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

2. ©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.

3. ©CMBI 2001 Amino Acids Backbones run from the amino to the carboxy end, or in other words, from N-terminus to C-terminus.

4. ©CMBI 2001 Zwitterion At pH 7, the amino group and the carboxyl groups are both ionised. In this state the amino group is protonated and thus positive, and the carboxyl group is de-protonated, and thus negative. An amino acid in this polarised state is called a zwitterion. In a protein, there is only one H on the N, and only one O on the C.

5. ©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. Which dipeptide is this?

6. ©CMBI 2001 The Peptide Bond phi (  ) = torsion angle around N-CA bond psi (  ) = torsion angle around CA-C bond omega (  ) = always ~180 degrees, sometimes ~0 = bond between two amino acids; peptide bond NH 2 CH C O R 1 N CH C O OH R 2 H   

7. ©CMBI 2001 Phi-Psi

8. ©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

9. ©CMBI 2001 Direction of Protein Chain Lys-Val Val-Lys

10. ©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

11. ©CMBI 2001 The 20 Amino Acids

12. ©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/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, imino-acid) Several amino acids belong in more than one category.

13. ©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.

14. ©CMBI 2001 Hydrophobicity Hydrophobicity is the most important characteristic of amino acids. It is the hydrophobic effect that drives proteins towards folding. Actually, it is all done by water. Water does not like hydrophobic surfaces. When a protein folds, exposed hydrophobic side chains get buried, and release water of its sad duty to sit against the hydrophobic surfaces of these side chains. Water is very happy in bulk water because there it has on average 3.6 H-bonds and about six degrees of freedom. So, whenever we discuss protein structure, folding, and stability, it is all the entropy of water, and that is called the hydrophobic effect.

15. ©CMBI 2001 Secondary Structure Preference Amino acids form chains, the sequence or primary structure. These chains fold in  -helices,  -strands,  -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  - branched residues (Ile, Thr, Val) like to sit in  -strands.