Control of protein synthesis by amino acid availability is an active and centrally important area of research that has produced several recent advances in our understanding of how these substrates serve not only as precursors but also as signaling molecules. One particularly noteworthy advance is the identification of the unique specificity of leucine in signaling to stimulate protein synthesis in skeletal muscle. Leucine mediated signaling results in a stimulation of initiation of mRNA translation and involves increases in the phosphorylation status of the translational repression 4E-BP1 and the ribosomal protein S6 kinase S6K1. It requires sustained activation of the mammalian target of rapamycin protein kinase. Leucine, however, also signals to stimulate protein synthesis in skeletal muscle by a mammalian target of rapamycin protein kinase independent (i.e. rapamycin insensitive) pathway, suggesting that the amino acid may signal through multiple pathways. Furthermore, leucine signaling in skeletal muscle differs from that in liver, suggesting that various responses may be tissue specific. Finally, there continues to be active research on the beneficial effects of glutamine as a unique supplement in catabolic circumstances. In this case, however, the signaling properties and mechanism of action of glutamine remain as an unsolved mystery.