Question 1

During solid-phase peptide synthesis, dicyclohexylcarbodiimide is used

Accepted Answer

A)  as a blocking agent. 
B)  as an activating agent. 
C)  to cleave the peptide from the resin. 
D)  to couple amino acids during the synthesis. 
A)  as a blocking agent. 
B)  as an activating agent. 
C)  to cleave the peptide from the resin. 
D)  to couple amino acids during the synthesis.

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

Explain how proteins are separated using isoelectric focusing.

Accepted Answer

Proteins are applied to a gel strip cont

Question 4

Compare the order of migration and the separation of three proteins (25 kDa, 100 kDa, and 150 kDa) in an SDS-PAGE gel with 15% polyacrylamide gel.

Accepted Answer

The 25 kDa protein would migrate the far

Question 5

In tandem mass spectrometry, the first 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.

Question 6

Which technique can be combined with mass spectrometry to identify protein antigens in large cellular complexes?

Accepted Answer

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

Question 7

Explain the differences among the three types of column chromatography.

Accepted Answer

Gel filtration chromatography (size excl

Question 8

Predict the fragments of the following peptide after cleavage by the V-8 protease. CMVAADGKLEPVS

Accepted Answer

A)  CMVAAD GKLEPVS 
B)  CMVAADGKLE PVS 
C)  CMVAADG KLEPVS 
D)  CMVAAD GKLE PVS 
A)  CMVAAD GKLEPVS 
B)  CMVAADGKLE PVS 
C)  CMVAADG KLEPVS 
D)  CMVAAD GKLE PVS

Question 9

Two-dimensional polyacrylamide gel electrophoresis separates proteins based on

Accepted Answer

A)  pI and shape. 
B)  ligand affinity and molecular weight. 
C)  shape and ligand affinity. 
D)  pI and molecular weight. 
A)  pI and shape. 
B)  ligand affinity and molecular weight. 
C)  shape and ligand affinity. 
D)  pI and molecular weight.

Question 10

Analyze and interpret the 2-D PAGE gel shown below. What information can be determined about the proteins labeled A and B?

Accepted Answer

Protein A has a higher mass an

Question 11

After centrifugation, there is a 10% decrease in activity and a 75% decrease in total protein. What is purification of the target protein?

Accepted Answer

A)  0.28-fold 
B)  1.3-fold 
C)  3.6-fold 
D)  7.5-fold 
A)  0.28-fold 
B)  1.3-fold 
C)  3.6-fold 
D)  7.5-fold

Question 12

The advantage of using a native PAGE gel compared with an SDS-PAGE gel is that the native PAGE gel

Accepted Answer

A)  separates proteins only based on molar mass. 
B)  gives information on the charge or conformation of the protein. 
C)  results in a better separation of small proteins. 
D)  increases the resolution of large and small proteins. 
A)  separates proteins only based on molar mass. 
B)  gives information on the charge or conformation of the protein. 
C)  results in a better separation of small proteins. 
D)  increases the resolution of large and small proteins.

Question 13

When cells isolated from the spleen are fused with long-living cells, they produce

Accepted Answer

A)  B cells. 
B)  immortalized tumor cells. 
C)  hybridoma cells. 
D)  red blood cells. 
A)  B cells. 
B)  immortalized tumor cells. 
C)  hybridoma cells. 
D)  red blood cells.

Question 14

One of the most difficult steps in X-ray crystallography is

Accepted Answer

A)  using the correct radio frequency pulses to perturb the nuclear spin. 
B)  determining the phases of diffracted X-rays. 
C)  dissolving the protein in the appropriate solvent. 
D)  obtaining a large enough sample for analysis. 
A)  using the correct radio frequency pulses to perturb the nuclear spin. 
B)  determining the phases of diffracted X-rays. 
C)  dissolving the protein in the appropriate solvent. 
D)  obtaining a large enough sample for analysis.

Question 15

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

Accepted Answer

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

Question 16

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

Accepted Answer

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

Question 17

Why is the supply of polyclonal antibodies limited?

Accepted Answer

A)  They are time consuming to produce. 
B)  The yield is very low. 
C)  The animals the antibodies are isolated from eventually die. 
D)  The production is limited by the government. 
A)  They are time consuming to produce. 
B)  The yield is very low. 
C)  The animals the antibodies are isolated from eventually die. 
D)  The production is limited by the government.

Question 18

Which method uses mass to charge ratios as well as a bioinformatics approach to determine the amino acid composition of a protein?

Accepted Answer

A)  X-ray crystallography 
B)  nuclear magnetic resonance 
C)  tandem mass spectrometry 
D)  size exclusion chromatography 
A)  X-ray crystallography 
B)  nuclear magnetic resonance 
C)  tandem mass spectrometry 
D)  size exclusion chromatography

Question 19

What cells are shown at step number 5 in the figure below?

Accepted Answer

A)  B cells 
B)  immortalized tumor cell 
C)  hybridoma cells 
D)  red blood cells 
A)  B cells 
B)  immortalized tumor cell 
C)  hybridoma cells 
D)  red blood cells

Question 20

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

Accepted Answer

VEFDGSKLSS

Exam 5: Methods in Protein Biochemistry

During solid-phase peptide synthesis, dicyclohexylcarbodiimide is used

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

Explain how proteins are separated using isoelectric focusing.

Compare the order of migration and the separation of three proteins (25 kDa, 100 kDa, and 150 kDa) in an SDS-PAGE gel with 15% polyacrylamide gel.

In tandem mass spectrometry, the first mass spectrometer

Which technique can be combined with mass spectrometry to identify protein antigens in large cellular complexes?

Explain the differences among the three types of column chromatography.

Predict the fragments of the following peptide after cleavage by the V-8 protease. CMVAADGKLEPVS

Two-dimensional polyacrylamide gel electrophoresis separates proteins based on

Analyze and interpret the 2-D PAGE gel shown below. What information can be determined about the proteins labeled A and B?

After centrifugation, there is a 10% decrease in activity and a 75% decrease in total protein. What is purification of the target protein?

The advantage of using a native PAGE gel compared with an SDS-PAGE gel is that the native PAGE gel

When cells isolated from the spleen are fused with long-living cells, they produce

One of the most difficult steps in X-ray crystallography is

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

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

Why is the supply of polyclonal antibodies limited?

Which method uses mass to charge ratios as well as a bioinformatics approach to determine the amino acid composition of a protein?

What cells are shown at step number 5 in the figure below?

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

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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