© E.V. Blackburn, 2012 Amino Acids and Proteins

© E.V. Blackburn, 2012 The hydrolysis of most proteins produces about twenty different amino acids. an  -amino acid Structure of amino acids The acids have an amino group bonded to the  carbon:-

© E.V. Blackburn, 2012 Amino acid classification neutral - one amino and one carboxyl group acidic - one amino and two carboxyl groups basic - two amino and one carboxyl group The 20 amino acids are further classified:

© E.V. Blackburn, 2012 Neutral amino acids Name Symbol Structure Alanine Ala or A CH 3 CH(NH 2 )CO 2 H Asparagine Asn or N H 2 NCOCH 2 CH(NH 2 )CO 2 H Cysteine Cys or C HSCH 2 CH(NH 2 )CO 2 H Glutamine Gln or Q H 2 NCOCH 2 CH 2 CH(NH 2 )CO 2 H Glycine Gly or G CH 2 (NH 2 )CO 2 H Isoleucine Ile or I CH 3 CH 2 CH(CH 3 )CH(NH 2 )CO 2 H Leucine Leu or L (CH 3 ) 2 CHCH 2 CH(NH 2 )CO 2 H Methionine Met or M CH 3 SCH 2 CH 2 CH(NH 2 )CO 2 H Phenylalanine Phe or F C 6 H 5 CH 2 CH(NH 2 )CO 2 H Proline Pro or P

© E.V. Blackburn, 2012 Name Symbol Structure Threonine Thr or T HOCH(CH 3 )CH(NH 2 )CO 2 H Tryptophane Try or W Neutral amino acids Serine Ser or S HOCH 2 CH(NH 2 )CO 2 H Valine Val or V (CH 3 ) 2 CHCH(NH 2 )CO 2 H Tyrosine Tyr or Y

© E.V. Blackburn, 2012 Aspartic acid Asp or D HO 2 CCH 2 CH(NH 2 )CO 2 H Acidic amino acid Name Symbol Structure Glutamic acid Glu or E HO 2 CCH 2 CH 2 CH(NH 2 )CO 2 H

© E.V. Blackburn, 2012 Arginine Arg or R HN=C-H(CH 2 ) 3 CH(NH 2 )CO 2 H NH 2 Histidine His or H Lysine Lys or K H 2 N(CH 2 ) 4 CH(NH 2 )CO 2 H Name Symbol Structure Basic amino acids

© E.V. Blackburn, 2012 Essential amino acids Humans can synthesize only 10 of these amino acids. The remaining amino acids must be obtained from dietary sources and are so called essential amino acids. These are: Isoleucine, Leucine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine, Arginine, Histidine, and Lysine.

© E.V. Blackburn, 2012 Stereochemistry of  -Amino Acids Most naturally occurring amino acids have the same configuration about the  carbon: L-(-)-glyceraldehydeL-(-)-serinenatural amino acids

© E.V. Blackburn, 2012 Acid-base Properties of Amino Acids

© E.V. Blackburn, 2012 Physical Properties very water soluble insoluble in non-polar organic solvents such as ether high melting points with decomposition

© E.V. Blackburn, 2012 Isoelectric Points - the pH of a dilute aqueous solution of the amino acid at which the amino acid is exactly neutral. The isoelectric point of neutral amino acids lies between pH = 4.8 and 6.3. For the basic amino acids, it is in the range 7.8 to The range is 2.7 to 3.2 for acidic amino acids.

© E.V. Blackburn, 2012 At a pH above the isoelectric point, amino acids form anions; at a lower pH, protonation occurs and cations form. An amino acid is the least soluble at its isoelectric point. Isoelectric Points

© E.V. Blackburn, 2012 Electrophoresis The amino acid is spotted on a strip of paper (or gel) on a center line. The strip is moistened with a buffer solution of a given pH. Electrodes are attached to the ends of the slip and a potential applied. Depending on the amino acid’s charge, it will migrate either to the positive or negative electrode. The rate and direction of migration depends on the buffer pH and the isoelectric point of the amino acid. Electrophoresis uses isoelectric point differences to separate amino acids and proteins.

© E.V. Blackburn, 2012 Synthesis of amino acids - the Hell-Volhard-Zelinsky reaction alanine

© E.V. Blackburn, 2012 Synthesis of amino acids - the Strecker synthesis NH 3 adds first to give an imine then CN - attacks

© E.V. Blackburn, 2012 The Peptide Bond The principal chain contains the amide bonds; the substituents, R, make up the side chains. The individual amino acids which make up the peptide are often referred to as amino acid residues. In some proteins, two or more polypeptide chains are joined together by disulfide bridges.

© E.V. Blackburn, 2012 Nomenclature Starting from the free amine end of the peptide, the names of the amino acids are joined together with each amino acid being considered as a substituent of the following amino acid. The name ends with the name of the final amino acid: phenylalanylleucylthreonine Phe-Leu-Thr

© E.V. Blackburn, 2012 Aspartame an artificial sweetener sold under the trade name Nutrasweet aspartylphenylalanine methyl ester Asp-Phe-OCH 3 the ester ending is indicated by -OCH 3 in the abridged notation. H 3 N-CH-C-NH-CH-C-OCH 3 O O CH 2 CO 2 - CH 2 -C 6 H 5 +

© E.V. Blackburn, 2012 Angiotensin II Angiotensin II is a blood pressure regulating hormone. It contains 8 amino acid residues. It is possible to arrange these in 40,320 different ways only one of which corresponds to the hormone! Its structure is actually: Asp-Arg-Val-Tyr-Ile-His-Pro-Phe.

© E.V. Blackburn, 2012 Sequential Degradation of Peptides Step 1: breaking disulfide linkages and purification of products Many polypeptides consist of two or more chains which are joined together by disulfide bridges. These bridges must be broken and the fragment products separated. This is done by an oxidation: chain A chain B chain A chain B

© E.V. Blackburn, 2012 Purification The various methods used to separate polypeptides depend on size, solubility in a given solvent, charge or ability to become bonded to a support material (chromatography). dialysis - filtration through a semi-permeable membrane ion exchange chromatography electrophoresis chromatography

© E.V. Blackburn, 2012 The polypeptide is completely hydrolyzed (HCl 6M, 110C, 24hr) to give a mixture of the free amino acids: Step 2. What amino acids are present?

© E.V. Blackburn, 2012 Amino Acid Analysis The mixture is separated using an automated system. The apparatus includes an ion exchange column with a negatively charged support (usually carboxylate or sulfonate). The amino acid mixture, in weakly acidic solution, is added to the column. According to structure, the amino acids are more or less protonated and so will be retained more or less strongly on the column. The pH of the eluant is gradually increased which results in deprotonation and the subsequent elution of the amino acids. Elution begins with the strongest acid and ends with the weakest.

© E.V. Blackburn, 2012 Amino Acid Analysis The eluant then passes into an analyzer which holds a special indicator, ninhydrin. The amino acid eluant forms a violet-purple color by reaction with the ninhydrin and the color’s intensity is proportional to the quantity of acid present.

© E.V. Blackburn, 2012 There are a number of methods used to determine the N-terminal amino acid of a peptide. They are all based on the fact that it is the only amino acid with a free amino group. Step 3. The sequential analysis of amino acids starting at the free amino end

© E.V. Blackburn, 2012 Sanger Degradation

© E.V. Blackburn, 2012 Edman Degradation Phenyl isothiocyanate, C 6 H 5 N=C=S, is a reagent which permits the progressive removal and identification of the N-terminal amino acid. The rest of the chain is not affected by the reaction therefore progressive removal is possible.

© E.V. Blackburn, 2012 Edman Degradation

© E.V. Blackburn, 2012 Specific Cleavage of Peptides A number of enzymes catalyze the hydrolysis of peptide bonds at specific points in an amino acid sequence. These enzymes are called proteases, peptidases or proteolytic enzymes. Trypsin is an example. It catalyzes the hydrolysis of polypeptides at the acyl group of arginine or lysine residues. Chymotrypsin cleaves at the acyl side of the aryl substituted acids phenylalanine, tyrosine and tryptophan.

© E.V. Blackburn, 2012 C-terminal residue The enzyme carboxypeptidase cleaves the C-terminal amide bond in a peptide. The peptide is incubated with the enzyme until the first amino acid is detected.

© E.V. Blackburn, 2012 Treatment of a peptide with 2,4-dinitrofluorobenzene followed by hydrolysis gives N-dinitrophenylvaline. Leucine is the free acid. The peptide contains one of each of the following amino acid residues Leu, Ser, Phe, Pro, Tyr, Lys, Gly and Val. Partial hydrolysis gives four peptides which contain the indicated amino acids: peptide A:- Leu, Ser, Phepeptide B:- Ser, Pro, Tyr, Lys peptide C:- Tyr, Lys, Glypeptide D:- Lys, Val, Gly A peptide!

© E.V. Blackburn, 2012 A peptide has the following amino acid composition: 2 Arg, 2 Ile, Glu, 2 Gly, Leu, Lys, Phe, Pro, Ser, Trp Reaction with Edman’s reagent releases PTH-Leu. Trypsin, a digestive enzyme of intestinal liquids, cleaves polypeptides only at the carboxy (acid) end of arginine (Arg) and Lysine (Lys). Chymotrypsin which is also found in mammalian intestines, cleaves the carboxy end of phenylalanine (Phe), tryptophan (Trp) and tyrosine (Tyr). Hydrolysis by trypsin produces Gly-Arg, Ile-Trp-Phe-Pro-Gly- Arg, Leu-Lys, and Ser-Glu-Ile. Hydrolysis by chymotrypsin produces one peptide with a partial sequence of Leu-Lys-Gly … and another with partial sequence Phe-Pro-Gly-Arg-Ser...