To reconstruct past diet of archaeological skeletal material, by chemical analysis, researchers have used stable carbon isotope ratios (13C/12C) of archaeological bone collagen to calculate the proportion of C-3 versus C-4 plants or marine versus terrestrial resources in the diet. However, evidence from animal studies indicates that different animal tissue types have different fractionation factors with regard to diet which may result in part from differential contributions of dietary carbohydrate, lipid, and protein to like fractions in the animal. This view of metabolism is in contrast to the theory that dietary nutrients are broken down into small molecules and then reassembled. Since collagen is a protein, the dietary fractions contributing components to its synthesis are important if the dietary fractions are not isotopically equivalent and the diet is less than ideally balanced. Based on the amino acid proportion given for modern bovine bone and considering as essential those amino acids essential for growth, 81per thousand of collagen residues are nonessential amino acids and 71per thousand of the carbon atoms are from nonessential amino acids. Dispensable amino acids can be synthesized from products of glycolysis or products of the citric acid cycle. Since the latter is the final common metabolic pathway of carbohydrates, proteins, and fatty acids, a certain scrambling of carbon atoms from different dietary fractions may be involved in collagen synthesis. This paper will discuss the fates of individual carbon atoms and the bulk relationships among metabolic processes and their implications for reconstructing diet from archaeological skeletal material.