Question 1

In tandem mass spectrometry, the second mass spectrometer

Accepted Answer

A)  determines the nuclear spin of the atoms. 
B)  determines the mass of peptide subfragments. 
C)  uses bioinformatics to compare the masses of the peptides. 
D)  uses electrospray ionization to select peptide fragments. 
A)  determines the nuclear spin of the atoms. 
B)  determines the mass of peptide subfragments. 
C)  uses bioinformatics to compare the masses of the peptides. 
D)  uses electrospray ionization to select peptide fragments. B

Question 2

Contrast the way that SDS-PAGE and native PAGE gels separate proteins.

Accepted Answer

SDS-PAGE gels use several chemicals (including the SDS) that denature the protein into polypeptide chains. The addition of the SDS negates the charge and the shape of the protein, so the protein is only separated based on molar mass. In a native PAGE, the protein is not denatured and is separated based on size, molar mass, and charge.

Question 3

The majority of serum proteins and nonspecific antibodies are removed during the generation of polyclonal antibodies by

Accepted Answer

A)  washing with a low pH buffer. 
B)  gel electrophoresis. 
C)  size exclusion chromatography. 
D)  salting out. 
A)  washing with a low pH buffer. 
B)  gel electrophoresis. 
C)  size exclusion chromatography. 
D)  salting out. A

Question 4

Which percentage of polyacrylamide would give the best separation for small proteins?

Accepted Answer

A)  5% 
B)  7.5% 
C)  10% 
D)  20% 
A)  5% 
B)  7.5% 
C)  10% 
D)  20%

Question 5

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 6

The step in solid-phase peptide synthesis that occurs at number 2 is

Accepted Answer

A)  deblocking of the residue attached to the resin. 
B)  coupling of the amino acid. 
C)  cleavage from the resin. 
D)  activation of the Fmoc blocked residue. 
A)  deblocking of the residue attached to the resin. 
B)  coupling of the amino acid. 
C)  cleavage from the resin. 
D)  activation of the Fmoc blocked residue.

Question 7

You are employed in a prominent biochemistry lab, ProteinsRUs. The company offers a $500 bonus to the person who can develop a way to perform Western blotting without having to wait to make a unique antibody for proteins under analysis. How would you propose to do this? Explain the method you would use in two to three sentences and give an example.

Accepted Answer

A faster way to perform the analysis wou

Question 8

What is the advantage of using sodium dodecyl sulfate (SDS) in gel electrophoresis?

Accepted Answer

Gel electrophoresis separates molecules

Question 9

In solid-phase peptide synthesis, which reagent is used to remove the peptide from the solid resin support?

Accepted Answer

A)  HF 
B)  DCC 
C)  Fmoc 
D)  PITC 
A)  HF 
B)  DCC 
C)  Fmoc 
D)  PITC

Question 10

Protein-specific antibodies can be used to detect proteins within cells conserving the cell architecture using

Accepted Answer

A)  immunofluorescence. 
B)  Western blot. 
C)  immunoprecipitation. 
D)  ELISA. 
A)  immunofluorescence. 
B)  Western blot. 
C)  immunoprecipitation. 
D)  ELISA.

Question 11

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

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 12

Which animal is most often used to generate monoclonal antibodies?

Accepted Answer

A)  rabbit 
B)  chicken 
C)  goat 
D)  mouse 
A)  rabbit 
B)  chicken 
C)  goat 
D)  mouse

Question 13

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 14

A polypeptide was digested by trypsin and chymotrypsin. Use the following information to determine the polypeptide sequence.

Accepted Answer

A)  ECFGMREDWKYLM 
B)  LMYKWMGFCEDER 
C)  LMYKWDERMGFCE 
D)  CELMYKWDERMGF 
A)  ECFGMREDWKYLM 
B)  LMYKWMGFCEDER 
C)  LMYKWDERMGFCE 
D)  CELMYKWDERMGF

Question 15

Most secondary antibodies used in Western blots are covalently linked to the enzyme

Accepted Answer

A)  luciferase. 
B)  horseradish peroxidase. 
C)  catalase. 
D)  hydrolase. 
A)  luciferase. 
B)  horseradish peroxidase. 
C)  catalase. 
D)  hydrolase.

Question 16

Describe how polyclonal antibodies are generated.

Accepted Answer

Either a rabbit, chicken, or goat is inj

Question 17

Which of the following peptides would be eluted last when separated using gel filtration chromatography?

Accepted Answer

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

Question 18

Monoclonal antibodies

Accepted Answer

A)  recognize a single epitope. 
B)  recognize multiple epitopes. 
C)  are isolated from leukocytes. 
D)  are isolated from red blood cells. 
A)  recognize a single epitope. 
B)  recognize multiple epitopes. 
C)  are isolated from leukocytes. 
D)  are isolated from red blood cells.

Question 19

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 20

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.

Exam 5: Methods in Protein Biochemistry

In tandem mass spectrometry, the second mass spectrometer

Contrast the way that SDS-PAGE and native PAGE gels separate proteins.

The majority of serum proteins and nonspecific antibodies are removed during the generation of polyclonal antibodies by

Which percentage of polyacrylamide would give the best separation for small proteins?

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

The step in solid-phase peptide synthesis that occurs at number 2 is

What is the advantage of using sodium dodecyl sulfate (SDS) in gel electrophoresis?

In solid-phase peptide synthesis, which reagent is used to remove the peptide from the solid resin support?

Protein-specific antibodies can be used to detect proteins within cells conserving the cell architecture using

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

Which animal is most often used to generate monoclonal antibodies?

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

A polypeptide was digested by trypsin and chymotrypsin. Use the following information to determine the polypeptide sequence.

Most secondary antibodies used in Western blots are covalently linked to the enzyme

Describe how polyclonal antibodies are generated.

Which of the following peptides would be eluted last when separated using gel filtration chromatography?

Monoclonal antibodies

Epitopes on protein antigens are generally located

Co-immunoprecipitation proteins are separated through

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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