As part of our investigations into the development of representational competence, we report results from a study in which we elicited sixteen graduate students’ expressed mental models of commonly-used terms for describing organic reactions – functional group, nucleophile/electrophile, acid/base – and for diagrams of transformations and their mechanisms. The students had the greatest difficulty in articulating a verbal description of functional groups. Most of the participants conceived of functional groups as book-keeping devices for determining the changes that occur in a reaction. Their conceptions of functional groups lacked any indication of function. Furthermore, this lack of process-oriented thinking resulted in descriptions of reactions that were focused on structural changes with relatively little mechanistic information. Consistent with previous research in chemistry and other STEM fields, the students in this study exhibited an overall superficial approach in their explanations of the diagrams; thus limiting the information they could extract from them.