Molecular Genetics assignment questions

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

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

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

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

Cas9

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

DNA

The D N A fragment sizes run from 150 bases at the top of the gel down to 1 base at the bottom of the gel. The promoter numbering starts at +75 at the top of the gel and goes down to +1, which is the transcription start sites. The numbering then becomes negative, down to -75 at the bottom of the gel. This figure shows the outcome of what type of experiment?

DNase I footprinting

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

DNase I footprinting

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

DNase I footprinting

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

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

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

Double-strand break

Match the phase of real-time PCR with the accumulation of products. Accumulation of the product levels off as one or more reagents are used up.

Plateau

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

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

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

Site-directed mutagenesis

__________-_________ ___________ allows a researcher to produce a mutation at a specific sequence.

Site-directed mutagenesis

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

Spacer region

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

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

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

The primary antibody

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

True

A cloned gene becoming integrated into the genome by nonhomologous recombination is called gene ________________ .

addition

The jellyfish gene for GFP was inserted into the zebrafish genome by gene ______.

addition

Reverse transcriptase PCR can be used to ______.

detect and quantify the amount of a specific RNA.

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

dideoxy

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

single guide or s g

Molecular pharming can refer to ______. Multiple select question. the use of livestock to gather DNA molecules the manufacture of medical products in agricultural plants collection of natural livestock proteins for use in medicine production of medically important proteins in the mammary glands of livestock

the manufacture of medical products in agricultural plants production of medically important proteins in the mammary glands of livestock

To perform PCR, a machine called a ___________ automates the timing of each cycle.

thermocycler

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

to provide defense against bacteriophages

A gene from one species that is introduced into another species is called a(n) _______________ .

transgene

the steps in the production of human insulin from bacteria.

1.) The coding sequence of either A or B chain is placed next to the coding sequence of the E. coli protein B-galactosidase. 2.) The B-galactosidase fusion protein is purified from bacteria. 3.) Fusion protein is treated with cyanogen bromide (CNBr), which cleaves fusion protein after methionine found between b-galactosidase and A or B chain. 4.) Both purified chains are mixed together under conditions in which they will fold properly to produce a functional protein.

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

A thermocycler that can detect fluorescence

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

As amplification increases, fluorescence increases.

What technique is useful for studying protein-DNA interactions?

Electrophoretic mobility shift assay

Match the phase of real-time PCR with the accumulation of products. The amount of product nearly doubles with each cycle but may be difficult to detect as the amounts are small.

Exponential

What keeps the chains of insulin from being degraded in bacterial cells?

Fusion with β-galactosidase

The __________________ is a brand of transgenic zebrafish that glows with bright green, red, or yellow fluorescent color.

GloFish

What makes reverse transcriptase PCR so sensitive?

It can detect small amounts of RNA from one cell.

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

Why is Taq polymerase used in PCR?

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

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

The break region may incur a small deletion. Frameshift mutation may occur in the coding sequence of the gene.

The use of living organisms or the materials they produce in the development of goods or processes that are beneficial to humans is called _____________ .

biotechnology

Gene knockins are used to study the effects of ______.

consistent gene expression

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

cycle threshold

Gene knockout allows researchers to study

how the loss of normal gene function affects an organism.

Vectors such as pUC18 and others of the pUC series contain a large number of restriction enzyme sites clustered in one region. Which term describes this advantageous arrangement of restriction sites?

multiple cloning site

The production of medically important proteins in the mammary glands of livestock is called molecular _____________ .

pharming

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

polymerase chain reaction PCR

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

real-time

A researcher has a DNA sample that was generated from the mRNA extracted from a cell line. The researcher wants to determine specifically how much of gene A was expressed in that cell line. What is one experiment that could be done to quantitively measure the expression of gene A?

real-time PCR

Incorporation of a growth hormone-regulating gene and promoter from other species produced a genetically modified ______ that can grow year round instead of only during specific seasons.

salmon

Assume that a plasmid (circular) is 3200 base pairs in length and has restriction sites at the following locations: 400, 700, 1400, 2600. Give the expected sizes of the restriction fragments following complete digestion.

300, 700, 1000, 1200

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

A chain reaction

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

What components are required for a PCR? (Check all that apply.) DNA ligase Primers DNA polymerase DNA template Deoxyribonucleotides Restriction endonucleases

Primase DNA polymerase DNA template Deoxyribonucleotides

The gel retardation assay is also known as the ______.

electrophoretic mobility shift assay

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

the accumulation of fluorescence is significantly greater than the background level

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

Which scientist developed the polymerase chain reaction?

Kary Mullis

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

Protein-DNA

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

The secondary antibody

Altering the sequence of a gene, such as with the CRISPR-Cas system, is known as ______.

gene modification

With a goal toward using GloFish to detect water pollution, scientists placed the green fluorescent protein (GFP) gene next to a promoter that ______.

turns the GFP gene on in the presence of environmental toxins

By adding the green fluorescent protein (GFP) gene next to a promoter that turns the gene on in the presence of certain environmental toxins, GloFish can be used to detect ______________ pollution.

water

In Western blotting, what probe is used to detect the protein of interest?

An antibody

Taq polymerase starts copying at __________.

DNA primers attached to the template of the desired gene

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

DNA replication

To perform many cycles of PCR, you need a machine that can change temperatures at exact times. What do you call this machine?

Thermocycler

Taq polymerase was first isolated from a bacterium called ________________ ______________

Thermus aquaticus

What type of probe is used in Northern blotting?

Labeled DNA

Insulin is a hormone composed of two different polypeptides, the _______________ and the __________________ chains, which can be produced separately in bacteria, then purified and mixed together to form functional human insulin.

alpha , beta

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

primers

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

reverse transcriptase

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

sequence of DNA

To perform PCR, a machine called a _______________ automates the timing of each cycle.

thermocycler

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

at a specific sequence of DNA

steps in performing a Western blot

1.) Separate the proteins in a mixture using SDS-PAGE. 2.) Blot the proteins onto a nylon membrane. 3.) Incubate the nylon membrane with the primary antibody 4.) Incubate the nylon membrane with the secondary antibody 5.) Treat the nylon mesh with a reagent that causes a color change.

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

Northern blotting

What is the purpose of Northern blotting?

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

What type of probe is used in Northern blotting?______.

Labeled DNA

Match the phase of real-time PCR with the accumulation of products. Accumulation of the product shows a directly proportional relationship to cycle number.

Linear

In biotechnology, what is used to benefit humans? Multiple select question. Computer generated organisms Living organisms Materials produced by living organisms Dead organisms

Living organisms Materials produced by living organisms

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

flank the region of DNA to be amplified

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

fluorescent dye

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

Real-time PCR

After Cas9 makes a double strand break, which characteristics are observed for repair of the break by homologous recombination repair (HRR)?

Researcher includes donor DNA that is homologous to the region where the break occurs. Can be used to make a specific point mutation.

Considering a diploid cell, how many copies of a gene already present in the genome would be present immediately following gene addition (assume the cell has not progressed through the cell cycle)?

3 Reason: A diploid cell would have two copies of a gene, plus the cloned copy integrated into the genome by nonhomologous recombination.

True or false: Reproductive cloning can only occur as a result of laboratory manipulations.

False

Methods that produce two or more genetically identical individuals are referred to as reproductive ___________.

cloning

During the initial phase of a real-time PCR experiment, called the ___________ phase, the amount of PCR products is small and reagents are not limiting, so the amount of product nearly doubles with each cycle.

exponential

The larger fish at the back of the photo has grown faster and larger due to the incorporation of a __________-factor regulating gene from another salmon species.

growth

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

They are complementary to the flanking sequences.

What is the term for an organism that has received genetic material from a different species?

Transgenic organism

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

True

steps in Northern Blotting

1.) Extract and purify RNA from living cells. 2.) Load RNA onto agarose gel. 3.) Separate RNA molecules according to size 4.) Blot RNAs onto a nylon membrane. 5.) Probe with a labeled fragment of DNA.

The purpose of PCR is to __________.

make many copies of an organism's DNA sequence

The process of gene ____________ aims to alter the sequence of a gene.

modification

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

Western blotting

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

crRNA tracrRNA

Which of the following is not a type of PCR? Multiple Choice Real-Time PCR Ct PCR Correct Reverse transcriptase PCR TaqMan PCR

ctPCR

A gene __________ is a gene ______________ in which a gene of interest has been added to a particular site in the mouse genome.

knockin , addition or insertion

In a type of gene replacement called gene _______________ , a cloned gene is rendered inactive and replaces a normal gene at its chromosomal location.

knockout

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

Western blotting