PCB 3023 Exam 3 questions and
answers graded A+ passed
Restriction enzymes cut DNA - correct answer at a specific sequence, whether in cells or in a test
tube
FEEDBACK: Restriction enzymes are enzymes that recognize and cut specific sequences. While
matching sequences are protected in the host bacterium's genome, this is an effective way to cleave
any DNA of foreign origin. Restriction enzymes are widely used in laboratories to cut DNA at a
specific sequence, regardless of DNA's origin.
DNA migrates through the pores of an agarose gel towards the ________ electrode; larger fragments
travel more________. - correct answer positive; slowly
FEEDBACK:
DNA fragments can be separated by size by forcing their migration through a dense gel matrix; the
larger fragments are slower to migrate because they are impeded by the matrix. The DNA fragments
move toward the positive electrode due to their negative charge generated by the phosphate groups
in the molecule's backbone.
DNA in a gel is most often visualized by - correct answer staining with a UV-reactive dye.
FEEDBACK:
DNA itself is colorless under visible light or blacklight. The DNA bands are visualized by adding a UV-
reactive dye that interacts between bases of DNA molecules and observing under UV light.
Which feature of a cloning vector enables bacterial cells to replicate a plasmid to make many more
copies? - correct answer replication origin
FEEDBACK: For a piece of DNA to be replicated by the cell's machinery, it requires a replication origin,
which is a sequence recognized by the cell for the cellular polymerase and other replication enzymes,
in order to begin the copying process. Investigators take advantage of this phenomenon to isolate
many copies of a desired plasmid.
,A genomic library is a collection of plasmids, each containing different chromosomal fragments from
the genome of an organism. A cDNA library, on the other hand, contains only the ________ genome
of an organism. - correct answer coding sequences of genes
FEEDBACK: A cDNA library is a library of DNA fragments that are made from reverse transcription of
mRNA transcripts. This type of library contains only the coding sequences of each gene, since introns
are spliced out of mature mRNAs.
The first step of PCR requires that the DNA to be amplified is - correct answer denatured.
FEEDBACK: In PCR, the target DNA must first be heated to denature the molecule into single-
stranded DNA. This allows the primers to bind in the second step by base-pairing with their
complementary sequence.
Approximately how many double-stranded DNA molecules will be formed from one starting
molecule after three rounds of PCR? - correct answer 8
FEEDBACK: After the first cycle of a PCR reaction, each starting target DNA molecule serves as the
template for generating two new daughter molecules, comparable to DNA replication in cell. The
second cycle will then duplicate each of the molecules from the first cycle, producing four total
molecules, and the third cycle duplicates each of those four molecules into eight.
The DNA polymerase enzyme used in PCR is different from the one used in human cells because it is
able to - correct answer withstand the high temperatures needed for denaturation.
FEEDBACK: PCR uses a polymerase that was isolated from a thermophilic bacterium. This enzyme can
withstand the high heat needed to denature the DNA strands in step one of PCR.
The chain-termination method of sequencing relies on the formation of partial copies of the DNA
fragment that terminate at each position in the sequence. The fragments are separated by size and
the terminating nucleotide is identified by - correct answer the position in the capillary and a unique
fluorescent tag on each nucleotide.
FEEDBACK: The chain-termination method of sequencing (or Sanger sequencing) amplifies the DNA
of interest to form many molecules that are randomly terminated by the incorporation of one of four
different fluorescently labeled dideoxynucleotides. The fragments are separated by size in a capillary
gel matrix and the fluorescent tags are read to reveal the sequence of the DNA molecule.
,The CRISPR system can be used to activate a gene by altering the Cas9 enzyme in what way? - correct
answer fusing an inactive Cas9 to a transcriptional activator
FEEDBACK: Instead of targeting a Cas9 nuclease to a site for making a double-strand break for
genome editing, CRISPR can be used to target various activities to specific locations in the genome.
This is done by inactivating the Cas9 so that it is no longer a nuclease, and then attaching a protein
with a desired activity.
Shown here is an expression vector. For the gene of interest to be expressed in the cells, the gene of
interest must be cloned where in this vector? - correct answer next to the promoter, in the proper
orientation
FEEDBACK: Expression vectors contain a promoter that drives transcription of the gene of interest.
Promoters have directionality, so for the gene to be expressed, the gene must be placed in the
proper location relative to the promoter.
If a protein with a specific activity is isolated, how can the encoding gene be identified? - correct
answer It can be identified by mass spectrometry followed by gene database searching.
FEEDBACK: Proteins of interest can be identified using mass spectrometry to determine many short
amino acid sequences read from the protein. These sequences can then be compared to a database
of all known protein-coding genes to identify the gene that encodes this protein.
Gel electrophoresis separates DNA fragments from each other by virtue of which feature? - correct
answer length
FEEDBACK: Correct. Gel electrophoresis separates DNA fragments from each other by virtue of their
length. Certain types of gels can differentiate between fragments that differ in length by a single
nucleotide pair.
When a mixture of DNA fragments of different sizes is loaded into an agarose gel and a voltage is
applied, the DNA will migrate in the gel. Which molecules will migrate the fastest? - correct answer
the smallest fragments
FEEDBACK: Correct. When a mixture of DNA fragments of different sizes is loaded onto an agarose
gel and a voltage is applied, the smallest DNA fragment will migrate the fastest in the gel. The
, lowermost bands on the gel will contain the smallest DNA fragments. If the voltage is applied for too
long, those fragments can actually run off the end of the gel.
What does the term "DNA cloning" refer to? - correct answer making many identical copies of a DNA
molecule
FEEDBACK: Correct. DNA cloning is the act of making many identical versions of a DNA molecule.
When the cloning plasmid is inserted into a bacterial cell, the cell replicates (or clones) the plasmid
many times.
When making a DNA library from a starting material of mRNA, which enzyme is first required to copy
the mRNA molecules into DNA molecules? - correct answer reverse transcriptase
FEEDBACK: Correct. This same type of enzyme allows RNA viruses such as HIV to replicate their
genomes and integrate into a host cell's DNA
What is the starting material for making a cDNA library? - correct answer mRNA
FEEDBACK: Correct. mRNA is the starting material, or the template, for making a cDNA library. The
DNA that goes into a cDNA library is not genomic DNA; it is DNA copied from the mRNAs present in a
particular type of cell. To prepare a cDNA library, all of the mRNAs are extracted, and double-
stranded DNA copies of these mRNAs are produced.
Identify each enzyme step by dragging the enzyme label to its correct target. There are four labels
and only two targets, so two labels are not used. - correct answer B, C
FEEDBACK: Correct. To insert a piece of DNA into a plasmid vector, the purified plasmid DNA is
opened up by a restriction enzyme that cleaves it at a single site, and the DNA fragment to be cloned
is then spliced into that site using DNA ligase.
Growth hormone, secreted by the pituitary gland, is important for organismal growth. Individuals
with two mutated, nonfunctional copies of the growth hormone gene exhibit dwarfism. Early
treatments relied on injecting patients with growth hormone isolated from the pituitary glands of
cadavers, an expensive procedure that unfortunately infected some recipients with prion particles
that caused Creutzfeldt-Jakob disease. Researchers sought a safer source of growth hormone via the
production of human growth hormone in E. coli bacteria. Put in order the series of steps undertaken
to create human growth hormone producing transgenic E. coli. - correct answer 1. Isolate mRNA
from pituitary gland.
answers graded A+ passed
Restriction enzymes cut DNA - correct answer at a specific sequence, whether in cells or in a test
tube
FEEDBACK: Restriction enzymes are enzymes that recognize and cut specific sequences. While
matching sequences are protected in the host bacterium's genome, this is an effective way to cleave
any DNA of foreign origin. Restriction enzymes are widely used in laboratories to cut DNA at a
specific sequence, regardless of DNA's origin.
DNA migrates through the pores of an agarose gel towards the ________ electrode; larger fragments
travel more________. - correct answer positive; slowly
FEEDBACK:
DNA fragments can be separated by size by forcing their migration through a dense gel matrix; the
larger fragments are slower to migrate because they are impeded by the matrix. The DNA fragments
move toward the positive electrode due to their negative charge generated by the phosphate groups
in the molecule's backbone.
DNA in a gel is most often visualized by - correct answer staining with a UV-reactive dye.
FEEDBACK:
DNA itself is colorless under visible light or blacklight. The DNA bands are visualized by adding a UV-
reactive dye that interacts between bases of DNA molecules and observing under UV light.
Which feature of a cloning vector enables bacterial cells to replicate a plasmid to make many more
copies? - correct answer replication origin
FEEDBACK: For a piece of DNA to be replicated by the cell's machinery, it requires a replication origin,
which is a sequence recognized by the cell for the cellular polymerase and other replication enzymes,
in order to begin the copying process. Investigators take advantage of this phenomenon to isolate
many copies of a desired plasmid.
,A genomic library is a collection of plasmids, each containing different chromosomal fragments from
the genome of an organism. A cDNA library, on the other hand, contains only the ________ genome
of an organism. - correct answer coding sequences of genes
FEEDBACK: A cDNA library is a library of DNA fragments that are made from reverse transcription of
mRNA transcripts. This type of library contains only the coding sequences of each gene, since introns
are spliced out of mature mRNAs.
The first step of PCR requires that the DNA to be amplified is - correct answer denatured.
FEEDBACK: In PCR, the target DNA must first be heated to denature the molecule into single-
stranded DNA. This allows the primers to bind in the second step by base-pairing with their
complementary sequence.
Approximately how many double-stranded DNA molecules will be formed from one starting
molecule after three rounds of PCR? - correct answer 8
FEEDBACK: After the first cycle of a PCR reaction, each starting target DNA molecule serves as the
template for generating two new daughter molecules, comparable to DNA replication in cell. The
second cycle will then duplicate each of the molecules from the first cycle, producing four total
molecules, and the third cycle duplicates each of those four molecules into eight.
The DNA polymerase enzyme used in PCR is different from the one used in human cells because it is
able to - correct answer withstand the high temperatures needed for denaturation.
FEEDBACK: PCR uses a polymerase that was isolated from a thermophilic bacterium. This enzyme can
withstand the high heat needed to denature the DNA strands in step one of PCR.
The chain-termination method of sequencing relies on the formation of partial copies of the DNA
fragment that terminate at each position in the sequence. The fragments are separated by size and
the terminating nucleotide is identified by - correct answer the position in the capillary and a unique
fluorescent tag on each nucleotide.
FEEDBACK: The chain-termination method of sequencing (or Sanger sequencing) amplifies the DNA
of interest to form many molecules that are randomly terminated by the incorporation of one of four
different fluorescently labeled dideoxynucleotides. The fragments are separated by size in a capillary
gel matrix and the fluorescent tags are read to reveal the sequence of the DNA molecule.
,The CRISPR system can be used to activate a gene by altering the Cas9 enzyme in what way? - correct
answer fusing an inactive Cas9 to a transcriptional activator
FEEDBACK: Instead of targeting a Cas9 nuclease to a site for making a double-strand break for
genome editing, CRISPR can be used to target various activities to specific locations in the genome.
This is done by inactivating the Cas9 so that it is no longer a nuclease, and then attaching a protein
with a desired activity.
Shown here is an expression vector. For the gene of interest to be expressed in the cells, the gene of
interest must be cloned where in this vector? - correct answer next to the promoter, in the proper
orientation
FEEDBACK: Expression vectors contain a promoter that drives transcription of the gene of interest.
Promoters have directionality, so for the gene to be expressed, the gene must be placed in the
proper location relative to the promoter.
If a protein with a specific activity is isolated, how can the encoding gene be identified? - correct
answer It can be identified by mass spectrometry followed by gene database searching.
FEEDBACK: Proteins of interest can be identified using mass spectrometry to determine many short
amino acid sequences read from the protein. These sequences can then be compared to a database
of all known protein-coding genes to identify the gene that encodes this protein.
Gel electrophoresis separates DNA fragments from each other by virtue of which feature? - correct
answer length
FEEDBACK: Correct. Gel electrophoresis separates DNA fragments from each other by virtue of their
length. Certain types of gels can differentiate between fragments that differ in length by a single
nucleotide pair.
When a mixture of DNA fragments of different sizes is loaded into an agarose gel and a voltage is
applied, the DNA will migrate in the gel. Which molecules will migrate the fastest? - correct answer
the smallest fragments
FEEDBACK: Correct. When a mixture of DNA fragments of different sizes is loaded onto an agarose
gel and a voltage is applied, the smallest DNA fragment will migrate the fastest in the gel. The
, lowermost bands on the gel will contain the smallest DNA fragments. If the voltage is applied for too
long, those fragments can actually run off the end of the gel.
What does the term "DNA cloning" refer to? - correct answer making many identical copies of a DNA
molecule
FEEDBACK: Correct. DNA cloning is the act of making many identical versions of a DNA molecule.
When the cloning plasmid is inserted into a bacterial cell, the cell replicates (or clones) the plasmid
many times.
When making a DNA library from a starting material of mRNA, which enzyme is first required to copy
the mRNA molecules into DNA molecules? - correct answer reverse transcriptase
FEEDBACK: Correct. This same type of enzyme allows RNA viruses such as HIV to replicate their
genomes and integrate into a host cell's DNA
What is the starting material for making a cDNA library? - correct answer mRNA
FEEDBACK: Correct. mRNA is the starting material, or the template, for making a cDNA library. The
DNA that goes into a cDNA library is not genomic DNA; it is DNA copied from the mRNAs present in a
particular type of cell. To prepare a cDNA library, all of the mRNAs are extracted, and double-
stranded DNA copies of these mRNAs are produced.
Identify each enzyme step by dragging the enzyme label to its correct target. There are four labels
and only two targets, so two labels are not used. - correct answer B, C
FEEDBACK: Correct. To insert a piece of DNA into a plasmid vector, the purified plasmid DNA is
opened up by a restriction enzyme that cleaves it at a single site, and the DNA fragment to be cloned
is then spliced into that site using DNA ligase.
Growth hormone, secreted by the pituitary gland, is important for organismal growth. Individuals
with two mutated, nonfunctional copies of the growth hormone gene exhibit dwarfism. Early
treatments relied on injecting patients with growth hormone isolated from the pituitary glands of
cadavers, an expensive procedure that unfortunately infected some recipients with prion particles
that caused Creutzfeldt-Jakob disease. Researchers sought a safer source of growth hormone via the
production of human growth hormone in E. coli bacteria. Put in order the series of steps undertaken
to create human growth hormone producing transgenic E. coli. - correct answer 1. Isolate mRNA
from pituitary gland.
