Structure and Function is one of five core concepts for biological literacy identified in Vision and Change for Undergraduate Biological Education. Students must understand the relationship between three-dimensional structures and their functions in order to predict enzyme binding. The Automated Analysis of Constructed Response (AACR) research group develops computer-automated tools that analyze students’ writing by creating scoring models to predict human scoring using a combination of computer trained scoring and statistical analyses. We developed three versions of a constructed response (CR) question about enzyme binding to determine which, if any, most effectively elicit student’s conceptions about the role of structure and function in enzyme binding in terms of three dimensional shape and energetics. The three versions were administered randomly as post-instruction homework in an upper level Biochemistry course at a large Midwestern research University. Version 1 asked students to describe how an enzyme binds in order to reduce the possibility of incorrect interactions (n=48). Version 2 asked the students to explain the mechanism that allows binding and reduces the possibility of incorrect interactions (n=48). Version 3 also asked the students for the mechanism, however asked them to describe how it allows an enzyme to bind to the correct molecule (n=51). We found that there were no qualitative differences in responses between the three versions. The content of the responses from the three version was similar as many students explained the structure of enzymes in terms of lock-and-key or induced fit binding, rather than interactions between functional groups. This might be attributed to many textbooks focusing more in depth on structure rather than energetic function. These preliminary results suggest that the three versions of the question are isomorphic and may be used for pre- and post-instruction assessment of students’ understanding of enzyme binding.