CHAPTER 3 (Figures)

CHAPTER 3 (Figures) - David L. Nelson and Michael M. Cox...

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Lehninger Principles of Biochemistry Fourth Edition Chapter 3: Amino Acids, Peptides, and Proteins David L. Nelson and Michael M. Cox
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2 Amino Acids i. The structure of the α -amino acids All 20 amino acids are α -amino acids. The have a general structure given in Fig. 3-2 except for Prolin e. A carbonyl group Amino group Hydrogen, and Side chain (R) They differ from each other in their side chain. R vary in structure, size and electronic charge. For all amino acids except glycine, the α -carbon is a chiral center The amino acid residues are all L-stereoisomers. ii. Classification of amino acids ( Fig. 3-5 and Table 3-1 ) Amino acids are classified by R group. a) Nonpolar aliphatic R-group The R groups are nonpolar and hydrophobic. The side chains of alanine , valine , leucine and isoleucine stabilize the structure by hydrophobic interactions Glycine has the simplest structure Although it is formally nonpolar, its very small side makes no real contribution to hydrophobic interactions.
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Gly-G Ala – A Pro- P Val-V Leu – L Ile- I Met-M Ser-S Thr-T Cys-C Asn- N Glu-Q
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4 Amino Acids a) Nonpolar aliphatic R-group (cont.) Methionine has a nonpolar thioester group in its side chain. Proline’s aliphatic side chain has distinctive cyclic structure. The secondary amino (imino) group of Pro residue is held in a rigid conformation that reduces the structural flexibility. b) Aromatic R-group Phenylalanine, tyrosine and trytophan all participate in hydrophobic interactions. Tyrosine and tryptophan are significantly more polar than phenylalanine because the tyrosine’s hydroxyl group (can form H-bonds) and the nitrogen of the tryptophan indole ring. Tryptophan and tyrosine, and to much less extent phenylalanine absorb UV light ( Fig. 3-6 ). This accounts for the characteristics strong absorbance of light by most proteins at wavelength of 280 nm .
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Phe-F Tyr-Y Trp-W
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7 Amino Acids c) Polar, uncharged R groups R groups are soluble in water (hydrophilic) because they contain groups that form H-bonds with water. This class include, serine, threonine, cystein, asparagine and glutamine . Cystein is readily oxidized to form a covalent linked dimeric amino acids The disulfide-linked residues are strongly hydrophobic. d) Positively charged (BASIC) R groups Lysine has a second primary amine group at the ε position. Arginine has a positively charged guanidino group. Histidine has an imidazole group. Histidine is the only standard amino acid having an ionizable side chain with pKa near neutrality. In many enzyme-catalyzed reactions, His residues facilitates the reaction by serving
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CHAPTER 3 (Figures) - David L. Nelson and Michael M. Cox...

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