Question 1

Due primarily to single nucleotide polymorphisms, each human differs from every other human, on average, by what percentage of the human genome?

Accepted Answer

A)  6% 
B)  15% 
C)  0.1% 
D)  98% 
E)  1.5% 
A)  6% 
B)  15% 
C)  0.1% 
D)  98% 
E)  1.5%

Question 2

When cloning a gene into a plasmid, which enzyme would you use to covalently attach the gene to the plasmid DNA?

Accepted Answer

A)  DNA polymerase 
B)  exonuclease III 
C)  DNA Ligase 
D)  alkaline phosphatase 
E)  a restriction endonuclease 
A)  DNA polymerase 
B)  exonuclease III 
C)  DNA Ligase 
D)  alkaline phosphatase 
E)  a restriction endonuclease

Question 3

What happens in PCR if you use DNA polymerase derived from E. coli instead of from a thermostable source?

Accepted Answer

Polymerase Chain Reaction (PCR) is a tec

Question 4

The PCR reaction mixture does NOT include:

Accepted Answer

A)  all four deoxynucleoside triphosphates. 
B)  DNA containing the sequence to be amplified. 
C)  DNA ligase. 
D)  heat-stable DNA polymerase. 
E)  oligonucleotide primer(s). 
A)  all four deoxynucleoside triphosphates. 
B)  DNA containing the sequence to be amplified. 
C)  DNA ligase. 
D)  heat-stable DNA polymerase. 
E)  oligonucleotide primer(s).

Question 5

Which factor is required to accurately determine the relative amount of gene expression of two or more genes in an organism using qPCR?

Accepted Answer

A)  a "no template" control 
B)  an oligonucleotide probe labeled with a fluorophore and a quenching molecule at its ends 
C)  use of reverse transcriptase to copy the RNA products into DNA 
D)  All of the answers are correct. 
E)  None of the answers is correct. 
A)  a "no template" control 
B)  an oligonucleotide probe labeled with a fluorophore and a quenching molecule at its ends 
C)  use of reverse transcriptase to copy the RNA products into DNA 
D)  All of the answers are correct. 
E)  None of the answers is correct.

Question 6

Which analytical technique does NOT help illuminate a gene's cellular function?

Accepted Answer

A)  DNA microarray analysis 
B)  protein chip analysis 
C)  Southern blotting 
D)  two-dimensional gel electrophoresis 
E)  two-hybrid analysis 
A)  DNA microarray analysis 
B)  protein chip analysis 
C)  Southern blotting 
D)  two-dimensional gel electrophoresis 
E)  two-hybrid analysis

Question 7

What is a polylinker?

Accepted Answer

A)  a type of cloning vector 
B)  a DNA fragment with multiple recognition sequences for restriction endonucleases 
C)  a type of expression vector 
D)  an enzyme that joins DNA molecules together 
E)  a method of getting DNA into a cell 
A)  a type of cloning vector 
B)  a DNA fragment with multiple recognition sequences for restriction endonucleases 
C)  a type of expression vector 
D)  an enzyme that joins DNA molecules together 
E)  a method of getting DNA into a cell

Question 8

Match each feature of the plasmid pBR322 (at left) with one appropriate description presented (at right) (see illustration of pBR322 below). Descriptions may be used more than once.   ____ ampR sequence
(a) Permits selection of bacteria containing the plasmid.
____ ori sequence
(b) A sequence required for packaging recombinant plasmids
____ tetR
into bacteriophage.
____ BamHI sequence
(c) Origin of replication.
____ PstI sequence
(d) Cleavage of the plasmid here does not affect antibiotic
sequence resistance genes.
(e) Insertion of foreign DNA here permits identification of
bacteria containing recombinant plasmids .

Accepted Answer

Question 9

If you want to determine what other proteins might be interacting with the protein you have been studying, what type of fusion tag would you add to your protein to aid in purification of both the protein you have been studying and the proteins interacting with it?

Accepted Answer

A)  a green fluorescent protein fusion tag 
B)  a tandem affinity purification tag 
C)  a maltose-binding protein tag 
D)  an epitope tag 
E)  a $\beta$-galactosidase tag 
A)  a green fluorescent protein fusion tag 
B)  a tandem affinity purification tag 
C)  a maltose-binding protein tag 
D)  an epitope tag 
E)  a $\beta$-galactosidase tag

Question 10

If you want to express two different genes on different plasmids in a bacterial host, which procedure will NOT be successful?

Accepted Answer

A)  using plasmids that have the same promoter sequence 
B)  using EcoRI and BamHI restriction endonucleases to clone the genes into their respective plasmids 
C)  placing different fusion tags on each of the genes when cloning them 
D)  using plasmids with the same origin of replication 
E)  using plasmids that have different selectable markers 
A)  using plasmids that have the same promoter sequence 
B)  using EcoRI and BamHI restriction endonucleases to clone the genes into their respective plasmids 
C)  placing different fusion tags on each of the genes when cloning them 
D)  using plasmids with the same origin of replication 
E)  using plasmids that have different selectable markers

Question 11

Genes that have sequence and functional relationships to each other within a single species are called:

Accepted Answer

A)  orthologs. 
B)  paralogs. 
C)  analogs. 
D)  homologs. 
E)  lincolnlogs. 
A)  orthologs. 
B)  paralogs. 
C)  analogs. 
D)  homologs. 
E)  lincolnlogs.

Question 12

A method of comparing the relative gene expression of all the genes in an organism at two different stages of its development is:

Accepted Answer

A)  a DNA microarray. 
B)  yeast two-hybrid analysis. 
C)  tandem affinity purification. 
D)  immunofluorescence. 
E)  quantitiative PCR. 
A)  a DNA microarray. 
B)  yeast two-hybrid analysis. 
C)  tandem affinity purification. 
D)  immunofluorescence. 
E)  quantitiative PCR.

Question 13

Which amino acid when repeated six to ten times at the N- or C-terminal ends of a protein allows that protein to bind to Ni2+ ions?

Accepted Answer

A)  Glu 
B)  His 
C)  Ala 
D)  Tyr 
E)  Asp 
A)  Glu 
B)  His 
C)  Ala 
D)  Tyr 
E)  Asp

Question 14

A method of determining if proteins are interacting in vivo that makes use of a transcription factor involved in regulating galactose metabolism genes is:

Accepted Answer

A)  a DNA microarray. 
B)  yeast two-hybrid analysis. 
C)  tandem affinity purification. 
D)  immunofluorescence. 
E)  quantitiative PCR. 
A)  a DNA microarray. 
B)  yeast two-hybrid analysis. 
C)  tandem affinity purification. 
D)  immunofluorescence. 
E)  quantitiative PCR.

Question 15

Which statement regarding plasmid-cloning vectors is CORRECT?

Accepted Answer

A)  Circular plasmids do not require an origin of replication to be propagated in E. coli. 
B)  Foreign DNA fragments up to 45,000 base pairs can be cloned in a typical plasmid. 
C)  Plasmids do not need to contain genes that confer resistance to antibiotics. 
D)  Plasmid vectors must carry promoters for inserted gene fragments. 
E)  The copy number of plasmids may vary from a few to several hundred. 
A)  Circular plasmids do not require an origin of replication to be propagated in E. coli. 
B)  Foreign DNA fragments up to 45,000 base pairs can be cloned in a typical plasmid. 
C)  Plasmids do not need to contain genes that confer resistance to antibiotics. 
D)  Plasmid vectors must carry promoters for inserted gene fragments. 
E)  The copy number of plasmids may vary from a few to several hundred.

Question 16

The E. coli recombinant plasmid pBR322 has been widely utilized in genetic engineering experiments. Which feature does pBR322 NOT have?

Accepted Answer

A)  a number of conveniently located recognition sites for restriction enzymes 
B)  a number of palindromic sequences near the EcoRI site, which permit the plasmid to assume a conformation that protects newly inserted DNA from nuclease degradation 
C)  a replication origin, which permits it to replicate autonomously 
D)  resistance to two different antibiotics, which permits rapid screening for recombinant plasmids containing foreign DNA 
E)  small overall size, which facilitates entry of the plasmid into host cells 
A)  a number of conveniently located recognition sites for restriction enzymes 
B)  a number of palindromic sequences near the EcoRI site, which permit the plasmid to assume a conformation that protects newly inserted DNA from nuclease degradation 
C)  a replication origin, which permits it to replicate autonomously 
D)  resistance to two different antibiotics, which permits rapid screening for recombinant plasmids containing foreign DNA 
E)  small overall size, which facilitates entry of the plasmid into host cells

Question 17

What is a DNA microarray? How does it resemble and how does it differ from a DNA library?

Accepted Answer

A DNA microarray is a tool used in molec

Question 18

Which tag is NOT used to study protein function?

Accepted Answer

A)  green fluorescent protein (GFP) 
B)  synteny tag 
C)  tandem affinity purification (TAP) 
D)  Gal4p DNA binding domain 
E)  Gal4p activation domain 
A)  green fluorescent protein (GFP) 
B)  synteny tag 
C)  tandem affinity purification (TAP) 
D)  Gal4p DNA binding domain 
E)  Gal4p activation domain

Question 19

The technique known as two hybrid analysis for detecting interacting gene products depend on:

Accepted Answer

A)  activation of DNA polymerase by the nearby binding of hybridizing protein complexes. 
B)  direct binding of a Gal4p activation domain to a DNA sequence in the promoter region. 
C)  having a promoter that responds directly to one of the two proteins whose interactions is being measured. 
D)  hybridization of DNA segments corresponding to the two genes being examined. 
E)  stimulation of transcription by interaction of two Gal4p domains via fused protein sequences. 
A)  activation of DNA polymerase by the nearby binding of hybridizing protein complexes. 
B)  direct binding of a Gal4p activation domain to a DNA sequence in the promoter region. 
C)  having a promoter that responds directly to one of the two proteins whose interactions is being measured. 
D)  hybridization of DNA segments corresponding to the two genes being examined. 
E)  stimulation of transcription by interaction of two Gal4p domains via fused protein sequences.

Question 20

Common problems with expression of eukaryotic proteins in bacteria may include proteins:

Accepted Answer

A)  aggregating into inclusion bodies. 
B)  not folding correctly due to absence of chaperones. 
C)  not undergoing posttranslational modification. 
D)  All of the answers are correct. 
E)  None of the answers is correct. 
A)  aggregating into inclusion bodies. 
B)  not folding correctly due to absence of chaperones. 
C)  not undergoing posttranslational modification. 
D)  All of the answers are correct. 
E)  None of the answers is correct.

Exam 9: DNA-Based Information Technologies

Due primarily to single nucleotide polymorphisms, each human differs from every other human, on average, by what percentage of the human genome?

When cloning a gene into a plasmid, which enzyme would you use to covalently attach the gene to the plasmid DNA?

What happens in PCR if you use DNA polymerase derived from E. coli instead of from a thermostable source?

The PCR reaction mixture does NOT include:

Which factor is required to accurately determine the relative amount of gene expression of two or more genes in an organism using qPCR?

Which analytical technique does NOT help illuminate a gene's cellular function?

What is a polylinker?

If you want to determine what other proteins might be interacting with the protein you have been studying, what type of fusion tag would you add to your protein to aid in purification of both the protein you have been studying and the proteins interacting with it?

If you want to express two different genes on different plasmids in a bacterial host, which procedure will NOT be successful?

Genes that have sequence and functional relationships to each other within a single species are called:

A method of comparing the relative gene expression of all the genes in an organism at two different stages of its development is:

Which amino acid when repeated six to ten times at the N- or C-terminal ends of a protein allows that protein to bind to Ni2+ ions?

A method of determining if proteins are interacting in vivo that makes use of a transcription factor involved in regulating galactose metabolism genes is:

Which statement regarding plasmid-cloning vectors is CORRECT?

The E. coli recombinant plasmid pBR322 has been widely utilized in genetic engineering experiments. Which feature does pBR322 NOT have?

What is a DNA microarray? How does it resemble and how does it differ from a DNA library?

Which tag is NOT used to study protein function?

The technique known as two hybrid analysis for detecting interacting gene products depend on:

Common problems with expression of eukaryotic proteins in bacteria may include proteins:

The Foundations of Biochemistry

Water

Amino Acids, Peptides, and Proteins

The Three-Dimensional Structure of Proteins

Protein Function

Enzymes

Carbohydrates and Glycobiology

Nucleotides and Nucleic Acids

Lipids

Biological Membranes and Transport

Biosignaling

Bioenergetics and Biochemical Reaction Types

Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway

Principles of Metabolic Regulation

The Citric Acid Cycle

Fatty Acid Catabolism

Amino Acid Oxidation and the Production of Urea

Oxidative Phosphorylation and Photophosphorylation

Carbohydrate Biosynthesis in Plants and Bacteria

Lipid Biosynthesis

Biosynthesis of Amino Acids, Nucleotides, and Related Molecules

Hormonal Regulation and Integration of Mammalian Metabolism

Genes and Chromosomes

DNA Metabolism

RNA Metabolism

Protein Metabolism

Regulation of Gene Expression

Filters

Which amino acid when repeated six to ten times at the N- or C-terminal ends of a protein allows that protein to bind to Ni²⁺ ions?