Big ideas in science education are meant to be interpretive frameworks that empower student learning. Unfortunately, outside of the broad conception of scientific evaluation, there are few theoretical explanations of how this might happen. Therefore, we contribute one such explanation, an instructional concept called integrative analysis wherein students use a big idea to interconnect isolated scenarios and enrich their meanings. We illustrate the characteristics and value of integrative analysis within an empirical study of student learning in 9th-grade biology. The study focused on using energy transfer as a big idea for teaching cellular respiration. Fifty-nine students were randomly assigned to one of two instructional conditions. In the "analysis" condition, students processed a set of three manipulatives representing cellular respiration molecules; then, they abstracted the deep energy transfer structure of these manipulatives as a big idea. In the "recognition" condition, students processed the same molecule-manipulatives, but without energy interpretations. Instead, they constructed additional manipulatives using novel materials. Then, students in both conditions received an identical lesson where they used their knowledge of the manipulatives to learn about one cellular respiration process, glycolysis. Specifically, students processed a sequence of three texts describing glycolysis, annotating the texts with either their deep energy transfer structure (analysis condition) or their contextualized knowledge of the manipulatives (recognition condition). A posttest showed that in the analysis condition, this process was significantly integrative as evidenced by analysis students' advantage over recognition students in connecting glycolysis to novel phenomena and generating causal explanations about glycolysis.