“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 NH3 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 NH3 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: +H3N-Lys-Val-Phe-Ala-Met-Cys-Leu-Leu-Arg-Val-COO- Or (in one-lettercode): KVFAMCLLRV ©CMBI 2001

The 20 Amino Acids A Ala Alanine C Cys Cysteine D Asp Aspartic acid (Aspartate) E Glu Glutamic acid (Glutamate) F Phe Phenylalanine G Gly Glycine H His Histidine I Ile Isoleucine K Lys Lysine L Leu Leucine M Met Methionine N Asn Asparagine P Pro Proline Q Gln Glutamine R Arg Arginine S Ser Serine T Thr Threonine V Val Valine W Trp Tryptophan Y Tyr Tyrosine ©CMBI 2001

20 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/hydrophobic Ala, Leu, Ile, Val Polar Asn, Gln Alcoholic Ser, Thr, (Tyr) Sulfur-containing Met, Cys Aromatic Phe, Tyr, Trp, (His) Charged Arg, Lys, Asp, Glu, (His) Special Gly (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. ©CMBI 2001

Secondary Structure Preference Amino acids form chains, the sequence or primary structure. These chains fold in -helices, b-strands, b-turns, and loops (or for short, helix, strand, turn and loop), the secondary structure. These secondary structure elements fold further to make whole proteins, but more about that later. There are relations between the physico-chemical characteristics of the amino acids and their secondary structure preference. I.e., the b- branched residues (Ile, Thr, Val) like to sit in b-strands. For now, just remember Helix: AMELK; Strand:VITWYF; Turn: PSDNG. (Later we will find out why) ©CMBI 2001