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Chapter 22

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Lana Mikhaylichenko

Chapter 22: Amino Acids, Peptides and Proteins Classification and Nomenclature of Amino Acids • Amino Acid: a carboxylic acid with an ammonium group on the α-carbon. • Amino Acid Residues: repeating units of amino acids. • Dipeptide: contains 2 amino acid residues, and so on. • Proteins: naturally occurring polypeptides made up of 40 to 4000 amino acid residues. o Fibrous Proteins: contain long chains of polypeptides arranged in bundles and are insoluble in water. o Globular Proteins: have spherical shapes and are soluble in water. • Amino acids differ only in the substituent (R) attached to the α-carbon. • There are two acidic amino acids: aspartate and glutamate. • There are two basic amino acids: lysine and arginine. • Indole is a very weak base because the lone pair on the nitrogen atom is needed for the compound’s aromaticity. • There are 10 essential amino acids as we cannot synthesize them at all or cannot synthesize them in adequate amounts. Configuration of the Amino Acids • α-carbon of all the naturally occurring amino acids is an asymmetric center except glycine. o They can exist as enantiomers; the D and L notation is used. o D-Amino Acid: the amino group is on the right when drawn in a Fisher projection. o L-Amino Acid: the amino group is on the left when drawn in a Fisher projection. o Most amino acids found in nature have the L-configuration. o Naturally occurring monosaccharides have the D-configuration. Acid-Base Properties of Amino Acids • Every amino acid has a carboxyl group and an amino group and each group can exist in an acidic form or a basic form, depending on the pH of the solution in which the amino acid is dissolved. • At pH~0, both groups (amino and carboxyl groups) will be in their acidic forms. • At pH=7, carboxyl group will be in its basic form and amino group will be in its acidic form. • At pH~11, both groups will be in their basic forms. • The amino acid can never exist as an uncharged compound, regardless of the pH. • Zwitterion: a compound that has a negative charge on one atom and a positive charge on a nonadjacent atom. The Isoelectric Point • Isoelectric Point (pI): the pH at which it has no net charge; it is the pH at which the amount of positive charge on an amino acid exactly balances the amount of negative charge. o pI = pH at which there is no net charge. o An amino acid will be positively charged if the pH of the solution is less than the pI of the amino acid and will be negatively charged if the pH of the solution is greater than the pI of the amino acid. • The pI of most amino acids that have an ionizable side chain is the average of the pKa values of the similarly ionizing groups. Separation of Amino Acids • Electrophoresis: separates amino acids on the basis of their pI values. o When the paper or the gel is placed in a buffered solution between two electrodes and an electric field is applied, an amino acid with a pI greater than the pH of the solution will have an overall positive charge and will migrate toward the cathode (-). o The farther the amino acid’s pI is from the buffer, the more positive the amino acid will be and the farther it will migrate toward the cathode in a given amount of time. o An amino acid with a pI less than the pH of the buffer will have an overall negative charge and will migrate toward the anode (+). • Paper Chromatography: separates amino acids on the basis of polarity. o The more polar the amino acid, the more strongly it is adsorbed onto the relatively polar paper. o The less polar amino acids travel up the paper more rapidly, since they have a greater affinity for the mobile phase. o The colored spot closest to the origin is the most polar amino acid and the spot farthest away from the origin is the least polar amino acid. o The most polar amino acids are those with charged side chains, the next most polar are those with side chains that can form hydrogen bonds and the least polar are those with hydrocarbon sidechains. o For amino acid with hydrocarbon side chains, the larger the alkyl group, the less polar the amino compound. • Ion-Exchange Chromatography: preparative separation in which larger amounts of amino acids are separated for use in subsequent processes. o Cations bind most strongly to cation-exchange resins. o Anions bind most strongly to anion-exchange resin. o Amino Acid Analyzer: an instrument that automates ion-exchange chromatography. Synthesis of Amino Acids • Hell-Volhard-Zelinski Reaction: it replaces the α-hydrogen of a carboxylic acid with a bromine using Br 2PBr 3nd H O;2the resulting compound undergoes an SN2 reaction with ammonia to form the amino acid. • Amino acids can also be synthesized by reductive amination of α-keto acids using excess ammonia. • N-Phthalimidomalonic Ester Synthesis: combines the malonic ester synthesis and the Gabriel synthesis. o α-Bromomalonic ester and potassium phthalimide undergo S 2 Neaction. o A proton is easily removed from the α-carbon of N-phthalimidomalonic ester since it is flanked by two ester groups. o The resulting carboanion undergoes S N reaction with an alkyl halide. o Heating in an acidic aqueous solution hydrolyzes both ester groups and both amide groups and decarboxylates the 3-oxocarboxylic acid. • Strecker Synthesis: an aldehyde reacts with ammonia forming an imine; an addition reaction with cyanide ion forms an intermediate which, when hydrolyzed, forms the amino acid. Resolution of Racemic Mixtures of Amino Acids • When amino acids are synthesized in nature, only the L-enantiomer is formed. • Enzyme-Catalyzed Reaction: the enzyme, being chiral, will react at a different rate with each of the enantiomers (pig kidney caralyzes the hydrolysis of L- amino acids but not D-amino acids). • Kinetic Resolution: the resolution of the enantiomers depends on the difference in the rates of reaction of the enzyme with the two N-acetylated compounds. Peptide Bonds and Disulfide Bonds • Peptide Bonds: amide bonds that link amino acid residues. • The amino acids are numbered starting with N-terminal end, usually on the left. • A peptide bond has about 40% double-bond character because of electron delocalization. • Steric hindrance in the cis configuration causes the trans configuration about the amide linkage to be more stable, so the α-carbon of adjacent amino acids are trans to each other. • Partial double-bond character prevents free rotation about the peptide bond, so the carbon and nitrogen atoms and the two
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