This study reports on the theoretical- and empirical-based design and evaluation of cell membrane biology learning activities within the Model of Educational Reconstruction and experiential realism. First, we designed analogy-based learning activities by considering students’ and scientists’ conceptions as described in the literature. Secondly, we carried out two video-taped teaching experiments to study students’ learning processes when interacting with the learning activities. Interpreting students’ conceptual development as thinking pathways enabled us to identify and understand the roots of their learning difficulties. Due to inherent ontological and epistemological presumptions, the students had difficulties in understanding that cell membrane structure determines their two-fold function: to separate and to connect environments in order to maintain living processes. The multiple analogies we employed helped foster conceptual development because they highlighted aspects of the concrete everyday experiences the students already had, but had not thought about. As a result of the learning activities, the students revised their conceptions regarding the terms barrier, gatekeeper and environment and connected these to a more coherent conceptual structure of cell membrane biology. Methods and outcomes of the study may contribute to a better understanding of how this important concept can be brought to science classrooms.