This paper reports on our use of a fine-grained learning progression to assess secondary students' reasoning through carbon-transforming processes (photosynthesis, respiration, biosynthesis). Based on previous studies, we developed a learning progression with four progress variables: explaining mass changes, explaining energy transformations, explaining subsystems, and explaining large-scale systems. For this study, we developed a 2-week teaching module integrating these progress variables. Students were assessed before and after instruction, with the learning progression framework driving data analysis. Our work revealed significant overall learning gains for all students, with the mean post-test person proficiency estimates higher by 0.6 logits than the pre-test proficiency estimates. Further, instructional effects were statistically similar across all grades included in the study (7th-12th) with students in the lowest third of initial proficiency evidencing the largest learning gains. Students showed significant gains in explaining the processes of photosynthesis and respiration and in explaining transformations of mass and energy, areas where prior research has shown that student misconceptions are prevalent. Student gains on items about large-scale systems were higher than with other variables (although absolute proficiency was still lower). Gains across each of the biological processes tested were similar, despite the different levels of emphasis each had in the teaching unit. Together, these results indicate that students can benefit from instruction addressing these processes more explicitly. This requires pedagogical design quite different from that usually practiced with students at this level.