Question 1

Which of these are commonly used to cleave peptide bonds in polypeptides?

Accepted Answer

A) 2-mercaptoethanol ($\beta$-M
E)  
B) dansyl chloride 
C) iodoacetate 
D) sodium dodecyl sulfate 
E) trypsin 
A) 2-mercaptoethanol ($\beta$-M
E)  
B) dansyl chloride 
C) iodoacetate 
D) sodium dodecyl sulfate 
E) trypsin E

Question 2

Although a protein's 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.

Accepted Answer

A) phosphorylation 
B) disulfide crosslinks 
C) glycosylation 
D) acetylation 
E) all of the above 
A) phosphorylation 
B) disulfide crosslinks 
C) glycosylation 
D) acetylation 
E) all of the above E

Question 3

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

Accepted Answer

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. 
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. B

Question 4

Adding additional salt to a protein solution can cause:

Accepted Answer

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 
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

Question 5

A phylogenetic tree depicts ___________ of proteins.

Accepted Answer

A) folding patterns 
B) hypervariable residues 
C) invariable residues 
D) evolutionary relationships 
E) gene sequences 
A) folding patterns 
B) hypervariable residues 
C) invariable residues 
D) evolutionary relationships 
E) gene sequences

Question 6

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:
   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?

Accepted Answer

a.On a size (mass)basis: gel permeation

Question 7

Matching
-To help prevent denaturation of proteins in solution, steps are taken to avoid _________ and adsorption to surfaces.

Accepted Answer

A) electrophoresis 
B) hydrophobic interaction 
C) enzyme-linked immunosorbent assay 
D) three-dimensional shape 
E) N-terminal amino acid
F)negative charge
G)nucleases
H)chromophore
I)foaming
J)high level expression
K)2-mercaptoethanol
L)positive charge
M)cation exchange
N)pI
O)chymotrypsin
P)C-terminal amino acid
Q)Sodium dodecyl sulfate 
A) electrophoresis 
B) hydrophobic interaction 
C) enzyme-linked immunosorbent assay 
D) three-dimensional shape 
E) N-terminal amino acid
F)negative charge
G)nucleases
H)chromophore
I)foaming
J)high level expression
K)2-mercaptoethanol
L)positive charge
M)cation exchange
N)pI
O)chymotrypsin
P)C-terminal amino acid
Q)Sodium dodecyl sulfate

Question 8

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?

Accepted Answer

a.cation exchange chromatography and ani

Question 9

SDS-PAGE separates proteins primarily due to differences in

Accepted Answer

A) isoelectric point. 
B) mass. 
C) polarity. 
D) solubility. 
E) amino acid sequence. 
A) isoelectric point. 
B) mass. 
C) polarity. 
D) solubility. 
E) amino acid sequence.

Question 10

Which of these techniques is used to separate proteins mainly based on mass?

Accepted Answer

A) polyacrylamide gel electrophoresis (in the absence of SDS) 
B) SDS-PAGE 
C) isoelectric focusing 
D) immunoblotting 
E) Western blotting 
A) polyacrylamide gel electrophoresis (in the absence of SDS) 
B) SDS-PAGE 
C) isoelectric focusing 
D) immunoblotting 
E) Western blotting

Question 11

Which of the following has the most dramatic influence on the characteristics of an individual protein?

Accepted Answer

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 $\alpha$-carbon 
E) the sequence of tRNA molecules involved in its translation 
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 $\alpha$-carbon 
E) the sequence of tRNA molecules involved in its translation

Question 12

______________ has emerged as a technique for protein sequencing.

Accepted Answer

A) NMR spectroscopy 
B) Mass spectrometry 
C) Gel electrophoresis 
D) Phylogenetic analysis 
E) Limited proteolysis 
A) NMR spectroscopy 
B) Mass spectrometry 
C) Gel electrophoresis 
D) Phylogenetic analysis 
E) Limited proteolysis

Question 13

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?

Accepted Answer

A) cytochrome c (12 kDa) 
B) RNA polymerase (99 kDa) 
C) glutamine synthetase (621 kDa) 
D) interferon-$\gamma$ (34 kDa) 
E) hemoglobin (62 kDa) 
A) cytochrome c (12 kDa) 
B) RNA polymerase (99 kDa) 
C) glutamine synthetase (621 kDa) 
D) interferon-$\gamma$ (34 kDa) 
E) hemoglobin (62 kDa)

Question 14

A fast way for nature to generate new proteins is:

Accepted Answer

A) generation of pseudogenes. 
B) mutation by neutral drift. 
C) shuffling protein domains or motifs. 
D) hypervariable positions. 
E) liberal substitution. 
A) generation of pseudogenes. 
B) mutation by neutral drift. 
C) shuffling protein domains or motifs. 
D) hypervariable positions. 
E) liberal substitution.

Question 15

___________ is an example of a very slowly evolving protein.

Accepted Answer

A) Histone H4 
B) Hemoglobin 
C) Cytochrome c 
D) Fibrinopeptides 
E) none of the above 
A) Histone H4 
B) Hemoglobin 
C) Cytochrome c 
D) Fibrinopeptides 
E) none of the above

Question 16

A fast and common method for determining the protein concentration in column effluent is

Accepted Answer

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. 
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.

Question 17

The peptide Leu─Cys─Arg─Ser─Gln─Met 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.

Accepted Answer

A) PTH─Leu, PTH─Cys, PTH─Arg, PTH─Ser, PTH─Gln, and PTH─Met 
B) PTH─Leu─Cys─Arg─Ser─Gln─Met 
C) PTH─Met and Leu─Cys─Arg─Ser─Gln─Met 
D) PTH─Leu─Cys and PTH─Arg─Ser─Gln─Met 
E) PTH─Leu and Cys─Arg─Ser─Gln─Met 
A) PTH─Leu, PTH─Cys, PTH─Arg, PTH─Ser, PTH─Gln, and PTH─Met 
B) PTH─Leu─Cys─Arg─Ser─Gln─Met 
C) PTH─Met and Leu─Cys─Arg─Ser─Gln─Met 
D) PTH─Leu─Cys and PTH─Arg─Ser─Gln─Met 
E) PTH─Leu and Cys─Arg─Ser─Gln─Met

Question 18

Which of the following amino acids would be first to elute at pH 8.0 from an anion-exchange column?

Accepted Answer

A) lysine 
B) alanine 
C) glutamic acid 
D) asparagine 
E) glycine 
A) lysine 
B) alanine 
C) glutamic acid 
D) asparagine 
E) glycine

Question 19

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?

Accepted Answer

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 
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

Question 20

Which of the following substances cannot be used to cleave peptide bonds in polypeptides?

Accepted Answer

A) trypsin 
B) cyanogen bromide 
C) endopeptidases 
D) 2-mercaptoethanol 
E) pepsin 
A) trypsin 
B) cyanogen bromide 
C) endopeptidases 
D) 2-mercaptoethanol 
E) pepsin

Exam 5: Proteins: Primary Structure

Which of these are commonly used to cleave peptide bonds in polypeptides?

Although a protein's 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.

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

Adding additional salt to a protein solution can cause:

A phylogenetic tree depicts ___________ of proteins.

Matching -To help prevent denaturation of proteins in solution, steps are taken to avoid _________ and adsorption to surfaces.

SDS-PAGE separates proteins primarily due to differences in

Which of these techniques is used to separate proteins mainly based on mass?

Which of the following has the most dramatic influence on the characteristics of an individual protein?

______________ has emerged as a technique for protein sequencing.

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 fast way for nature to generate new proteins is:

___________ is an example of a very slowly evolving protein.

A fast and common method for determining the protein concentration in column effluent is

Which of the following amino acids would be first to elute at pH 8.0 from an anion-exchange column?

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?

Which of the following substances cannot be used to cleave peptide bonds in polypeptides?

Introduction to the Chemistry of Life

Water

Nucleotides, Nucleic Acids, and Genetic Information

Amino Acids

Proteins: Three-Dimensional Structure

Protein Function Part I: Myoglobin and Hemoglobin

Carbohydrates

Lipids and Biological Membranes

Membrane Transport

Enzyme Catalysis

Enzyme Kinetics, Inhibition and Control

Biochemical Signaling

Introduction to Metabolism

Glycogen Metabolism and Gluconeogenesis

Glucose Catabolism

Citric Acid Cycle

Electron Transport and Oxidative Phosphorylation

Photosynthesis

Lipid Metabolism

Amino Acid Metabolism

Mammalian Fuel Metabolism: Integration and Regulation

Nucleotide Metabolism

Nucleic Acid Structure

Dna Replication, Repair and Recombination

Transcription and Rna Processing

Translation

Regulation of Gene Expression

Filters

The pK₁, pK₂, and pK_R of the amino acid histdine are 1.8, 9.3, and 6.0, respectively.The pK₁, pK₂, and pK_R 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?