Amino Acids and Peptides

Transcription

1 Amino Acids Amino Acids and Peptides Amino acid a compound that contains both an amino group and a carboxyl group α-amino acid an amino acid in which the amino group is on the carbon adjacent to the carboxyl group although α-amino acids are commonly written in the unionized form, they are - more properly R- C-C written in R- the C-C zwitterion (internal salt) form 2 3 unionized form zwitterion Page 2 Chirality of Amino Acids Chirality of Amino Acids With the exception of glycine, all protein-derived amino acids have at least one stereocenter (the α-carbon) and are chiral the vast majority of α-amino acids have the L- configuration at the α-carbon Comparison of the stereochemistry of alanine and glyceraldehyde (Fischer projection formulas) the naturally occurring form C - 3 C - 3 C - 3 C - 3 C 3 D-Alanine C 3 L-Alanine C 3 C 3 D-Alanine L-Alanine (Fischer projections) the naturally occurring form C C 2 D-Glyceraldehyde C C 2 L-Glyceraldehyde Page 3 Page 4 onpolar side chains (predominant form at p 7.0) glycine (gly, G) phenylalanine (phe, F) - alanine (ala, A) C 3 - tryptophan (trp, W) valine (val, V) (C 3 ) 2 C leucine (leu, L) (C 3 ) 2 CC 2 - isoleucine (ile, I) proline (Pro, P) C 3 C 2 C( C 3 )- methionine (met, M) C 3 C 2 C 2 - Polar side chains (predominant form at p 7.0) asparagine (asn, ) serine (ser, ) 2 CC 2 - glutamine (glu, G) 2 CC 2 C 2 - C 2 - threonine (thr, T) C 3 C- Page 5 Page 6 1

2 Acidic side chains (predominant form at p 7.0) aspartic acid (asp, D) glutamic acid (glu, E) - CC CC 2 C 2 - cysteine (cys, C) tyrosine (tyr, Y) C 2 - C 2 - Basic side chains (predominant form at p 7.0) arginine (arg, R) histidine (his, ) 2 2 CC 2 C 2 C 2 - C 2 - lysine (lys, K) 3 C 2 C 2 C 2 C 2 - Page 7 Page 8 Uncommon Amino Acids ote these structural features 1. All 20 are α-amino acids 2. For 19 of the 20, the α-amino group is primary; for proline, it is secondary 3. With the exception of glycine, the α-carbon of each is a stereocenter 4. Isoleucine and threonine contain a second stereocenter 5. The sulfhydryl group (pk a 8.3) of cysteine, the imidazole group (pk a 6.0) of histidine, and the phenolic hydroxyl (pk Page 9 a 10.1) of phenylalanine are partially ionized at p 7.0, but the ionic form is not Each example is derived from a common amino acid by the modification shown in color I I 3 C - C - C - 3 I I 3 ydroxylysine ydroxyproline Thyroxine hydroxylysine and hydroxyproline are found only in a few connective tissues such as collagen thyroxine is found only in the thyroid gland Page 10 Ionization of Amino Acids 1 charge 0 charge -1 charge 3 C pka = C - 2 C - pk a = 9.69 Isoelectric zwitterion Titration of Amino Acids Figure (a) Titration of alanine with a 2 charge 3 C pk a = charge 3 C - 0 charge 3 C - pk a = 6.04 pk a = charge 2 C - Page 11 Isoelectric zwitterion Page 12 2

3 Titration of Amino Acids Acidity α-c Groups Figure (b) Titration of histidine with a The average an α-carboxyl group is 2.19, which makes them considerably stronger acids than acetic acid (pk a 4.76) the greater acidity of the amino acid carboxyl group is due to the electron-withdrawing inductive effect of the - 3 group The ammonium ion has an electron-withdrawing inductive effect RCC 2 pk a = 2.19 RCC Page 13 Page 14 Acidity α- 3 groups Basicity Guanidine Group The average value of pk a for an α- 3 group is 9.47, compared with a value of for a 2 alkylammonium ion pk a = 9.47 RCC - 2 RCC pk a = C 3 CC 3 2 C 3 CC The side chain of arginine is a considerably stronger base than an aliphatic amine basicity of the guanido group is attributed to the large resonance stabilization of the protonated form relative 2 to the neutral 2 form 2 R C 2 R C R C 3 2 R C 2 pk a = Page 15 Page 16 Basicity Imidazole Group Ionization vs p The imidazole group on the side chain of histidine is a heterocyclic aromatic amine C 2 CC - 2 C 2 CC Given the value of each functional group, we can calculate the ratio of each acid to its conjugate base as a function of p Consider the ionization of an α-c pk a = 2.00 α C α C this lone pair is not a part of the aromatic sextet; it is the proton acceptor C 2 CC pk a 6.04 writing the acid ionization constant and rearranging terms gives [ α-c - ] K a = [ 3 ] [ α-c - ] K = a or [ α-c ] [ α-c ] [ 3 ] Page 17 Page 18 3

4 Ionization vs p Ionization vs p substituting the value of K a (1 x 10-2 ) for the hydrogen [ α-c ion - concentration ] K = a 1.00 at p x 10-2 = 7.0 = ( x ) gives [ α-c ] [ 3 ] 1.00 x 10-7 We can also calculate the ratio of acid to conjugate base for an α- 3 group; for this calculation, assume a value 10.0 for pk a α 3 2 pk a = α 2 3 at p 7.0, the α-carboxyl group is virtually 100% in the ionized or conjugate base form, and has a net charge of -1 we can repeat this calculation at any p and determine the ratio of [α C - ]to[α C] and Page 19 writing the acid ionization constant and rearranging gives [ α- 2 ] K [ α- = a 3 ] [ 3 ] Page 20 Ionization vs p enderson-asselbalch substituting values for K a of an α- 3 group and the hydrogen ion concentration at p 7.0 gives [ α- 2 ] K a 1.00 x [ α- = 3 ] [ 3 = = 1.00 x 10-3 ] 1.00 x 10-7 at p 7.0, the ratio of α- 2 to α- 3 is approximately 1 to 1000 at this p, an α-amino group is 99.9% in the acid or protonated form and has a charge of 1 Page 21 We have calculated the ratio of acid to conjugate base for an α-carboxyl group and an α-amino group at p 7.0 We can do this for any weak acid and its conjugate base at any p using the enderson-asselbalch equation Page 22 [conjugate base] p = pk a log [weak acid] enderson-asselbalch Isoelectric p using the enderson-asselbalch equation, we can calculate the percent of charged or uncharged form present and the net charge on 100% 86% 99% 100% 88% 100% serine at p 3.0, 7.0, and C-C- 3 - C-C C-C- - C 2 C 2 C 2 p 3.0 p 7.0 p 10.0 et charge 1 et charge 0 et charge -1 Isoelectric p, pi the p at which the majority of molecules of a compound in solution have no net charge the pi for glycine, for example, falls midway between the pk a values for the carboxyl and amino groups pi = 1 2 (pk a α C p K a α 3 ) = 1 ( ) = Page 23 given in the following tables are isoelectric p values for the 20 protein-derived amino acids Page 24 4

5 Isoelectric p (pi) Table 3.2 pk a and pi of α-amino acids Isoelectric p (pi) Table 3.2 (cont'd) onpolar & polar side chains α C α 3 alanine asparagine glutamine glycine isoleucine leucine methionine phenylalanine proline serine threonine tryptophan valine Page 25 ide Chain pi Page 26 Acidic ide Chains α C α C α 3 α 3 ide Chain aspartic acid glutamic acid cysteine tyrosine Basic ide Chains ide Chain arginine histidine lysine pi pi Electrophoresis Electrophoresis(Process) Electrophoresis the process of separating compounds on the basis of their electric charge electrophoresis of amino acids can be carried out using paper, starch, agar, certain plastics, and cellulose acetate as solid supports in paper electrophoresis, a paper strip saturated with an aqueous buffer of predetermined p serves as a bridge between two electrode vessels Page 27 a sample of amino acids is applied as a spot (the origin) on the solid support strip an electric potential is applied to the electrode vessels and amino acids migrate toward the electrode with charge opposite their own molecules with a high charge density move faster than those with a low charge density molecules at their isoelectric point remain at the origin after separation is complete, the strip is dried and developed to make the separated amino acids Page 28 Polypeptides In 1902, Emil Fischer proposed that proteins are long chains of amino acids joined by amide bonds to which he gave the name peptide bonds Peptide bond the special name given to the amide bond between the α- carboxyl group of one amino acid and the α-amino group of another erylalanine (er-ala) 2 C C 3 erine (er) Alanine (Ala) peptide bond 2 C 3 - C3 erylalanine (er-ala) Page 29 Page 30 5

6 Peptides Geometry of Peptide Bond peptide the name given to a short polymer of amino acids joined by peptide bonds; they are classified by the number of amino acids in the chain dipeptide a molecule containing two amino acids joined by a peptide bond tripeptide a molecule containing three amino acids joined by peptide bonds polypeptide a macromolecule containing many amino acids joined by peptide bonds protein a biological macromolecule of molecular Page 31 the four atoms of a peptide bond and the two alpha carbons joined to it lie in a plane with bond angles of 120 about C and to account for this geometry, Linus Pauling proposed that a peptide bond is most accurately represented as a hybrid of two contributing structures - C α C α the hybrid has C considerable C- double C bond character and C α rotation about the Cpeptide α bond is restricted Page 32 (1) (2) Writing Peptides ome mall Peptides By convention, peptides are written from the left, beginning with the free - 3 group and ending with the free -C - group the repeat pattern, starting from the -terminal amino acid, is ---> α-carbon ---> carbonyl carbon etc. -terminal amino acid 3 peptide bonds er-met-asn - 2 C-terminal amino acid 3 -C- C--C-C-C 3 C 2 C 2 C - C 6 5 L-Aspartyl-L-phenylalanine methyl ester (Aspartame) 3 -C 2 -C 2 -C-- C-C - C 2 β-alanyl-l-histidine (Carnosine) Page 33 Page 34 Glutathione Enkephalins - 3 Glutathione, G (reduced form) - 2e - oxidation 2e - reduction Glutathione, G-G (oxidized form) - - A disulfide bond Leucine enkephalin Tyr-Gly-Gly-Phe-Leu = Y-G-G-F-L Methionine enkephalin Tyr-Gly-Gly-Phe-Met = Y-G-G-F-M Page 35 Page 36 6

7 xytocin & Vasopressin 3 -Cys-Tyr-Ile Gln Cys-Asn Pro-Leu-Gly-C- 2 xytocin 3 -Cys-Tyr-Phe Gln Cys-Asn Pro-Arg-Gly-C- 2 Vasopressin End Page 37 Page 38 7