Here we revew what we’ve learned so far and introduce a quantitative evaluation of the flow of energy through the cycle through the lens of a clinical application: how to interpret the citric acid metabolite section of a urinary organic acids test. We begin with an explanation of the curious absence of oxaloacetate on these tests, which takes us back to the basic principles of chemical bonding. Ultimately, we identify patterns reflecting three conditions: energy overload, oxidative stress, and thiamin deficiency.