The Organic Chemistry of Amino Acids, 6th Edition Paula Yurkanis Bruice Chapter 23 The Organic Chemistry of Amino Acids, Peptides, and Proteins

Peptides and proteins are polymers of amino acids linked together by amide bonds:

Classification of Amino Acids Hydrophobic: water-fearing, nonpolar side chains Alkyl side chain Hydrophilic: water-loving side chains Polar, neutral side chains Anionic Cationic

Nonpolar Side Chains

Polar, Neutral Side Chains

Polar, Acidic Side Chains

Basic, Polar Side Chains

Configuration of Amino Acids

Acid–Base Properties of Amino Acids An amino acid can never exist as an uncharged compound

Some amino acids have ionizable hydrogens on their side chains:

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

The pI of an amino acid that has an ionizable side chain is the average of the pKa values of ionized groups of the same charge:

A mixture of amino acids can be separated by electrophoresis on the basis of their pI values: Ninhydrin is used to detect the individual amino acids

A mixture of amino acids can also be separated on the basis of polarity:

Ion-exchange chromatography can be used to perform preparative separation of amino acids: Negatively charged resin binds selectively to positively charged amino acids

Ion-Exchange Chromatography Cations bind most strongly to cation-exchange resins. Anions bind most strongly to anion-exchange resins. An amino acid analyzer is an instrument that automates ion-exchange chromatography.

Synthesis of Amino Acids HVZ reaction followed by reaction with ammonia: Reductive amination:

A more efficient way of synthesizing amino acids:

The Strecker Synthesis

Resolution of Racemic Mixtures of Amino Acids

Formation of a Peptide

A peptide bond has 40% double-bond character:

Formation of Disulfide Bonds Disulfides can be reduced to thiols

The disulfide bridge in proteins contributes to the overall shape of a protein:

Peptide Examples Tyr-Gly-Gly-Phe-Leu Tyr-Gly-Gly-Phe-Met ENKEPHALINS Natural ligands for opioid receptors Tyr-Gly-Gly-Phe-Leu Tyr-Gly-Gly-Phe-Met NUTRASWEET Peptide-based sweetener GLUTATHIONE Antioxidant and electrophile trap

Because amino acids have two functional groups, amide bond formation with a mixture of two amino acids affords four products:

Strategy for Making a Specific Peptide Bond

t-BOC protection of an amine group: The t-BOC protecting group is stable during amide bond formation but is removed under acidic conditions

Carboxylic acid activation by DCC:

Amide bond formation:

Amino acids can be added to the growing C-terminal end by repeating these two steps:

When the desired number of amino acids has been added to the chain, the protecting group can be removed:

An Improved Peptide Synthesis Strategy C-terminal amino acid Attachment of N-protected amino acid to resin

Removal of t-BOC protecting group Carboxylic acid activation of second amino acid

Amide bond formation Removal of t-BOC protecting group

Carboxylic acid activation of N-terminal amino acid Amide bond formation Removal of t-BOC protecting group

Release of tripeptide from Merrifield resin

Sequencing Proteins N-terminal amino acid? C-terminal amino acid? What is in between?

The first step in determining the sequence of amino acids in a peptide or protein is to cleave the disulfide bridges:

The next step is to determine the number and kinds of amino acids in the peptide or protein by hydrolysis and then analysis of the mixture:

The N-terminal amino acid of a peptide or a protein can be determined by Edman degradation:

The particular PTH–amino acid can be identified by chromatography using known standards

The C-terminal amino acid can be identified by treating the protein with carboxypeptidase: Carboxypeptidase B: ONLY Arg and Lys Carboxypeptidase A: ALL amino acids EXCEPT Arg and Lys

The peptide or protein can be partially hydrolyzed using endopeptidases: Trypsin: C-side of Arg and Lys Chymotrypsin: C-side of Phe, Tyr, Trp Elastase: C-side of Gly and Ala No cleavage for any endopeptidase if Pro on either side Example of trypsin hydrolysis:

Cyanogen bromide causes the hydrolysis of the amide bond on the C-side of a methionine residue:

Mechanism for cleavage of a peptide bond by cyanogen bromide:

Secondary Structure of Proteins Describes the repetitive conformations assumed by segments of the backbone of a peptide or protein Three factors determine the choice of secondary structure: The regional planarity about each peptide bond Maximization of the number of peptide groups that engage in hydrogen bonding Adequate separation between nearby R groups

The a-helix is stabilized by hydrogen bonds:

Not all amino acids are able to fit into an -helix: Prolines distort the helix. Two adjacent Val, Ile, or Thr cannot fit into a helix. Two adjacent residues with the same charges cannot fit into a helix.

Two Types of b-Pleated Sheets

Most globular proteins have coil or loop conformations:

The tertiary structure is the three-dimensional arrangement of all the atoms in the protein:

The tertiary structure is defined by the primary structure The stabilizing interactions include covalent bonds, hydrogen bonds, electrostatic attractions, and hydrophobic interactions Disulfide bonds are the only covalent bonds that can form when a protein folds

Quaternary Structure of Proteins Proteins that have more than one polypeptide chain are called oligomers The individual chains are called subunits