Biological systems and living processes involve a complex interplay of biochemicals and macromolecular structures that can be challenging for undergraduate students to comprehend and, thus, misconceptions abound. Protein synthesis, or translation, is an example of a biological process for which students often hold many misconceptions. This article…

Reading the primary literature in a journal club format is an excellent practice where undergraduate students can develop their abilities in experimental data analysis and critical thinking, learn about new ideas and methods, and gain a foothold in scientific discourse. However, students are not familiar with the format, writing style, and depth…

Teaching by night and reflecting on a subject by day is the way that Salman Khan sees education evolving in the age of online lectures. Khan believes he is onto something in what he styles the "flipped classroom." In Khan's view, there is no need for students to be divided into grades by age. Instead, they should learn at their own pace, moving on…

This article describes a 13-week laboratory course called Human Toxicology taught at the University of Otago, New Zealand. This course used a guided inquiry based laboratory coupled with formative assessment and collaborative learning to develop in undergraduate students the skills of problem solving/critical thinking, data interpretation and…

Dynamic light scattering (DLS) analyses are routinely used in biology laboratories to detect aggregates in macromolecular solutions, to determine the size of proteins, nucleic acids, and complexes or to monitor the binding of ligands. This article is written for graduate and undergraduate students with access to DLS and for faculty members who…

3D visualization assists in identifying diverse mechanisms of protein-DNA recognition that can be observed for transcription factors and other DNA binding proteins. We used Proteopedia to illustrate transcription factor-DNA readout modes with a focus on DNA shape, which can be a function of either nucleotide sequence (Hox proteins) or base pairing…

Terms to be familiar with before you start to solve the test: transcription, pre-mRNA, RNA processing, RNA transport, RNA polymerase II, direct and indirect immunofluorescence staining, cell fractionation by centrifugation, oligo(dT)-cellulose chromatography, washing and elution of the column, ribonuclease, SDS-polyacrylamide gel electrophoresis,…

In proteomics, complex mixtures of proteins are separated (usually by chromatography or electrophoresis) and identified by mass spectrometry. We have created 2DE Tandem MS, a computer program designed for use in the biochemistry, proteomics, or bioinformatics classroom. It contains two simulations--2D electrophoresis and tandem mass spectrometry.…

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…

Although the biochemistry education community is far from avoiding conversations about improving teaching and learning, reexamining individual and community teaching practices through the lens of the scholarship of teaching and learning (SoTL) is critical for continued growth and improvement. The contemporary vision of SoTL, which has been…

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…

An undergraduate biochemistry laboratory experiment is described that will teach students the practical and theoretical considerations for measuring the equilibrium dissociation constant (K[subscript D]) for a protein/DNA interaction using electrophoretic mobility shift assays (EMSAs). An EMSA monitors the migration of DNA through a native gel;…

The ultimate goal of "student-centered" education is to empower students to learn beyond educational programs. This means nurturing students' autonomy and fostering the development of their own motivation and mechanisms to become self-directed learners. This idea has been embodied in the "lifelong learning" mantra that pervades contemporary views…

Biological systems, from the molecular to the ecological, involve dynamic interaction networks. To examine student thinking about networks we used graphical responses, since they are easier to evaluate for implied, but unarticulated assumptions. Senior college level molecular biology students were presented with simple molecular level scenarios;…

Exopolysaccharide (EPS) production by the rhizobacterium "Sinorhizobium meliloti" is essential for root nodule formation on its legume host (alfalfa), and for establishment of a nitrogen-fixing symbiosis between the two partners. Production of EPS II (galactoglucan) by certain "S. meliloti" strains results in a mucoid colony phenotype. Other…