Following is a table listing the one-letter symbols, the three-letter symbols, and the chemical properties of the side chains of the standard amino acids. The masses listed are based on weighted averages of the elemental
isotopes at their
natural abundances. Forming a
peptide bond results in elimination of a molecule of
water. Therefore, the protein's mass is equal to the mass of amino acids the protein is composed of minus 18.01524 Da per peptide bond.
General chemical properties Side-chain properties §: Only ionizable residues have a meaningful pKa. Values for Asp, Cys, Glu, His, Lys & Tyr were determined using the amino acid residue placed centrally in an alanine pentapeptide. The value for Arg is from Pace
et al. (2009). The value for Sec is from Byun & Kang (2011). Note: the pKa value of an amino-acid residue in a small peptide is typically slightly different when it is inside a protein.
Protein pKa calculations are sometimes used to calculate the change in the pKa value of an amino-acid residue in this situation.
Gene expression and biochemistry • UAG is normally the
amber stop codon, but in organisms containing the biological machinery encoded by the pylTSBCD cluster of genes the amino acid pyrrolysine will be incorporated. • UGA is normally the opal (or umber) stop codon, but encodes selenocysteine if a
SECIS element is present. † The
stop codon is not an amino acid, but is included for completeness. †† UAG and UGA do not always act as stop codons (see above). ‡ An essential amino acid cannot be synthesized in humans and must, therefore, be supplied in the diet. Conditionally essential amino acids are not normally required in the diet, but must be supplied
exogenously to specific populations that do not synthesize it in adequate amounts. & Occurrence of amino acids is based on 135 Archaea, 3775 Bacteria, 614 Eukaryota proteomes and human proteome (21 006 proteins) respectively.
Mass spectrometry In
mass spectrometry of peptides and proteins, knowledge of the masses of the residues is useful. The mass of the peptide or protein is the sum of the residue masses plus the mass of
water (
Monoisotopic mass = 18.01056 Da; average mass = 18.0153 Da). The residue masses are calculated from the tabulated chemical formulas and atomic weights. In
mass spectrometry, ions may also include one or more
protons (
Monoisotopic mass = 1.00728 Da; average mass* = 1.0074 Da). *Protons cannot have an average mass, this confusingly infers to Deuterons as a valid isotope, but they should be a different species (see
Hydron (chemistry)) §
Monoisotopic mass Stoichiometry and metabolic cost in cell The table below lists the abundance of amino acids in
E.coli cells and the metabolic cost (ATP) for synthesis of the amino acids. Negative numbers indicate the metabolic processes are energy favorable and do not cost net ATP of the cell. The abundance of amino acids includes amino acids in free form and in polymerization form (proteins).
Remarks Catabolism Amino acids can be classified according to the properties of their main products: • Glucogenic, with the products having the ability to form
glucose by
gluconeogenesis • Ketogenic, with the products not having the ability to form glucose: These products may still be used for
ketogenesis or
lipid synthesis. • Amino acids catabolized into both glucogenic and ketogenic products == See also ==