Chapter 5: Proteins: Primary Structure

Matching
A)
B)
C)
D)
E)
F)
G)
H)
I)
J)
K)
L)
M)
N)
O)
P)
Q

electrophoresis
hydrophobic interaction
enzyme-linked immunosorbent assay
three-dimensional shape
N-terminal amino acid
negative charge
nucleases
chromophore
foaming
high level expression
2-mercaptoethanol
positive charge
cation exchange
pI
chymotrypsin
C-terminal amino acid
Sodium dodecyl sulfate

1. One of the reasons the primary structure is important for a protein is that it determines the
__three-dimentional shape____ the molecule adopts in aqueous solutions.
Ans: D
Level of Difficulty: Easy
Section: 5.1
Learning objective: Polypeptide Diversity
2. If the cDNA for a protein has been cloned, it may be possible to obtain large quantities of the
protein by __high level expression_______________ in bacteria.
Ans: J
Level of Difficulty: Easy
Section: 5.2.A
Learning objective: Protein Purification and Analysis

3. To help prevent denaturation of proteins in solution, steps are taken to avoid

__foamin_______ and adsorption to surfaces.
Ans: I
Level of Difficulty: Moderate
Section: 5.2.A
Learning objective: Protein Purification and Analysis
4. Molecules that contain a(n) __chromophor____ are capable of absorbing light.
Ans: H
Level of Difficulty: Easy
Section: 5.2.A
Learning objective: Protein Purification and Analysis
5. If antibodies to the protein being assayed are available, a(n) ______ can be carried out.
Ans: C
Level of Difficulty: Moderate
Section: 5.2.A
Learning objective: Protein Purification and Analysis
6. In general, proteins are least soluble in water when the pH is close to the _pI_____.
Ans: N
Level of Difficulty: Moderate
Section: 5.2.B
Learning objective: Protein Purification and Analysis
7. ___hydrophoic interaction___ chromatography is a method of fractionating a protein mixture
according to differences in polarity.
Ans: B
Level of Difficulty: Easy
Section: 5.2.C
Learning objective: Protein Purification and Analysis

8. In order for DEAE to act as an anion exchanger, it must have a __positive____.

Ans: L
Level of Difficulty: Easy
Section: 5.2.C
Learning objective: Protein Purification and Analysis
9. In ___cation exchange___ chromatography, a protein mixture must be applied to the column
at a low pH so that the proteins will have a net positive charge and bind to the column.
Ans: M
Level of Difficulty: Moderate
Section: 5.2.C
Learning objective: Protein Purification and Analysis
10. In SDS-PAGE, disulfide-linked polypeptides can be separated after reacting the protein first
with _
K) 2-mercaptoethanol
_____.
Ans: K
Level of Difficulty: Easy
Section: 5.2.D
Learning objective: Protein Purification and Analysis
11. Either dansyl chloride or Edman's reagent can be used to identify the _N-terminal_____ of a
protein.
Ans: E
Level of Difficulty: Moderate
Section: 5.3.A
Learning objective: Protein Sequencing
12. The endoprotease chyrotrpsin______ cleaves polypeptides on the C-terminal side of certain
bulky hydrophobic amino acid residues.
Ans: O
Level of Difficulty: Moderate
Section: 5.3.B
Learning objective: Protein Sequencing

Multiple Choice
13. Proteins are synthesized in vivo by the translation of
A) cDNA.
B) tRNA.
C) rRNA.
D) exons.
E) mRNA.
Ans: E
Level of Difficulty: Easy
Section: 5.1
Learning objective: Polypeptide Diversity
14. Since there are 20 standard amino acids, the number of possible linear polypeptides of length
N can be expressed as:
A) n 20
B) 20n
C) 20 10n
D) n20
E) n 1020
Ans: B
Level of Difficulty: Easy
Section: 5.1
Learning objective: Polypeptide Diversity
15. Natural proteins most commonly contain linear polypeptides between 100 and 1000 residues
in length. One of the reasons polypeptides outside this range may be disfavored is that
A) larger polypeptides would likely be insoluble.
B) smaller polypeptides do not form stable folded structures.
C) smaller polypeptides typically assemble into prion-like aggregates.
D) amide linkages are not strong enough to keep larger polypeptides intact.
E) ribosomes are unable to synthesize larger polypeptides.
Ans: B
Level of Difficulty: Easy
Section: 5.1
Learning objective: Polypeptide Diversity

16. The vast majority of polypeptides contain between ______ amino acid residues.
A) 10 and 50
B) 50 and 100
C) 100 and 1000
D) 1000 and 2000
E) 2000 and 34,000
Ans: C
Level of Difficulty: Easy
Section: 5.1
Learning objective: Polypeptide Diversity
17. Which of the following has the most dramatic influence on the characteristics of an
individual protein?
A) the amino-acid sequence
B) the amino-acid composition
C) the location of its encoding gene within the genome
D) the stereochemistry at the -carbon
E) the sequence of tRNA molecules involved in its translation
Ans: A
Level of Difficulty: Easy
Section: 5.1
Learning objective: Polypeptide Diversity
18. Which statement about insulin is correct?
A) Insulin is composed of two polypeptides, the A chain and the B chain.
B) Insulin contains an intrachain disulfide bond.
C) Insulin contains interchain disulfide bonds.
D) The A chain and the B chain of insulin are encoded by a single gene.
E) All of the above are correct.
Ans: E
Level of Difficulty: Easy
Section: 5.1
Learning objective: Polypeptide Diversity

19. A fast and common method for determining the protein concentration in column effluent is
A) tandem mass spectrometry.
B) salting in with ammonium sulfate.
C) drying a portion and weighing the solid.
D) measuring light absorption at 280 nm.
E) Edman degradation.
Ans: D
Level of Difficulty: Easy
Section: 5.2.A
Learning objective: Protein Purification and Analysis
20. The salting in of proteins can be explained by:
A) salt counter-ions reducing electrostatic attractions between protein molecules.
B) salt ions reducing the polarity of the solution.
C) salt ions increasing the hydrophobic interactions.
D) releasing hydrophobic proteins from nonpolar tissue environments.
E) hydration of the salt ions reducing solubility of proteins.
Ans: A
Level of Difficulty: Moderate
Section: 5.2.A
Learning objective: Protein Purification and Analysis
21. The quantitation of proteins due to their absorbance at ~280 nm (UV region) is due to the
large absorbtivity of the ________ amino acids.
A) anionic
B) dansylated
C) cleaved
D) polar
E) aromatic
Ans: E
Level of Difficulty: Easy
Section: 5.2.A
Learning objective: Protein Purification and Analysis

22. Which of the following assays would be most specific for a particular protein?
A) Bradford assay
B) UV absorptivity
C) radioimmunoassay
D) molar absorptivity
E) amino acid analysis
Ans: C
Level of Difficulty: Moderate
Section: 5.2.A
Learning objective: Protein Purification and Analysis
23. An enzyme-linked immunosorbent assay requires
A) a radioactive substrate.
B) a radioactive standard for binding to the antibody.
C) aromatic amino acids.
D) an antibody that binds the protein of interest.
E) a catalytic antibody.
Ans: D
Level of Difficulty: Moderate
Section: 5.2.A
Learning objective: Protein Purification and Analysis
24. ELISA is an example of a(n):
A) enzyme assay.
B) biological assay.
C) binding assay.
D) immunological assay.
E) none of the above
Ans: D
Level of Difficulty: Easy
Section: 5.2.A
Learning objective: Protein Purification and Analysis

25. You are purifying a nuclease by affinity chromatography. To determine which fractions
contain the protein of interest, you test samples of all fractions for their ability to break down
DNA. This is an example of
A) a binding assay.
B) a biological assay.
C) an enzyme assay.
D) an immunological assay.
E) none of the above
Ans: C
Level of Difficulty: Easy
Section: 5.2.A
Learning objective: Protein Purification and Analysis
26. A radioimmunoassay requires
A) an enzyme-linked antibody.
B) a coupled enzymatic reaction.
C) a radiolabeled antibody.
D) a catalytic antibody.
E) a radiolabeled standard protein that is used to compete for binding to the antibody.
Ans: E
Level of Difficulty: Moderate
Section: 5.2.A
Learning objective: Protein Purification and Analysis

27. Five graduate students prepare extracts from 5 different tissues. Each student measures the
total amount of alcohol dehydrogenase and the total amount of protein in his or her extract.
Which extract has the highest specific activity?
Total protein (mg)
A
B
C
D
E

300
200
3000
5000
1000

Total alcohol
dehydrogenase activity
(units)
60,000
80,000
96,000
100,000
200,000

Ans: B
Level of Difficulty: Easy
Section: 5.2.A
Learning objective: Protein Purification and Analysis

28. Which physical characteristic is not commonly used in protein separation?

A) solubility
B) stereochemistry
C) size
D) charge
E) polarity
Ans: B
Level of Difficulty: Easy
Section: 5.2.B
Learning objective: Protein Purification and Analysis
29. Adding additional salt to a protein solution can cause:
A) an increase in solubility called salting in.
B) a decrease in solubility called salting out.
C) protein precipitation from solution.
D) all of the above
E) none of the above
Ans: D
Level of Difficulty: Easy
Section: 5.2.B
Learning objective: Protein Purification and Analysis
30. A first step in purifying a protein that was initially associated with fatty substances would be
A) Coomassie Brilliant Blue dye staining.
B) analytical ultracentrifugation.
C) ELISA.
D) Western blotting.
E) hydrophobic interaction chromatography.
Ans: E
Level of Difficulty: Moderate
Section: 5.2.C
Learning objective: Protein Purification and Analysis

31. The acronym HPLC stands for

A) hydrophobic protein liquid chromatography.
B) high performance liquid chromatography.
C) hydrophilic partition liquid chromatography.
D) high priced liquid chromatography.
E) hydrostatic process liquid chromatography.
Ans: B
Level of Difficulty: Easy
Section: 5.2.C
Learning objective: Protein Purification and Analysis
32. A technique that can be used to separate proteins based primarily on the presence of nonpolar residues on their surface is called
A) ion-exchange chromatography.
B) gel filtration chromatography.
C) affinity chromatography.
D) gel electrophoresis.
E) hydrophobic interaction chromatography.
Ans: E
Level of Difficulty: Easy
Section: 5.2.C
Learning objective: Protein Purification and Analysis
33. A technique that can be used to separate proteins based primarily on their pI is called
A) ion-exchange chromatography.
B) gel filtration chromatography.
C) affinity chromatography.
D) isoelectric focusing.
E) hydrophobic interaction chromatography.
Ans: D
Level of Difficulty: Easy
Section: 5.2.C
Learning objective: Protein Purification and Analysis

10

34. Which of the following amino acids would be last to elute at pH 8.0 from an anion-exchange
column?
A) lysine
B) alanine
C) glutamic acid
D) asparagine
E) glycine
Ans: C
Level of Difficulty: Moderate
Section: 5.2.C
Learning objective: Protein Purification and Analysis
35. Which of the following amino acids would be first to elute at pH 8.0 from an anionexchange column?
A) lysine
B) alanine
C) glutamic acid
D) asparagine
E) glycine
Ans: A
Level of Difficulty: Moderate
Section: 5.2.C
Learning objective: Protein Purification and Analysis
36. The pK1, pK2, and pKR of the amino acid lysine are 2.2, 9.1, and 10.5, respectively. The pK1,
pK2, and pKR of the amino acid arginine are 1.8, 9.0, and 12.5, respectively. A student at SDSU
wants to use ion exchange chromatography to separate lysine from arginine. What pH is likely
to work best for this separation?
A) 1.5
B) 2.5
C) 5.5
D) 7.5
E) 10.5
Ans: E
Level of Difficulty: Difficult
Section: 5.2.C
Learning objective: Protein Purification and Analysis

11

37. The pK1, pK2, and pKR of the amino acid histdine are 1.8, 9.3, and 6.0, respectively. The
pK1, pK2, and pKR of the amino acid arginine are 1.8, 9.0, and 12.5, respectively. You have a
mixture of histidine and arginine, how would you try to separate these two amino acids?
A) anion exchange chromatography at pH 2
B) anion exchange chromatography at pH 4
C) cation exchange chromatography at pH 2
D) cation exchange chromatography at pH 4
E) cation exchange chromatography at pH 9
Ans: E
Level of Difficulty: Difficult
Section: 5.2.C
Learning objective: Protein Purification and Analysis
38. What can be done to increase the rate at which a protein of interest moves down an ionexchange chromatography column?
A) reduce the ion concentration in the eluant
B) add a small amount of a non-ionic detergents to the eluant
C) change the pH of the eluant
D) add a protease inhibitor to the eluant
E) reduce the temperature of the eluant
Ans: C
Level of Difficulty: Moderate
Section: 5.2.C
Learning objective: Protein Purification and Analysis
39. Hydrophobic interaction chromatography can be used to separate proteins based on
differences in
A) ionic charge.
B) solubility.
C) size.
D) polarity.
E) binding specificity.
Ans: D
Level of Difficulty: Easy
Section: 5.2.C
Learning objective: Protein Purification and Analysis

12

40. You are trying to separate five proteins, which are listed below, by gel filtration
chromatography. Which of the proteins will elute first from the column?
A) cytochrome c (12 kDa)
B) RNA polymerase (99 kDa)
C) glutamine synthetase (621 kDa)
D) interferon- (34 kDa)
E) hemoglobin (62 kDa)
Ans: C
Level of Difficulty: Moderate
Section: 5.2.C
Learning objective: Protein Purification and Analysis
41. SDS-PAGE separates proteins primarily due to differences in
A) isoelectric point.
B) mass.
C) polarity.
D) solubility.
E) amino acid sequence.
Ans: B
Level of Difficulty: Easy
Section: 5.2.D
Learning objective: Protein Purification and Analysis
42. Which of these techniques is used to separate proteins mainly based on mass?
A) polyacrylamide gel electrophoresis (in the absence of SDS)
B) SDS-PAGE
C) isoelectric focusing
D) immunoblotting
E) Western blotting
Ans: B
Level of Difficulty: Easy
Section: 5.2.D
Learning objective: Protein Purification and Analysis

13

43. Which of these techniques uses antibodies to detect very small amounts of specific proteins
following separation by SDS-PAGE.
A) immunoblotting
B) silverstaining
C) Coomassie Brilliant Blue staining
D) ELISA
E) RIA
Ans: A
Level of Difficulty: Easy
Section: 5.2.D
Learning objective: Protein Purification and Analysis
44. Disulfide bonds can be cleaved using
A) iodoacetate.
B) dansyl chloride.
C) 2-mercaptoethanol (-ME).
D) trypsin.
E) phenylisothiocyanate.
Ans: C
Level of Difficulty: Easy
Section: 5.3.A
Learning objective: Protein Sequencing
45. Which of these reagents is commonly used to determine the number of polypeptides in a
protein?
A) iodoacetate
B) dansyl chloride
C) 2-mercaptoethanol (-ME)
D) cyanogen bromide
E) DEAE
Ans: B
Level of Difficulty: Easy
Section: 5.3.A
Learning objective: Protein Sequencing

14

46. Enzymes that hydrolyze the internal peptide bonds (not the peptide bonds of the terminal
amino acids) of a protein are classified as
A) oxidoreductases.
B) lyases.
C) endopeptidases.
D) nucleases.
E) exopeptidases.
Ans: C
Level of Difficulty: Easy
Section: 5.3.B
Learning objective: Protein Sequencing
47. Which of the following substances cannot be used to cleave peptide bonds in polypeptides?
A) trypsin
B) cyanogen bromide
C) endopeptidases
D) 2-mercaptoethanol
E) pepsin
Ans: D
Level of Difficulty: Moderate
Section: 5.3.B
Learning objective: Protein Sequencing
48. Which of these are commonly used to cleave peptide bonds in polypeptides?
A) 2-mercaptoethanol (-ME)
B) dansyl chloride
C) iodoacetate
D) sodium dodecyl sulfate
E) trypsin
Ans: E
Level of Difficulty: Moderate
Section: 5.3.B
Learning objective: Protein Sequencing

15

49. The peptide LeuCysArgSerGlnMet is subjected to Edman degradation. In the first

cycle the peptide first reacts with phenylisothiocyanate under basic conditions. The product of
this reaction is incubated with anhydrous trifluoroacetic acid and subsequently with an aqueous
acid. What are the products generated in the first cycle.
A)
B)
C)
D)
E)

PTHLeu, PTHCys, PTHArg, PTHSer, PTHGln, and PTHMet

PTHLeuCysArgSerGlnMet
PTHMet and LeuCysArgSerGlnMet
PTHLeuCys and PTHArgSerGlnMet
PTHLeu and CysArgSerGlnMet

Ans: E
Level of Difficulty: Moderate
Section: 5.3.C
Learning objective: Protein Sequencing
50. Edman degradation can be used to
A) identify the N-terminal amino acid of a polypeptide.
B) identify the C-terminal amino acid of a polypeptide.
C) separate the subunits of a multi-subunit protein.
D) cleave a protein at specific sites.
E) cleave disulfide bonds within a protein so that the individual polypeptides can be separated.
Ans: A
Level of Difficulty: Easy
Section: 5.3.C
Learning objective: Protein Sequencing
51. Although a proteins primary sequence can be inferred from the nucleotide sequence,
modifications such as ______ can be determined most easily by tandem mass spectrometry
followed by protein database searching.
A) phosphorylation
B) disulfide crosslinks
C) glycosylation
D) acetylation
E) all of the above
Ans: E
Level of Difficulty: Easy
Section: 5.3.D
Learning objective: Protein Sequencing

16

52. The positive charge on proteins in electrospray ionization mass spectrometry is the result of
A) protons fired at the gas-phase protein molecules.
B) protonated side chains of Asp and Glu residues.
C) protonated side chains of Arg and Lys residues.
D) a high pH.
E) electrons fired at the gas-phase protein molecules.
Ans: C
Level of Difficulty: Moderate
Section: 5.3.D
Learning objective: Protein Sequencing
53. ______________ has emerged as a technique for protein sequencing.
A) NMR spectroscopy
B) Mass spectrometry
C) Gel electrophoresis
D) Phylogenetic analysis
E) Limited proteolysis
Ans: B
Level of Difficulty: Easy
Section: 5.3.D
Learning objective: Protein Sequencing
54. Protein sequences are customarily reconstructed from sequenced fragments because
A) protein purification invariably results in the fragmentation of the protein of interest.
B) proteins are naturally and inevitably cleaved by proteolytic enzymes.
C) proteins are composed of multiple subunits.
D) large polypeptides cannot be directly sequenced.
E) all of the above
Ans: D
Level of Difficulty: Easy
Section: 5.3.E
Learning objective: Protein Sequencing

17

55. You have purified a new peptide hormone. To determine its amino acid sequence you have
digested the polypeptide with trypsin and in a separate reaction you have cleaved the polypeptide
with cyanogen bromide.
Cleavage with trypsin yielded 5 peptides that were sequenced by Edman degradation as shown in
the following.
1.
2.
3.
4.
5.

SerLeu
AspValArg
ValMetGluLys
SerGlnMetHisLys
IlePheMetLeuCysArg

Cleavage with cyanogen bromide yielded 4 peptides that were sequenced by Edman degradation:
1.
2.
3.
4.

HisLysSerLeu
AspValArgValMet
GluLysIlePheMet
LeuCysArgSerGlnMet

Determine the identity of the N-terminal amino acid after reconstructing the intact protein.
A)
B)
C)
D)
E)

Asp
Ser
His
Glu
Ile

Ans: A
Level of Difficulty: Difficult
Section: 5.3.E
Learning objective: Protein Sequencing
56. In two homologous proteins, which residue is most likely to replace a Glu residue as a
conservative substitution?
A) Asp
B) Trp
C) Met
D) Ile
E) Lys
Ans: A
Level of Difficulty: Easy
Section: 5.4.A
Learning objective: Protein Evolution

18

57. A phylogenetic tree depicts ___________ of proteins.

A) folding patterns
B) hypervariable residues
C) invariable residues
D) evolutionary relationships
E) gene sequences
Ans: D
Level of Difficulty: Easy
Section: 5.4.A
Learning objective: Protein Evolution
58. A protein that has had few changes in its amino acid sequence over evolutionary history is
labeled
A) a fibrinopeptide.
B) evolutionarily conserved.
C) random.
D) a product of pseudogenes.
E) phylogenetic.
Ans: B
Level of Difficulty: Easy
Section: 5.4.B
Learning objective: Protein Evolution
59. Paralogous genes are
A) genes that do not encode protein.
B) genes of slowly evolving proteins.
C) relics of genes that are not expressed.
D) genes of rapidly evolving proteins.
E) the results of gene duplication.
Ans: E
Level of Difficulty: Moderate
Section: 5.4.B
Learning objective: Protein Evolution

19

60. A fast way for nature to generate new proteins is:

A) generation of pseudogenes.
B) mutation by neutral drift.
C) shuffling protein domains or motifs.
D) hypervariable positions.
E) liberal substitution.
Ans: C
Level of Difficulty: Easy
Section: 5.4.B
Learning objective: Protein Evolution
61. ___________ is an example of a very slowly evolving protein.
A) Histone H4
B) Hemoglobin
C) Cytochrome c
D) Fibrinopeptides
E) none of the above
Ans: A
Level of Difficulty: Moderate
Section: 5.4.B
Learning objective: Protein Evolution
62. Proteins are often constructed from multiple segments of 40-200 amino acid residues,
commonly called
A) pseudogenes.
B) hypervariable residues.
C) protolytic fragments.
D) domains.
E) subunits.
Ans: D
Level of Difficulty: Easy
Section: 5.4.B
Learning objective: Protein Evolution

20

SHORT ANSWER
63. Proteins can vary in size from approximately 40 to 34,000 amino acids.
a. Why is there a lower limit to the size of proteins?
b. Why is there an upper limit to the size of polypeptides?
Ans: a. Polypeptides shorter than 40 residues are unable to maintain a stable fold (probably
because there are not enough functional groups to help stabilize the folded structure).
b. The longer the polypeptide, the longer the corresponding mRNA and gene, resulting in an
increase in mistakes made during transcription and translation. Beyond a certain size every
protein encoded for by a very large gene will include debilitating mistakes.
Level of Difficulty: Moderate
Section: 5.1
Learning objective: Polypeptide Diversity
64. We are able to purify proteins because they differ from each other in various physical or
chemical properties. List 5 physicochemical properties of proteins that can be used as basis for
their separation. Give a method of separation based on each of these properties (match the
method with the property).
Ans: 1. solubility salting out; 2. ionic charge ion exchange chromatography,
electrophoresis (in the absence of SDS), or isoelectric focusing; 3. polarity hydrophobic
interaction chromatography; 4. size (mass) gel filtration chromatography (size exclusion
chromatography) or SDS-PAGE 5. ability to bind to specific molecules affinity
chromatography
Level of Difficulty: Moderate
Section: 5.2A
Learning objective: Protein Purification and Analysis

21

65. One technique commonly used in protein purification is chromatography.

a. Explain briefly the general principle of column chromatography
b. Name four types of chromatography and indicate for each of these types the basis for
separation (match types of chromatography with the properties that form the basis for
separation).
Ans: a. In chromatography there are two phases, the stationary phase and the mobile phase.
The stationary phase is the column material and the mobile phase is the buffer that runs through
the column. Proteins or molecules are separated based on their relative affinities for these two
phases. A molecule with very high affinity for the stationary phase will spend most of its time
associated with the column material and will move very slowly down the column. A molecule
with high affinity for the mobile phase will spend most of its time suspended in the buffer and
will move quickly through the column. Molecules with high affinity for the stationary phase will
elute late from the column. Molecules with a high affinity for the mobile phase will elute early.
b. 1. ion-exchange chromatography ionic charge; 2. gel filtration chromatography size
(mass); 3.
hydrophobic interaction chromatography polarity; 4. affinity chromatography ability to
bind to specific molecules.
Level of Difficulty: Moderate
Section: 5.2C
Learning objective: Protein Purification and Analysis
66. Ion exchange chromatography is a commonly used method for separation of biomolecules.
a. What are the two types of ion exchange chromatography?
b. In what order would Arg, Val, and Glu elute from a carboxymethyl column at pH 6.0.
Carboxymethyl is negatively charged at pH 6.0.
c. You are trying to purify a protein using ion exchange chromatography. Unfortunately, your
protein remains bound to the ion exchange column or it is eluting very slowly. What are the two
changes you can make, to try to elute your protein more quickly from this column?
Ans: a. cation exchange chromatography and anion exchange chromatography.
b. First Glu, then Val, followed last by Arg, because at pH 6.0 Glu is has an electric charge of -1,
Val is neutral, and Arg has an electric charge of +1.
c. To make your protein move more quickly through the column you need to reduce the
interactions with the column material. This can be done by changing the pH (changing the
charge on your protein) or by increasing the ion concentration in the eluant (ions will compete
with your protein for binding to the column material).
Level of Difficulty: Moderate
Section: 5.2C
Learning objective: Protein Purification and Analysis

22

67. A variety of chromatographic techniques are available for protein purification.

a. Explain briefly the principle of hydrophobic interaction chromatography.
b. Name three changes that can be made to the eluant that can be used to speed up elution of the
protein of interest from a hydrophobic interaction chromatography column.
Ans: a. The column material is substituted with nonpolar groups. Proteins with nonpolar
regions on their surface will be driven to interact with the column material as a result of the
hydrophobic affect.
b. To weaken the interaction between the column material and the nonpolar regions on your
protein you can include detergents (they will shield nonpolar regions on proteins from interacting
with water or other nonpolar groups), change the pH (will change the polarity of your protein), or
reduce the ion concentration of the eluant (this will make it less polar).
Level of Difficulty: Moderate
Section: 5.2C
Learning objective: Protein Purification and Analysis
68. You are interested in receptor protein-tyrosine kinases and you are purifying a novel
phosphotyrosine-binding protein (NPBP-1). In order to characterize this protein you need to
separate it from three other proteins (X, Y, and Z) that are still present in your partially purified
material. The proteins in your preparation have the following properties:

protein X
protein Y
protein Z
NPBP-1

binds to
phosphotyrosine
yes
yes
no
yes

Size (kDa)
85
29
31
28

pI
7.2
2.9
7.4
7.5

a. What type of separation technique can be used to separate protein NPBP-1 from protein X?
b. What type of separation technique can be used to separate protein NPBP-1 from protein Y?
c. What type of separation technique can be used to separate protein NPBP-1 from protein Z?
Ans: a. On a size (mass) basis: gel permeation chromatography, SDS-PAGE, or
ultracentrifugation.
b. On a charge basis: ion exchange chromatography or isoelectric focusing
c. On a binding behavior basis: phosphotyrosine affinity chromatography
Level of Difficulty: Moderate
Section: 5.2C
Learning objective: Protein Purification and Analysis

23

69. You have purified the receptor for a hormone by affinity chromatography. During gel
filtration chromatography under native conditions the receptor elutes between pyruvate
decarboxylase (250 kDa) and glutamine synthetase (620 kDa). During SDS-PAGE, in the
absence of reducing agents, the receptor migrates as a single band of approximately 230 kDa.
When SDS-PAGE is carried out in the presence of 2-mercaptoethanol the receptor migrates as
two bands of approximately 95 and 135 kDa. Explain this result.
Ans: The receptor is a heterotetramer composed of two subunits of 95 kDa and two subunits
of 135 kDa. Heterodimers of one subunit and one subunit are stabilized by disulfide bonds.
Two heterodimers are held together by hydrophobic interactions. In the absence of detergents
during gel filtration all subunits stay together and we observe a 460 kDa protein. During SDSPAGE (in the absence of reducing agents) SDS interferes with the hydrophobic interactions that
hold the two dimers together and we observe a 230 kDa protein. Finally, when we add 2mercaptoethanol during SDS-PAGE the disulfide bonds are broken and we observe 2
polypeptides of 135 and 95 kDa.

Level of Difficulty: Moderate

Section: 5.2D
Learning objective: Protein Purification and Analysis

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