Though student understanding of the nature of matter has been studied extensively, little is known about student knowledge of the biological molecules. This study examined understanding of proteins, carbohydrates, and lipids in 25 undergraduate students in order to document logical structures within student alternative concepts. Student knowledge of the particulate nature of matter (PNM) was collected in a pre-survey. Their knowledge of the biological molecules was collected via pre- and post-surveys, embedded questions, and interviews. No relationship was found between initial PNM knowledge and knowledge of molecules at the start of the course. By the end, however, strong correlations were found between initial PNM knowledge and knowledge of molecules. Students displayed alternative ways of categorizing biomolecules, using overlapping functional categories based on perceived nutritional roles. Their underlying assumptions about molecules fell into six categories: as goes macro, so goes micro; source = substance; molecule/energy equivalence; like acts upon like; functional equivalence; functional limitation. Student alternative conceptions displayed logical structure; their conceptions "worked" in their everyday lives. However, alternative categorizations of biomolecules used by low-PNM students interfered with their ability to understand biological processes that involved these molecules: enzyme activity, photosynthesis, and DNA synthesis. Educational implications of these findings are discussed.