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Anticipated learning outcomes (LOs) were defined and used for the backward design of a Course-based Undergraduate Research Experience (CURE). These LOs reflect the inquiry-based nature of CUREs and capture key knowledge and skills inherent to scientific practice and essential in research. The LOs were used to plan a formative and summative assessment strategy to support and evaluate student achievement. A research question was identified that aligned with the learning goals of the course, provided an opportunity for discovery and iteration, and introduced a variety of molecular, cellular, and biochemical techniques. The course is offered to students in the final year of their degree and delivered over a 12-week period with two 3-hr labs each week. These LOs, and the rigorous assessment strategy used to support them, could be adapted to different projects. Likewise, the laboratory exercises are presented as a series of modules highlighting opportunities for adaptation to a variety of schedules.

The three-dimensional structures of the inactive protein precursors (zymogens) of the serine, cysteine, aspartic, and metalloprotease classes of proteolytic enzymes are known. Comparisons of these structures with those of the mature, active proteases reveal that, in general, the preformed, active conformations of the residues involved in catalysis are rendered sterically inaccessible to substrates by the residues of the zymogens' N-terminal extensions or prosegments. The prosegments interact in nonsubstrate-like fashions with the residues of the active sites in most of the cases. The gastric aspartic proteases have a well-characterized zymogen conversion pathway. Structures of human progastricsin, the inactive intermediate 2, and active human pepsin are known and have been used to define the conversion pathway. The structure of the zymogen precursor of plasmepsin II, the malarial aspartic protease, shows a new twist on the mode of inactivation used by the gastric zymogens. The prosegment of proplasmepsin disrupts the active conformation of the two catalytic aspartic acid residues by inducing a major reorientation of the two domains of the mature protease. The picornaviral 2A and 3C proteases have a chymotrypsin-like tertiary structure but with a cysteine nucleophile. These enzymes cleave themselves from the viral polyprotein in cis (intramolecular cleavage) and carry out trans cleavages of other scissile peptides important for the virus life cycle. Although the structure of the precursor viral polyprotein is unknown, it probably resembles the organization of the proenzymes of the bacterial serine proteases, subtilisin, and [Alpha]-lytic protease. Cleavage of the prosegment is known to occur in cis for these precursor molecules.