An understanding of protein folding relies on a solid foundation of a number of critical chemical concepts, such as molecular structure, intra-/intermolecular interactions, and relating structure to function. Recent reports show that students struggle on all levels to achieve these understandings and use them in meaningful ways. Further, several…

It is often difficult for students to develop an intuition about molecular processes, which occur in a realm far different from day-to-day life. For example, thermal fluctuations take on hurricane-like proportions at the molecular scale. Students need a way to visualize realistic depictions of molecular processes to appreciate them. To this end,…

The main topics of this dissertation are: 1) the development and discussion of a new molecular balance for measuring alkyl-alkyl interactions in a wide array of organic solvents, 2) the development of linear solvation energy relationships between solvent interaction parameters and solvent accessible surface area (SASA) in CH-arene interactions,…

Ubiquitin is essential for eukaryotic life and varies in only 3 amino acid positions between yeast and humans. However, recent deep sequencing studies indicate that ubiquitin is highly tolerant to single mutations. We hypothesized that this tolerance would be reduced by chemically induced physiologic perturbations. To test this hypothesis, a class…

Only a few pedagogical experiments have been published dealing specifically with the hydrophobic interaction though it plays a central role in biochemistry. A set of experiments is presented in which students partition a variety of colorful indicator dyes in biphasic water/organic solvent mixtures. Students monitor the partitioning visually and…

Measurement of protein denaturation and protein folding is a common laboratory technique used in undergraduate biochemistry laboratories. Differential scanning fluorimetry (DSF) provides a rapid, sensitive, and general method for measuring protein thermal stability in an undergraduate biochemistry laboratory. In this method, the thermal…

A fluorescence spectroscopy experiment is described where students integrated biochemistry and instrumental analysis, while characterizing the green fluorescent protein excitation and emission spectra in terms of its phenolic and phenolate chromophores. Students studied the combined effect of pH and temperature on the protein's fluorescence,…

Research on external representations in biochemistry has uncovered student difficulties in comprehending and interpreting external representations. This project focuses on students' understanding of three external representations of the potassium ion channel protein. This is part I of a two-part study, which focuses on the affordances and…

Research that has focused on external representations in biochemistry has uncovered student difficulties in comprehending and interpreting external representations. This study focuses on students' understanding of three external representations (ribbon diagram, wireframe, and hydrophobic/hydrophilic) of the potassium ion channel protein. Analysis…

A basic introduction to concept of a solvation shell around an apolar solute as well as its detection is presented. The hydrophobic solvation of toluene is found to be a good teaching example which connects macroscopic, phenomenological thermodynamic results with an atomistic point of view.

Fugacity and bioavailability can be used to facilitate students' understanding of potential environmental risks associated with toxic chemicals and, therefore, should be incorporated in environmental chemistry and science laboratories. Although the concept of concentration is easy to grasp, fugacity and bioavailability can be challenging…

Understanding diffusion of water into and out of the cell through osmosis is fundamental to the learning and teaching of biology. Although this process is thought of as occurring directly across the lipid bilayer, the majority of water transport is actually mediated by specialised transmembrane water-channels called aquaporins. This study…

Discusses the physical basis and current understanding of hydrophobic effects. The thermodynamic background of the effects, hydrophobic hydration, and hydrophobic interactions are described. Four existing controversies are outlined. (YP)

A microscale laboratory experiment to investigate the formation and utility of microemulsions is described. Microemulsions are technologically important fluids that can reduce the use of toxic organic solvents. In the experiment, students prepare a microemulsion and compare the solubility of sudan III dye in the microemulsion and in dodecane. They…

Background information, list of materials needed, and procedures used are provided for a demonstration involving the transformation of a hydrophobic liquid to a partially hydrophobic semisolid. Safety considerations are noted. (JN)