There is great variation in the carbon isotope composition of amino acids within a single organism. In cyanobacteria, Macko et al. observed a ~30‰ range in δC values amongst the amino acids. Amino acids produced from the same precursors also had widely varying compositions. It is difficult to explain these trends because of limited data on the kinetic isotope effects associated with reactions that synthesize amino acid carbon skeletons. Nevertheless, some insights can be gained by applying the logic above to the reaction networks responsible for amino acid biosynthesis.
Consider the amino acids synthesized from pyruvate. Pyruvate is produced during glycolysis and can be decarboxylated by pyruvate dehydrogenase to generate acetyl groups. These acetyl groups enter the citric acid cycle as acetyl-CoA or can be used to synthesize lipids. There is a large kinetic isotope effect associated with this reaction, so the remaining pyruvate pool becomes enriched in C relative to the acetyl groups. This enriched pyruvate can be transaminated to produce alanine. In the experiments by Macko et al., alanine indeed had a δC value slightly higher than that of cyanobacterial photosynthate.
Valine is synthesized by the addition of a C depleted acetyl group to pyruvate. Consistent with this mechanism, Takano et al. found valine to be depleted in C relative to alanine in anaerobic methanotrophic archaea. However, in cyanobacteria, Macko et al. observed a higher δC value for valine than alanine. This could be due to the branch point at the intermediate α-ketoisovalerate, which can be transaminated to produce valine or further acetylated to generate leucine. There may be different isotope effects associated with the addition of an amino or acetyl group at position C-2 in α-ketoisovalerate. As discussed above, the isotopic consequences of this branch point would depend on the relative rates of leucine vs valine production.
One would also expect relative depletion of C in leucine because its synthesis requires the addition of another isotopically light acetyl group. In Escherichia coli, the carboxyl carbon in leucine (derived from acetyl-CoA) has a δC value roughly 13‰ lower than that of the entire molecule. Curiously, the same depletion is not observed in photoautotrophs. Further, there is little consistency in the δC of most amino acids between cyanobacteria and eukaryotic photoautotrophs. These discrepancies demonstrate the limits of our understanding of the mechanisms that set amino acid isotopic compositions. Regardless, isotopic variations between different taxa have been used to great effect in ecology.