of copies of sequences beyond the 5′ or 3′ end of the desired sequence.
C)It cannot be used to amplify cDNAs or mRNAs.
D)It will amplify only sequences present in multiple copies in the DNA sample.
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30
Which of the following statements about RNA interference (or RNAi) is FALSE?
A)RNAi is a natural mechanism used to regulate genes.
B)During the process of RNAi, hybridization of a small RNA molecule with the mRNA degrades the mRNA.
C)Because RNAi depends on the introduction of a double-stranded RNA into a cell or an organism, it is not a process that can cause heritable changes in gene expression.
D)In C.elegans, RNAi can be introduced into the animals by feeding them with bacteria that produce the inhibitory RNA molecules.
A)RNAi is a natural mechanism used to regulate genes.
B)During the process of RNAi, hybridization of a small RNA molecule with the mRNA degrades the mRNA.
C)Because RNAi depends on the introduction of a double-stranded RNA into a cell or an organism, it is not a process that can cause heritable changes in gene expression.
D)In C.elegans, RNAi can be introduced into the animals by feeding them with bacteria that produce the inhibitory RNA molecules.
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31
A double-stranded DNA molecule can be separated into single strands by heating it to 90°C because
A)heat disrupts the hydrogen bonds holding the sugar-phosphate backbone together.
B)DNA is negatively charged.
C)heat disrupts hydrogen-bonding between complementary nucleotides.
D)DNA is positively charged.
A)heat disrupts the hydrogen bonds holding the sugar-phosphate backbone together.
B)DNA is negatively charged.
C)heat disrupts hydrogen-bonding between complementary nucleotides.
D)DNA is positively charged.
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32
Second-generation sequencing differs from Sanger sequencing because
A)second-generation sequencing does not depend on chain-terminator nucleoside triphosphates.
B)second-generation sequencing does not require DNA polymerase.
C)for the cost per base sequenced, second-generation sequencing is much more expensive than Sanger sequencing.
D)second-generation sequencing can sequence millions of pieces of DNA at the same time on a single glass slide.
A)second-generation sequencing does not depend on chain-terminator nucleoside triphosphates.
B)second-generation sequencing does not require DNA polymerase.
C)for the cost per base sequenced, second-generation sequencing is much more expensive than Sanger sequencing.
D)second-generation sequencing can sequence millions of pieces of DNA at the same time on a single glass slide.
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33
Which of the following techniques is not appropriate if you want to examine whether a gene is expressed in a specific tissue?
A)in situ hybridization
B)production of a cDNA library
C)RNA-Seq
D)next generation genome sequencing
A)in situ hybridization
B)production of a cDNA library
C)RNA-Seq
D)next generation genome sequencing
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34
Why is an excess of normal deoxyribonucleoside triphosphate molecules (dNTPs) needed during dideoxy sequencing?
A)DNA polymerase uses the dNTPs to synthesize a DNA molecule complementary to the molecule being sequenced.
B)dNTPs are consumed as energy to fuel the sequencing reactions.
C)When dNTP levels are too low, there will be very few chain-termination events.
D)The dNTPs can hybridize to the fragment to be sequenced and serve as primers for DNA polymerase.
A)DNA polymerase uses the dNTPs to synthesize a DNA molecule complementary to the molecule being sequenced.
B)dNTPs are consumed as energy to fuel the sequencing reactions.
C)When dNTP levels are too low, there will be very few chain-termination events.
D)The dNTPs can hybridize to the fragment to be sequenced and serve as primers for DNA polymerase.
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35
Your friend works at the Centers for Disease Control and Prevention and has discovered a brand-new virus that has recently been introduced into the human population.She has just developed a new assay that allows her to detect the virus by using PCR products made from the blood of infected patients.The assay uses primers in the PCR assay that hybridize to sequences in the viral genome.
Your friend is distraught because of the result she obtained (see Figure 10-28) when she looked at PCR products made using the blood of three patients suffering from the viral disease, using her own blood, and using a leaf from her petunia plant.
You advise your friend not to panic, as you believe she is missing an important control.Which one of the choices listed below is the best control for clarifying the results of her assay? Explain your answer.
Figure 10-28
A)a PCR assay using blood from a patient who is newly infected but does not yet show symptoms
B)a PCR assay using blood from a dog
C)a PCR assay using blood from an uninfected person
D)repeating the experiments she has already done with a new tube of polymerase
Your friend is distraught because of the result she obtained (see Figure 10-28) when she looked at PCR products made using the blood of three patients suffering from the viral disease, using her own blood, and using a leaf from her petunia plant.
You advise your friend not to panic, as you believe she is missing an important control.Which one of the choices listed below is the best control for clarifying the results of her assay? Explain your answer.

Figure 10-28
A)a PCR assay using blood from a patient who is newly infected but does not yet show symptoms
B)a PCR assay using blood from a dog
C)a PCR assay using blood from an uninfected person
D)repeating the experiments she has already done with a new tube of polymerase
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36
Figure 10-25 shows a restriction map of a piece of DNA containing your favorite eukaryotic gene.The arrow indicates the position and orientation of the gene in the DNA.In part (B) of the figure are enlargements showing the portions of the DNA whose sequences have been used to make PCR primers A, B, C, and D.Which primer or primers can be used to amplify the gene? (A)

(B)
Figure 10-25
A)primers A and B
B)primers A and C
C)primers A and D
D)primer A alone

(B)

A)primers A and B
B)primers A and C
C)primers A and D
D)primer A alone
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37
You have been hired to create a cat that will not cause allergic reactions in cat-lovers.Your coworkers have cloned the gene encoding a protein found in cat saliva, expressed the protein in bacteria, and shown that it causes violent allergic reactions in people.But you soon realize that even if you succeed in making a knockout cat lacking this gene, anyone who buys one will easily be able to make more hypoallergenic cats just by breeding them.Which of the following will ensure that people will always have to buy their hypoallergenic cats from you?
A)Inject the modified embryonic stem (ES) cells into embryos that have a genetic defect to prevent the mature adult from reproducing.
B)Implant the injected embryos into a female cat that is sterile as a result of a genetic defect.
C)Sell only the offspring from the first litter of the female cat implanted with the injected embryos.
D)Surgically remove the sexual organs of all the knockouts before you sell them.
A)Inject the modified embryonic stem (ES) cells into embryos that have a genetic defect to prevent the mature adult from reproducing.
B)Implant the injected embryos into a female cat that is sterile as a result of a genetic defect.
C)Sell only the offspring from the first litter of the female cat implanted with the injected embryos.
D)Surgically remove the sexual organs of all the knockouts before you sell them.
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38
Which of the following statements about Illumina sequencing is FALSE?
A)The nucleoside triphosphates that are used have a fluorescent marker.
B)The nucleoside triphosphates that are used have a 3′ chemical group that will terminate DNA synthesis.
C)The termination of DNA synthesis by the nucleoside triphosphates that are used is reversible.
D)Both normal and modified nucleoside triphosphates are used to synthesize DNA.
A)The nucleoside triphosphates that are used have a fluorescent marker.
B)The nucleoside triphosphates that are used have a 3′ chemical group that will terminate DNA synthesis.
C)The termination of DNA synthesis by the nucleoside triphosphates that are used is reversible.
D)Both normal and modified nucleoside triphosphates are used to synthesize DNA.
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39
Which of the following statements about PCR is FALSE?
A)PCR uses a DNA polymerase from a thermophilic bacterium.
B)PCR is particularly powerful because after each cycle of replication, there is a linear increase in the amount of DNA available.
C)For PCR, every round of replication is preceded by the denaturation of the double-stranded DNA molecules.
D)The PCR will generate a pool of double-stranded DNA molecules, most of which will have DNA from primers at the 5′ ends.
A)PCR uses a DNA polymerase from a thermophilic bacterium.
B)PCR is particularly powerful because after each cycle of replication, there is a linear increase in the amount of DNA available.
C)For PCR, every round of replication is preceded by the denaturation of the double-stranded DNA molecules.
D)The PCR will generate a pool of double-stranded DNA molecules, most of which will have DNA from primers at the 5′ ends.
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40
PCR involves a heating step, followed by a cooling step, and then DNA synthesis.What is the primary reason for why this cooling step is necessary?
A)Cooling the reaction ensures the integrity of the covalent bonds holding the nucleotides together in the DNA strand.
B)Cooling the reaction gives the DNA polymerase an opportunity to rest from the previous cycle so that it will be ready for the next round of synthesis.
C)Transcription takes place during the cooling step.
D)Cooling the reaction brings the temperature down to a level that is compatible with the short primers forming stable hydrogen bonds with the DNA to be amplified.
A)Cooling the reaction ensures the integrity of the covalent bonds holding the nucleotides together in the DNA strand.
B)Cooling the reaction gives the DNA polymerase an opportunity to rest from the previous cycle so that it will be ready for the next round of synthesis.
C)Transcription takes place during the cooling step.
D)Cooling the reaction brings the temperature down to a level that is compatible with the short primers forming stable hydrogen bonds with the DNA to be amplified.
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41
You have been asked to consult for a biotech company that is seeking to understand why some fungi can live in very extreme environments, such as the high temperatures inside naturally occurring hot springs.The company has isolated two different fungal species, F.cattoriae and W.gravinius, both of which can grow at temperatures exceeding 95°C.The company has determined the following things about these fungal species:
By sequencing and examining their genomes, the biotech company hopes to understand why these species can live in extreme environments.However, the company only has the resources to sequence one genome, and would like your input as to which species should be sequenced and whether you believe a shotgun strategy will work in this case.(Be sure to explain your answer.)

By sequencing and examining their genomes, the biotech company hopes to understand why these species can live in extreme environments.However, the company only has the resources to sequence one genome, and would like your input as to which species should be sequenced and whether you believe a shotgun strategy will work in this case.(Be sure to explain your answer.)
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42
Indicate whether a cDNA library or a genomic DNA library will be more appropriate for use in the following applications.
A.You want to study the promoter of gene A.
B.Gene A encodes a tRNA and you wish to isolate a piece of DNA containing the full-length sequence of the tRNA.
C.You discover that gene A is alternatively spliced and you want to see which predicted alternative splice products the cell actually produces.
D.You want to find both gene A and the genes located near gene A on the chromosome.
E.You want to express gene A in bacteria to produce lots of protein A.
A.You want to study the promoter of gene A.
B.Gene A encodes a tRNA and you wish to isolate a piece of DNA containing the full-length sequence of the tRNA.
C.You discover that gene A is alternatively spliced and you want to see which predicted alternative splice products the cell actually produces.
D.You want to find both gene A and the genes located near gene A on the chromosome.
E.You want to express gene A in bacteria to produce lots of protein A.
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43
To study gene function, scientists use various methods to disrupt the sequence of the gene.In some cases, this is not possible and conditional knockouts must be used instead.Which of the following statements about the Cre-Lox system for creating conditional knockouts is TRUE?
A)Conditional knockouts can be produced because the gene of interest is flanked by LoxP sites only in the cell type of interest.
B)Conditional knockouts can be produced by expressing the Cre recombinase gene only in the cell type of interest.
C)The gene of interest is not expressed in the cell type of interest in a conditional mutant because Cre recombinase acts to inhibit RNA polymerase when it binds to the LoxP site.
D)Nontarget tissues do not have the Cre recombinase gene, and thus do not produce Cre recombinase.
A)Conditional knockouts can be produced because the gene of interest is flanked by LoxP sites only in the cell type of interest.
B)Conditional knockouts can be produced by expressing the Cre recombinase gene only in the cell type of interest.
C)The gene of interest is not expressed in the cell type of interest in a conditional mutant because Cre recombinase acts to inhibit RNA polymerase when it binds to the LoxP site.
D)Nontarget tissues do not have the Cre recombinase gene, and thus do not produce Cre recombinase.
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44
What is the main reason for using a cDNA library rather than a genomic library to isolate a human gene from which you wish to make large quantities of the human protein in bacteria?
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45
Some plasmids from cDNA libraries can have defects because of the way in which a cDNA library is constructed.For each dilemma (A to D) listed below, indicate which of the outcomes (1 to 4) you might encounter, and explain why.Outcomes may be used more than once.
Table 10-54

Table 10-54
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46
Why is a heat-stable DNA polymerase from a thermophilic bacterium (the Taq polymerase) used in the polymerase chain reaction rather than a DNA polymerase from E.coli or humans?
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47
You have created a piece of recombinant DNA by placing a cDNA from a gene you believe is important for the differentiation of liver cells (called LC1) onto an expression plasmid that contains all the sequences necessary for propagation of this DNA in bacteria and for the production of the LC1 protein in bacteria.A picture of this plasmid is shown in Figure 10-66A, with the segment of the DNA containing the LC1 gene depicted as a gray rectangle; the promoter sequence is depicted as a white rectangle.The LC1 protein is phosphorylated on serine 54; the nucleotide sequence of the portion of the DNA that encodes this region is shown below the diagram.All HindIII and SalI restriction sites have also been mapped on the plasmid; the recognition sequences for these restriction nucleases are shown in Figure 10-66B.
Table 10-56
Figure 10-66
A.Given the information above, write out the amino acids 52 to 57, encoded by the nucleotide sequence shown above.Be sure to number the amino acids appropriately.(Hint: Remember, serine is amino acid number 54.)
B.You want to create a mutant version of the LC1 gene that replaces the serine 54 found on this peptide with a glycine.You want to do this by changing only one nucleotide, and you also want to destroy the HindIII recognition sequence with this change.Write out a 21-nucleotide DNA sequence that can accommodate these changes.Be sure to (i) write out the DNA and label the 5′ and 3′ ends, (ii) underline the mutated HindIII recognition site, and (iii) circle any change made to the original sequence.

Table 10-56

Figure 10-66
A.Given the information above, write out the amino acids 52 to 57, encoded by the nucleotide sequence shown above.Be sure to number the amino acids appropriately.(Hint: Remember, serine is amino acid number 54.)
B.You want to create a mutant version of the LC1 gene that replaces the serine 54 found on this peptide with a glycine.You want to do this by changing only one nucleotide, and you also want to destroy the HindIII recognition sequence with this change.Write out a 21-nucleotide DNA sequence that can accommodate these changes.Be sure to (i) write out the DNA and label the 5′ and 3′ ends, (ii) underline the mutated HindIII recognition site, and (iii) circle any change made to the original sequence.
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48
Figure 10-45A depicts the restriction map of one segment of the human genome for four restriction nucleases W, X, Y, and Z.Figure 10-45B depicts the restriction maps of four individual BAC clones that contain segments of human DNA from the region depicted in Figure 10-45A. (A)

(B)

Figure 10-45
From this information, how would you order these BAC clones, from left to right?
A)1, 2, 3, 4
B)2, 1, 4, 3
C)3, 4, 2, 1
D)4, 1, 3, 2

(B)

Figure 10-45
From this information, how would you order these BAC clones, from left to right?
A)1, 2, 3, 4
B)2, 1, 4, 3
C)3, 4, 2, 1
D)4, 1, 3, 2
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49
Which of the restriction nucleases listed below can potentially cleave a segment of cDNA that encodes the peptide KIGDACF?
Table 10-56

Table 10-56

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50
You want to amplify the DNA between the two stretches of sequence shown in Figure 10-58.Of the listed primers, choose the pair that will allow you to amplify the DNA by PCR.
Figure 10-58

Figure 10-58
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51
Assume that defects in a hypothetical gene X have been linked to a disease.Two copies of a defective gene X will predispose a child to the disease, while a single copy of the gene seems to produce no symptoms.Because early treatment can counteract the effects of the disease, a program of voluntary genetic testing is being performed with prospective parents.Caril Ann is pregnant with Charles's child.You obtain DNA samples from Charles, Caril Ann, and the fetus.You conduct PCR from these DNA samples using two different primer sets that will detect two commonly found deletions in gene X that are associated with the disease.The gene and location of these primer sets are shown in Figure 10-61A.Your results are shown in Figure 10-61B.
Figure 10-61
A.Which of the three individuals have defects in gene X?
B.Which individuals have a single defective gene and which have two defective copies of the gene?
C.Indicate the location of each individual's defects on gene X.

Figure 10-61
A.Which of the three individuals have defects in gene X?
B.Which individuals have a single defective gene and which have two defective copies of the gene?
C.Indicate the location of each individual's defects on gene X.
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52
Which of the restriction nucleases listed below can potentially cleave a segment of cDNA that encodes the peptide KIGDACF?
Table 10-56

Table 10-56

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53
You have the amino acid sequence of a protein and wish to design PCR primers that will allow you to amplify this gene by PCR from genomic DNA.Using this protein sequence, you deduce a particular DNA sequence that can encode this protein.Why is it unwise to use only this DNA sequence you have deduced to design PCR primers for isolating the gene encoding your protein of interest from genomic DNA?
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54
How does the Cas9 system target where it produces a double-strand break in the DNA?
A)A guide RNA molecule is associated with Cas9 and will direct Cas9 to bind at sequences complementary to the guide RNA.
B)The Cas9 protein contains amino acids that can interact with specific sequences in the DNA, targeting Cas9 to those specific sites.
C)The Cas9 protein binds to a recombinase, allowing it to disable the gene of interest.
D)A guide RNA molecule associated with Cas9 provides the catalytic activity to cleave the DNA where Cas9 binds.
A)A guide RNA molecule is associated with Cas9 and will direct Cas9 to bind at sequences complementary to the guide RNA.
B)The Cas9 protein contains amino acids that can interact with specific sequences in the DNA, targeting Cas9 to those specific sites.
C)The Cas9 protein binds to a recombinase, allowing it to disable the gene of interest.
D)A guide RNA molecule associated with Cas9 provides the catalytic activity to cleave the DNA where Cas9 binds.
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55
You are studying a protein that contains the peptide sequence RDWKLVI.The part of the DNA encoding this peptide is included in the sequence shown below.
Table 10-56
5′-GGCGTGACTGGAAGCTAGTCATC-3′
3′-CCGCACTGACCTTCGATCAGTAG-5′
This sequence does not contain any HindIII restriction enzyme sites; the target sequence for the HindIII restriction nuclease is shown in Figure 10-65.
Figure 10-65A
Your goal is to create a HindIII site on this plasmid without changing the coding sequence of the protein.Explain how you would do this.

Table 10-56
5′-GGCGTGACTGGAAGCTAGTCATC-3′
3′-CCGCACTGACCTTCGATCAGTAG-5′
This sequence does not contain any HindIII restriction enzyme sites; the target sequence for the HindIII restriction nuclease is shown in Figure 10-65.

Figure 10-65A
Your goal is to create a HindIII site on this plasmid without changing the coding sequence of the protein.Explain how you would do this.
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56
You are studying a protein, and a small fragment of its sequence is shown below.You have decided that the glutamine in the protein segment has an important role in its function.You decide to change this glutamine to a lysine by changing only one base.Given the partial mRNA sequence that codes for this stretch of protein below, write the new sequence for this stretch of RNA if you were to make this change.Be sure to label the 5′ and 3′ ends.
Table 10-56
F D P Q G S H
5′-UUCGACCCGCAGGGCAGCCAC-3′

Table 10-56
F D P Q G S H
5′-UUCGACCCGCAGGGCAGCCAC-3′
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57
The sequencing of the human genome was a technological accomplishment.Which of the following did NOT contribute to the sequencing of the human genome in the early 2000s?
A)shotgun sequencing
B)restriction site mapping of BACs
C)automated Sanger sequencing
D)Illumina sequencing
A)shotgun sequencing
B)restriction site mapping of BACs
C)automated Sanger sequencing
D)Illumina sequencing
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58
For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below.Not all words or phrases will be used; use each word or phrase only once.
DNA sequencing polymerase chain reaction
DNA ligase recombinant DNA
endonucleases restriction enzymes
gel electrophoresis ribonucleases
Nucleases that cut DNA only at specific short sequences are known as __________.DNA composed of sequences from different sources is known as __________.__________ can be used to separate DNA fragments of different sizes.Millions of copies of a DNA sequence can be made entirely in vitro by the __________ technique.
DNA sequencing polymerase chain reaction
DNA ligase recombinant DNA
endonucleases restriction enzymes
gel electrophoresis ribonucleases
Nucleases that cut DNA only at specific short sequences are known as __________.DNA composed of sequences from different sources is known as __________.__________ can be used to separate DNA fragments of different sizes.Millions of copies of a DNA sequence can be made entirely in vitro by the __________ technique.
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59
The Cas9 enzyme used in the CRISPR system
A)was created by scientists by modifying restriction enzymes.
B)was discovered in bacteria as part of a mechanism to protect themselves from foreign DNA.
C)was found as part of a natural mechanism used by plants to protect themselves from viruses.
D)was found in cultured mouse embryonic stem (ES) cells.
A)was created by scientists by modifying restriction enzymes.
B)was discovered in bacteria as part of a mechanism to protect themselves from foreign DNA.
C)was found as part of a natural mechanism used by plants to protect themselves from viruses.
D)was found in cultured mouse embryonic stem (ES) cells.
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