Recent calls asking science teachers to increase student authority by diversifying instruction appear stalled by a lack of empirical evidence supporting the actual implementation of any such shifts. To better support the practical integration of more student‐directed inquiry into the science classroom, we consider one teacher's day‐to‐day praxis within the context of a yearlong chemistry curriculum. Using cultural historical activity theory (CHAT) we analyze how the interplay of key classroom elements (i.e., the classroom community, subjects, division of labor, mediating artifacts, rules, objects, and outcomes) varies within and across three distinct participant structures, and thus shapes what students experience as science. We construct CHAT activity models of each of the participant structures in order to examine how the teacher's differentiated use of traditional classroom mechanisms (e.g., whole class discussions and critique) scaffolds students' developing ability to direct their own inquiries. Our study demonstrates how a teacher can link elements within and between a diverse set of participant structures in ways that systematically create real opportunities for student‐directed inquiry and collaboration while assuring students learn to act with disciplinary authority. © 2014 Wiley Periodicals, Inc. J Res Sci Teach 51: 606–634, 2014