Ch. 9 - Biotechnology

A graduate student wants to clone a particular gene into a plasmid. The sequence includes AluI and BamHI sites on both sides of the desired fragment. AluI cuts symmetrically directly between the G and C nucleotides in a palindromic 5' AGCT 3' sequence. BamHI cuts asymmetrically directly between the G and G nucleotides in a palindromic 5' GGATCC 3' sequence. Which of the two restriction endonucleases should the graduate student choose, and why? A) BamHI to cut both sides-since this enzyme cuts asymmetrically, it'll leave the sticky, cohesive single-strand DNA ends that will make it easier to ligate into a BamHI-cut plasmid DNA sequence. B) AluI to cut both sides-it's always easier to ligate together blunt ends of DNA. She should also use AluI on the plasmid she wants to put the fragment into. C) BamHI on the fragment, and AluI on the plasmid-this will give her the matching sequences to anneal/ligate together on the fragment/plasmid combination. D) BamHI on one side of the fragment, and AluI on the other side-this would keep the fragment from sticking right back to where it was cut out from in the original DNA. E) Neither of these endonucleases will really be useful; she should look for a single enzyme that creates either blunt ends or sticky ends, depending on the plasmid that she is using as a vector.

A

HPV is a non-enveloped, double stranded DNA virus. What are the components of this virus? A) DNA and protein B) RNA and protein C) DNA, RNA, and protein D) DNA, protein, and phospholipids E) RNA, protein, and phospholipids

A

Host cells containing recombinant DNA can be selected on the basis of the properties of the A) vector. B) ribosomes. C) enzymes. D) virus. E) introns.

A

Identify the correct sequence in which the steps below occur during a single PCR cycle. 1) Complementary base pairing between primers and target DNA. 2) Addition of DNA nucleotides by Taq DNA polymerase. 3) Heat separation of strands of target DNA. A) 3; 1; 2 B) 1; 2; 3 C) 1; 3; 2 D) 2; 3; 1 E) 2; 1; 3

A

If PCR is carried out on a sample using primers specific for HPV 16 and no DNA is amplified, can a person assume that they are HPV-free? A) No. The person likely does not have HPV16 but they may have another HPV strain. B) Yes. If there is no HPV16 present, there definitely won't be any other strain of HPV present either. C) Yes. Primers specific for HPV 16 would also detect all other strains of HPV, so a negative test indicates the person is free of any HPV. D) No. The negative result simply indicates that HPV is not a DNA virus but is in fact an RNA virus. E) No. The negative result simply indicates that HPV is not a DNA virus but is in fact a bacterium which has a different type of DNA.

A

Selecting for transformants involves A) identifying organisms that have taken up recombinant DNA. B) identifying organisms that have taken up recombinant RNA. C) identifying organisms that are producing proteins. D) identifying organisms that are producing DNA. E) identifying organisms that are producing antibiotics.

A

Short tandem repeats (STRs) A) are useful in identifying specific individuals. B) are important sites in vectors where foreign DNA can be integrated. C) are errors that can arise during DNA sequencing. D) are DNA fragments generated during PCR. E) are generally found in exons.

A

The entire set of cloned fragments of the complete human genome is termed a A) DNA library. B) book of genes. C) recombinant gene. D) restructured genome. E) genetic set.

A

The polymerase chain reaction is used to duplicate small sections of A) DNA. B) RNA. C) proteins. D) lipids. E) lipopolysaccharides.

A

Which of the following is NOT True about laboratory strains of E. coli being desirable hosts for genetic engineering? A) E. coli is fastidious but can usually be grown in the lab. B) The genetics of E. coli is very well known. C) E. coli is especially able to express foreign genes. D) E. coli has known phenotypic characteristics. E) All of the answer choices are correct.

A

Why are primers needed in DNA sequencing? A) DNA polymerase needs a primer because it can only add nucleotides to an existing nucleotide strand. B) DNA polymerase needs a primer to help it recognize a vector for gene insertion. C) DNA polymerase needs a primer for proofreading and mismatch repair after a gene has been sequenced. D) The primer acts as a template for the dideoxynucleotides and deoxynucleotides. E) All of the answer choices are correct.

A

Why must an agarose gel be placed in a buffer solution for DNA gel electrophoresis? A) Ions in the buffer conduct the electric current needed to move the DNA fragments in the gel matrix. B) The DNA fragments will disintegrate unless there is a buffer present to prevent this from happening. C) Even distilled, autoclaved water has a high number of DNases in it that would destroy the DNA. D) The buffer contains phosphates, and the DNA fragments must be phosphorylated before they move in agarose. E) DNA cannot be detected unless buffer is added to the system; the buffer colors the DNA fragments for visualization.

A

You are examining the DNA profile of an unknown pathogen. The pathogen's DNA has been digested with EcoRI restriction enzyme. There are 7 bands on DNA on the gel. Which of the following is NOT True? A) The original piece of DNA has seven EcoRI restriction sites. B) The original piece of DNA has six EcoRI restriction sites. C) The DNA has not been completely restricted. D) The restriction enzyme has been denatured. E) The restriction enzyme EcoRI was isolated from E. coli.

A

A common way to identify the E. coli that carries the desired recombinant DNA is by using a(n) A) vector. B) probe. C) host. D) plasmid. E) antibiotic.

B

A danger in using E. coli in cloning is that A) E. coli could cause disease. B) the outer membrane is toxic to humans. C) the human cells may reject the insertion. D) the exons may invert the introns. E) working with E. coli requires a BSL3 laboratory.

B

All of the following are True about DNA probes EXCEPT they A) may be obtained from denatured tagged dsDNA. B) are usually tagged dsRNA. C) may be obtained from similar genes from another organism. D) may be synthesized usually using information based on the protein sequence. E) may be tagged with a fluorescent dye.

B

Dideoxynucleotides A) are useful in nucleic acid sequencing AND have two additional hydroxyl groups at the 2' and 3' carbons. B) are useful in nucleic acid sequencing AND act as chain terminators. C) act as chain initiators AND have two additional hydroxyl groups at the 2' and 3' carbons. D) act as chain initiators AND are useful in nucleic acid sequencing. E) are useful in generating proteins AND act as chain terminators.

B

HPV is a DNA virus and can be detected in a sample using PCR. Is it possible to detect an RNA virus using this technique or something similar? A) No; there is no known process by which RNA can be copied because the subunits of RNA are amino acids and these cannot be amplified without the use of ribosomes. B) Yes; a variation of PCR is RT-PCR in which an enzyme called reverse transcriptase generates cDNA from mRNA in a sample, and that cDNA is then amplified exponentially. C) Yes; Taq polymerase is a unique DNA polymerase that can copy either RNA or DNA, so it doesn't matter what type of virus is present-the enzyme will still detect it in a PCR reaction. D) No; PCR can only be carried out on a double-stranded molecule such as DNA, and RNA is a single-stranded molecule. E) There is no answer to this question because nobody has ever tried to amplify RNA; viruses contain both DNA and RNA so it is always possible to detect the DNA component.

B

In a FISH experiment, what would happen if unbound probe was not washed off? A) Nothing-it's not necessary to wash off the unbound probe and doing so just adds an extra step to the procedure. B) You would get False-positive results in different areas where the probe hadn't actually bound, but it was still sitting there and lighting up. C) Your FISH would be floating at the top of the tank due to the toxicity of the probe building up within them. D) Nothing-the target nucleotide sequences are labeled, not the probe. Therefore, excess unbound probe wouldn't matter for the experiment. E) You would get an intermediate color on the array because of the presence of both bound and unbound probes that fluoresce at different temperatures.

B

Mitochondrial DNA (mtDNA) in humans A) is always donated to the offspring from both parents. B) can be used to identify related people. C) can be isolated only from intact embryos. D) can be used to establish paternity. E) is linear, single-stranded DNA.

B

Polymerase chain reaction (PCR) can be used to perform DNA sequencing reactions. In this case, are two primers (a forward and a reverse) necessary? A) Yes-you can't perform PCR without two specific primers to amplify the region in question in the DNA. B) No-dideoxynucleotide sequencing depends on different length fragments being formed and then separated based on size. This can take place with only a specific forward OR a specific reverse primer. C) No-you actually need a primer pair for each round of DNA amplification ... so you'll need many, many primer pairs, depending how many rounds you plan to do. D) Yes-and it will be important to make sure that the primer pairs are made with dideoxynucleotides that are labeled with fluorescent dyes. Otherwise, you won't be able to detect the fragments that are made in the PCR process. E) Yes-if you only have one primer, you will only be able to determine the dideoxynucleotide sequence of RNA, which is a single-stranded molecule.

B

The Ti plasmid is naturally found in A) Escherichia. B) Agrobacterium. C) Pseudomonas. D) Staphylococcus. E) E. coli AND Staphylococcus.

B

The energy to separate fragments during agarose gel electrophoresis is supplied by A) gravity. B) electricity. C) active transport. D) agarosis. E) buffers.

B

The gene for human insulin has been successfully cloned in A) S. aureus. B) E. coli. C) rhinovirus. D) human cells. E) pig cells.

B

The molecule(s) that act as molecular glue to bind DNA fragments together is/are A) DNAse. B) DNA ligase. C) ligandase. D) polymerase. E) DNAse AND ligandase.

B

The molecules used to cut target DNA in genetic engineering are A) exonucleases. B) restriction enzymes. C) proteases. D) RNA polymerases. E) DNA ligases.

B

The polymerase chain reaction is used to A) amplify mRNA. B) amplify certain sections of DNA. C) produce proteins. D) produce long polymers of carbohydrates to be used in electrophoresis. E) produce long polymers of amino acids to be used in electrophoresis.

B

What would the outcome be if you forgot to do the washing step when carrying out FISH on a sample containing bacteria? A) Nothing. The washing step is recommended but is not necessary and can be omitted. B) Unbound probe would remain on the slide and would fluoresce, making it impossible to see individual cells. C) The unbound probe would anneal strongly to the glass slide in random patterns that would look like bacteria. D) The unbound probe would cause lysis of the target bacterial cells, destroying their nuclei and mitochondria. E) Nothing. Unbound probe will not fluoresce, so even if it is present, it will not affect the results.

B

When a vector that uses the lacZ gene as a second marker is used in a cloning experiment, bacteria that contain the recombinant DNA will give rise to A) red colonies. B) white colonies. C) blue colonies. D) cream colonies. E) All of the answer choices are correct.

B

Agarose gel electrophoresis separates nucleic acid fragments according to A) density. B) shape. C) size. D) nucleobase sequence. E) type of 5C sugar.

C

DNA molecules that contain pieces of DNA from two different sources are defined as A) biotechnology. B) gene cloning. C) recombinant DNA. D) genetic engineering. E) mutation.

C

Identify the statement about digestion of DNA by restriction enzymes that is NOT True. A) It produces sticky ends. B) It produces blunt ends. C) One strand of the DNA molecule is cut. D) It generates restriction fragments. E) All of the answer choices are correct.

C

In a recent research article describing the use of FISH to detect LNTB, the authors noted that they used probes that were only 20 base pairs (bp) in length rather than the conventional 100 bp-500 bp. Given what you know about acid-fast bacteria, why do you think they took this approach? A) The nature of the Mycobacterial cytoplasmic membrane likely makes is difficult for larger probes to enter the cell. B) The nature of the Mycobacterial capsule likely makes is difficult for larger probes to enter the cell. C) The nature of the Mycobacterial cell wall likely makes is difficult for larger probes to enter the cell. D) Mycobacteria have a lipopolysaccharide outer membrane through which larger probes cannot enter. E) Mycobacteria have smaller ribosomes than any other bacteria and the probes are targeted at rRNA.

C

PCR produces A) DNA fragments of all possible sizes. B) DNA fragments that are one nucleotide larger than the next fragment. C) DNA fragments of a particular size. D) protein fragments of all possible sizes. E) DNA fragments that are three nucleotides smaller than the previous fragment.

C

Possessing the entire sequence of a particular human genome may not be as useful as we think. Why not? A) Every human genome is different enough that knowing ONE human's DNA sequence can't tell us almost anything about ALL humans. B) It's not the DNA sequence that matters-we need to know the mRNA sequence of the human genome. C) Due to the presence of introns/exons, and splicing of RNA after transcription, the DNA sequence doesn't necessarily tell us the exact number/type of proteins that will eventually be made from it. D) The amount of "junk DNA" present in the human genome masks any useful genetic information that we'd like to obtain. E) Due to the presence of introns/exons, and pre-transcriptional modification, the protein profile varies considerably among people, so it would be better to determine that.

C

Restriction enzymes have proved so useful in manipulating DNA because A) they cut at defined sites AND the sticky ends make it very easy to allow recombination of DNA with RNA. B) they cut at random sites AND the sticky ends make it very easy to allow recombination of any type of DNA. C) they cut at defined sites AND the sticky ends make it very easy to allow recombination of any type of DNA. D) they protect eukaryotes against virus attack AND they cut both RNA and DNA. E) they protect eukaryotes against virus attack AND the sticky ends make it very easy to allow recombination of DNA with RNA.

C

Starting with a single piece of dsDNA, after 3 PCR cycles there are A) 2 additional pieces of dsDNA. B) 4 additional pieces of dsDNA. C) 8 additional pieces of dsDNA. D) 16 additional pieces of dsDNA. E) 1 additional piece of dsDNA.

C

The Ti plasmid is used as a vector to transfer DNA into A) viruses. B) bacteria. C) plant cells. D) animal cells. E) protozoa.

C

The agarose used in electrophoresis A) interacts electrically with the DNA. B) chemically binds to the DNA. C) separates DNA fragments by size. D) selectively sorts recombinant DNA from host DNA. E) denatures DNA/RNA.

C

The size of the amplified DNA fragment generated during PCR is determined by A) how many cycles are performed. B) the size of the template DNA. C) the location to which the primers anneal. D) how much Taq polymerase is used. E) the time for each cycle.

C

When detecting microorganisms, a probe that hybridizes to sequences on ribosomal RNA (rRNA) is generally used. This is because A) not all bacteria have DNA but they all have large quantities of ribosomal RNA. B) rRNA is in the cytoplasm so is easy to detect but DNA is in the nucleus so is harder to detect. C) cells that are dividing can have thousands of copies of rRNA, increasing the technique's sensitivity. D) RNA is a single-stranded molecule but DNA is a triple helix and must be denatured. E) These are all reasons that rRNA is targeted.

C

Which is the CORRECT definition of PCR? A) Use of the enzyme reverse transcriptase to generate cDNA from mRNA, and then amplifying the cDNA exponentially using RNA polymerase. B) In vitro process of determining the nucleotide sequence of a DNA molecule using a variety of enzymes. C) In vitro technique used to repeatedly duplicate (amplify) a specific region of a DNA molecule, increasing the number of copies exponentially. D) Procedure in which a fragment of DNA is inserted into a vector and then transferred into another cell, where it then replicates. E) The process in which two complementary strands of DNA from different sources are annealed to create a hybrid double-stranded molecule.

C

Which of the following about DNA microarray technology is NOT True? A) It may use many DNA fragments that function like probes. B) It involves attaching nucleotides to a solid support such as a glass slide. C) It relies on visual detection of the labeled probes after hybridization. D) It uses nucleic acid hybridization. E) It involves the use of fluorescently labeled singe-stranded cDNA.

C

Which of the following genera has proved useful for manipulating plant cells? A) Escherichia B) Bacillus C) Agrobacterium D) Pseudomonas E) Rhizobium

C

Which of the following is NOT True about an ideal vector? A) A vector may be a plasmid or bacteriophage. B) A vector has a restriction enzyme recognition site. C) A vector contains an RNA primer. D) A vector contains an origin of replication. E) A vector contains a selectable marker.

C

A dye often used for its ease and sensitivity to visualize nucleic acid after agarose gel electrophoresis is A) nigrosin. B) malachite green. C) gold oxide. D) ethidium bromide. E) crystal violet.

D

During PCR, which primer anneals to template DNA at its 3' end? A) The forward primer only. B) The reverse primer only. C) Either the forward primer or the reverse primer. D) Both the forward primer and the reverse primer. E) Primers don't bind to template DNA.

D

Fluorescence in situ hybridization (FISH) A) uses virus hosts, uses a labeled probe, AND is useful in microbial ecology. B) uses a labeled probe, allows identification of particular bacterial groups in mixed samples, AND uses virus hosts. C) is useful in microbial ecology, allows identification of particular bacterial groups in mixed samples AND depends on electron microscopy. D) uses a labeled probe, is useful in microbial ecology, AND allows identification of particular bacterial groups in mixed samples. E) is useful in microbial ecology, allows identification of particular bacterial groups in mixed samples AND uses virus hosts.

D

Genetic engineering A) allows the use of bacteria as production factories for a number of molecules AND is dependent on RNA enzymes. B) relies on recombinant DNA technology AND relies completely on conjugation. C) allows the use of bacteria as production factories for a number of molecules AND relies completely on conjugation. D) allows the use of bacteria as production factories for a number of molecules AND relies on recombinant DNA technology. E) is dependent on RNA enzymes AND relies on recombinant DNA technology.

D

Genetic engineering of plants has so far produced A) pest-resistant plants. B) plants that are herbicide resistant. C) plants with increased nutritional value. D) All of the answer choices are correct. E) None of the answer choices is correct.

D

Genetically modified food has raised some concerns because A) it contains radioactive nucleic acids. B) it contains very dangerous allergens. C) it releases radioactivity into the environment. D) the modified DNA may transfer to other organisms. E) All of these are valid concerns.

D

How are target cells identified using the FISH technique? A) Using an electron microscope. B) Using DNA microarrays. C) Using DNA sequencing. D) Using a fluorescence microscope. E) By detecting UV levels.

D

Human DNA cut with restriction enzyme A can be joined to A) uncut human DNA. B) uncut bacterial DNA. C) bacterial DNA cut with restriction enzyme H. D) bacterial DNA cut with restriction enzyme A. E) bacterial DNA cut with a human restriction enzyme.

D

In order to get around the lack of ability of prokaryotes to remove introns from precursor RNA, it may be necessary to A) use the DNA directly. B) use the DNA after it has been processed. C) use different promoters. D) generate cDNA from mRNA. E) turn cDNA into mRNA.

D

PCR generates a DNA fragment of a distinct size even when the whole viral chromosome is used as a template. What determines the boundaries of the amplified fragment? A) The concentration of one particular deoxynucleotide in the reaction. B) The length of time of the elongation step in each cycle. C) The position of a termination sequence, which causes the Taq polymerase to fall off the template. D) The sites on the template DNA to which the specific primers used in the reaction anneal. E) The temperature at which the elongation step in each cycle is carried out.

D

Taq polymerase is A) a reverse transcriptase. B) an RNA polymerase. C) an enzyme from Escherichia coli. D) a heat-stable DNA polymerase from Thermus aquaticus. E) an RNA polymerase AND an enzyme from Escherichia coli.

D

The DNA polymerase used in PCR comes from the bacterium thermophile Thermus aquaticus, and is called Taq polymerase. Why is this enzyme used, and not a DNA polymerase from an organism such as E. coli? A) The DNA synthesis step of the PCR cycle occurs at 95ᵒC; Taq polymerase is from a bacterium that grows in high temperatures and can function at this temperature, while DNA polymerase from a mesophile such as E. coli would be denatured at this temperature. B) The DNA synthesis step of the PCR cycle occurs at 72ᵒC; Taq polymerase can function at this temperature, while DNA polymerase from a mesophile such as E. coli requires significantly higher temperatures in order to function correctly. C) E. coli is an RNA organism and therefore depends on RNA polymerase for its replication cycle; it is not possible to obtain DNA polymerase from this bacterium. D) The DNA synthesis step of the PCR cycle occurs at 72ᵒC; Taq polymerase is from a bacterium that grows in high temperatures and can function at this temperature, while DNA polymerase from a mesophile such as E. coli would be denatured at this temperature. E) DNA polymerase from Thermus aquaticus is a very active enzyme. It is able to synthesize DNA at a faster rate than any other known DNA polymerase which is important because the key to successful PCR is a speedy reaction.

D

The sequence of cDNA synthesized from an mRNA template with the sequence AUGGUA would be ________. This cDNA probe would hybridize to gene chip DNA with the sequence ________. A) UACCAU; ATGGTA B) TACCAT; AUGGUA C) AUGGUA; AUGGUA D) TACCAT; ATGGTA E) AUGGUA; TACCAT

D

Common vectors used for cloning genes are A) bacteria. B) viruses. C) nucleotides. D) plasmids. E) viruses AND plasmids.

E

Double-stranded DNA will separate into two strands when exposed to A) high temperature AND low pH B) high pH AND low salt C) low temperature AND high salt D) low salt AND low pH E) high temperature AND high pH.

E

Goal(s) of gene cloning may be to produce A) a protein. B) many copies of the gene to be used as a probe. C) many copies of the gene for sequencing. D) more copies of the host cell. E) a protein, many copies of the gene to be used as a probe, AND many copies of the gene for sequencing.

E

Knowing the sequence of a genome is useful in A) identifying genetic alterations associated with disease AND studying evolutionary relationships. B) studying evolutionary relationships AND determining protein sequences. C) determining protein sequences AND identifying genetic alterations associated with disease. D) determining protein sequences BUT not identifying genetic changes. E) identifying genetic alterations associated with disease, studying evolutionary relationships, AND determining protein sequences.

E

PCR is particularly useful in A) detecting viable yet non-culturable organisms. B) assessing impure (multiple types of bacteria present) samples. C) dealing with very small numbers of bacteria. D) relatively quickly producing results. E) All of the answer choices are correct.

E

Plasmids work well for insertion of foreign DNA into a cell. Which statement is False? A) Plasmids have an origin of replication. B) Plasmids are relatively small compared with a chromosome. C) Plasmids can replicate independent of the chromosome. D) Plasmids usually contain a selectable marker such as antibiotic resistance. E) All known bacteria contain plasmids of some kind.

E

Scientists have cloned the human insulin gene into E. coli. Which of the following would NOT have been used in the procedure? A) A plasmid B) Competent bacteria C) A restriction enzyme D) DNA ligase E) A bacteriophage

E

The primer used in Sanger (dideoxy chain termination) sequencing A) can have any random nucleotide sequence. B) has a nucleotide sequence complementary to the 5' end or the 3' end of the region to be copied. C) has a nucleotide sequence complementary to the 5' end of the region to be copied. D) must have a sequence beginning and ending with the same nucleotide. E) has a nucleotide sequence complementary to the 3' end of the region to be copied.

E

When a tissue sample such as lymph node tissue is to be analyzed by FISH, it must first be treated with chemicals. Which of the following is NOT a reason that this step is needed? A) To maintain cell shape. B) To inactivate enzymes that might otherwise degrade the nucleic acid of the cells. C) To make the cells more permeable so that the labeled probe can easily enter. D) To inactivate enzymes that might otherwise degrade the nucleic acid of the cells AND to maintain cell shape. E) To break down the cellulose walls of the tissue so that the probes can enter those cells.

E

Which nitrogenous base does the dideoxynucleotide ddNTP contain? A) Adenine B) Thymine C) Cytosine D) Guanine E) A, T, G or C

E

Bacteria use CRISPR for gene editing.

False

Most eukaryotic genes are cloned directly into the vector for expression in prokaryotes.

False

PCR typically results in the generation of fragments of all sizes.

False

When using lacZ containing vectors, colonies containing intact vector turn white.

False

A DNA microarray contains oligonucleotides that contain a label.

True

A very common vector is a plasmid.

True

Agarose gel electrophoresis may be considered as a partial purification technique

True

DNA probes are used to find regions of complementary DNA.

True

FISH uses labeled probes to detect specific whole cells.

True

It is useful to have a reference sequence when assembling DNA sequence data in high through-put methods because assembly will be quicker if two sequences can be compared.

True

PCR is useful for amplifying a particular section of DNA.

True

Vectors must have at least one restriction enzyme recognition site.

True