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Sample Test

Introduction to Biotechnology, 3e (Thieman)

Chapter 3   Recombinant DNA Technology and Genomics

 

1) You just cloned a new gene from mice. Which of the following techniques would be the best choice to use if you wanted to determine the number of copies of this gene in the mouse genome?

1.    A) Northern blot analysis

2.    B) RT-PCR

3.    C) Western blot analysis

4.    D) Southern blot analysis

5.    E) In situ hybridization

Answer:  D

 

2) Which of the following techniques involves hybridizing a cDNA sample to a chip containing thousands of single-stranded DNA sequences, allowing one to study the expression of thousands of genes simultaneously?

1.    A) PCR

2.    B) Southern blot

3.    C) FISH

4.    D) Agarose gel electrophoresis

5.    E) DNA microarray

Answer:  E

 

3) When making a complementary DNA (cDNA) library, which enzyme is used to copy mRNA into DNA?

1.    A) DNA ligase

2.    B) DNA polymerase

3.    C) Primase

4.    D) RNA polymerase

5.    E) Reverse transcriptase

Answer:  E

 

4) In a recombinant DNA experiment, which enzyme is used to join together DNA fragments by forming phosphodiester bonds between nucleotides? Recall that this same enzyme joins together Okazaki fragments on the lagging strand during DNA replication.

1.    A) DNA primase

2.    B) DNA polymerase

3.    C) DNA helicase

4.    D) DNA ligase

5.    E) Reverse transcriptase

Answer:  D

 

 

5) During library screening, PCR, Southern blotting, and other techniques, binding two pieces of DNA to each other by hydrogen bonding is called ________.

1.    A) autoradiography

2.    B) hybridization

3.    C) DNA ligation

4.    D) reverse transcription

5.    E) polyadenylation

Answer:  B

6) ________ is a DNA-binding dye that fluoresces when DNA in an agarose gel is illuminated with ultraviolet light.

1.    A) Casein

2.    B) Ethidium bromide

3.    C) Malt

4.    D) Lactic acid

5.    E) Ethanol

Answer:  B

 

7) Which of the following vectors would be the best choice for gene transfer in plant cells?

1.    A) Cosmid

2.    B) Bacterial artificial chromosome

3.    C) Bacteriophage vector

4.    D) Ti vector

5.    E) Plasmid

Answer:  D

 

8) A ________ is a single-stranded DNA molecule attached to a radioactive or fluorescent compound that is complementary to a specific sequence of DNA. Such pieces of DNA are used to identify and study cloned genes in hybridization experiments.

1.    A) polypeptide

2.    B) promoter

3.    C) vector

4.    D) probe

5.    E) plasmid

Answer:  D

 

9) Transformation in a cloning experiment is ________.

1.    A) ligating pieces of foreign DNA together

2.    B) inserting DNA into bacteria cells

3.    C) cutting DNA with restriction enzymes

4.    D) using PCR to clone a gene

5.    E) a technique for determining gene copy number in a genome

Answer:  B

 

 

10) Which of the following is an INCORRECT statement about restriction enzymes?

1.    A) Most restriction enzymes are isolated from bacteria.

2.    B) Restriction enzymes usually recognize palindromic sequences.

3.    C) Restriction enzymes create phosphodiester bonds between pieces of DNA in a cloning experiment.

4.    D) Restriction enzymes can cut to create overlapping single-stranded ends of DNA.

5.    E) Restriction enzymes can cut to create blunt-ended pieces of DNA.

Answer:  C

11) Based on what you know about which organisms naturally produce restriction enzymes and how restriction enzymes are named, which of the following enzymes is isolated from the bacterium Bacillus amyloliquefaciens?

1.    A) EcoRI

2.    B) BamHI

3.    C) SmaI

4.    D) PstI

5.    E) HindIII

Answer:  B

 

12) Imagine you wanted to use a human genomic DNA library to clone the human gene for insulin. You will be using the rat insulin gene sequence as your DNA probe. In what order would you perform the following steps to accomplish this goal?

1.    Use autoradiography to identify colonies containing DNA that hybridized to the probe

2.    Grow transformed cells on media with antibiotics and X-gal for blue-white screening

3.    Ligate genomic DNA and vector DNA

4.    Cut genomic DNA and vector DNA with restriction enzymes

5.    Hybridize library DNA with labeled probe for the rat insulin gene

6.    Transform bacteria with recombinant plasmid

 

1.    A) 2, 3, 6, 5, 4, 1

2.    B) 1, 2, 5, 6, 4, 3

3.    C) 4, 3, 6, 2, 5, 1

4.    D) 4, 3, 5, 2, 6, 1

5.    E) 2, 6, 5, 3, 1, 4

Answer:  C

 

13) Approximately how large is the human genome?

1.    A) 20,000 bp

2.    B) 1 billion bp

3.    C) 3 billion bp

4.    D) 13 million bp

5.    E) 30 billion bp

Answer:  C

 

 

14) Approximately how many genes are present in the human genome?

1.    A) 3 billion genes

2.    B) 20 billion genes

3.    C) 100,000 genes

4.    D) 20,000 genes

5.    E) 50,000 genes

Answer:  D

 

15) Which of the following techniques is the best choice for amplifying DNA?

1.    A) Southern blot analysis

2.    B) PCR

3.    C) DNA sequencing

4.    D) Affinity chromatography

5.    E) Microarray analysis

Answer:  B

16) Which of the following techniques is most commonly used to separate and analyze DNA by size?

1.    A) PCR

2.    B) Agarose gel electrophoresis

3.    C) DNA microarray analysis

4.    D) Hybridization

5.    E) DNA libraries

Answer:  B

 

17) A ________ consists of cloned DNA fragments for all expressed genes in a particular tissue

1.    A) genomic DNA library

2.    B) cDNA library

3.    C) PCR library

4.    D) Guggenheim library

5.    E) shotgun library

Answer:  B

 

18) Which of the following techniques is most efficient for transforming bacterial cells?

1.    A) Gene gun

2.    B) ES cell transfer

3.    C) Electroporation

4.    D) Pronuclear microinjection

5.    E) Sperm-mediated transfer

Answer:  C

 

 

19) Which of the following statements about the human genome is INCORRECT?

3.    A) There are approximately 3.1 billion bp in the human genome.

4.    B) Human share a majority of genes with other species.

5.    C) Less than 2 percent of the genome codes for proteins.

6.    D) The human genome contains approximately 100,000 genes.

7.    E) The functions of most human genes are still unknown.

Answer:  D

 

20) Dideoxyribonucleotides (ddNTPs) used for DNA sequencing lack oxygen atoms at ________.

1.    A) the 1′ carbon of the pentose sugar

2.    B) the 1′ and 2′ carbons of the pentose sugar

3.    C) the 2′ and 3′ carbons of the pentose sugar

4.    D) the 3′ and 5′ carbons of the pentose sugar

5.    E) the 5′ carbon of the pentose sugar

Answer:  C

 

21) A recombinant DNA molecule is produced artificially and contains sequences ________.

1.    A) from bacteria only

2.    B) from yeast only

3.    C) from unrelated organisms

4.    D) from cells that have been chemically modified

5.    E) from prokaryotic genes

Answer:  C

22) A linear strand of DNA is 1,000 bp long. A recognition sequence for the restriction enzyme Eco R1 is located 300 base pairs (bp) from the 5′ end of this linear DNA molecule.  Digesting this DNA molecule with Eco RI would produce ________.

1.    A) one DNA fragment, 1,000 bp long

2.    B) three DNA fragments, two of them 300 bp long and one 400 bp long

3.    C) two DNA fragments, one 300 bp long and one 700 bp long

4.    D) two fragments, each 500 bp long

5.    E) none of the above

Answer:  C

 

23) During molecular cloning, a gene of interest (insulin) is inserted into a bacterial structure called a ________ and enters a bacterial cell through a process called ________.

1.    A) chromosome; electrophoresis

2.    B) nucleus; transformation

3.    C) plasmid; transcription

4.    D) plasmid; transformation

5.    E) genome; transformation

Answer:  D

 

 

24) Which of the following might lead to the generation of several incorrect PCR products?

1.    A) An annealing temperature that is too low

2.    B) An annealing temperature that is too high

3.    C) Performing 30 cycles of PCR

4.    D) Using the correct primers

5.    E) Including an extension step

Answer:  A

 

25) A bacteriophage is ________.

1.    A) a small cloning vector used in humans

2.    B) a large cloning vector used in humans

3.    C) a type of bacterial protein

4.    D) a virus that specifically infects bother viruses

5.    E) a virus that specifically infects bacteria

Answer:  E

 

26) Explain the use of an antibiotic (e.g., ampicillin) resistance gene on a vector.

Answer:  The antibiotic resistance gene is found on the vector (also known as the plasmid). This gene confers resistance to the recombinant DNA plasmid when transformed into bacterial cells and plated on agar media containing the antibiotic, such as ampicillin.  Only bacterial cells that have taken up the vector can grow on media containing ampicillin, thus allowing for selection of colonies that have taken up the vector.

 

27) Describe two advantages for cloning a gene from a cDNA library versus a genomic DNA library.

Answer:  A cDNA library is free of introns and it is enriched for the gene of interest because it is made from mRNA from the desired tissue type.  In contrast, a genomic DNA library still has introns and it has every gene in the genome, making it more difficult to find the gene of interest.

28) Describe three reagents used and the three steps in the process of polymerase chain reaction.

Answer:  The reaction calls for Taq polymerase, a pool of nucleotides, primers, and a thermo cycler. The three steps in the process are as follows: denaturation, which occurs at 94ºC to separate the DNA strand; annealing, in which the temperature varies depending on the primers but is usually between 50ºC and 60ºC and allows the primers to adhere to the DNA strands; and extension, which occurs at 72ºC, allowing for elongation of the DNA from the primer.

 

29) Explain the meaning and utility of RNA interference.

Answer:  RNA interference (RNAi) is a process within living cells that moderates the activity of their genes.

 

 

30) Explain the dideoxy sequencing method.

Answer:  Sanger’s method, which is also referred to as chain termination, is based on the use of dideoxynucleotides (ddNTP’s) in addition to the normal nucleotides (NTP’s) found in DNA. Dideoxynucleotides are essentially the same as nucleotides except they contain a hydrogen group on the 3′ carbon instead of a hydroxyl group (OH). These modified nucleotides, when integrated into a sequence, prevent the addition of further nucleotides. This occurs because a phosphodiester bond cannot form between the dideoxynucleotide and the next incoming nucleotide, and thus the DNA chain is terminated. A nested set of products can then be used to determine the actual nucleotide sequence.

 

 

Introduction to Biotechnology, 3e (Thieman)

Chapter 4   Proteins as Products

 

1) Which recombinant protein is widely used to digest milk proteins for making cheeses?

1.    A) Casein

2.    B) Chymosin

3.    C) Erythropoietin

4.    D) Insulin

5.    E) DNA ligase

Answer:  B

 

2) Which of the following is NOT a recombinant protein isolated from bacteria?

1.    A) Interferon

2.    B) Factor VIII

3.    C) Insulin

4.    D) Erythropoietin

5.    E) Cellulase

Answer:  E

 

3) Isolating and purifying a protein from biological materials to make a biotech product is known as ________.

1.    A) bioprospecting

2.    B) bioprocessing

3.    C) bioremediation

4.    D) biofermentation

5.    E) bioengineering

Answer:  B

 

4) Quaternary structure of a protein refers to ________.

1.    A) the sequence of amino acids in a polypeptide

2.    B) alpha-helical or beta-sheet arrangements of protein structure

3.    C) three-dimensional coil of a polypeptide around itself

4.    D) the association of multiple polypeptide subunits to form a functional protein

5.    E) the number of amino acids in a polypeptide chain

Answer:  D

 

5) Which of the following techniques is designed for separating and analyzing proteins according to their size?

1.    A) Agarose gel electrophoresis

2.    B) Affinity chromatography

3.    C) Polyacrylamide gel electrophoresis

4.    D) Microarray analysis

5.    E) Sanger sequencing

Answer:  C

 

 

6) ________ chromatography involves separating proteins by binding them to ligands.

1.    A) Affinity

2.    B) Polyacrylamide

3.    C) Size-exclusion

4.    D) Ion-exchange

5.    E) Electrophoresis

Answer:  A

7) ________ involves separating proteins by differences in electrostatic charge.

1.    A) Affinity chromatography

2.    B) Mass spectroscopy

3.    C) Size-exclusion chromatography

4.    D) Ion-exchange chromatography

5.    E) Gel-filtration chromatography

Answer:  D

 

8) Bioprocessing a protein often involves growing cells in carefully controlled environments using containers called ________.

1.    A) bioreactors

2.    B) proteomes

3.    C) centrifuges

4.    D) chromatography

5.    E) electrophoresis

Answer:  A

 

9) Cheese manufacturing involves enzymatic or microbial processing of the milk protein ________ to form a coagulated mixture called curd.

1.    A) chymosin

2.    B) rennin

3.    C) malt

4.    D) lactic acid

5.    E) casein

Answer:  E

 

10) Recombinant forms of what protease are used in laundry detergents to remove stains?

1.    A) Casein

2.    B) Subtilisin

3.    C) Erythropoietin

4.    D) Insulin

5.    E) Streptokinase

Answer:  B

 

 

11) Which recombinant protein is used to stimulate red blood cell growth and production?

1.    A) Erythropoietin

2.    B) Insulin

3.    C) Factor VIII

4.    D) Interleukin

5.    E) Streptokinase

Answer:  A

 

12) Alpha helices and β-pleated sheets represent the ________ structure of a protein.

1.    A) primary

2.    B) secondary

3.    C) tertiary

4.    D) quaternary

5.    E) All of the above

Answer:  B

13) Which of the following is NOT an enzyme?

1.    A) Lactose

2.    B) Amylase

3.    C) Catalase

4.    D) Protease

5.    E) Isomerase

Answer:  A

 

14) Adding a carbohydrate group to a protein is known as ________.

1.    A) phosphorylation

2.    B) acetylation

3.    C) glycosylation

4.    D) isomerization

5.    E) kinase activation

Answer:  C

 

15) Adding a phosphate or sugar group to a newly made protein is an example of ________.

1.    A) a posttranscriptional modification

2.    B) a pretranscriptional modification

3.    C) an intron removal

4.    D) gene silencing

5.    E) a posttranslational modification

Answer:  E

 

16) Inclusion bodies ________.

1.    A) are important for a protein’s function

2.    B) can only be found in the primary structure

3.    C) assist in protein purification

4.    D) are insoluble clumps of foreign protein

5.    E) are often part of the final protein product

Answer:  D

 

17) An advantage of using bacterial cells to express proteins is that ________.

1.    A) they are simple to grow

2.    B) they perform posttranslational modifications

3.    C) they are most like human cells

4.    D) they fold proteins correctly

5.    E) their media is expensive

Answer:  A

 

18) A disadvantage of using bacterial cells to grow proteins is that ________.

1.    A) they are simple to grow

2.    B) their media is inexpensive

3.    C) they are most like human cells

4.    D) they do not correctly fold all proteins

5.    E) they grow quickly

Answer:  D

19) Cells must be lysed to release the protein of interest if ________.

1.    A) the protein is secreted into the media

2.    B) the protein is intracellular

3.    C) the protein is hydrophobic

4.    D) the protein is positively charged

5.    E) the protein is hydrophilic

Answer:  B

 

20) HPLC is ________.

1.    A) high-performance liquid chromatography

2.    B) high-pressure lyophilized chromatin

3.    C) heat pressure and liquid contents

4.    D) heat performance lyophilized chromatin

5.    E) heat particulate liquid chromatin

Answer:  A

 

21) Name and define the four levels of structure of a protein. Are all proteins required to have all four levels of structures?

Answer:  Primary, which is the string of amino acids that define the protein; secondary, in which the protein folds into alpha helices and beta sheets; Tertiary, which is the binding within alpha helices and beta sheets; and quaternary, which happens when two or more proteins must associate into a final three-dimensional shape to be active.

A protein does not need all four levels; only two or more associated proteins forms a quaternary structure.

 

22) If you are purifying a protein from an SEC column, what fractions do you want to collect?

Answer:  It depends on whether or not your protein is large or small. Large proteins elute first because they go around the beads whereas small proteins go within the beads. So, for large proteins, you collect the first set of fractions. For smaller proteins, you collect the second set of proteins.

 

23) Define upstream and downstream processing when producing a protein.

Answer:  Upstream processing is the actual cell line expression of the protein of interest. Downstream is the purification of the protein from all the other components in the cell to ensure purity.

 

24) What is meant by lyophilization of proteins and why is it done?

Answer:  It is the freeze-drying of a protein to prepare it to be placed into its final container. It helps to stabilize the protein in transit to the pharmacy or doctor’s office, and it gives the protein better long-term storage capabilities.