05 - CHAPTER 5 Amino Acids, Peptides, and Proteins...

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Biochemistry: The Molecular Basis of Life, 4/e McKee/McKee Copyright © 2009 by Oxford University Press, Inc. C H A P T E R 5 Amino Acids, Peptides, and Proteins
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FIGURE 5.1 Protein Diversity Overview Life is protein-based (developed from RNA world). Proteins: ~ ½ of cell dry mass. Most diverse functions of all biomolecules (!) 20 aa blocks – variety of combinations. Protein diversity: - theoretical – 20 N , where N is the number of aa in a protein - reality – 10 6-7 (?) Peptide = < 50 aa Protein > 50 aa Polypeptide, oligopeptide
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FIGURE 5.2 The Standard Amino Acids 5.1 Amino acids Standard aa – commonly found in proteins (20). Nonstandard – chemically modified in the protein or not in common proteins. Standard aa – primary amino groups except for P. R confers unique properties. Amino acid classes (interaction with water) (1) hydrophobic (nonpolar): G, A, V, L, I, P – hydrocarbon R F, W – aromatic R M, C – sulfur (2) polar: S, T, Y, N, Q H-bonds (3) acidic: D, E ‘-’ charged in cells (4) basic: K, R, H H is a weak base. α FIGURE 5.3 General Structure of the α -Amino Acids
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Biologically active amino acids (aa functions not as parts of proteins) 1. Chemical messengers - neurotransmitters (signaling between nerve cells) - hormones (signaling between non-neuronal cells) 2. Biosynthetic precursors of N-containing organic molecules: nt, heme, chlorophyll 3. Metabolic intermediates FIGURE 5.5 Some Derivatives of Amino Acids FIGURE 5.6 Citrulline and Ornithine Modified aa in proteins FIGURE 5.7 Some Modified Amino Acid Residues Found in Polypeptides prothrombin collagen signal transduction
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Stereoisomers α -C is linked to 4 different groups, ie asymmetrical = chiral . Stereoisomers = molecules that differ only in the spatial arrangement of their atoms. Enantiomers = stereoisomers that are mirror images. They have identical physical properties but rotate plane-polarized light in opposite directions (‘+’ = D-form vs. ‘-’ = L-form). Glyceraldehyde = reference compound for optical isomers. Most biomolecules are either D (sugars) or L (aa). FIGURE 5.8 Two Enantiomers FIGURE 5.9 D- and L-Glyceraldehyde
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Titration of amino acids 2 (most aa) or 3 titratable groups Aa pK 1 COOH pK 2 NH 3 + pK R Gly 2.34 9.6 Ala 2.34 9.69 Ph e 1.83 9.13 Asp 2.09 9.82 3.86 Glu 2.19 9.67 4.25 Arg 2.17 9.04 12.48 + H 3 N-CH-COOH I CH 2 I CH 2 I COOH + H 3 N-CH-COO - I CH 2 I CH 2 I COOH + H 3 N-CH-COO - I CH 2 I CH 2 I COO - H 2 N-CH-COO - I CH 2 I CH 2 I COO - pK 1 pK 2 pK R FIGURE 5.10 Titration of Two Amino Acids Isoelectric point = neutral (uncharged) form: pI Ala = (pK 1 + pK 2 ) / 2 = (2.34 + 9.69)/ 2 = 6.02
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FIGURE 5.11 Formation of a Dipeptide FIGURE 5.12 The Peptide Bond Amino acid reactions - Peptide (amide) bond - Disulfide bridge - Schiff base Peptide bond formation Acyl substitution reaction Dehydration = release of H 2 O O O II II R−C−X + Y - R−C−Y
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05 - CHAPTER 5 Amino Acids, Peptides, and Proteins...

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