In this article we analyze how the joint cognitive system of teacher and student actions mediated by cultural tools develops sense making of science concepts, and the use of concepts as tools for explaining phenomena and processes related to energy and energy transformation. We take a sociocultural approach to the analysis of how material and digital learning resources become tools for thinking and reasoning. We combined ethnographic descriptions with analysis of video records of classroom interactions in a high school and examined how a teacher and a group of students engaged in a computer-supported collaborative inquiry. Our results show that students through inquiry are enabled to make sense of concepts and their experiences with resources and also to use science concepts as explanatory tools. However, this is mediated by the teachers' practices for supporting students, such as providing relevant clues for them to continue their inquiry, eliciting their initial understanding of concepts thereby making them available for further development, pressing for explanations, and reformulating their explanations. The teacher is continuously alternating between withdrawing and making students inquire by themselves and supporting their inquiry. In and through such social interactions, materials and digital tools become tools for thinking. We argue that one of the practical implications of our study is that it is crucial that teachers explicitly draw students into their system of activity throughout the entire learning trajectory and that the teachers and students together make sense of science concepts for explaining energy transformation.