Question 1

One method used to prevent disulfide bond interference with protein sequencing procedures is:

Accepted Answer

A)  cleaving proteins with proteases that specifically recognize disulfide bonds. 
B)  protecting the disulfide bridge against spontaneous reduction to cysteinyl sulfhydryl groups. 
C)  reducing disulfide bridges and preventing their re-formation by further modifying the -SH groups. 
D)  removing cystines from protein sequences by proteolytic cleavage. 
E)  sequencing proteins that do not contain cysteinyl residues. 
A)  cleaving proteins with proteases that specifically recognize disulfide bonds. 
B)  protecting the disulfide bridge against spontaneous reduction to cysteinyl sulfhydryl groups. 
C)  reducing disulfide bridges and preventing their re-formation by further modifying the -SH groups. 
D)  removing cystines from protein sequences by proteolytic cleavage. 
E)  sequencing proteins that do not contain cysteinyl residues.

Question 2

The "signature sequence" shown below represents a portion of a protein from four different organisms. The proteins can be classified as:

Accepted Answer

A)  homologs. 
B)  orthologs. 
C)  paralogs. 
D)  both homologs and orthologs. 
E)  both homologs and paralogs. 
A)  homologs. 
B)  orthologs. 
C)  paralogs. 
D)  both homologs and orthologs. 
E)  both homologs and paralogs.

Question 3

Which statement is CORRECT with respect to the amino acid composition of proteins?

Accepted Answer

A)  Larger proteins have a more uniform distribution of amino acids than smaller proteins. 
B)  Proteins contain at least one each of the 20 different standard amino acids. 
C)  Proteins with different functions usually differ significantly in their amino acid composition. 
D)  Proteins with the same molecular weight have the same amino acid composition. 
E)  The average molecular weight of an amino acid in a protein increases with the size of the protein. 
A)  Larger proteins have a more uniform distribution of amino acids than smaller proteins. 
B)  Proteins contain at least one each of the 20 different standard amino acids. 
C)  Proteins with different functions usually differ significantly in their amino acid composition. 
D)  Proteins with the same molecular weight have the same amino acid composition. 
E)  The average molecular weight of an amino acid in a protein increases with the size of the protein.

Question 4

According to the diagram, how many titratable groups does this amino acid have?

Accepted Answer

A)  0 
B)  1 
C)  2 
D)  3 
E)  It cannot be determined by this diagram. 
A)  0 
B)  1 
C)  2 
D)  3 
E)  It cannot be determined by this diagram.

Question 5

You are trying to determine the sequence of a protein that you know is pure. Give the most likely explanation for each of the following experimental observations. You may use a simple diagram for your answer.
(a) The Sanger reagent (FDNB, fluorodinitrobenzene) identifies Ala and Leu as amino-terminal residues, in roughly equal amounts.
(b) Your protein has an apparent Mr of 80,000, as determined by SDS-polyacrylamide gel electrophoresis. After treatment of the protein with performic acid, the same technique reveals two proteins of Mr 35,000 and 45,000.
(c) Size-exclusion chromatography (gel filtration) experiments indicate the native protein has an apparent Mr of 160,000.

Accepted Answer

(a) The most likely explanation for the

Question 6

In one or two sentences, describe the usefulness of each of the following reagents or reactions in the analysis of protein structure:
(a) Edman reagent (phenylisothiocyanate)
(b) protease
(c) reducing agent (dithiothreitol or $\beta$-mercaptoethanol)

Accepted Answer

(a) The Edman reagent (phenylisothiocyan

Question 7

The uncommon amino acid selenocysteine has an R group with the structure -CH2-SeH (pKa $\approx$5). In an aqueous solution, pH = 7.0, selenocysteine would:

Accepted Answer

A)  be a fully ionized zwitterion with no net charge. 
B)  be found in proteins as D-selenocysteine. 
C)  never be found in a protein. 
D)  be nonionic. 
E)  not be optically active. 
A)  be a fully ionized zwitterion with no net charge. 
B)  be found in proteins as D-selenocysteine. 
C)  never be found in a protein. 
D)  be nonionic. 
E)  not be optically active.

Question 8

Briefly describe the five major groupings of amino acids.
79.
A
B
C
D
E
Tyr-Lys-Met
Gly-Pro-Arg
Asp-Trp-Tyr
Asp-His-Glu
Leu-Val-Phe
Which one of the above tripeptides:
____ (a) is most negatively charged at pH 7?
____ (b) will yield DNP-tyrosine when reacted with l-fluoro-2,4-dinitrobenzene and hydrolyzed in acid?
____ (c) contains the largest number of nonpolar R groups?
____ (d) contains sulfur?
____ (e) will have the greatest light absorbance at 280 nm?

Accepted Answer

Amino acids, the building blocks of prot

Question 9

At the isoelectric pH of a tetrapeptide:

Accepted Answer

A)  only the amino and carboxyl termini contribute charge. 
B)  the amino and carboxyl termini are not charged. 
C)  the total net charge is zero. 
D)  there are four ionic charges. 
E)  two internal amino acids of the tetrapeptide cannot have ionizable R groups. 
A)  only the amino and carboxyl termini contribute charge. 
B)  the amino and carboxyl termini are not charged. 
C)  the total net charge is zero. 
D)  there are four ionic charges. 
E)  two internal amino acids of the tetrapeptide cannot have ionizable R groups.

Question 10

The formation of a peptide bond between two amino acids is an example of a(n) _____ reaction.

Accepted Answer

A)  cleavage 
B)  condensation 
C)  group transfer 
D)  isomerization 
E)  oxidation reduction 
A)  cleavage 
B)  condensation 
C)  group transfer 
D)  isomerization 
E)  oxidation reduction

Question 11

According to the diagram, at pH 2, what is the average net charge on this amino acid?

Accepted Answer

A)  +1 
B)  + 0.5 
C)  0 
D)  -0.5 
E)  -1 
A)  +1 
B)  + 0.5 
C)  0 
D)  -0.5 
E)  -1

Question 12

How can isoelectric focusing be used in conjunction with SDS gel electrophoresis?

Accepted Answer

Isoelectric focusing (IEF) can be used i

Question 13

How does the shape of a titration curve confirm the fact that the pH region of greatest buffering power for an amino acid solution is around its pK's?

Accepted Answer

A titration curve for an amino acid solu

Question 14

The structure below is a molecule used in the sweeteners Equal® and NutraSweet®. When heated, the peptide bond will hydrolyze into methanol and which two amino acids?

Accepted Answer

A)  asparagine and tyrosine 
B)  aspartic acid and phenylalanine 
C)  glutamic acid and phenylalanine 
D)  aspartic acid and tryptophan 
E)  glutamic acid and histidine 
A)  asparagine and tyrosine 
B)  aspartic acid and phenylalanine 
C)  glutamic acid and phenylalanine 
D)  aspartic acid and tryptophan 
E)  glutamic acid and histidine

Question 15

For each of these methods of separating proteins, describe the principle of the method, and tell what property of proteins allows their separation by this technique.
(a) ion-exchange chromatography
(b) size-exclusion (gel filtration) chromatography
(c) affinity chromatography

Accepted Answer

(a) Ion-exchange chromatography: The pri

Question 16

Which pair of amino acids can be used to measure the concentration of proteins based on absorption of UV light?

Accepted Answer

A)  proline and valine 
B)  serine and threonine 
C)  aspartate and glutamate 
D)  lysine and histidine 
E)  tyrosine and tryptophan 
A)  proline and valine 
B)  serine and threonine 
C)  aspartate and glutamate 
D)  lysine and histidine 
E)  tyrosine and tryptophan

Question 17

All of the 20 common amino acids contain an R-group that is attached to the:

Accepted Answer

A)  carboxyl group. 
B)  amino group. 
C)  $\alpha$ carbon. 
D)  $\beta$ carbon. 
E)  It depends on the amino acid 
A)  carboxyl group. 
B)  amino group. 
C)  $\alpha$ carbon. 
D)  $\beta$ carbon. 
E)  It depends on the amino acid

Question 18

According to the diagram, which pH range offers the GREATEST buffering power for this amino acid?

Accepted Answer

A)  0.5-1.5 
B)  0-1 
C)  1-2 
D)  2-3 
E)  1-3 
A)  0.5-1.5 
B)  0-1 
C)  1-2 
D)  2-3 
E)  1-3

Question 19

A nonapeptide was determined to have the following amino acid composition: (Lys)2, (Gly) 2, (Phe) 2, His, Leu, Met. The native peptide was incubated with 1-fluoro-2,4-dinitrobenzene (FDNB) and then hydrolyzed; 2,4-dinitrophenylhistidine was identified by HPLC. When the native peptide was exposed to cyanogen bromide (CNBr), an octapeptide and free glycine were recovered. Incubation of the native peptide with trypsin gave a pentapeptide, a tripeptide, and free Lys. 2,4-Dinitrophenyl-histidine was recovered from the pentapeptide, and 2,4-dinitrophenylphenylalanine was recovered from the tripeptide. Digestion with the enzyme pepsin produced a dipeptide, a tripeptide, and a tetrapeptide. The tetrapeptide was composed of (Lys) 2, Phe, and Gly. The native sequence was determined to be:

Accepted Answer

A)  Gly-Phe-Lys-Lys-Gly-Leu-Met-Phe-His. 
B)  His-Leu-Gly-Lys-Lys-Phe-Phe-Gly-Met. 
C)  His-Leu-Phe-Gly-Lys-Lys-Phe-Met-Gly. 
D)  His-Phe-Leu-Gly-Lys-Lys-Phe-Met-Gly. 
E)  Met-Leu-Phe-Lys-Phe-Gly-Gly-Lys-His. 
A)  Gly-Phe-Lys-Lys-Gly-Leu-Met-Phe-His. 
B)  His-Leu-Gly-Lys-Lys-Phe-Phe-Gly-Met. 
C)  His-Leu-Phe-Gly-Lys-Lys-Phe-Met-Gly. 
D)  His-Phe-Leu-Gly-Lys-Lys-Phe-Met-Gly. 
E)  Met-Leu-Phe-Lys-Phe-Gly-Gly-Lys-His.

Question 20

Why do smaller molecules elute after large molecules when a mixture of proteins is passed through a size-exclusion (gel filtration) column?

Accepted Answer

Size-exclusion chromatography, also know

Exam 3: Amino Acids, Peptides, and Proteins

One method used to prevent disulfide bond interference with protein sequencing procedures is:

The "signature sequence" shown below represents a portion of a protein from four different organisms. The proteins can be classified as:

Which statement is CORRECT with respect to the amino acid composition of proteins?

According to the diagram, how many titratable groups does this amino acid have?

In one or two sentences, describe the usefulness of each of the following reagents or reactions in the analysis of protein structure: (a) Edman reagent (phenylisothiocyanate) (b) protease (c) reducing agent (dithiothreitol or β\betaβ -mercaptoethanol)

The uncommon amino acid selenocysteine has an R group with the structure -CH2-SeH (pKa ≈\approx≈ 5). In an aqueous solution, pH = 7.0, selenocysteine would:

At the isoelectric pH of a tetrapeptide:

The formation of a peptide bond between two amino acids is an example of a(n) _____ reaction.

According to the diagram, at pH 2, what is the average net charge on this amino acid?

How can isoelectric focusing be used in conjunction with SDS gel electrophoresis?

How does the shape of a titration curve confirm the fact that the pH region of greatest buffering power for an amino acid solution is around its pK's?

The structure below is a molecule used in the sweeteners Equal® and NutraSweet®. When heated, the peptide bond will hydrolyze into methanol and which two amino acids?

For each of these methods of separating proteins, describe the principle of the method, and tell what property of proteins allows their separation by this technique. (a) ion-exchange chromatography (b) size-exclusion (gel filtration) chromatography (c) affinity chromatography

Which pair of amino acids can be used to measure the concentration of proteins based on absorption of UV light?

All of the 20 common amino acids contain an R-group that is attached to the:

According to the diagram, which pH range offers the GREATEST buffering power for this amino acid?

Why do smaller molecules elute after large molecules when a mixture of proteins is passed through a size-exclusion (gel filtration) column?

The Foundations of Biochemistry

Water

The Three-Dimensional Structure of Proteins

Protein Function

Enzymes

Carbohydrates and Glycobiology

Nucleotides and Nucleic Acids

DNA-Based Information Technologies

Lipids

Biological Membranes and Transport

Biosignaling

Bioenergetics and Biochemical Reaction Types

Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway

Principles of Metabolic Regulation

The Citric Acid Cycle

Fatty Acid Catabolism

Amino Acid Oxidation and the Production of Urea

Oxidative Phosphorylation and Photophosphorylation

Carbohydrate Biosynthesis in Plants and Bacteria

Lipid Biosynthesis

Biosynthesis of Amino Acids, Nucleotides, and Related Molecules

Hormonal Regulation and Integration of Mammalian Metabolism

Genes and Chromosomes

DNA Metabolism

RNA Metabolism

Protein Metabolism

Regulation of Gene Expression

Filters

In one or two sentences, describe the usefulness of each of the following reagents or reactions in the analysis of protein structure: (a) Edman reagent (phenylisothiocyanate) (b) protease (c) reducing agent (dithiothreitol or $\beta$ -mercaptoethanol)

The uncommon amino acid selenocysteine has an R group with the structure -CH₂-SeH (pK_a $\approx$ 5). In an aqueous solution, pH = 7.0, selenocysteine would: