Question 1

Which component used in a Western blot is covalently linked to an enzyme?

Accepted Answer

A)  SDS-PAGE gel 
B)  primary antibody 
C)  secondary antibody 
D)  filter membrane 
A)  SDS-PAGE gel 
B)  primary antibody 
C)  secondary antibody 
D)  filter membrane

Question 2

Calculate the specific activity when 500 mg of protein has an activity of 18,000 units.

Accepted Answer

A)  0.28 units/mg protein 
B)  36 units/mg protein 
C)  9000 units/mg protein 
D)  13,000 units/mg protein 
A)  0.28 units/mg protein 
B)  36 units/mg protein 
C)  9000 units/mg protein 
D)  13,000 units/mg protein

Question 3

Which technique ionizes polypeptides by embedding the tryptic fragments into a light-absorbing matrix and exposing it to a laser?

Accepted Answer

A)  ESI 
B)  MALDI 
C)  NMR 
D)  X-ray crystallography 
A)  ESI 
B)  MALDI 
C)  NMR 
D)  X-ray crystallography

Question 4

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

Accepted Answer

Both methods are used to ionize peptides

Question 5

What cells are shown at step number 2 in the figure below?

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 6

In isoelectric focusing,

Accepted Answer

A)  negatively charged proteins migrate toward the cathode. 
B)  negatively charged proteins migrate toward the anode. 
C)  small proteins migrate the fastest. 
D)  large proteins migrate the fastest. 
A)  negatively charged proteins migrate toward the cathode. 
B)  negatively charged proteins migrate toward the anode. 
C)  small proteins migrate the fastest. 
D)  large proteins migrate the fastest.

Question 7

The Fab immunoglobin fragment

Accepted Answer

A)  is generally found within $\beta$-barrels. 
B)  is located in polar surface groups in loop regions. 
C)  contains the high-affinity antigen binding site. 
D)  is responsible for the solubility of the antibody. 
A)  is generally found within $\beta$-barrels. 
B)  is located in polar surface groups in loop regions. 
C)  contains the high-affinity antigen binding site. 
D)  is responsible for the solubility of the antibody.

Question 8

After using the salting out method to isolate proteins, how is ammonium sulfate removed from the solution?

Accepted Answer

A)  sonication 
B)  French press 
C)  dialysis 
D)  centrifugation 
A)  sonication 
B)  French press 
C)  dialysis 
D)  centrifugation

Question 9

Using the figure below describing monoclonal antibody generation, identify the step where the B cells are fused with the tumor cells.

Accepted Answer

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

Question 10

The part of the Western blot that contains the protein-specific recognition and facilitates the antigen-antibody interactions is the

Accepted Answer

A)  SDS-PAGE gel. 
B)  primary antibody. 
C)  tertiary antibody. 
D)  filter membrane. 
A)  SDS-PAGE gel. 
B)  primary antibody. 
C)  tertiary antibody. 
D)  filter membrane.

Question 11

During solid-phase peptide synthesis, 9-fluorenylmethoxycarbonyl 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 12

The figure below shows three proteins that are separated using gel filtration chromatography. Which protein is the largest?

Accepted Answer

A)  squares 
B)  circles 
C)  triangles 
D)  Not enough information is included to determine the protein. 
A)  squares 
B)  circles 
C)  triangles 
D)  Not enough information is included to determine the protein.

Question 13

In isoelectric focusing,

Accepted Answer

A)  positively charged proteins migrate toward the cathode. 
B)  positively charged proteins migrate toward the anode. 
C)  small proteins migrate the fastest. 
D)  large proteins migrate the fastest. 
A)  positively charged proteins migrate toward the cathode. 
B)  positively charged proteins migrate toward the anode. 
C)  small proteins migrate the fastest. 
D)  large proteins migrate the fastest.

Question 14

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 15

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 16

Which enzyme or reagent cleaves a peptide at the carboxyl side of a methionine residue?

Accepted Answer

A)  trypsin 
B)  chymotrypsin 
C)  V-8 protease 
D)  cyanogen bromide 
A)  trypsin 
B)  chymotrypsin 
C)  V-8 protease 
D)  cyanogen bromide

Question 17

The step in solid-phase peptide synthesis that occurs at number 3 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 18

Compare and contrast the three MOST commonly used homogenization techniques to prepare a cell extract.

Accepted Answer

All three methods are used to disrupt or

Question 19

Protein NMR is more useful than X-ray crystallography for studying

Accepted Answer

A)  secondary structure elements. 
B)  large proteins. 
C)  protein unfolding. 
D)  static protein structures. 
A)  secondary structure elements. 
B)  large proteins. 
C)  protein unfolding. 
D)  static protein structures.

Question 20

Predict the fragments of the following peptide after cleavage by trypsin. GLMKTYPDSTA

Accepted Answer

A)  GLM KTYPDSTA 
B)  GLMK TYPDSTA 
C)  GLMKTY PDSTA 
D)  GLMKTYPD STA 
A)  GLM KTYPDSTA 
B)  GLMK TYPDSTA 
C)  GLMKTY PDSTA 
D)  GLMKTYPD STA

Exam 5: Methods in Protein Biochemistry

Which component used in a Western blot is covalently linked to an enzyme?

Calculate the specific activity when 500 mg of protein has an activity of 18,000 units.

Which technique ionizes polypeptides by embedding the tryptic fragments into a light-absorbing matrix and exposing it to a laser?

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

What cells are shown at step number 2 in the figure below?

In isoelectric focusing,

The Fab immunoglobin fragment

After using the salting out method to isolate proteins, how is ammonium sulfate removed from the solution?

Using the figure below describing monoclonal antibody generation, identify the step where the B cells are fused with the tumor cells.

The part of the Western blot that contains the protein-specific recognition and facilitates the antigen-antibody interactions is the

During solid-phase peptide synthesis, 9-fluorenylmethoxycarbonyl is used

The figure below shows three proteins that are separated using gel filtration chromatography. Which protein is the largest?

In isoelectric focusing,

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.

Which enzyme or reagent cleaves a peptide at the carboxyl side of a methionine residue?

The step in solid-phase peptide synthesis that occurs at number 3 is

Compare and contrast the three MOST commonly used homogenization techniques to prepare a cell extract.

Protein NMR is more useful than X-ray crystallography for studying

Predict the fragments of the following peptide after cleavage by trypsin. GLMKTYPDSTA

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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