A standard part of biology curricula is a project-based assessment of cell structure and function. However, these are often individual assignments that promote little problem-solving or group learning and avoid the subject of organelle chemical interactions. I evaluate a model-based cell project designed to foster group and individual guided inquiry, and review how the project stimulates problem-solving at a cellular system level. Students begin with four organism cell types, label organelles, describe their structures, and affix chemicals produced or needed for each organelle's function. Students simulate cell signaling, cell recognition, and transport of molecules through membranes. After describing the project, I present measures of student participation and a rubric, compare individual versus group work, and highlight future modifications, including alignment with the Next Generation Science Standard of “Structure, Function, and Information Processing.”