Bio E2 Ch.10
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.
PCR was invented in _______. (a) the 1800s. (b) the 1950s. (c) the 1980s. (d) 2009.
(c) the 1980s
10-21 DNA can be introduced into bacteria by a mechanism called ____________. (a) transcription. (b) ligation. (c) replication. (d) transformation.
(d) transformation.
Figure x 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. 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) Polymerase will fill in the staggered end to create a blunt end.
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.
You want to design a DNA probe used for hybridization to isolate a clone from a cDNA library. Which of the following statements about DNA probes is true? (a) The shorter the DNA probe used to probe the library, the greater the number of colonies to which the probe might hybridize. (b) A DNA probe that contains sequences that span two exons is better suited to the purpose than a DNA probe that only contains sequences from one exon. (c) A DNA probe that contains sequences immediately upstream of the DNA that codes for the first methionine in the open reading frame will usually not hybridize to clones in a cDNA library. (d) Hybridization of a DNA probe to the plasmid of interest will permit the detection of the clone of interest; labeling of the DNA probe is not necessary.
(a) The shorter the DNA probe used to probe the library, the greater the number of colonies to which the probe might hybridize.
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.
Which of the following techniques is not appropriate if you want to examine the transcriptome of a specific tissue? (a) in situ hybridization (b) production of a cDNA library (c) RNA-Seq (d) microarray analysis
(a) in situ hybridization
You have a circular plasmid that can be cut by the restriction nuclease HindIII, as diagrammed in Figure Q10-4. 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
(a) one linear piece of DNA
During gel electrophoresis, the 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.
You have a piece of circular DNA that can be cut by the restriction nucleases XhoI and SmaI, as indicated in Figure Q10-5. 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
(b) 2
Figure A depicts the restriction map of one segment of the human genome for four restriction nucleases W, X, Y, and Z. Figure Q10-64B depicts the restriction maps of four individual BAC clones that contain segments of human DNA from the region depicted in Figure Q10-64A.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) 2, 1, 4, 3
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
(b) 7
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 hybridizes to a DNA probe.
(b) By placing the library DNA into bacteria, the bacteria can be used to amplify the desired DNA fragments from the DNA library.
Which of the following statements about gel-transfer hybridization (or Southern blotting) is false? (a) This technique involves the transfer of DNA molecules from gel onto nitrocellulose paper or nylon paper. (b) In this technique, single-stranded DNA is separated by electrophoresis. (c) A labeled DNA probe binds to the DNA by hybridization. (d) The DNA that is separated on a gel is not labeled.
(b) In this technique, single-stranded DNA is separated by electrophoresis.
Figure x shows the cleavage sites of several restriction nucleases.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) NcoI
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.
(b) PCR is particularly powerful because after each cycle of replication, there is a linear increase in the amount of DNA available.
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.
(b) Restriction nucleases recognize specific sequences on single-stranded DNA.
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.
(b) The creation of transgenic pigs that expressed insulin was very expensive compared to the cost of creating bacteria that expressed insulin.
you have a linear piece of DNA that can be cut by the restriction nucleases HindIII and EcoRI. If you were to cut this linear DNA with HindIII, what type of DNA fragments do you predict you will obtain? If you were to cut this linear DNA with HindIII, what type of DNA fragments do you predict you will 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
(b) two linear pieces of DNA, only one of which can be cut by EcoRI
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) 1930s. (b) 1950s. (c) 1970s. (d) 1990s.
(c) 1970s
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.
(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.
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.
(c) Incorporation of a dideoxyribonucleoside triphosphate leads to the termination of replication for that strand.
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) NotI GCGGCCGC (d) XzaI GAAGGATCCTTC
(c) NotI GCGGCCGC
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 clone that hybridizes to your probe. (b) The larger the size of the fragments used to make the library, the more difficult it will be to find your gene of interest once you have identified a clone that hybridizes to your probe. (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 clone.
(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.
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.
(c) heat disrupts hydrogen-bonding between complementary nucleotides.
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
(c) promoter DNA sequences
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.
(c) re-form a double helix if the two strands have complementary sequences.
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
(c) sequences of the telomeres (the ends of the chromosomes)
With fully automated Sanger sequencing, all four chain-terminating ddNTPs can be added into a single reaction. This is different from the traditional slab gel Sanger sequencing, where a different reaction had to be carried out for each ddNTP. The mixing of all four ddNTPs can be carried out because ______________. (a) the fully automated Sanger sequencing reactions are loaded onto a capillary gel. (b) the fully automated 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 fully automated 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.
(c) the fully automated 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.
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
(c) the specific location within the cell of the protein encoded by this gene
You are interested in a single-stranded DNA molecule that contains the following sequence:Which molecule can be used as a probe that will hybridize to your sequence of interest? (a) 5′-GATTGCAT-3′ (b) 5′-TACGTTAG-3′ (c) 5′-CTAACGTA-3′ (d) 5′-ATGCAATC-3′
(d) 5′-ATGCAATC-3′
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.
(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.
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
(d) DNA replication
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.
(d) Surgically remove the sexual organs of all the knockouts before you sell them.
You want to design a DNA probe used for hybridization to isolate a clone from a cDNA library. Which of the following concerns about DNA probe design is the most legitimate? (a) You must be careful when designing your probe to take into account which DNA strand was transcribed in mRNA and choose a probe complementary to the mRNA. (b) You must be careful not to include any DNA sequences in your probe that are upstream (5′) of the AUG start codon. (c) You must make sure that all the DNA sequences in your probe lie within an exon, and do not span two exons. (d) You must make sure that all the DNA sequences in your probe are not located downstream (3′) of the polyadenylation signal.
(d) You must make sure that all the DNA sequences in your probe are not located downstream (3′) of the polyadenylation signal.
Second-generation sequencing differs from Sanger sequencing because _____________. (a) second-generation sequencing does not depend on chain-terminator ddNTPs. (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 tens of millions of pieces of DNA at the same time on a single glass slide.
(d) second-generation sequencing can sequence tens of millions of pieces of DNA at the same time on a single glass slide.
you have a piece of circular DNA that can be cut by the restriction nucleases EcoRI, HindIII, and NotI. Which statement 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) two DNA fragments of unequal size will be created when this DNA is cut by both HindIII and EcoRI.
During gel __________________, DNA fragments can be loaded into one end of an agarose slab to separate the fragments on the basis of charge. As ____________________ is applied across the agarose slab, the DNA molecules, which have a __________________ charge, will migrate toward the ___________________ electrode. Because _________________ DNA fragments will migrate more quickly, they will be found furthest away from the area of the gel where the DNA fragments were loaded. One method to visualize the DNA on the agarose slab involves staining the DNA with a dye that will __________________ under ultraviolet light. centrifugation negative digested neutral electrophoresis posistive fluoresce radioactive gravity sequencing irradiate smaller larger voltage
10-10
A nuclease hydrolyzes the __________________ bonds in a nucleic acid. 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 phosphodiester endonucleases polymerase chain reaction exonucleases recombinant DNA gel electrophoresis restriction nucleases hydrogen ribonucleases nucleic acid hybridization
A nuclease hydrolyzes the phosphodiester bonds in a nucleic acid. Nucleases that cut DNA only at specific short sequences are known as restriction nucleases. DNA composed of sequences from different sources is known as recombinant DNA. Gel electrophoresis 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 polymerase chain reaction technique.
