The pedagogical value of having biochemistry and organic chemistry students build and manipulate physical models of chemical species is well established in the literature. Nevertheless, for the most part, the use of molecular models is generally limited to several laboratory exercises or to demonstrations in the classroom setting. A simple methodology using Maruzen or Darling molecular models, transparent, ziplock plastic bags, and a carefully designed questioning strategy has been developed and used over many years. Student-constructed models were turned in on a daily or weekly basis in the lecture portion of an introductory biochemistry course and graded. The models ranged from simple amino acids to silk fibroin to one turn of a DNA double helix; construction of complex structures were small-group efforts. These activities were observed to actively engage students in understanding biochemical structures. The use of models in the ways described resulted in students providing more sophisticated answers on exams than in years when such model building exercises were not part of the instructional methods. (Contains 2 figures and 2 tables.)