©CMBI 2001 Amino Acids “ When you understand the amino acids, you understand everything ”

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©CMBI 2001 Amino Acids “ When you understand the amino acids, you understand everything ”

©CMBI 2001 Amino Acids Proteins are macromolecules made up from 20 different amino acids. The heart of the amino acid is the so-called C . To which are bound: an amino group, a carboxyl group, a hydrogen, and the side chain. The C , C, N and O atoms are called backbone atoms. R denotes any one of the 20 possible side chains.

©CMBI 2001 Di-peptide Amino acids bind, to form a protein. Upon binding, two protons from the NH 3 and one oxygen from the carboxyl join to form a water. So the peptide bond has at the one side a C=O and at the other side an N-H. Only the ends of the chain are NH 3 or carboxylic, and thus charged. Which dipeptide is this? Where are the charges?

©CMBI 2001 Phi-Psi

©CMBI 2001 Amino Acid Sequence The amino acid sequence (also called primary structure) of a protein is the order of the amino acids in the protein chain. The sequence is always read from the N-terminus to the C- terminus of the protein. For example: +H 3 N-Lys-Val-Phe-Ala-Met-Cys-Leu-Leu-Arg-Val-COO- Or (in one-lettercode): KVFAMCLLRV

©CMBI 2001 The 20 Amino Acids AAlaAlanine C CysCysteine D Asp Aspartic acid (Aspartate) E GluGlutamic acid (Glutamate) F PhePhenylalanine G GlyGlycine H HisHistidine I IleIsoleucine K LysLysine L LeuLeucine M MetMethionine N AsnAsparagine P ProProline Q GlnGlutamine R ArgArginine S SerSerine T ThrThreonine V ValValine W TrpTryptophan Y TyrTyrosine

©CMBI Amino Acids The side chains, R, determine the differences in the structural and chemical properties of the 20 ‘natural’ amino acids. The 20 amino acids can, for example, be classified as follows: Aliphatic/hydrophobicAla, Leu, Ile, Val PolarAsn, Gln AlcoholicSer, Thr, (Tyr) Sulfur-containingMet, Cys AromaticPhe, Tyr, Trp, (His) ChargedArg, Lys, Asp, Glu, (His) SpecialGly (no R), Pro (cyclic) Several amino acids belong in more than one category.

©CMBI 2001 Amino Acid Characteristics There are many ways to characterize the properties of amino acids. The ones most useful and most commonly used are: Hydrophobicity Size Charge Secondary structure preference Alcoholicity Aromaticity And on top of that there are some special characteristics like bridge forming by cysteines, rigidity of prolines, titrating at physiological pH of histidine, flexibility of glycines, etc.