____ DNA technology uses in vitro molecular techniques that combine DNA fragments to produce novel arrangements.

Recombinant

A molecule that has covalently linked DNA fragments from at least two sources is called a ____ ____ molecule.

recombinant DNA

Making many copies of a particular DNA segment using vectors or the polymerase chain reaction is called gene

cloning

You would ____ a gene to make many copies of that gene.

Blank 1: clone or amplify

Which of the following is pharmaceutical product that is produced by bacteria expressing the human gene?

Multiple choice question.

Insulin

Simvastatin

Oxycodone

Aspirin

Insulin

What is recombinant DNA technology?

Multiple choice question.

The only way to cure disease

The production of new arrangements of DNA

Double-stranded breaks in chromosomes

The control of expression of bacterial genes

The production of new arrangements of DNA

A particular gene to be cloned is often isolated from ______.

Multiple choice question.

bacterial DNA only

in vitro constructed DNA

chromosomal DNA

RNA

chromosomal DNA

A recombinant DNA molecule has covalently linked DNA fragments from ______.

Multiple choice question.

bacteria and viruses

genes that encode protein and pseudogenes

at least two different sources

bacteria and humans only

at least two different sources

What is a cloning vector?

Multiple choice question.

A molecule that carries the DNA to be cloned

A large DNA molecule with many genes

A molecule that creates mutations in DNA segments

A cell from the Domain Archaea

A molecule that carries the DNA to be cloned

The replication of recombinant DNA molecules inside a host cell is one form of ______.

Multiple choice question.

DNA sequencing

mutagenesis

gene cloning

Northern blotting

gene cloning

What is the term that describes a cell that contains a DNA cloning vector?

Multiple choice question.

Site-directed mutant

Vectorized cell

Bacteriophage

Host cell

Host cell

What is the purpose of gene cloning?

Multiple choice question.

To determine what vectors are plasmids

To analyze DNA binding proteins

To track the inheritance of an allele

To produce many copies of a DNA molecule of interest

To produce many copies of a DNA molecule of interest

A small circular DNA molecule that is often used as a vector in gene cloning is called a(n)

plasmid

Select all that apply

Which of the following are common uses of gene cloning?

Multiple select question.

The expression of a cloned gene can be used to discover its cellular function.

Cloned genes can be introduced into bacteria to make medicines.

Cloned genes are always used in forensic investigations.

Cloned genes can be used in trials of gene therapy.

The expression of a cloned gene can be used to discover its cellular function.

Cloned genes can be introduced into bacteria to make medicines.

Cloned genes can be used in trials of gene therapy.

Naturally occurring plasmids that confer resistance to antibiotics are called

Blank 1: R

Blank 2: plasmids, factors, or factor

True or false: Chromosomal DNA is a common source of cloned DNA.

True

Reason:

Although any DNA can be cloned, it is convenient to separate the gene of interest from the chromosomal DNA.

A vector requires an origin of replication so that it can be ______.

Multiple choice question.

analyzed through DNA sequencing

altered by the host cell

used to express proteins

copied many times by the host cell

copied many times by the host cell

A DNA molecule that acts as a carrier of DNA that is to be cloned is called a(n) ______.

Multiple choice question.

cloning vector

initiation complex

transfer RNA

selectable marker

cloning vector

A cell that harbors a vector is called a

host cell

Which sequence determines whether or not a vector can replicate in a particular cell?

Multiple choice question.

The origin of replication

The translation start site

The antibiotic resistance site

An Eco RI restriction site

The origin of replication

What is a plasmid?

Multiple choice question.

A gene for a selectable marker, such as antibiotic resistance

A small circular DNA molecule often used as a vector in gene cloning

A virus that is missing several genes and is often used as a vector in gene cloning

A large linear DNA molecule with an origin of replication

A small circular DNA molecule often used as a vector in gene cloning

A vector must contain the ____ ____ that is recognized by the species of the host cell and allows the host cell to make lots of copies of the vector.

origin of replication

R factors make useful vectors because they ______.

Multiple choice question.

confer resistance to antibiotics

can accept chromosomal DNA

do not contain an origin of replication

are especially small

confer resistance to antibiotics

Why would one use a vector with a selectable marker?

Multiple choice question.

To identify protein-binding DNA sequences

To identify cells containing the vector

To create site-directed mutants

To allow the enzymes of the host cell to replicate the vector

To identify cells containing the vector

Reason:

Genes for enzymes that replicate the vector are on the host cell chromosome.

What do you call the DNA sequence in a vector that allows the replication enzymes of the cell to make lots of copies of the vector?

Multiple choice question.

Antibiotic resistance gene

Promoter and operator

Origin of replication

Selectable marker

Origin of replication

True or false: Viruses cannot be used as vectors in gene cloning.

False

Reason:

Viruses can be used as vectors, typically to carry small pieces of DNA.

What is a cloning vector?

Multiple choice question.

A cell from the Domain Archaea

A molecule that creates mutations in DNA segments

A large DNA molecule with many genes

A molecule that carries the DNA to be cloned

A molecule that carries the DNA to be cloned

Which of the following vectors would you use to clone a large piece of DNA?

Multiple choice question.

R plasmid

Host cell

Cosmid

Virus

Cosmid

Reason:

Viruses are commonly used to clone small segments of DNA.

The sequence of the ____ of ____ determines whether or not a vector can replicate in a particular type of host cell.

Blank 1: origin

Blank 2: replication

Enzymes that bind to a specific DNA sequence and cut the DNA backbone are called

Blank 1: restriction

Blank 2: endonucleases or enzymes

In gene cloning, how is a suitable vector chosen?

Multiple choice question.

It must be a very specific size

It must contain 3 or more antibiotic resistance genes

It must replicate in only one cell type

It must replicate in the appropriate cell type

It must replicate in the appropriate cell type

Many species of bacterial cells make restriction enzymes to protect themselves from invasion by

Blank 1: bacteriophages, viruses, DNA, or phages

A resistance gene that allows a host cell containing a vector to grow on a toxic substance is called a(n)

selectable marker

Viruses can be used as ____ to carry other pieces of DNA.

vectors

"Sticky ends" created by cutting DNA with a restriction enzyme are useful in cloning because they ______.

Multiple choice question.

allow the identification of host cells containing vectors

are only created in vector DNA

are important in producing RNA

are areas where two pieces of DNA can hydrogen bond

are areas where two pieces of DNA can hydrogen bond

Reason:

Genetic markers are used to identify host cells that contain vectors.

Select all that apply

Select all vectors that can be used to clone large segments of DNA.

Multiple select question.

BACs

Plasmids

Cosmids

YACs

BACs

Cosmids

YACs

When cloning a gene into a vector, the sugar-phosphate backbone of each DNA molecule is covalently linked by the enzyme DNA

ligase

Restriction endonucleases are used in gene cloning to ______.

Multiple choice question.

cut the DNA backbone and reveal protein-binding sequences

create site-directed mutants

cut the DNA backbone prior to inserting the DNA to be cloned

identify host cells containing vectors

cut the DNA backbone prior to inserting the DNA to be cloned

Reason:

There are other protein-binding sequences besides the ones recognized by restriction enzymes.

Fill in the blank question.

A DNA sequence in one strand that is identical when read in the opposite direction in the other strand is called a ____ sequence.

palindromic

How does a bacterial cell use restriction enzymes?

Multiple choice question.

To determine the nucleotide sequence of the cloned DNA

To help the replication enzymes make many copies of the vector

To protect the cell against engulfment by a white blood cell

To protect the cell against invasion by bacteriophages

To protect the cell against invasion by bacteriophages

Select the sequence that is palindromic.

Multiple choice question.

5'-AAGGAA-3' 3'-TTCCTT-5'

5'-CCACCA-3' 3'-GGTGGT-5'

5'-GGATCC-3' 3'-CCTAGG-5'

5'-GGATCC-3' 3'-CCTAGG-5'

Single-stranded stretches of DNA created by restriction enzymes, such as those shown on the left and right sides of the molecule in the figure, are called

sticky ends

Click and drag on elements in order

Order the following steps in cloning a gene, putting the first step at the top.

The digested chromosomal DNA and plasmid DNA are incubated together.

Ligation by DNA ligase.

Chromosomal DNA is isolated and cut with a restriction enzyme; the plasmid DNA is cut with the same enzyme.

1. Chromosomal DNA is isolated and cut with a restriction enzyme; the plasmid DNA is cut with the same enzyme.
2. The digested chromosomal DNA and plasmid DNA are incubated together.
3. Ligation by DNA ligase.

What does the enzyme DNA ligase do?

Multiple choice question.

It cuts the DNA backbone at a specific sequence.

It binds to DNA and prevents other enzymes from cutting the backbone.

It covalently links the sugar-phosphate backbone of DNA.

It binds to DNA and prevents RNA polymerase form binding.

It covalently links the sugar-phosphate backbone of DNA.

A recombinant vector ______.

Multiple choice question.

has ligated back to its original form

never contains foreign DNA

contains a piece of chromosomal DNA

always has the same restriction sites

contains a piece of chromosomal DNA

Restriction enzymes usually recognize ____ sequences in which the sequence in one strand is identical to the complementary strand read in the opposite direction.

palindromic

If the two ends of a vector cut with a restriction enzyme ligate back together without an insert, a ____ vector has been created.

recircularized

Cells that can take up DNA from the medium are considered ____ cells.

competent

In a palindromic sequence, The sequence in one strand ______.

Multiple choice question.

is the same in the complementary strand when read in the same direction

is the same when read 5' to 3' or 3' to 5'

is the same in the complementary strand when read in the opposite direction

is the same in the complementary strand when read in the opposite direction

When cloning a gene, why must the chromosomal DNA and the plasmid DNA be cut with the same restriction enzyme?

Multiple choice question.

The sticky ends of the plasmid DNA will be complementary to the sticky ends of the chromosomal DNA.

The chromosomal DNA fragments will have sticky ends, but the plasmid DNA will not.

The chromosomal DNA and the plasmid will both be cut into many small pieces.

The chromosomal DNA and the plasmid DNA will both have their selectable markers cleaved.

The sticky ends of the plasmid DNA will be complementary to the sticky ends of the chromosomal DNA.

Transformation occurs when ______.

Multiple choice question.

a piece of chromosomal DNA is ligated into a plasmid vector

competent cells take up DNA from the medium

restriction enzymes cut the DNA backbone and create sticky ends

a virus is used as a vector instead of a plasmid

competent cells take up DNA from the medium

Reason:

The ligation of a gene into a vector is not the same as transformation, the uptake of extracellular DNA into a cell.

Fill in the blank question.

A vector that contains a piece of chromosomal DNA is referred to as a ____ vector.

recombinant

A recircularized vector is one that has ______.

Multiple choice question.

been transformed into a host cell

ligated with a second, different vector

ligated with itself

many copies of the chromosomal DNA insert

ligated with itself

Reason:

A recircularized vector does not contain any inserts.

If bacteria are transformed with a plasmid carrying an antibiotic-resistance gene, one would expect progeny of that cell to ______ when exposed to the antibiotic.

Multiple choice question.

lyse

remain in stasis

grow

die

grow

In gene cloning, cells are treated with agents that ______, creating competent cells.

Multiple choice question.

make them resistant to antibiotics

protect them against bacteriophage invasion

make them permeable to DNA

make them glow in the dark

make them permeable to DNA

Select the sequence that is palindromic.

Multiple choice question.

5'-AAGGAA-3' 3'-TTCCTT-5'

5'-CCACCA-3' 3'-GGTGGT-5'

5'-GGATCC-3' 3'-CCTAGG-5'

5'-GGATCC-3' 3'-CCTAGG-5'

The enzyme that uses RNA as a template to make a complementary strand of DNA is called

reverse transcriptase

The process by which competent cells take up DNA from the extracellular medium is called

transformation

Select all that apply

Select the reagents needed to make cDNA.

Multiple select question.

Taq polymerase

Poly-dT primer

mRNA

Reverse transcriptase

dNTPs

Poly-dT primer

mRNA

Reverse transcriptase

dNTPs

What is the name of the enzyme that partially digests the RNA in a DNA - RNA hybrid?

Multiple choice question.

RNaseH

Reverse transcriptase

RNA polymerase

DNA ligase

RNaseH

Reason:

This enzyme produces a DNA strand complementary to an RNA molecule.

Following exposure to a plasmid containing the ampicillin resistance gene, a bacterial cell that was previously sensitive now grows in the presence of the antibiotic. What happened?

Multiple choice question.

The bacterial cell was mutated so that it is now resistant to ampicillin.

The bacterial cell merged with other bacterial cells to become a super organism.

The bacterial cell was transformed with a plasmid carrying the ampicillin resistance gene.

The ampicillin was rendered non-lethal by the procedure.

The bacterial cell was transformed with a plasmid carrying the ampicillin resistance gene.

DNA made using RNA as the starting material is called ______ DNA.

Multiple choice question.

RNA copied

copied cloned

complementary

reverse

complementary

What is an advantage of using cDNA in cloning?

Multiple choice question.

A cDNA molecule contains uracils.

A cDNA molecule contains introns but no exons.

A cDNA molecule contains the coding regions but not introns.

A cDNA molecule can only be expressed in eukaryotic cells.

A cDNA molecule contains the coding regions but not introns.

You have a piece of RNA, and you want to synthesize a complementary strand of DNA. What enzyme would you use?

Multiple choice question.

Reverse transcriptase

DNA polymerase

β-galactosidase

RNA polymerase

Reverse transcriptase

A researcher may use restriction enzymes to digest the DNA of an organism. The fragments of DNA are then ligated individually into many vectors. This collection of recombinant vectors is called a

Blank 1: DNA or genomic

Blank 2: library

Why would you use a poly-dT primer when making cDNA?

Multiple choice question.

Reverse transcriptase only works when the primer is a poly-dT oligonucleotide.

It would be complementary to the poly-A tail at the 3' end of the mRNA.

There are fewer hydrogen bonds in an oligonucleotide with many dNTP's.

It would bind to the poly-dT tail at the 3' end of the mRNA.

It would be complementary to the poly-A tail at the 3' end of the mRNA.

Reason:

The 3' end of the mRNA has a poly-A tail.

When all of the chromosomal DNA of an organism is used to produce a collection of recombinant vectors, the collection is known as a ______ library.

Multiple choice question.

transcriptomic

cDNA

proteomic

genomic

genomic

RNaseH partially digests the RNA in a DNA - RNA hybrid molecule. Why would you use this enzyme when making cDNA?

Multiple choice question.

RNaseH helps DNA ligase repair the phosphodiester bonds in the DNA backbone.

RNaseH also acts as a restriction enzyme.

The short RNAs that result from digestion can be used as primers by DNA polymerase.

The short RNAs that result from digestion can be used as primers by DNA polymerase.

Reason:

DNA polymerase is used to make the second DNA strand in cDNA.

Fill in the blank question.

When DNA is made using RNA as the starting material, the DNA is called ____ DNA.

Blank 1: complementary, c, or copy

A DNA library made with DNA generated by reverse transcriptase is called a ____ library.

cDNA

Why is cloning a cDNA molecule easier than cloning an entire eukaryotic gene?

Multiple choice question.

A cDNA molecule has several origins of replication.

A cDNA molecule does not have introns, which can be quite large.

A cDNA molecule does not contain protein-coding sequences.

A cDNA molecule does not have exons, which can be quite large.

A cDNA molecule does not have introns, which can be quite large.

Reason:

A cDNA molecule is derived from the protein-coding sequences found in mRNA.

What is a DNA library?

Multiple choice question.

A collection of recombinant vectors

A collection of bacterial cells, each containing one foreign gene

A repository of restriction fragments generated by treating the DNA of an organism with one restriction enzyme

A collection of journal articles about cloning

A collection of recombinant vectors

Reason:

Restriction fragments must be ligated into vectors to produce a DNA library.

In 1985, Kary Mullis developed a way to copy DNA without vectors or host cells. This technique is called

Blank 1: polymerase or P

Blank 2: chain or C

Blank 3: reaction, R, or reactions

After digesting all of the chromosomal DNA of an organism with restriction enzymes and recombining the DNA into vectors, the collection of recombinant vectors resulting is called a

Blank 1: genomic or DNA

Blank 2: library

When using PCR to amplify DNA, short oligonucleotides called primers ______.

Multiple choice question.

contain restriction sites useful for inserting DNA into vectors

are made of ribonucleotides

are complementary to the 3' end of the mRNA

flank the region of DNA to be amplified

flank the region of DNA to be amplified

True or false: PCR can amplify one segment of DNA from a mixture.

True

Reason:

PCR can amplify one segment of DNA because of the specificity of the primers.

If you wanted a collection of only transcribed DNA, you would construct a ______.

Multiple choice question.

DNA library without vectors

genomic library

DNA library with viral vectors

cDNA library

cDNA library

Reason:

A genomic library would contain both transcribed and non-transcribed sequences.

What is an advantage of using cDNA in cloning?

Multiple choice question.

A cDNA molecule contains uracils.

A cDNA molecule contains the coding regions but not introns.

A cDNA molecule contains introns but no exons.

A cDNA molecule can only be expressed in eukaryotic cells.

A cDNA molecule contains the coding regions but not introns.

In PCR, the two primers bind to specific sites in the ____ and flank the gene to be amplified.

DNA

Which scientist developed the polymerase chain reaction?

Multiple choice question.

Kary Mullis

Charles Yanofsky

Edwin Southern

James Watson

Kary Mullis

If a gene is amplified by PCR so that there are many copies, it can be said to be ______.

Multiple choice question.

controlled

cloned

translated

transcribed

cloned

Short oligonucleotides that flank the region of DNA to be amplified by PCR are called

primers

Primers are chosen for PCR based on ______.

Multiple choice question.

knowing the DNA sequence flanking the gene of interest

knowing the species of the organism with the gene of interest

the restriction site in the vector to be used

the species of the host cell

knowing the DNA sequence flanking the gene of interest

How can PCR amplify one segment of DNA from a complex mixture of potential template molecules?

Multiple choice question.

Primers can be designed to flank a specific segment of DNA.

Only one primer is needed for specific amplification.

Taq polymerase only recognizes very specific DNA sequences.

The use of a thermocycler results in specific amplification.

Primers can be designed to flank a specific segment of DNA.

In PCR, the template DNA is ______.

Multiple choice question.

the DNA on either side of the sequence to be amplified

a palindromic sequence

another name for the vector

the DNA to be amplified

the DNA to be amplified

Reason:

Primers are designed to bind to DNA on either side of the sequence to be amplified.

Why is Taq polymerase used in PCR?

Multiple choice question.

The DNA polymerase must come from a bacterium that is competent.

The DNA polymerase must be thermostable as PCR involves cycles of heating.

The primers only work with Taq polymerase.

Taq polymerase comes from Thermus aquaticus, a frequently used host cell.

The DNA polymerase must be thermostable as PCR involves cycles of heating.

Reason:

This cell lives in hot springs so its DNA polymerase is heat stable.

In PCR, why do the primers bind to specific sites in the DNA on either side of the gene of interest?

Multiple choice question.

They are complementary to the flanking sequences.

They are random, so the binding is lucky.

They have a high G-C content, so they will bind even if the sequences do not match.

They are identical to the flanking sequences.

They are complementary to the flanking sequences.

True or false: Amplifying a gene by PCR results in many copies, just like cloning using a vector and host cell.

True

Reason:

Both amplification and cloning with a vector and host cell result in many copies of a gene.

In PCR, each cycle uses the products of the previous cycle as templates. What do you call this?

Multiple choice question.

A genomic library

A chain reaction

Cloning

Annealing

A chain reaction

Reason: Annealing

The answer refers to the increase in the number of templates with each PCR cycle.

Knowing the sequence of the DNA ______ the gene of interest allows scientists to design appropriate primers.

Multiple choice question.

complementary to

one kilobase downstream from

in the middle of

flanking

flanking

Reason: complementary to

A primer is complementary to a region adjacent to the gene of interest.

In PCR, the temperature must be ______ from the denaturation temperature in order for primers to anneal.

Multiple choice question.

raised

lowered exactly 37 degrees

lowered

raised 10 degrees

lowered

Reason:

The temperature must be lowered from the denaturation temperature to promote annealing of the primers.

Fill in the blank question.

In PCR, the DNA to be amplified is called the ____ DNA.

template

In PCR, primer extension refers to the synthesis of ______ starting at the primers.

Multiple choice question.

complementary DNA

a strand of dideoxyribonucleotides

complementary RNA

a small protein

complementary DNA

Taq polymerase was first isolated from a bacterium called

Blank 1: Thermus

Blank 2: aquaticus

A typical PCR run consists of between ______ cycles.

Multiple choice question.

50 and 60

100 and 200

five and ten

20 and 30

20 and 30

Fill in the blank question.

In PCR, the two primers bind to specific sites in the ____ and flank the gene to be amplified.

DNA

After ______ cycles of PCR, a DNA sequence may be amplified a million-fold.

Multiple choice question.

about 1,000

about 20

about 1,000,000

1-2

about 20

Click and drag on elements in order

Order the steps in one cycle of a PCR reaction, putting the first step at the top.

Denaturation

Primer extension

Primer annealing

1. Denaturation

2. Primer annealing

3. Primer extension

Primer annealing occurs when ______.

Multiple choice question.

the two complementary strands of DNA come apart

Taq polymerase makes complementary strands of DNA starting at a short oligonucleotides

short oligonucleotides bind to complementary DNA flanking the gene of interest

a restriction enzyme makes a double-stranded cut in the DNA backbone

short oligonucleotides bind to complementary DNA flanking the gene of interest

Taq polymerase synthesizes complementary DNA in the 5' to 3' direction extending from the primer.

During PCR, the process of ____ ____ results when the Taq polymerase catalyzes the synthesis of complementary DNA, starting at the primers.

primer extension

Reverse transcriptase PCR can be used to ______.

Multiple choice question.

detect and quantify the amount of a specific RNA.

create specific restriction sites that will be useful in cloning

create site-directed mutants

create DNA that can be expressed in Thermus aquaticus

detect and quantify the amount of a specific RNA.

Reason:

RNA molecules are amplified into DNA in this process, regardless of the presence of restriction sites.

One typical PCR cycle lasts ______ minutes.

Multiple choice question.

two to three

30 to 60

90

between 10 and 15

two to three

True or false: Reverse transcriptase PCR can detect very small amounts of a specific RNA.

True

Reason:

Reverse transcriptase is extraordinarily sensitive.

After 20 PCR cycles, a DNA sequence may be amplified ______-fold.

Multiple choice question.

100-million

ten

a thousand

a million

a million

Fill in the blank question.

____-____ PCR allows one to assess the amount of DNA produced during a PCR amplification as it is happening.

Blank 1: Real

Blank 2: Time

How is the amount of DNA produced during real-time PCR measured?

Multiple choice question.

By measuring the fluorescence emitted by the probe added to the PCR mixture

By stopping the thermocycler at various times during the PCR run and running samples on a gel

By blotting the product of the run onto a solid support so that it can be probed

By transforming bacteria with samples taken from various times during the run

By measuring the fluorescence emitted by the probe added to the PCR mixture

Reason:

Fluorescent detector molecules are used in this method.

The ____ probe is an oligonucleotide that can be used to follow real-time PCR. It has a reporter molecule at one end and a quencher molecule at the other end.

TaqMan

The enzyme ____ ____ is used when PCR is employed to detect and quantify the amount of a specific RNA.

reverse transcriptase

Click and drag on elements in order

Place the steps in a real-time PCR experiment in order from first to last, putting the first step at the top.

Taq polymerase cleaves the oligonucleotide in TaqMan.

More and more TaqMan probes are digested and the level of fluorescence increases.

A primer and the TaqMan probe both anneal to template DNA.

The reporter can emit unquenched fluorescence that can be measured.

1. A primer and the TaqMan probe both anneal to template DNA.

2. Taq polymerase cleaves the oligonucleotide in TaqMan.

3. The reporter can emit unquenched fluorescence that can be measured.

4. More and more TaqMan probes are digested and the level of fluorescence increases.

Click and drag on elements in order
Order the three steps of a PCR cycle from the first to last step, starting at the top.

1. Heating to denature/ separate DNA strands
2. Lowering the temperature to allow for primer annealing to template DNA
3. Incubating at a temperature that allows the synthesis of the complementary strand.

Click and drag on elements in order
Scientists can use the CRISPR/Cas9 system to "edit" the genome of a cell in vivo. Put the steps in the process in the correct order, starting at the top.
Instructions

1. A guide RNA is designed and synthesized that matches the sequence of DNA that will be edited.

2. The CRISPR/Cas9 system is loaded with the guide RNA and introduced into cells.

3. The CRISPR/Cas9 system associates with the DNA sequence complementary to the guide RNA.

4. Cas 9 cuts the DNA.

5. Inaccurate repair of the cut DNA results in a small detections or insertions, which lead to loss of gene function.

What makes reverse transcriptase PCR so sensitive?

Multiple choice question.

It can detect small amounts of RNA from one cell.

It can detect small amounts of DNA from one bacterial colony.

It can detect small amounts of protein after SDS-PAGE.

It can make large amounts of RNA from only one primer.

It can detect small amounts of RNA from one cell.

Reason:

Reverse transcriptase PCR is used to amplify RNA.

What is the technique that allows one to determine the amount of template DNA present when the PCR cycles began?

Multiple choice question.

Real-time PCR

Reverse transcription

Cloning in plasmid vectors

DNA sequencing

Real-time PCR

In real-time PCR, the cycle threshold is reached when ______.

Multiple choice question.

fluorescence is detected for the first time in an experiment

the accumulation of fluorescence is the same as the background level

the accumulation of fluorescence is significantly greater than the background level

the accumulation of fluorescence is significantly greater than the background level

What type of apparatus does one need to quantify the DNA produced during real-time PCR?

Multiple choice question.

A device to detect low levels of radioactivity

A microtiter-plate reader

A thermocycler that can detect fluorescence

Gel electrophoresis and a UV source

A thermocycler that can detect fluorescence

Reason:

An apparatus that can detect small quantities of DNA is needed.

How is the TaqMan probe used to monitor real-time PCR?

Multiple choice question.

As amplification increases, fluorescence increases.

As amplification increases, a color change is detected.

As amplification increases, the amount of probe decreases.

As amplification increases, fluorescence decreases.

As amplification increases, fluorescence increases.

Reason:

The TaqMan probe is an oligonucleotide that can be used to follow real-time PCR. It has a reporter molecule at one end and a quencher molecule at the other end. As amplification increases, fluorescence increases.

Click and drag on elements in order

Real-time PCR goes through three main phases with regard to product accumulation. Place them in order from first to last, with the first step at the top.

Exponential

Linear

Plateau

1. Exponential

2. Linear

3. Plateau

What activity of Taq polymerase separates the reporter from the quencher in the TaqMan molecule?

Multiple choice question.

3' to 5' endonuclease

5' to 3' endonuclease

5' to 3' exonuclease

Polymerase

3' to 5' exonuclease

5' to 3' exonuclease

True or false: Reverse transcriptase PCR can detect very small amounts of a specific RNA.

True

In a real-time PCR experiment, how is the standard detected separately from the sample of interest?

Multiple choice question.

Different radionucleotides are used to monitor each sample.

Different primers are used to amplify each sample.

The products are designed to be different sizes, and they are distinguished by size.

Different-colored fluorescent molecules are used to monitor each sample.

Different-colored fluorescent molecules are used to monitor each sample.

Reason:

Different primers are used to amplify each sample.

While this is true, this is not how the samples are detected.

Fill in the blank question.

A method in which the exponential phase of real-time PCR is analyzed to quantitate the initial template concentration is called the ____ ____ method.

Blank 1: cycle or CBlank 2: threshold or t

DNA sequencing enables researchers to determine the order of ______ ______ in a gene.

Multiple choice question.

amino acids

RNA nucleotides

DNA nucleotides

DNA nucleotides

The Maxam and Gilbert method of DNA sequencing used chemicals that cleaved the DNA at ______.

Multiple choice question.

A-T pairs only

random sequences

long stretches of A bases

specific bases

specific bases

This figure shows a real-time PCR experiment carried out at low, medium, and high concentrations of starting template DNA. Please match each curve (designated by a letter) with the corresponding amount of starting template. Fluorescence values are plotted on the Y axis.

A

B

C

Medium

Low

High

• A High
• B Medium
• C Low

Select all that apply

Select the types of standards that are commonly used in real-time PCR.

Multiple select question.

A random sequence of DNA from the sample is also amplified.

A repetitive sequence already present in the sample is also amplified.

A standard of known concentration is added to the PCR mixture.

Another gene that is already present in the sample is also amplified.

A standard of known concentration is added to the PCR mixture.

Another gene that is already present in the sample is also amplified.

Dideoxy sequencing was formulated based on scientists' knowledge of what process?

Multiple choice question.

DNA replication

Reverse transcription

Transcription

Translation

DNA replication

This technique enables researchers to determine the DNA bases in genes and other chromosomal regions.

Multiple choice question.

Southern blotting

Restriction mapping

Colony hybridization

DNA sequencing

DNA sequencing

If the oxygens on carbons 2 and 3 of the sugar of a nucleotide have been removed, the nucleotide is referred to as a

Blank 1: dideoxyribonucleotide, ddNTP, or dideoxyribonucleotides

Which scientist(s) developed an early method of DNA sequencing that involved base-specific chemical cleavage of DNA?

Multiple choice question.

Maxam and Gilbert

Kary Mullis

Monod and Jacob

Francis Crick

Maxam and Gilbert

Chain termination occurs when a dideoxyribonucleotide is incorporated into a growing DNA strand because there is no ______.

Multiple choice question.

phosphate

3'-OH group

amino

5'-OH group

3'-OH group

In automated sequencing, each dideoxyribonucleotide is labeled with a different colored ______.

Multiple choice question.

radioisotope

DNA primer

fluorescent dye

Taq polymerase

fluorescent dye

Click and drag on elements in order

Order the steps in DNA sequencing, putting the first step at the top.

High concentrations of all four unlabeled deoxyribonucleotides are added.

Low concentrations of all four fluorescently labeled dideoxyribonucleotides and DNA polymerase are added.

A laser and fluorescence detector are used to determine the color associated with each DNA strand.

Primers are added.

Many copies of a single-stranded vector containing the gene of interest are acquired.

Electrophoresis separates DNA strands according to their lengths.

Answer in the picture.

Fill in the blank question.

The DNA sequencing method developed by Frederick Sanger that became a commonly used method of DNA sequencing is called ____ sequencing.

dideoxy

In dideoxyribonucleotides, ____ oxygens are removed from the sugar compared with ribose.

2

Sequencing using the dideoxy method results in a sequencing ladder because ______.

Multiple choice question.

using the four labeled dideoxyribonucleotides results in chain termination at each nucleotide

using the four unlabeled deoxyribonucleotides results in chain termination at each nucleotide

the amount of DNA increases in discrete steps, like a ladder

using the four labeled dideoxyribonucleotides results in chain termination at each nucleotide

Reason:

The sizes of DNA molecules, rather than the amounts of DNA, are detected by this method.

In dideoxy sequencing, if a dideoxyribonucleotide is incorporated into the growing strand of DNA, the strand can no longer grow as there is no 3' OH group. This is called ______.

Multiple choice question.

chain termination

transposition

terminal acceptance

real-time PCR

chain termination

Fill in the blank question.

____-____ ____ allows a researcher to produce a mutation at a specific sequence.

Blank 1: Site

Blank 2: Directed

Blank 3: Mutagenesis

The use of dideoxyribonucleotides with different colored fluorescent dyes allows the detection of the ______.

Multiple choice question.

appropriate vector

sequence of DNA

amount of DNA

gene of interest

sequence of DNA

Reason:

A probe is needed to detect a gene of interest.

How is site-directed mutagenesis useful in the study of genes and proteins?

Multiple choice question.

Since site-directed mutagenesis introduces random mutations, new genes can be identified.

The mutated gene can be studied in vitro only.

The mutated gene can be introduced into a living organism to see how the mutation affects the organism.

The mutated gene can be introduced into a living organism to see how the mutation affects the organism.

To ensure that the automated sequencing is accurate, it is important that the sequencing mixture contains ______.

Multiple choice question.

equal concentrations of unlabeled deoxyribonucleotides and labeled dideoxyribonucleotides

high concentrations of unlabeled deoxyribonucleotides and low concentrations of labeled dideoxyribonucleotides

high concentration of labeled dideoxyribonucleotides and low concentrations of unlabeled deoxyribonucleotides

high concentrations of unlabeled deoxyribonucleotides and low concentrations of labeled dideoxyribonucleotides

Reason:

All four types of deoxyribonucleotides are added at a high concentration and all four types of dideoxyribonucleotides (ddA, ddT, ddG, or ddC), which are fluorescently labeled, are added at a low concentration.

Dideoxy sequencing was formulated based on scientists' knowledge of what process?

Multiple choice question.

Reverse transcription

Transcription

Translation

DNA replication

DNA replication

The dideoxy sequencing method results in mixtures of DNA strands of different lengths which are run on a gel. The gel is read from the bottom up. This is referred to as a

Blank 1: sequencing or sequence

Blank 2: ladder

Site-directed mutagenesis allow a researcher to make a mutation ______.

Multiple choice question.

in the DNA flanking the gene of interest

at a specific sequence of DNA

in the vector DNA

at the ends of chromosomes

at a specific sequence of DNA

Site-directed mutagenesis is sometimes referred to as ____-directed mutagenesis.

oligonucleotide

If a scientist wanted to determine how a specific mutation in a gene of interest affected an organism, what technique would be most useful?

Multiple choice question.

Real-time PCR

Reverse transcriptase PCR

Site-directed mutagenesis

DNA sequencing

Site-directed mutagenesis

Click and drag on elements in order

Place the steps in site-directed mutagenesis in order from first to last, with the first step on top.

Design an oligonucleotide primer that is complementary to the DNA of interest, except for a mismatched region.

Add dNTPs, DNA polymerase, and DNA ligase.

Anneal the primer to the template DNA.

Introduce the DNA into a living cell.

Answer in the picture.

Which component in the CRISPR-Cas9 system makes a double-strand break in DNA?

Multiple choice question.

tracrRNA

Cas9

crRNA

Cas9

Fill in the blank question.

When the CRISPR-Cas system is used for gene mutagenesis, tracrRNA and crRNA are linked together in a molecule called the ____ ____ RNA.

Blank 1: single or s

Blank 2: guide or g

What is the most important feature of a primer used in site-directed mutagenesis?

Multiple choice question.

It contains a region that is not complementary to the template.

It comes from a natural source.

It is 20 nucleotides long.

It is exactly complementary to the template DNA.

It contains a region that is not complementary to the template.

Reason:

A mutation will not be produced if the primer is exactly complementary to the template.

How does one analyze a site-directed mutation?

Multiple choice question.

By cutting it with restriction enzymes

By sequencing it using the dideoxy method

By introducing it into a living organism

With a Southern blot

By introducing it into a living organism

Reason:

The sequence is already known, the analysis involves testing the effects of the mutation.

The natural function of the CRISPR-Cas system in bacteria is to ______.

Multiple choice question.

to make changes throughout the bacterial chromosome

to provide defense against bacteriophages

to provide defense against other bacteria

to provide defense against bacteriophages

When CRISPR-Cas is used for gene mutagenesis, what type of change does Cas9 make in the gene of interest?

Multiple choice question.

Double-strand break

Nucleotide transition

Single-strand break

Nucleotide transversion

Double-strand break

Select all that apply

When the CRISPR-Cas system is used for gene mutagenesis, which two components are combined in the single guide (sgRNA)?

Multiple select question.

Gene of interest

crRNA

Cas9

tracrRNA

crRNA

tracrRNA

Fill in the blank question.

In gene mutagenesis by CRISPR-Cas, a DNA break can be repaired by ____ end ____ or by homologous ____ ____.

Blank 1: nonhomologous

Blank 2: joining

Blank 3: recombination

Blank 4: repair

The dideoxy sequencing method results in mixtures of DNA strands of different lengths which are run on a gel. The gel is read from the bottom up. This is referred to as a

Blank 1: sequencing or sequence

Blank 2: ladder

Select all that apply

CRISPR-Cas technology has been used to mutate genes in ______.

Multiple select question.

human cell lines

human embryos

plant cells

adult mice

roundworms

mouse embryos

human cell lines

plant cells

adult mice

roundworms

mouse embryos

Reason:

While there are some recent reports of attempts to alter human genes, the outcomes have a high degree of uncertainty. The scientific community considers these attempts to be unethical.

In the CRISPR-Cas system, what part of the sgRNA is designed to be complementary to the gene to be mutated?

Multiple choice question.

Repeat region

Spacer region

tracrRNA

Linker region

Spacer region

Select all that apply

After Cas9 makes a double strand break, which characteristics are observed for repair of the break by nonhomologous end joining (NHEJ)?

Multiple select question.

The break region may incur a small deletion.

Frameshift mutation may occur in the coding sequence of the gene.

Can be used to make a specific point mutation.

Researcher includes donor DNA that is homologous to the region where the break occurs.

The break region may incur a small deletion.

Frameshift mutation may occur in the coding sequence of the gene.

What is the purpose of Northern blotting?

Multiple choice question.

To identify a specific protein within a mixture of proteins

To identify a specific DNA fragment within a mixture of DNA molecules

To identify a specific DNA molecule within a mixture of RNA molecules and proteins

To identify a specific RNA molecule within a mixture of RNA molecules

To identify a specific RNA molecule within a mixture of RNA molecules

A major advantage of CRISPR-Cas technology over site-directed mutagenesis is that it can be used directly on ____ cells.

Blank 1: living, live, or alive

Click and drag on elements in order

Place in order from first to last the steps in Northern Blotting. with the first step at the top.

Extract and purify RNA from living cells.

Load RNA onto an agarose gel.

Probe with a labeled fragment of DNA.

Blot RNAs onto a nylon membrane.

Separate RNA molecules according to size.

Answer in the picture.

How does one analyze a site-directed mutation?

Multiple choice question.

By cutting it with restriction enzymes

With a Southern blot

By sequencing it using the dideoxy method

By introducing it into a living organism

By introducing it into a living organism

Reason:

The sequence is already known, the analysis involves testing the effects of the mutation.

You wish to determine if a protein is made at a particular stage of development. What technique would you use?

Multiple choice question.

Southern blotting

Northern blotting

Western blotting

Polymerase chain reaction

Western blotting

This technique is used to identify a specific RNA molecule within a mixture of RNA molecules.

Multiple choice question.

Eastern blotting

Southern blotting

Northern blotting

Western blotting

Northern blotting

In the Western blot, to what is the enzyme that will give the colored reaction coupled?

Multiple choice question.

The primary antibody

The nylon membrane

The protein of interest

The secondary antibody

The secondary antibody

Reason:

The primary antibody binds to one or more proteins separated by gel electrophoresis.

What type of probe is used in Northern blotting?

Multiple choice question.

Labeled protein

Labeled antibody

Labeled RNA

Labeled DNA

Labeled DNA

For Western blotting, what type of probe is used to identify the protein of interest?

Multiple choice question.

antigen

epitope

labeled DNA

antibody

labeled RNA

antibody

What technique is used to identify a particular protein in a mixture of proteins?

Multiple choice question.

Northern blotting

Real-time PCR

Southern blotting

Western blotting

Western blotting

In the Western blot, what binds to the protein of interest?

Multiple choice question.

An oligonucleotide

The secondary antibody

An enzyme

The primary antibody

The primary antibody

Reason:

The secondary antibody binds to the primary antibody.

Antibodies bind to three-dimensional structures found within a protein that are called ______.

Multiple choice question.

receptors

domains

secondary antibodies

epitopes

epitopes

Fill in the blank question.

In the technique of Western blotting, a primary ____ binds to an ____ to identify a specific protein.

Blank 1: antibody

Blank 2: antigen or epitope

You wish to determine if a protein is made at a particular stage of development. What technique would you use?

Multiple choice question.

Northern blotting

Polymerase chain reaction

Western blotting

Southern blotting

Western blotting

After Cas9 makes a double strand break, which characteristics are observed for repair of the break by nonhomologous end joining (NHEJ)?

Multiple select question.

Can be used to make a specific point mutation.

The break region may incur a small deletion.

Frameshift mutation may occur in the coding sequence of the gene.

Researcher includes donor DNA that is homologous to the region where the break occurs.

The break region may incur a small deletion.

Frameshift mutation may occur in the coding sequence of the gene.

What technique is useful for studying protein-DNA interactions?

Multiple choice question.

Real-time PCR

Electrophoretic mobility shift assay

The construction of a DNA library

The western blot

Electrophoretic mobility shift assay

Reason:

This method identifies a protein through antibody binding.

An antigen has one or more three dimensional structures called ______ to which a(n) ______ will bind.

Multiple choice question.

antibodies; epitopes

active sites; antibody

receptors; antibody

epitopes; antibody

epitopes; antibody

For Western blotting, what type of probe is used to identify the protein of interest?

Multiple choice question.

labeled DNA

antibody

antigen

labeled RNA

epitope

antibody

How does the binding of a protein to a DNA fragment affect the ability of the fragment to migrate through a gel during electrophoresis?

Multiple choice question.

It slows the fragment's migration.

It has no effect on the fragment's migration.

It depends on the protein.

It accelerates the fragment's migration.

It slows the fragment's migration.

Which of the following techniques is used to study protein-DNA interactions?

Multiple choice question.

DNase I footprinting

The Western blot

The Northern blot

The Southern blot

DNase I footprinting

The gel retardation assay is also known as the ______.

Multiple choice question.

Southern blot

colony hybridization assay

electrophoretic mobility shift assay

Western blot

electrophoretic mobility shift assay

This figure shows the outcome of what type of experiment?

Multiple choice question.

Western blotting

DNA sequencing

DNase I footprinting

Real time PCR

DNase I footprinting

If RNA polymerase holoenzyme is bound to the promoter of a specific gene, what will be the outcome of DNase I footprinting of this promoter region?

Multiple choice question.

The promoter will be completely digested by the DNase I enzyme.

A few sites within the promoter will be cleaved by DNase I.

The promoter will be protected from DNase I digestion.

The promoter will be protected from DNase I digestion.

The ______ assay is used to identify protein-DNA interactions because the binding of a protein to a DNA fragment slows the ability of the fragment to migrate through a gel during electrophoresis.

Multiple choice question.

Western blot

real-time PCR

dideoxyribonucleotide

electrophoretic mobility shift

electrophoretic mobility shift

The DNase I footprinting technique is used to study ____-____ interactions.

Blank 1: DNA

Blank 2: protein or binding

Which technique can identify the DNA region that interacts with a DNA-binding protein?

Multiple choice question.

DNase I footprinting

Northern blotting

Western blotting

Site-directed mutagenesis

DNase I footprinting

In a DNase I footprinting experiment, a region of DNA bound to protein will be ______ cleavage by the DNAse I enzyme.

Multiple choice question.

moderately susceptible to

highly susceptible to

protected from

protected from

How does the binding of a protein to a DNA fragment affect the ability of the fragment to migrate through a gel during electrophoresis?

Multiple choice question.

It accelerates the fragment's migration.

It depends on the protein.

It has no effect on the fragment's migration.

It slows the fragment's migration.

It slows the fragment's migration.