This study aims at exploring how interrogative processes may foster making sense of biological concepts that related to the phenomena protein synthesis such as positive transcription factors, enzyme, DNA, mRNA destroyer, as they are learned in a multiple representational environment that consists of biological simulation and mathematical representation. Five pairs of high school students which they 17 years old participated in this study, which was guided by the logic of inquiry approach and the variation theory. We analyzed the data by identifying the students’ questions through their engagements with the digital tool and the students’ transitions between mathematical representation and biological simulation. The results indicated that the digital tool supports the students in posing several kinds of questions, and the answers to these questions support the students in making sense of the biological knowledge embodied in the digital tool.