Shown is a model of the F1F1F1S1F1F1F10-helical conformation of a protein. Show any two of the many hydrogen bonds that are responsible for maintenance of the F1F1F1S1F1F1F10-helical conformation. In each hydrogen bond, identify the donor atom and the acceptor atom, then show the hydrogen bond itself with a line.

Recall that an alpha helix has a conform

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.

a. The carboxylic acid is labeled as 14 C a

Exam 27: Amino Acids, Peptides, and Proteins

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.

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Question 1

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The side chain of MNAPPA is the same as the side chain for arginine. The guanidino group is positively charged at physiological pH and will interact with the Asp₁₈₉ in the binding pocket. The hydrocarbon chain on MNAPPA is the same length as arginine and will interact favorably with the hydrophobic walls of the pocket.

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

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The Strecker synthesis starts with an aldehyde and reacts with ammonia to form an imine. Cyanide then adds to form an -amino nitrile. The nitrile is then hydrolyzed to give a carboxylic acid.

The R group and hydrogen bonded to the alpha carbon on the amino acid must come from the aldehyde. So, the synthesis will be:

The configuration of all the naturally occurring -amino acids is as follows: $The configuration of all the naturally occurring -amino acids is as follows: All but one of the naturally occurring -amino acids have the S configuration at the asymmetric carbon. In the one amino acid that has the R configuration, the R group is (a) - \mathrm { CH } _ { 2 } \mathrm { SH } (b) - \mathrm { CH } _ { 2 } \mathrm { OH } (c) (d) - \mathrm { CH } _ { 2 } \mathrm { CH } _ { 2 } \mathrm { SCH } _ { 3 }$ 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) $The configuration of all the naturally occurring -amino acids is as follows: All but one of the naturally occurring -amino acids have the S configuration at the asymmetric carbon. In the one amino acid that has the R configuration, the R group is (a) - \mathrm { CH } _ { 2 } \mathrm { SH } (b) - \mathrm { CH } _ { 2 } \mathrm { OH } (c) (d) - \mathrm { CH } _ { 2 } \mathrm { CH } _ { 2 } \mathrm { SCH } _ { 3 }$ (d) $- \mathrm { CH } _ { 2 } \mathrm { CH } _ { 2 } \mathrm { SCH } _ { 3 }$

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Question 3

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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.

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Question 4

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.

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Question 5

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

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Question 6

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.

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Question 7

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?

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Question 8

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

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Question 9

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.

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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.

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Question 11

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

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Question 12

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.

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Question 13

Predict the major organic product for the reaction:

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Question 14

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

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Question 15

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

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Question 16

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

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Question 17

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.

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Question 18

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):

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Question 19

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)?

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Question 20

Showing 1 - 20 of 25

Exam 27: Amino Acids, Peptides, and Proteins

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.

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

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.

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.

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 Strecker synthesis of amino acids involves what functional group intermediate?

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.

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

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.

Predict the major organic product for the reaction:

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

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

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

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

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

Chemical Bonding and Chemical Structure

Alkanes and Organic Nomenclature

The Curved-Arrow Notation, Resonance, Acids and Bases, and Chemical Equilibrium

Introduction to Alkenes and Alkynes

Addition Reactions of Alkenes and Alkynes

Principles of Stereochemistry

Cyclic Compounds and Reaction Stereochemistry

Nomenclature and Noncovalent Intermolecular Interactions

The Chemistry of Alkyl Halides

Free-Radical Reactions, Main-Group Organometallic Compounds, and Carbenes

The Chemistry of Alcohols and Thiols

The Chemistry of Ethers, Epoxides, Glycols, and Sulfides

Introduction to Spectroscopy

Nuclear Magnetic Resonance Spectroscopy

Dienes and Aromaticity

The Chemistry of Benzene and Its Derivatives

Allylic and Benzylic Reactivity

The Chemistry of Aryl Halides, Vinylic Halides, and Phenols

The Chemistry of Aldehydes and Ketones

The Chemistry of Carboxylic Acids

The Chemistry of Carboxylic Acid Derivatives

The Chemistry of Enolate Ions, Enols, and Α,β-Unsaturated Carbonyl Compounds

The Chemistry of Amines

Carbohydrates

The Chemistry of Thioesters, Phosphate Esters, and Phosphate Anhydrides

The Chemistry of the Aromatic Heterocycles and Nucleic Acids

Pericyclic Reactions

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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.

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):

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)?