The structure and function relationship is a core concept identified by physiology faculty. Prior research has shown this may be a difficult concept for students to understand. Formative written assessments, such as short answer essay questions, allow students to demonstrate their thinking by encouraging students to use their diverse ideas to construct their responses. Varying the context of a question, such as the inclusion of a scenario, may be used to provide insight into the different stages of students' emerging biological expertise. Short answer questions based on the core concept structure[left right arrow]function were administered to students in a junior level General Physiology course and a sophomore level Human Anatomy and Physiology course at a large southeastern public university. Questions were based on the integumentary, muscular, digestive, and cardiovascular systems. Student responses were scored with a conceptual rubric developed for each question prompt as well as each organ system represented in the question prompts. Students were interviewed to determine if their responses to the short answer questions accurately reflected their thinking. Less than half of the student responses in this study demonstrated a conceptual understanding of the structure-function relationship. Students demonstrated different conceptual understanding of structure[left right arrow]function concepts depending on the question prompt with a scenario versus the question prompt without a scenario. The question prompts with scenarios versus non-scenarios provided a different context, which may have influenced student explanations. These results suggest that instructors should provide students with questions in varying contexts to allow students to demonstrate their heterogeneous ideas about a concept.