371 - Chapter 3 Outline.pdf

371 - Chapter 3 Outline.pdf - CHEM 371 Chapter 3 Amino...

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CHEM 371 Chapter 3: Amino Acids, Peptides, and Proteins C. Mouzakitis Proteins are polymers of covalently bonded amino acids. Once bound, an amino acid is called a residue , reflecting the loss of water in this bonding. The 20 common amino acids are α -amino acids , as they have a carboxyl group and an amino group bound to the same alpha carbon. Amino acids differ in their R group side chains, which influence their shape, charge, and solubility. There are additional, less common amino acids, which may be either residues modified after protein synthesis or amino acids that exist in organisms but are not part of proteins. Numbering carbons: highest priority given to carbon with the substituent containing the highest atomic number (usually the carbonyl carbon). The carbon immediately attached to C1 is the alpha carbon. The Greek letters are not used for heterocyclic R groups, as they would be ambiguous The alpha carbon is a chiral center for 19 amino acids (not glycine as R group is another H). Chirality results in two optically active, nonsuperimposable, mirror image stereoisomers called enantiomers . The nomenclature to specify this absolute configuration is the D, L system , based on similarity to glyceraldehyde . L-Amino acids are those with the α -amino group on the left, and D-amino acids have the α - amino group on the right. The L, D system does not refer to levorotatory (light – left) and dextrorotatory (light – right); not all L-amino acids are levorotatory. Amino acid residues in protein molecules are exclusively L stereoisomers . Since the active sites on enzymes are asymmetric, catalyzed reactions are stereospecific. Amino Acids are classified into five groups based on polarity , or tendency to interact with water at biological pH 7.0. 1. Nonpolar, Aliphatic R groups – hydrophobic: alanine, valine, leucine, isoleucine, glycine, methionine, and proline. a. Ala, Val, Leu, and Ile have severely hydrophobic side chains b. Gly does not contribute to hydrophobic interaction c. Pro has a rigid cyclic structure that reduces flexibility 2. Aromatic R groups: phenylalanine, tyrosine, and tryptophan a. Phe, Tyr, and Trp are relatively nonpolar b. Tyr has hydroxyl group that can form hydrogen bonds c. Tyr and Trp are more polar than Phe 3. Polar, Uncharged R groups: serine, threonine, cysteine, asparagine, and glutamine a. Side chains can form hydrogen bonds with water, thus making them more soluble or hydrophilic b. Ser and Thr have hydroxyl groups contributing to polarity c. Cys has sulfhydryl group contributing to polarity d. Asn and Gln have amide group contributing to polarity e. Asn and Gln are the amides of Asp and Glu (see structures) f. Cys can covalently link to another Cys to form cysteine via a disulfide bond .
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4. Positively Charged (Basic) R groups – very hydrophilic: lysine, arginine, and histidine a. Lys has primary amino group on the ε position, Arg has guanidino group, and His has imidazole group.
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