Physical and life science disciplines emphasize how basic structural units influence function, yet it is challenging for students to understand structure-function relationships, particularly at molecular scales. Undergraduates in our biology capstone course struggled to connect mutations in a gene encoding a key protein in a cell development regulation pathway to the function of that protein. We hypothesized that physical molecular models and interactive activities exploring the pathway would help students overcome this learning challenge. Four years of iterative assessment cycles, curricular revisions, and assessment rubrics based on these classroom strategies allowed us to pinpoint students' struggles to make specific connections between genetic structural mutations and protein function. Student scores on summative assessments and self-reports of learning improved over the 4 years. Furthermore, student comments both supported the summative data and helped us understand how these curricular materials are helpful. We present an evidence-based example in which STEM educators successfully incorporate a novel teaching material by integrating scaffolds that allow students to see how experts make sense of complex and dynamic systems.