Ensuring undergraduate students become proficient in relating protein structure to biological function has important implications. With current two-dimensional (2D) methods of teaching, students frequently develop misconceptions, including that proteins contain a lot of empty space, that bond angles for different amino acids can rotate equally, and that product inhibition is equivalent to allostery. To help students translate 2D images to 3D molecules and assign biochemical meaning to physical structures, we designed three 3D learning modules consisting of interactive activities with 3D printed models for amino acids, proteins, and allosteric regulation with coordinating pre- and post-assessments. Module implementation resulted in normalized learning gains on module-based assessments of 30% compared to 17% in a no-module course and normalized learning gains on a comprehensive assessment of 19% compared to 3% in a no-module course. This suggests that interacting with these modules helps students develop an improved ability to visualize and retain molecular structure and function.