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Lecture 2

Lecture 2 Text Notes amino acids

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Stavroula Andreopoulos

Lecture 2 Amino Acids Amino Acids - the structure of an amino acid is an alpha carbon covalently linked to both the amino and carboxyl groups – a variable side chain is also bonded to the carbon - side chain – R group – gives the amino acid its identity - in neutral solution/physiological pH, the carboxyl and amino groups exist as COO and NH - 3+ - because the amino acid has a positive and negative charge it is neutral – zwitterion - amino acids are chiral, except for glycine - amino and carboxyl groups of amino acids allows for polymerization to form peptides – react in a head-to-tail conformation by forming a covalent amide linkage – peptide bond - reaction equilibrium favours peptide bond hydrolysis - reaction produces polypeptides and proteins - all amino acids except proline have free α-amino and α-carboxyl groups - classifications of amino acids – (1) nonpolar or hydrophobic amino acids, (2) neutral (uncharged) but polar amino acids, (3) acidic amino acids which have a net negative charge at pH 7, (4) basic amino acids which have a net positive charge at pH 7 Nonpolar Amino Acids - important in the process of folding proteins - include all amino acids with alkyl R groups – alanine, valine, leucine, isoleucine - cyclic structure and aromatic amino acids – proline, phenylalanine, tryptophan - methionine is included as well - proline is not an amino acids but an α-imino acid Polar, Uncharged Amino Acids - contain R groups that can (1) form hydrogen bonds with water, (2) act as a nucleophile in enzyme reactions – glycine is the only exception - amide groups of asparagine and glutamine; hydroxyl groups of tyrosine, threonine, and serine; sulfahydryl group of cysteine – good at hydrogen bonding - glycine has R group of a single hydrogen – solubility attributed to polar amino and carboxyl groups Acidic Amino Acids - aspartic acid and glutamic acid – contain carboxyl group in R group – weaker acids than the α-carboxyl but still exist as COO at physiological pH and have a net negative charge - aspartic acid = aspartate, glutamic acid = glutamate - proteins that bind metal ions for structure or function contain metal binding sites that contain one or more aspartate or glutamate side chains Basic Amino Acids - net positive charge at neutral pH – histidine, arginine, lysine - imidazole group in histidine, guanidino group in arginine, protonated alkyl amino group in lysine - histidine has pKa 6.0 at physiological pH – important in protonation and deprotonation in enzyme reactions – peptides containing histidi
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