The 11th Misconception?

The recent excellentessayby Robic (2010) awakened an old concern of mine regarding whether “sequences,” be they protein or nucleic acid, have escaped the limits of their useful abstraction and acquired the status of a nonexistent physical reality. The original observation that formed the basis for this notion lies with the widespread belief that protein folding involves a change of dimensionality. My sense is that the way that the central dogma is taught and the use of schematic diagrams to teach protein folding (e.g., Branden and Tooze, 1999, p. 3) combine to reinforce students’ beliefs that protein folding involves a transformation from the one-dimensional sequence space to the threedimensional structure space. This erroneous belief is accentuated by classroom discussions about the folding problem, which are often initiated with a question about how amino acid sequence determines protein structure. I believe that students then come to visualize and conceptualize protein folding as the process through which a one-dimensional protein sequence is transformed to a three-dimensional protein structure. When my students display this conception, I respond by asking questions such as “What is the dimensionality of what comes out of the ribosome? Does the dimensionality of an unfolded polypeptide chain differ from a folded protein? In terms of electrostatics, molecular dynamics, bond formation, and solvent interactions, which is more complex—an unfolded or a folded protein? Is protein folding a change