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THE PRIMARY STRUCTURES OF PROTEINS AMINO ACIDS Introduction to proteins: Protein functions Enzymes (catalysts) Transporters (membrane spanning) Contraction, motion Defense (antibodies, venoms) Regulation (of catalysis, transport, motion) Nutrient storage (C,N sources) Structure (tensile strength) Other (luminescence, bonding...) Protein structures Primary structure (linear polymer of amino acids) Secondary structure (standard 3-D patterns) Tertiary structure (detailed 3-D conformation) Quaternary structure (combined polymer chains) The -carbon is chiral: L and D forms All protein amino acids are L forms Amino acids are: Amphoteric, amphiprotic: act as acid or base Ionic: electrolyte Ampholyte: amphoteric electrolyte (in a pH gradient under an electric field, moves to its isoelectric point) Amino acids are: Amphoteric, amphiprotic: act as acid or base Ionic: electrolyte Ampholyte: amphoteric electrolyte (in a pH gradient under an electric field, moves to its isoelectric point) + _ Amino acids can connect with a peptide bond involving amino and carboxylate groups Peptide bonds are planar and partially ionic Note the Directionality: Side chains (R groups): group amino acids by structure and function (Assignment: memorize amino acids by name, side chain, abbreviations, characteristic) Glycine and alanine have the smallest, simplest side chains. Both have side chains that are non-polar and neutral. Hydrophobicity (Go for transfer from butanol to water): -0.4 1.8 Valine, leucine, isoleucine, methionine, and proline are non-polar , neutral, and alaphatic. Hydrophobicities: 4.2 3.8 4.5 1.9 -1.6 Phenylalanine and tryptophan are non-polar, neutral, and aromatic. Hydrophobicities: 2.8 -0.9 Serine, threonine, and tyrosine are polar and neutral. Hydrophobicities: -0.8 -0.7 -1.3 Cysteine, asparagine, and glutamine are neutral and… non-polar polar polar. Hydrophobicities: 2.5 -3.5 -3.5 Lysine, arginine, and histidine are polar and positively charged. (+ charge below pH 7) Hydrophobicities: -3.9 -4.5 -3.2 Aspartate and glutamate are polar and negatively charged. Hydrophobicities: -3.5 -3.5 Titration of glutamate (Shoulders represent Transitions) - Titration of a small polypeptide: gly-lys-ala N C Note: shoulders in titration curve only for C-term, N-term, and side chains Assignment: memorize amino acids by name, side chain, abbreviations, characteristics (hydrophobic, polar, acidic, basic, etc.С donХt worry about values of hydrophobicity) There are different, non-protein amino acids. Three amino acids probably explain the toxicity of some deadly Chinese mushrooms: 2R-amino-4S-hydroxy-5-hexynoic acid; 2R-amino-5-hexynoic acid gamma-guanidinobutyric acid.