Chapter 22 The Organic Chemistry of Amino Acids, Peptides, and Proteins Paula Yurkanis Bruice University of California, Santa Barbara

Amino Acids and Peptides Peptides and proteins are polymers of amino acids linked together by amide bonds.

Proteins Have Diverse Functions

Lysine and Arginine The amino group is on the epsilon carbon. The guanidino group is on the delta carbon.

Histidine and Tryptophan Histidine is an imidazole-substituted alanine. Tryptophan is an indole-substituted alanine.

D-Sugars and L-Amino Acids

An Antibiotic

Ornithine Has One Less Methylene Group Than Lysine

The Structure of an Amino Acid An amino acid can never exist as an uncharged compound.

Some amino acids have ionizable hydrogens on their side chains. Histidine Some amino acids have ionizable hydrogens on their side chains.

The pI of Alanine The isoelectric point (pI) of an amino acid is the pH at which it has no net charge.

The pI of Lysine

The pI of Glutamic Acid

Electrophoresis Electrophoresis separates amino acids on the basis of their pI values. Ninhydrin is used to detect the individual amino acids.

Ninhydrin

Chromatography separates amino acids on the basis of their polarity.

A Cation-Exchange Resin The resin exchanges the Na+ counterions for positively charged groups.

Separation of Three Amino Acids

A Chromatogram a chromatogram obtained from separation of amino acids using an automated amino acid analyzer

Synthesizing an Amino Acid Using an HVZ Reaction

Synthesizing an Amino Acid by Reductive Animation

Synthesizing an Amino Acid Using the N-Phthalimidomalonic Ester Synthesis

Synthesizing an Amino Acid Using a Strecker Synthesis

Resolution of a Racemic Mixture of Amino Acids

A Tripeptide

Commas Indicate the Sequence is Not Known; Hyphens Indicate the Sequence is Known Val is the N-terminal amino acid. His is the C-terminal amino acid.

A Peptide Bond Has 40% Double Bond Character

The squares indicate the plane of each peptide bond. A Polypeptide Chain The squares indicate the plane of each peptide bond.

Mild Oxidation of a Thiol

The Mechanism

Reduction of a Disulfide

Oxidation of Cysteine Forms Cystine

Disulfide bridges contribute to the overall shape of the protein.

Straight and Curly Hair

Insulin Insulin has two interchain disulfide bridges and one intrachain disulfide bridge.

peptides synthesized by the body to control pain Enkephalins peptides synthesized by the body to control pain

Peptide Hormones Bradykinin inhibits inflammation of tissues. Vasopressin regulates the bond’s retention of water; it is released in response to stress. Oxytocin induces labor and stimulates milk production.

NutraSweet NutraSweet is the methyl ester of a dipeptide of aspartate and phenylalanine

Because amino acids have two functional groups, Synthesizing Gly-Ala Because amino acids have two functional groups, mixing Gly and Ala (and heating) would lead to four different dipeptides.

Strategy for Peptide Bond Synthesis To make a peptide bond, the N-terminal amino acid needs to have its amino group protected and its carboxyl group activated.

Protecting the Amino Group

Activating the Carboxyl Group

Forming a New Peptide Bond

Adding a Third Amino Acid

Removing the Protecting Group When the desired number of amino acids has been added to the chain, the protecting group can be removed.

Assuming an 80% Yield for Formation of Each Peptide Bond

Automated Solid-Phase Peptide Synthesis The N-protected C-terminal amino acid is added to the resin.

Automated Solid-Phase Peptide Synthesis The protecting group is removed. The next amino acid with its amino group protected and then its carboxyl group activated is added to the resin.

Automated Solid-Phase Peptide Synthesis The protecting group is removed. The next amino acid with its amino group protected and then its carboxyl group activated is added to the resin.

Removing the Protecting Group The protecting group is removed. The peptide is removed from the resin.

Protein Structure Primary structure: the sequence of amino acids and the location of disulfide bonds Secondary structure: the conformations assumed by the protein’s backbone when it folds Tertiary structure: the three-dimensional structure of the entire protein Quaternary structure: the way the individual peptide chains are arranged

Reducing the Disulfide Bridges in Proteins The first step in determining the sequence of amino acids is cleaving the disulfide bridges.

Acid-Catalyzed Hydrolysis of the Peptide Bonds The next step is to determine the number and kinds of amino acids in the peptide or protein by hydrolysis of all the amide bonds and then analysis of the mixture.

Identifying the N-Terminal Amino Acid

The Thiazoline Rearranges to a PTH-Amino Acid For the mechanism, see Problem 72. The particular PTH–amino acid can be identified by chromatography using known standards.

Carboxypeptidase is Used to Determine the C-Terminal Amino Acid Carboxypeptidase catalyzes the hydrolysis of the C-terminal peptide bond. Carboxypeptidase is an exopeptidase. Carboxypeptidase A cleaves off the C-terminal amino acid as long as it is not Arg or Lys. Carboxypeptidase B cleaves off the C-terminal amino acid only if it is Arg or Lys.

Trypsin is an Endopeptidase Trypsin cleaves on the right of amino acids with positively charged side chains (Arg and Lys).

Cleavage by Trypsin

Chymotrypsin is an Endopeptidase Chymotrypsin cleaves on the right of amino acids that contain amino acids with aromatic six-membered rings (Phe, Tyr, and Trp).

Elastase cleaves on the right of small amino acids (Gly and Ala). Elastase is an Endopeptidase Elastase cleaves on the right of small amino acids (Gly and Ala).

An Enzyme Will Not Hydrolyze a Peptide Bond if Proline is at the Cleavage Site

Cyanogen Bromide Cleaves on the Right Side of Methionine

The Mechanism

Three factors determine the secondary structure: The regional planarity about each peptide bond limits the conformations of the peptide chain. The number of peptide groups that engage in hydrogen bonding is maximized. The need for adequate separation between nearby R groups

Hydrogen Bonding Between Peptide Groups Proteins fold to maximize the number of hydrogen bonds between peptide groups.

The α-helix is stabilized by hydrogen bonds.

β-Pleated Sheets

The Secondary Structure of a Protein

The Tertiary Structure of a Protein

Stabilizing Interactions

The Quaternary Structure of Hemoglobin The individual chains are called subunits.