Proteins are highly specialized macromolecules performing essential functions in a biological system, such as controlling transport processes, stabilization of the cell structure, and enzymatic catalyzation of chemical reactions; others act as molecular motors in the complex machinery of molecular synthetization processes. Chemically, proteins are built up of sequences of amino acid residues linked by peptide bonds. The polypeptide chain consists of a linear backbone with the amino acid specific side chains attached to it. The atomic composition of the protein backbone is shown in Fig. 1.1. Typical proteins consist of up to N = 50, . . ., 3000residues. The 20 different types of amino acids occurring in bioproteins are shown in Fig. 1.2. The side chains of these amino acids govern the principal specificity of each amino acid in protein folding processes and differ in chemical and physical properties under the influence of the surrounding solvent. Solubility in an aqueous environment is dependent of the occurrence of polar groups in the side chain, such as, e.g., the hydroxylic groups in serine and threonine. Hydrophobic side chains are insoluble and little reactive in a polar environment. Typical large and strongly hydrophobic side chains such as, for example, phenylalanine or tryptophan, possess aromatic rings. Others, like alanine or leucine with methine (-CH), methylene (-CH2), or methyl (-CH3) groups in the side chain, are aliphatic, i.e., these side chains only contain hydrogen and carbon atoms.
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