Mitochondrial Electron Transport What explains the observation that FADH 2 oxidation yields one less ATP than NADH oxidation by the Electron Transport System? Solution There are in a total 3 spots in electrn transport system where the molecules NADH and FADH2 can deposit their electrons. Each of the spot in the ETC gives one ATP. The NADH enters in first protein and deposits its electrons , so its electrons go through all the three 3 spots , which makes 3 ATPs in all. The FADH2 dies not enter into first protein , it skips it. It then enters into second one , and deposits its electrons , so now its electrons can undergo through only two spots , which make 2 ATPs in total. So FADH2 oxidation yields one less ATP than NADH oxidation in ETC. .