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Exam 27: Amino Acids, Peptides, and Proteins

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Question 1

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

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Cystosine (C) will base pair w...

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Question 2

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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) $- \mathrm { CH } _ { 2 } \mathrm { SH }$ (b) $- \mathrm { CH } _ { 2 } \mathrm { OH }$ (c) (d) $- \mathrm { CH } _ { 2 } \mathrm { CH } _ { 2 } \mathrm { SCH } _ { 3 }$

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

F) A) and B)
G) C) and E)

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Question 3

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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.

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

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?

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.

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.

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 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.

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

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.

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

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.

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.

Predict the major organic product for the reaction:

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

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

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) :

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

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.