L3-5_Amino_Acids - Amino Acids-The Building Blocks of...

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10 Amino Acids-The Building Blocks of Protein Biomolecules The goal of biochemistry is to explain life in chemical terms Approximately 30 of the >90 naturally occurring chemical elements are essential to living organisms The four most abundant elements in organisms are Hydrogen Oxygen Nitrogen Carbon Trace elements are present in miniscule amounts but are essential because of specific roles they play Carbon The chemistry of living organisms is organized around carbon Functional groups are groups of atoms that confer specific properties on the molecule by nature of their arrangement in space and their identities. Affect a variety of parameters Structural Hydrogen bonding Reactivity Solubility Equally important to the presence of the functional groups is their arrangement in three-dimensional space This is their stereochemistry Stereoisomers : molecules with the same order of bonding but different spatial relationships. Amino Acids General Features 20 Standard amino acids All have a carboxylic end, an amino end and an R group Referred to as alpha amino acids all but one have a chiral (non-superimposable) center all amino acids found in proteins are of the L stereoisomer L = Life +H 3 N C C R O - O H
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11 Shorthand references are both three letter and one letter Classes and Characteristics of the amino acids: Have various different physicochemical properties polarity acidity basicity aromaticity bulk conformational flexibility ability to cross link ability to hydrogen bond chemical reactivity These several characteristics, many of which are interrelated are largely responsible for proteins' great range of properties. The classifications are somewhat arbitrary since many amino acids could fit in more than one class The classes are based on the R groups (the side-chains) of the amino acids. The classes are: i. Those with non-polar R groups ii. Those with uncharged polar R groups iii. Those with charged polar R groups Non-polar amino acids The aliphatic residues (6) Gly, Ala, Val, Leu, Ile, Met Have no reactive groups on their side chains Hydrophobic, do not interact favorably with water interact favorably with each other and other nonpolar atoms Typically found buried inside a proteins folded structure Variety in their shapes is important for their structural role Ala, A CH 3 Val, V CH CH 3 CH 3 Leu, L Ile, I CH 2 HC CH 3 CH 3 H Gly, G CH 2 CH CH 3 CH 3 CH 2 CH 2 S CH 3 Met, M
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12 The smallest amino acid (1) Glycine R group is a hydrogen The only amino acid that is not optically active Used in proteins where points of flexibility and low steric or chemical reactivity are advantageous The cyclic residue (1) Proline Actually is an imino acid No amide bond for use in hydrogen bonding or resonance stabilization Cyclic ring imposes rigid constraints on rotation about the N—C α bond.
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