Question 1

Compare and contrast electrospray ionization (ESI)and matrix-assisted laser desorption/ionization (MALDI).

Accepted Answer

Both methods are used to ionize peptides

Question 2

Why is the process of purifying proteins from cells considered challenging?

Accepted Answer

A)  Proteins are insoluble. 
B)  The process is expensive and time consuming. 
C)  There is no way to determine the structure of the protein. 
D)  There are 10,000 to 100,000 proteins in one sample. 
A)  Proteins are insoluble. 
B)  The process is expensive and time consuming. 
C)  There is no way to determine the structure of the protein. 
D)  There are 10,000 to 100,000 proteins in one sample.

Question 3

During the production of polyclonal antibodies,how are the antigen-specific antibodies purified?

Accepted Answer

A)  dialysis 
B)  gel electrophoresis 
C)  size exclusion chromatography 
D)  affinity chromatography 
A)  dialysis 
B)  gel electrophoresis 
C)  size exclusion chromatography 
D)  affinity chromatography

Question 4

Below are the steps of a Western blot.What is the correct order?
1)The membrane is incubated with the secondary antibody.
2)The membrane is incubated with the primary antibody.
3)The membrane is washed with a blocking solution.
4)Proteins are transferred to a nitrocellulose membrane.
5)Protein extracts are separated by gel electrophoresis.

Accepted Answer

A) 5,4,3,2,1 
B) 4,5,2,3,1 
C) 3,4,5,1,2 
D) 2,5,4,3,1 
A) 5,4,3,2,1 
B) 4,5,2,3,1 
C) 3,4,5,1,2 
D) 2,5,4,3,1

Question 5

Epitopes on protein antigens are generally located

Accepted Answer

A)  in the heavy chain domains. 
B)  on polar surface groups in loop regions. 
C)  in the light chain domains. 
D)  in association with variable domain amino acid residues. 
A)  in the heavy chain domains. 
B)  on polar surface groups in loop regions. 
C)  in the light chain domains. 
D)  in association with variable domain amino acid residues.

Question 6

Why is X-ray crystallography more commonly used than NMR spectroscopy when determining protein structure?

Accepted Answer

NMR is limited to proteins that are less

Question 7

The specific sites on the antibody that interacts with the antigen are

Accepted Answer

A)  epitopes. 
B)  immunoglobin light chains. 
C)  immunoglobin heavy chains. 
D)  variable-domain amino acid residues. 
A)  epitopes. 
B)  immunoglobin light chains. 
C)  immunoglobin heavy chains. 
D)  variable-domain amino acid residues.

Question 8

In an ELISA,the capture antibody is a __________ antibody.

Accepted Answer

A)  monoclonal primary 
B)  polyclonal primary 
C)  monoclonal secondary 
D)  polyclonal secondary 
A)  monoclonal primary 
B)  polyclonal primary 
C)  monoclonal secondary 
D)  polyclonal secondary

Question 9

Co-immunoprecipitation proteins are separated through

Accepted Answer

A)  affinity chromatography. 
B)  SDS-PAGE. 
C)  HPLC. 
D)  size exclusion chromatography. 
A)  affinity chromatography. 
B)  SDS-PAGE. 
C)  HPLC. 
D)  size exclusion chromatography.

Question 10

Below are the steps of solid-phase peptide synthesis:
1)The protecting groups of the amino acids are removed.
2)The peptide is released from the solid support resin.
3)An incoming amino acid is activated at the carboxyl group by DCC and added to the column.
4)Fmoc is removed by treatment with a base and the C-terminal amino acid is attached to the resin molecule.
5)The resin bound C-terminal amino acid and the incoming N-terminal amino acid are coupled.What is the appropriate order of these steps?

Accepted Answer

A) 3,5,4,2,1 
B) 1,4,2,5,3 
C) 4,3,5,1,2 
D) 2,4,5,3,1 
A) 3,5,4,2,1 
B) 1,4,2,5,3 
C) 4,3,5,1,2 
D) 2,4,5,3,1

Question 11

Which peptide would migrate the slowest in an SDS-PAGE gel? P

Accepted Answer

A)  A 
B)  B 
C)  C 
D)  D 
A)  A 
B)  B 
C)  C 
D)  D

Question 12

If a protocol for a Western blot calls for the use of rabbit anti-mouse antibody,what type of antibody would this be considered?

Accepted Answer

A)  monoclonal primary 
B)  polyclonal primary 
C)  monoclonal secondary 
D)  polyclonal secondary 
A)  monoclonal primary 
B)  polyclonal primary 
C)  monoclonal secondary 
D)  polyclonal secondary

Question 13

In isoelectric focusing,a protein with a pH below the pI would

Accepted Answer

A)  migrate toward the anode. 
B)  migrate toward the cathode. 
C)  stop migrating. 
D)  migrate, but there is no way to determine the direction. 
A)  migrate toward the anode. 
B)  migrate toward the cathode. 
C)  stop migrating. 
D)  migrate, but there is no way to determine the direction.

Question 14

Which type of chromatography separates proteins using specific binding properties?

Accepted Answer

A)  affinity chromatography 
B)  gel filtration chromatography 
C)  size exclusion chromatography 
D)  high-performance liquid chromatography 
A)  affinity chromatography 
B)  gel filtration chromatography 
C)  size exclusion chromatography 
D)  high-performance liquid chromatography

Question 15

Which technique uses highly specific monoclonal antibodies in a high-throughput form to detect small amounts of antigen?

Accepted Answer

A)  immunofluorescence 
B)  Western blot 
C)  SDS-PAGE gel 
D)  ELISA 
A)  immunofluorescence 
B)  Western blot 
C)  SDS-PAGE gel 
D)  ELISA

Question 16

During a Western blot,the membrane is washed with a blocking solution before being treated with the primary antibody to

Accepted Answer

A)  retain the position of the proteins in the transfer from gel to membrane. 
B)  facilitate antibody-antigen interactions. 
C)  decrease nonspecific antibody binding. 
D)  facilitate a chemical reaction that can be detected. 
A)  retain the position of the proteins in the transfer from gel to membrane. 
B)  facilitate antibody-antigen interactions. 
C)  decrease nonspecific antibody binding. 
D)  facilitate a chemical reaction that can be detected.

Question 17

Describe the major difference between the types of protein samples used in X-ray crystallography and NMR spectroscopy.Then explain how this difference limits each method.

Accepted Answer

Protein samples used in NMR are in solut

Question 18

Explain the difference between the primary and secondary antibody using a Western blot.

Accepted Answer

The primary antibody facilitates the ant

Question 19

Calculate the purification of the target protein when there is a 30% decrease in activity and a 55% decrease in total protein after centrifugation.

Accepted Answer

A)  0.55-fold 
B)  0.64-fold 
C)  1.6-fold 
D)  1.8-fold 
A)  0.55-fold 
B)  0.64-fold 
C)  1.6-fold 
D)  1.8-fold

Question 20

Explain the differences among the three types of column chromatography.

Accepted Answer

Gel filtration chromatography (size excl

Exam 5: Methods in Protein Biochemistry

Compare and contrast electrospray ionization (ESI)and matrix-assisted laser desorption/ionization (MALDI).

Why is the process of purifying proteins from cells considered challenging?

During the production of polyclonal antibodies,how are the antigen-specific antibodies purified?

Epitopes on protein antigens are generally located

Why is X-ray crystallography more commonly used than NMR spectroscopy when determining protein structure?

The specific sites on the antibody that interacts with the antigen are

In an ELISA,the capture antibody is a __________ antibody.

Co-immunoprecipitation proteins are separated through

Which peptide would migrate the slowest in an SDS-PAGE gel? P

If a protocol for a Western blot calls for the use of rabbit anti-mouse antibody,what type of antibody would this be considered?

In isoelectric focusing,a protein with a pH below the pI would

Which type of chromatography separates proteins using specific binding properties?

Which technique uses highly specific monoclonal antibodies in a high-throughput form to detect small amounts of antigen?

During a Western blot,the membrane is washed with a blocking solution before being treated with the primary antibody to

Describe the major difference between the types of protein samples used in X-ray crystallography and NMR spectroscopy.Then explain how this difference limits each method.

Explain the difference between the primary and secondary antibody using a Western blot.

Calculate the purification of the target protein when there is a 30% decrease in activity and a 55% decrease in total protein after centrifugation.

Explain the differences among the three types of column chromatography.

Principles of Biochemistry

Physical Biochemistry: Energy Conversion,water,and Membranes

Nucleic Acid Structure and Function

Protein Structure

Protein Function

Enzyme Mechanisms

Cell Signaling Systems

Glycolysis: a Paradigm of Metabolic Regulation

The Citrate Cycle

Oxidative Phosphorylation

Photosynthesis

Carbohydrate Structure and Function

Carbohydrate Metabolism

Lipid Structure and Function

Lipid Metabolism

Amino Acid Metabolism

Nucleotide Metabolism

Metabolic Integration

Dna Replication, repair, and Recombination

Rna Synthesis, processing, and Gene Silencing

Protein Synthesis, posttranslational Modification, and Transport

Gene Regulation

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