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Chapter 04 – Amino Acids and the Peptide Bond


1. The intrinsic properties of the 20 amino acids include all EXCEPT:

a. α-Carbon is symmetric.
b. The capacity to polymerize.
c. Novel acid-base properties.
d. Varied structure and chemical functionality in side chains.
e. Chirality.




2. The amino and carboxyl groups of amino acids react in a head-to-tail fashion, eliminating water, and forming a covalent ____ linkage typically referred to as a(n) ____ bond.

a. ester, aromatic
b. anhydride, phosphoanhydride
c. amide, peptide
d. dehydration, hydrogen
e. none of the above




3. All of the statements about the classification of these amino acids are correct EXCEPT:

a. Aspartic acid and asparagine are acidic amino acids.
b. Alanine and valine are neutral, nonpolar amino acids.
c. Serine and glutamine are polar, uncharged amino acids.
d. Lysine and arginine are basic amino acids.
e. Tyrosine and phenylalanine are aromatic amino acids.




4. The difference between serine and homoserine is the same as between cysteine and homocysteine. This change from the common amino acid is:

a. one additional methylene (−CH2−) group.
b. one additional carboxyl group.
c. two additional amine groups.
d. presence of a ring system.
e. one additional amine group.




5. Which of the following amino acids has more than one chiral carbon?

a. serine
b. lysine
c. threonine
d. cysteine
e. aspartic acid




6. Which of the listed amino acids is classified as a basic amino acid?

a. leucine
b. phenylalanine
c. aspartate
d. asparagine
e. lysine




7. All of the amino acids EXCEPT ____ have both free α-amino and free α-carboxyl groups.

a. aspartic acid
b. proline
c. asparagine
d. lysine
e. valine




8. The amino acid with a side-chain pKa near neutrality and which therefore plays an important role as proton donor and acceptor in many enzyme catalyzed reactions is:

a. histidine.
b. cysteine.
c. proline.
d. serine.
e. methionine.




9. The pKa of the α−carboxyl group of an amino acid is ____ by the presence on the amine group.

a. greatly increased (>2 pH units)
b. greatly decreased (> 2 pH units)
c. unchanged
d. slightly increased (1-2 pH units)
e. slightly decreased (1-2 pH units)




10. At which of the following pH values would histidine (pKa values of 1.8, 6.0 and 9.2) be found with a net negative charge?

a. 1.0
b. 4.0
c. 8.0
d. 11.0
e. none of the above




11. What is the pH of a serine solution in which the α−amine group (pKa 9.2) is 33% deprotonated?

a. 8.7
b. 8.9
c. 9.0
d. 9.5
e. 9.8




12. Glutamic acid has pKa values of 2.2, 4.3, and 9.7. Calculate the isoelectric point for glutamic acid.

a. 3.25
b. 4.3
c. 5.4
d. 7.0
e. 8.6




13. If the pI of a peptide is 4.6, ____ might be present while ____ would probably be absent.

a. Glu / Lys
b. His / Ser
c. Arg / His
d. Asp / Gly
e. Cys / Tyr




14. The pKa of the cysteine side chain ____ group is 8.32, so it is about 11% deprotonated at pH ____.

a. acid, 3.2
b. amino, 8.5
c. hydroxyl, 10.2
d. sulfhydryl, 7.4
e. none of the above




15. Which of the peptides would absorb light at 280 nm?

a. Ala-Lys-His
b. Ser-Gly-Asn
c. Ala-Ala-Trp
d. Val-Pro-Leu
e. Ser-Val-Ile




16. Which of the following amino acids absorbs light most strongly between 250 and 300 nm?

a. His
b. Phe
c. Trp
d. Tyr
e. None of the above absorb light in this range




17. All are true for stereoisomers EXCEPT:

a. A diastereomer is a nonsuperimposable non-mirror image.
b. An enantiomer is a nonsuperimposable mirror image.
c. Diastereomers have different melting points.
d. Diastereomers rotate plane polarized light in equal but opposite directions.
e. None, all are true.




18. All are true statements about L-isoleucine EXCEPT:

a. Its enantiomer is named D-isoleucine.
b. L-alloleucine would be its diastereomer.
c. It contains a total of two asymmetric or chiral carbons.
d. It can also be named as (2S,3S)-isoleucine using the (R,S) system.
e. Its diastereomer would be named D-leucine.




19. Which of the following is classified as a neutral polar amino acid?

a. Asp
b. Leu
c. His
d. Ser
e. Trp




20. For the peptide Ala-His-Glu-Val-Asp-Cys-Lys-Leu, what is the net charge at pH 3?

a. -1
b. 0
c. +1
d. +2
e. +3




21. Where Cα is the α-carbon, N represents the amide nitrogen and Co is the carbonyl carbon of amino acids in a peptide, the peptide backbone of a protein consists of the repeated sequence:

a. −Cα−N−Co
b. −N−Co−Cα
c. −N−Cα−Co
d. −Co−Cα−N−
e. none of the above




22. The peptide bond has partial ____ character.

a. hydrogen bond
b. double bond
c. triple bond
d. van der Waals bond
e. all of the above




23. Which of the following IS NOT a result of resonance in peptide bonds?

a. approximately 40% double bond (coplanar) character.
b. restricted rotation in the peptide backbone at the N−Cα bond and Cα−Co bond.
c. the coplanar six atoms of the peptide bond group of atoms.
d. a Cα−carbon that is out of the coplanar group of atoms.
e. Co−N bond distance that is shorter than normal, but longer than C=N bonds.




24. Which of the following atoms IS NOT contained within the amide plane of the peptide backbone?

a. Cα-carbon.
b. amide nitrogen.
c. side chain carbons.
d. carbonyl carbon.
e. none, all are included.




25. Discuss the amino acids that occur only rarely in proteins.​

ANSWER:   There are several amino acids that occur only rarely in proteins and are produced by modifications of one of the 20 amino acids already incorporated into a protein. Pyrrolysine and selenocysteine are incorporated naturally into proteins through specific modifications that occur during the reactions of protein synthesis. Both selenocysteine and pyrrolysine bring novel structural and chemical features to the proteins that contain them. Hydroxylysine and hydroxyproline are found mainly in the collagen and gelatin proteins. Pyroglutamic acid is found in a light-driven proton-pumping protein called bacteriorhodopsin. γ-carboxyglutamic acid is found in calcium-binding proteins.​
TOPICS:   4.1 What Are the Structures and Properties of Amino Acids?


26. Discuss the side-chain groups of amino acids that undergo ionizations.​

ANSWER:   ​Histidine contains an ionizable imidazolium proton, and arginine carries a guanidinium function. The β-carboxyl group of aspartic acid and the γ-carboxyl side chain of glutamic acid exhibit pKa values intermediate to the α-COOH on one hand and typical aliphatic carboxyl groups on the other hand. In a similar fashion, the -amino group of lysine exhibits a pKa that is higher than that of the α-amino group but similar to that for a typical aliphatic amino group. These intermediate side-chain pKa values reflect the slightly diminished effect of the a-carbon dissociable groups that lie several carbons removed from the side-chain functional groups. The para-OH group of tyrosine and the —SH group of cysteine also show a significant degree of dissociation.
TOPICS:   4.2 What Are the Acid-Base Properties of Amino Acids?


27. Explain the chirality of amino acid molecules.​

ANSWER:   A molecule that has four different groups attached to the α-carbon atom is said to be asymmetric or chiral. All amino acids except glycine are chiral. The two possible configurations for the α-carbon constitute nonsuperimposable mirror-image isomers, or enantiomers. Enantiomeric molecules display optical activity—the ability to rotate the plane of polarization of plane-polarized light. Clockwise rotation of incident light is referred to as dextrorotatory behavior, and counterclockwise rotation is called levorotatory behavior. The magnitude and direction of the optical rotation depend on the nature of the amino acid side chain. Some protein-derived amino acids at a given pH are dextrorotatory and others are levorotatory, even though all of them are of the L-configuration.​
TOPICS:   4.4 What Are the Optical and Stereochemical Properties of Amino Acids?


28. Discuss the principles on which methods of amino acid separation are based.​

ANSWER:   All the methods used for the separation and analysis of amino acids take advantage of the relative differences in the physical and chemical characteristics of amino acids, particularly ionization behavior and solubility characteristics. Separations of amino acids are usually based on partition properties (the tendency to associate with one solvent or phase over another) and separations based on electrical charge. In all of the partition methods, the molecules of interest are allowed (or forced) to flow through a medium consisting of two phases—solid-liquid, liquid-liquid, or gas-liquid. The molecules distribute themselves between the two phases depending on their particular properties and their consequent preference for associating with one or the other phase. Methods important for amino acid separations include ion exchange chromatography, gas chromatography (GC), and high-performance liquid chromatography (HPLC).​
TOPICS:   4.6 How Are Amino Acid Mixtures Separated and Analyzed?


29. Explain the classification of peptides based on the number of amino acids they contain.​

ANSWER:   Peptide is the name assigned to short polymers of amino acids. Peptides are classified according to the number of amino acid units in the chain. Each unit is called an amino acid residue, the word residue denoting what is left after the release of H2O when an amino acid forms a peptide link upon joining the peptide chain. Dipeptides have two amino acid residues, tripeptides have three, tetrapeptides four, and so on. After about 12 residues, this terminology becomes cumbersome, so peptide chains of more than 12 and less than about 20 amino acid residues are usually referred to as oligopeptides, and when the chain exceeds several dozen amino acids in length, the term polypeptide is used. The distinctions in this terminology are not precise.​
TOPICS:   4.7 What Is the Fundamental Structural Pattern in Proteins?