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

Amino Acids and DNA synthesis Amino acids are the source of Nitrogens for DNA and RNA synthesis. No amino acids no RNA, no DNA. This raises the question what was first? Amino acids are abundantly found on meteorites, mostly L-form, much less D-form. Purine and pyrimidines are in low amounts discovered.

Amino Acids distribution Finkelstein et al., J. Bioinformatics and Computational Biology 2006

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. O R The C , C, N and O atoms are called backbone atoms. R denotes any one of the 20 possible side chains. H2NH2N CHCH C OHOH  ©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 ©CMBI 2001 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

The 20 Amino Acids ©CMBI 2001 ACAC Ala Cys Alanine Cysteine DEFGHDEFGH Asp Glu Phe Gly His Aspartic acid (Aspartate) Glutamic acid (Glutamate) Phenylalanine Glycine Histidine IKLMNIKLMN Ile Lys Leu Met Asn Isoleucine Lysine Leucine Methionine Asparagine PQRSTPQRST Pro Gln Arg Ser Thr Proline Glutamine Arginine Serine Threonine VWYVWY Val Trp Tyr Valine Tryptophan Tyrosine

20 Amino Acids ©CMBI 2001 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 Polar Alcoholic Sulfur-containing Aromatic Charged Special Ala, Leu, Ile, Val Asn, Gln Ser, Thr, (Tyr) Met, Cys Phe, Tyr, Trp, (His) Arg, Lys, Asp, Glu, (His) Gly (no R), Pro (cyclic) Several amino acids belong in more than one category.

Amino Acid Characteristics ©CMBI 2001 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.

Secondary Structure Preference ©CMBI 2001 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. For now, just remember Helix: AMELK;Strand:VITWYF; Turn: PSDNG. (Later we will find out why)