Deck 27: Amino Acids, Peptides, and Proteins

Question 1

Aspartic acid is a naturally occurring amino acid. It is shown below in the form in which it exists in very acidic solutions. Its pK_a values are 1.9, 3.7, and 9.6.
What is the predominant form in which it exists at physiological pH (pH = 7.4)?

A) form A
B) form B
C) form C
D) form D
E) form Ef.
form F

Answer 1

D

Question 2

The configuration of all the naturally occurring -amino acids is as follows:
All but one of the naturally occurring -amino acids have the S configuration at the asymmetric carbon. In the one amino acid that has the R configuration, the "R" group is

A) group (a).
B) group (b).
C) group (c).
D) group (d).
E) None of these has the R configuration.

Answer 2

A

Question 3

Below are the structure and individual functional group pK_a values for the amino acid glutamic acid (abbreviated as Glu and/or E).
Select all the true statement(s):

A) At physiological pH (7.4), all the carboxylic acid groups in Glu are dissociated.
B) At physiological pH (7.4), none of the carboxylic acid groups in Glu are dissociated.
C) The net charge of Glu at pH 6 is +1.
D) The isoelectric point (pI) of Glu is 5.38.
E) The isoelectric point (pI) of Glu is 3.24.

Answer 3

A, E

Question 4

Which, if any, of the structures represents a D-amino acid?

A) compound A
B) compound B
C) compound C
D) none of these compounds

Question 5

Fill in the wedge and dash bond template provided to indicate the correct stereochemistry of this unnatural dipeptide.

Question 6

The amino acid arginine (Arg, R) exists at pH = 7.4 as the following structure:
a. The cation in the side chain is resonance stabilized. Complete the description of the resonance hybrid in the diagram above by drawing two other resonance structures and the curved-arrow notation used to derive them. (You can draw just the relevant part of the side chain.) Show all charges and unshared pairs!
b. Select the one true statement:
(1) Resonance makes this form of the amino acid a stronger base than it would be in the absence of such resonance.
(2) Resonance makes this form of the amino acid a weaker base than it would be in the absence of such resonance.
(3) Resonance makes this form of the amino acid a weaker acid than it would be in the absence of such resonance.
(4) Resonance makes this form of the amino acid a stronger acid than it would be in the absence of such resonance.

Question 7

A tripeptide is shown below. (a) Give the sequence of the peptide as their three letter abbreviations and (b) as the single-letter abbreviations for the amino acids. (c) Explain how the peptide will change when you increase the pH to 13.

Question 8

The pK_a values for glutamic acid are 2.16, 4.32, and 9.67.
a. Draw Glu at pH = 2.16, 4.32, and 9.67.
b. Calculate the isoelectric point (pI) of Glu.

Question 9

A student wishes to use ion-exchange chromatography to separate a mixture of three peptides: G-A-L, D-A-M, and E-W-E. Determine whether they should use an anionic or cationic column, then determine the order of elution.

Question 10

A tripeptide is shown below. Label the N-terminal amino acid, the C-terminal amino acid, and the peptide bond(s). Then classify the peptide as acidic, basic, or neutral.

Question 11

Show how the acetamidomalonate method can be used to prepare the unusual amino acid from the indicated starting material.

Question 12

The Strecker synthesis of amino acids involves what functional group intermediate?

A) a cyanohydrin
B) an imine
C) an enamine
D) an oxime

Question 13

Identify the reagents needed to make isoleucine using the Strecker synthesis.

Question 14

Predict the major organic product for the reaction:

Question 15

In the first step of a solid-phase peptide synthesis, an Fmoc-amino acid reacts with a chloromethyl group on the resin. (a) Draw a curved-arrow mechanism and draw the amino acid linked to the resin. (b) explain why a Fmoc group is needed and how to remove it.

Question 16

Given the DNA sequence, transcribe the sequence to mRNA.
5ʹ-CCTAGTA-3ʹ

Question 17

Translate the mRNA sequence shown to a peptide. Use the codon table provided in your book.
GAUACUUGUUGGAUCAGG

Question 18

Several techniques are available for carrying out amino acid analysis. The amide bonds of proteins and peptides can be hydrolyzed in acidic or basic aqueous solutions, then separated by chromatography and analyzed. Which statement is true?

A) Hydrolyzed amino acids react with AQC-NHS on the carboxylic acid.
B) In C18-HPLC, the amino acids with polar side chains are absorbed more strongly on the stationary phase.
C) Amino acid analysis gives the relative amounts of each amino acid residue.
D) Amino acid analysis gives the order of the amino acid residues.

Question 19

A pentapeptide is sequenced using trypsin and chymotrypsin.
Trypsin cleavage gave two fragments with the amino acids (in alphabetical order):
T1: Arg, Gly
T2: Lys, Met, Phe
Chymotrypsin cleavage gave two fragments with the amino acids (in alphabetical order).
C1: Arg, Gly, Phe
C2: Lys, Met
Deduce the sequence of the pentapeptide using the three-letter abbreviations.

Question 20

Draw the expected Edman degradation product of Leu-Val-Gly after one cycle.

Question 21

The figure shows a ribbon structure for the opioid receptor, a member of the "G-protein coupled receptor" family. This protein, as shown in the cartoon, is imbedded in the membrane so that the exterior of the protein is in contact with the membrane phospholipid bilayer.

Question 22

Here are two related observations about the conformations of synthetic peptides as a function of pH.
​
The synthetic peptide poly-L-lysine (. . .Lys-Lys-Lys-Lys. . .) adopts an -helical conformation at pH > 10, but as the pH is lowered to 7, the helix is converted into a random structure.
The synthetic peptide poly-L-glutamic acid (. . .Glu-Glu-Glu-Glu. . .) adopts an -helical conformation at pH < 3, but, as the pH is raised above 5, the helix is converted into a random structure.
Explain these two observations.

Question 23

Shown is a model of the -helical conformation of a protein. Show any two of the many hydrogen bonds that are responsible for maintenance of the -helical conformation. In each hydrogen bond, identify the donor atom and the acceptor atom, then show the hydrogen bond itself with a line.

Question 24

Outline a synthesis of the radiolabeled amino acids below. You can use Na¹⁴CN as a source of ¹⁴C. Deuterated compounds can be prepared from CD₃OH.
a.

b.

Question 25

The structure of MNAPPA is shown below, and it has been shown to be a selective and potent trypsin inhibitor. Analyze the structure and explain why MNAPPA binds to trypsin.