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Amino acids and peptides The “Lego” of proteins Amino Acids • Same general structure • Called alpha amino acids • L- isomer is physiologically active • Side chain or R group determines other properties • Acid-base properties O H3N+ O R Amino Acids, General • pK of carboxyl group around 2.3 – Deprotonated at physiological pH • R – COO- • pK of amino group around 9.5 – Protonated at physiological pH • H3N+-R • Some R-groups are acidic or basic Nonpolar amino acids O NH3+ C H2 NH3+ H C O glycine(G) O H2C H C H3C Leucine (L) O O CH3 CH3 Valine (V) O H + H N NH3+ O H3C CH3 NH3+ CH3 Alanine (A) O NH3+ O O C H CH 2 H3C Isoleucine (I) Proline (P) O O Aromatic Amino Acids O O H3N+ H3N+ O HO phenylalanine (F) pKr = 10.07 tyrosine (Y) O H3N+ O O N tryptophan (W) Polar Amino Acids, alcohols O H3N+ HO Serine (S) O O H3N+ H3C O OH Threonine (T) Polar Amino Acids (sulfur containing) O O H3N+ O N3N+ O HS S Cysteine (C) H3C Methionine (M) Polar amino acids (amides) O H3N+ O O H3N+ O H2N O Asparagine (N) H2N O Glutamine (Q) Charged Amino Acids (Acidic) O H3N+ O O H3N+ O O O Aspartate (D) pKr = 3.86 O O Glutamate (E) pKr = 4.25 Charged Amino Acids (Basic) O H3N+ O O H3N+ O H3N+ O HN N HN NH2+ NH3+ H2N Arginie (R) pKr = 12.48 Histidine (H) pKr = 6.0 Lysine (K) pKr = 10.53 O Titration of Amino acids • Titration of glycine Titration of Glutamate O pK = 9.67 H3N+ O pK = 2.19 O O Glutamate (E) pKr = 4.25 Purification of amino acids • Chromatography – Various types – Ion exchange • Uses net charge or can change with pH – Separate K, D and A – HPLC Electrophoresis • Using electricity to move particles through a gelatinous matrix • Isoelectric point • IEF Peptides • Peptide bond is amide linkage between amino acids • No free rotation about C-N bond due to partial double bond character of bond – resonance peptide bond H3N+ O O N H R1 - O O H3N+ R2 O + O N R1 R2 Tetrapeptide • Note planes of peptide bonds Peptides • Peptides are vectorial – Have N and C termini • Sequences read H3N+---COOP-I-G O H2N+ O N H O N H O Draw a tetrapeptide of L-A-R-D at physiological pH • Answer Biologically Interesting Peptides • Aspartame – L-aspartyl-Lphenylalanine methyl ester O H3N+ O O N H O O CH3 Other small interesting peptides • Enkephalins Y-G-G-F-L Y-G-G-F-M • Oxytocin C-Y-I-Q-N-C-P-L-G-NH2 • Has C—C disulfide • Vasopressin C-Y-F-Q-N-C-P-R-G-NH2 • Also disulfide Chemical Synthesis of Peptides • Why? • Done solid phase – Problem with in solution • Hard to make pure desired sequence – Purify by filtration • Side chains blocked • Made backwards ( C---N) Scheme for peptide synthesis Tetrapeptide answer A L O H3N+ O N H D R O N H O N H O O NH H2N+ • Back NH2 O