05 - Chapter 5 Proteins Their Primary Structure and...

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Chapter 5 Proteins: Their Primary Structure and Biological Functions . . . . . . . . . . . . . . . . . . . . . . . . Chapter Outline v Peptide or amide bond Carboxyl group joined to amino group with loss of water -condensation reaction incorporates amino acid residue Double bond characteristics •-bond and peptide bond resonance No free rotation about peptide bond C, O, N, H all in peptide plane v Peptide chains Peptides: dipeptide to dodecapeptide (2 to 12 amino acid residues, 1 to 11 peptide bonds) Oligopeptides: 12 to 20 residues Polypeptides: >20 amino acid residues Proteins Monomeric protein -single chain -polypeptide Multimeric protein -multiple chains: homomultimeric or heteromultimeric v Protein architecture Fibrous proteins Globular proteins Membrane proteins v Protein structure Primary structure: Sequence of amino acids Secondary structure: Helices and sheets formed by interactions between peptide planes Tertiary structure: 3-D shape Quaternary structure: How chains interact in multimeric protein Protein conformation determined by primary sequence and weak force interactions Configuration actual arrangement of atoms held together by covalent bonds v Amino acid composition 6N HCl, 110°C, 24, 48, 72 hr Ser/Thr extrapolate to zero time, Val/Ile extrapolate to infinity Trp destroyed, Asn/Gln converted to Asp/Glu v Protein purification Size distinction: Size exclusion chromatography, ultracentrifugation, ultrafiltration Solubility distinction: Ammonium sulfate (salts), organic solvent, pH (solubility minimum at isoelectric point) Differential interactions: Ion exchange chromatography, hydrophobic interaction chromatography v Protein sequencing Separation of polypeptide chains: Reduction of disulfide bonds and denaturation
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Chapter 5 . Proteins: Their Primary Structure and Biological Functions 62 Inactivation of sulfhydryl groups: Performic acid oxidation or reduction with β- mercaptoethanol followed alkylation Amino acid composition N- and C-terminus identification N-terminus chemistry: Edman degradation -phenylisothiocyanate to product PTH derivative of N-terminal amino acid C-terminus: Carboxypeptidase C or Y cleaves any C-terminal amino acid, carboxypeptidase B cleaves only Arg or Lys, carboxypeptidase A does not cleave Arg, Lys, or Pro Polypeptide chain fragmentation: Sets of short, overlapping peptides Trypsin: Carbonyl side of Arg, Lys Chymotrypsin: Carbonyl side of Phe, Tyr, Trp Clostripain: Carbonyl side of Arg Endopeptidase Lys-C: Carbonyl side of Lys Staphyloccal protease: Carbonyl side of Asp, Glu Cyanogen bromide: Carbonyl side of Met Hydroxylamine: Asn/Gly bond Acid hydrolysis: Asp/Pro Sequence determination Edman degradation Mass spectrometry Sequence reconstruction: Match sequence of members of set of overlapping peptides Location of disulfide bonds: Analysis of fragments from nonreduced protein by diagonal electrophoresis (first dimension nonreducing -second dimension reducing)
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This note was uploaded on 02/18/2011 for the course BIOCHEM 328 taught by Professor Joel during the Spring '11 term at Cal Poly.

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05 - Chapter 5 Proteins Their Primary Structure and...

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