Introduction
Amino acids are the basic building blocks of proteins. They are also the basic units of FoldIt. In the structure of a protein, each amino acid contributes one link in the protein backbone and one side chain. The backbone establishes the basic structural aspects of the protein, and the side chains determine the details of its biological function.
(This table comes from Wikipedia, and we can use it to get started on discussing individual amino acids. In the meantime, I'd like to get in touch with anyone who has access to jpegs of these compounds showing how they all look in Fold It. -- Diderot)
| Amino Acid | 3-Letter | 1-Letter | Side chain polarity | Side chain acidity or basicity of neutral species | Hydropathy index[1] |
|---|---|---|---|---|---|
| Alanine | Ala | A | nonpolar | neutral | 1.8 |
| Arginine | Arg | R | polar | basic (strongly) | -4.5 |
| Asparagine | Asn | N | polar | neutral | -3.5 |
| Aspartic acid | Asp | D | polar | acidic | -3.5 |
| Cysteine | Cys | C | polar | neutral | 2.5 |
| Glutamic acid | Glu | E | polar | acidic | -3.5 |
| Glutamine | Gln | Q | polar | neutral | -3.5 |
| Glycine | Gly | G | nonpolar | neutral | -0.4 |
| Histidine | His | H | polar | basic (weakly) | -3.2 |
| Isoleucine | Ile | I | nonpolar | neutral | 4.5 |
| Leucine | Leu | L | nonpolar | neutral | 3.8 |
| Lysine | Lys | K | polar | basic | -3.9 |
| Methionine | Met | M | nonpolar | neutral | 1.9 |
| Phenylalanine | Phe | F | nonpolar | neutral | 2.8 |
| Proline | Pro | P | nonpolar | neutral | -1.6 |
| Serine | Ser | S | polar | neutral | -0.8 |
| Threonine | Thr | T | polar | neutral | -0.7 |
| Tryptophan | Trp | W | nonpolar | neutral | -0.9 |
| Tyrosine | Tyr | Y | polar | neutral | -1.3 |
| Valine | Val | V | nonpolar | neutral | 4.2 |
Chemistry
In chemistry, an [amino acid] is a molecule containing both amine and carboxyl functional groups. In the alpha amino acids, the amino and carboxylate groups are attached to the same carbon, which is called the α–carbon. The various alpha amino acids differ in which side chain (R group) is attached to their alpha carbon. They can vary in size from just a hydrogen atom in glycine through a methyl group in alanine to a large heterocyclic group in tryptophan.
Beyond the amino acids that are found in all forms of life, many non-natural amino acids have vital roles in technology and industry. For example, the chelating agents EDTA and nitrilotriacetic acid are alpha amino acids that are important in the chemical industry.
Overview
Alpha-amino acids are the building blocks of proteins. Amino acids combine in a condensation reaction that releases water and the new "amino acid residue" that is held together by a peptide bond. Proteins are defined by their unique sequence of amino acid residues; this sequence is the primary structure of the protein. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a vast variety of proteins.
Twenty standard amino acids are used by cells in protein biosynthesis, and these are specified by the general genetic code. These 20 amino acids are biosynthesized from other molecules, but organisms differ in which ones they can synthesize and which ones must be provided in their diet. The ones that cannot be synthesized by an organism are called essential amino acids.
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