We have investigated the effects of an animation of ATP synthesis in mitochondria on students understanding of the process. University students were exposed to the animation without narration before their introductory course in cell metabolism. Our intention was to identify any visual aspects of the animation that helped students to understand the process, and how the animation influenced their reasoning. In a mixed-method design, individual questionnaires were administered and group discussions performed. We identified three features of the animation which helped the students to understand critical aspects of the process, namely 1) molecular dynamics, 2) an explicitly visualized coupling between the flow of protons through the protein complex and ATP-synthesis 3) movements and induced conformational changes in the proteins during the process. We also observed that students showed difficulties in predicting the reversibility of the reaction. Analogies might enhance the meaningfulness and provide qualitative insights of sub-microscopic explanations. Albeit so, our preliminary analysis of the group discussions indicates that they are also sometimes misleading and can act as traps that induce erroneous chemical reasoning.