Research on student thinking facilitates the design of instructional materials that build on student ideas. The pieces framework views student knowledge as consisting of independent pieces that students assemble in fluctuating ways based on the context at hand. This perspective affords important insights about the reasons students think the way they do. We used the pieces framework to investigate student thinking about the concept transformations of energy and matter with a specific focus on metabolism. We conducted think-aloud interviews with undergraduate introductory biology and biochemistry students as they solved a metabolism problem set. Through knowledge analysis, we identified two categories of knowledge elements cued during metabolism problem solving: (1) those about the visual representation of negative feedback inhibition; and (2) those pertaining to student focus on different metabolic compounds in a pathway. Through resource graph analysis, we found that participants tend to use knowledge elements independently and in a fluctuating way. Participants generally showed low representational competence. We recommend further research using the pieces perspective, including research on improving representational competence. We suggest that metabolism instructors teach metabolism as a concept, not a collection of example pathways, and explicitly instruct students about the meaning of visual representations associated with metabolism.