National calls to improve science education include focusing on scientific practices coupled with learning disciplinary core ideas. Among the practices is constructing explanations. In the field of cellular and molecular biology, explanations typically include a mechanism and can be used to make predictions about phenomena. In this work, we developed an assessment item about transcription, a key process in the biology core concept of genetic information flow. We used a mechanistic framework to develop a rubric that identifies undergraduate explanations that leverage molecular or sub-molecular mechanisms, descriptions, or use unlinked ideas. We applied this rubric to categorize 346 undergraduate written explanations and compare five-item versions. We found that one version elicited sub-molecular mechanistic explanations from 20% of students, compared to between 2% and 13% from other versions. This version included the element of time, by indicating that a new RNA was formed as part of transcription. We also developed and applied a conceptual rubric to capture the context students used in their explanations and found a median of two context ideas in student explanations of transcription. Our work demonstrates that with careful item wording, undergraduates can explain molecular processes like transcription by leveraging sub-molecular mechanisms.