Amino Acids are the organic compounds and the building blocks of peptides and proteins.
The Structure of Amino Acids
An α-amino acid contains four different substituents which are attached to a central carbon atom (the α-C atom):
the acid group (carboxylic acid group = carboxyl group, COOH, which Bachem abbreviates to -OH in the three-letter code)
a basic group (NH2, amino group, abbreviated H- in the three-letter code)
the variable side chain called R (It can vary greatly and thereby determines the properties of the peptide)
a hydrogen atom (H)
Accordingly, the α-C atom carries 4 groups with different chemical properties that play a very large role in what follows.
Proteinogenic Amino Acids
There are 20 different 'proteinogenic' amino acids from which proteins of the cell are made. They differ solely in the side chain R. In addition many other α-amino acids are found in nature, either free, as products of metabolism or incorporated into peptides/proteins. Examples are L-hydroxyproline (Hyp) in collagen, or L-ornithine (Orn) free in the urine. Other α-amino acids, e.g. L-norleucine (Nle) have so far only been obtained through chemical synthesis. Bachem calls non-proteinogenic amino acids such as Hyp and Nle 'unusual amino acids'. Often, they are designated as 'unnatural amino acids' irrespective of their occurrence in nature. Amino acids (whether proteinogenic or not) can be biologically active, e.g. L-tryptophan, L-glutamic acid.
The side chain R can
be a hydrogen atom: glycine, the simplest α-amino acid
carry an additional acid group (COOH): aspartic acid, glutamic acid or a modified acid group (an amide, CONH2 e.g. asparagine, glutamine)
be a hydrocarbon (non-polar): alanine (R = methyl), phenylalanine (R = benzyl), valine (R = isopropyl)
contain sulfur: cysteine, methionine
In addition to the α-amino acids from which peptides and proteins are built, Bachem has many other amino acids on offer, including those in which the amino group is bound to another carbon atom.
L- and D-amino acids
The four different substituents of the α-carbon atom are not arranged in one plane, but lie at four corners of a tetrahedron with the α-C atom in the center.
Therefore two forms of the amino acid molecule are possible that behave like mirror images of each other and are known as stereoisomers or enantiomers:
The two enantiomers do not differ in their physical properties, except that in solution, they rotate the plane of polarized light. Compounds that do this are called 'optically active'. Optical activity is found very widely in nature. Apart from glycine (R = H, image and mirror image identical), all proteinogenic amino acids show this phenomenon. Glucose (sugar) also rotates the light and this property is used to determine the concentration of glucose solutions, as does DNA and its building blocks.
All proteinogenic amino acids (apart from Gly) are L-enantiomers (L stands for laevus, Latin for 'left'), e.g. L-alanine.
Their 'mirror images', the D-amino acids, occur much less often in nature. D stands for dexter (Latin for 'right'). To reiterate this point, L or D denote the arrangement of the four different substituents on the α-C atom, i.e. the respective enantiomer.
The direction of rotation cannot be deduced from the designation L or D. In the case of L-amino acids, it can be positive or negative (see below), with the corresponding D-amino acids, it is always in the opposite direction.
The values of rotation are often stated as [α] on the ADS (Analytical Data Sheets) of amino acids and their derivatives, since they are characteristic for the particular compound. Values of rotation are often also measured for peptides.
L-alanine: + 14.3°
L-tryptophan: - 31.8°
D-tryptophan: + 30.7° (the discrepancies between the absolute values for the L- and corresponding
D-enantiomer lie within the range of accuracy of the method)
A 1:1 mixture of the two enantiomers is called a racemate. In this case, the rotations of the L- and D- form compensate each other.
In the Bachem notation, the L-form is not explicitly shown because of its ubiquity (e.g. L-alanine = H-Ala-OH). Only the less common D-form (D-alanine = H-D-Ala-OH) and the racemate, which is shown as DL, are designated as such.
Notation for amino acids
If the name of an amino acid is written out in full, the enantiomeric form is shown as well: L-alanine and D-alanine.
In the case of a racemate - as is common in organic chemistry - the DL is routinely omitted. Amino acids and peptides are represented by their three-letter codes (usually the first three letters of the name). In addition, there is also a one-letter code that is preferred, especially for longer peptides and proteins
L-alanine → Ala, L-Ala, H-Ala-OH (3-letter); A (1-letter)
L-arginine → Arg, L-Arg, H-Arg-OH (3-letter); R (1-letter)
The notation signifies that it is the L-form and that the amino and carboxyl groups are free. The abbreviations of the 20 proteinogenic amino acids are given in the Table above.
The one-letter code is only used for the 20 proteinogenic amino acids, for D-amino acids, the usual practice is to use small letters, e.g. f = D-Phe.
On the other hand, for many of the non-proteinogenic amino acids there is often also an obligatory three-letter code, e.g. Hyp (L-trans-hydroxyproline), Nle (L-norleucine), Orn (L-ornithine). Not all abbreviations usually found in the literature are also used by Bachem. For some amino acids, the non-abbreviated name is used, e.g. L-thiazolidine-4-carboxylic acid (otherwise Thz).