The function of proteins is governed by their three-dimensional structure. This structure is determined by the chemical characteristics and atomic interactions of amino acids. Students of biochemistry, with a particular focus on protein chemistry, benefit from looking at protein structures and understanding how proteins are built and fold. Due to…

Biochemistry is an important professional course to undergraduates majoring in rehabilitation therapy in medical colleges and universities. To deepen students' understanding of the taught content, enhance their application ability and cultivate their high-level thinking ability, we investigated the effect of integration of the nine-grid thinking…

This study examines secondary students' understanding of epigenetics, focusing on their scientific representations from a chemical perspective. The purpose was to identify common misconceptions and assess how technological interventions can enhance students' conceptual models of epigenetics. A mixed-methods approach was employed, incorporating…

Ionization of amino acids (AA) is very important concept in biochemistry. We integrate the mathematical concept of probability with biochemically relevant process of AA ionization. We visualize the ionization process with Mathematica software discussing intramolecular interactions between weakly acidic/basic functional groups and charge--pH…

Enzymes are nature's catalysts, mediating chemical processes in living systems. The study of enzyme function and mechanism includes defining the maximum catalytic rate and affinity for substrate/s (among other factors), referred to as enzyme kinetics. Enzyme kinetics is a staple of biochemistry curricula and other disciplines, from molecular and…

The central focus of my dissertation concerns the issue of representation. The issue of representation is important for science education research for two reasons: (1) the use of external representation in science teaching and learning, particularly in chemistry education, is ubiquitous as microscopic entities are not directly visible, and (2) the…

The central focus of my dissertation concerns the issue of representation. The issue of representation is important for science education research for two reasons: (1) the use of external representation in science teaching and learning, particularly in chemistry education, is ubiquitous as microscopic entities are not directly visible, and (2) the…

A critical skill that biochemistry students must develop is the interpretation of molecular images, ranging from macromolecular representations to the chemical structures of the building blocks that comprise them. Such analysis requires biomolecular visual literacy, which is not often explicitly taught, and can be challenging for instructors to…

Biochemistry is about structure and function, but it is also about data and this is where computers come in. From my time as a graduate student and post doc, whenever I encountered data I thought, "I can work this up by hand, but I think a computer could do a better job." Since that time, I have been working at the interface of…

Regulation is a key concept for understanding the dynamics of metabolism in bacteria. This report outlines a simple laboratory experiment aimed at studying a key form of regulation in bacterial metabolism, exemplifying how microbes switch the flux of carbon towards alternative metabolic fates as a function of nutrient availability and according to…

In neurons, mRNAs can be repressed postinitiation and assembled into granules enabling the transport and later, regulated reactivation of the paused mRNAs. It has been suggested that a large percentage of transcripts in neuronal processes are stored in these stalled polysomes. Given this, it is predicted that nascent peptides should be abundant in…

Understanding the relationship between protein structure and function can be challenging for students. Molecular visualization software aids students in this problem by allowing manipulation of structures from new and deeper perspectives. In this communication, an activity using iMolview Lite, structure visualization software for portable devices,…

Mental rotation (MR) is the ability to transform a mental representation of an object so as to accurately predict how the object would look from a different angle (Sci 171:701-703, 1971), and it is involved in a number of important cognitive and behavioral activities. In this review we discuss recent studies that have examined MR in infants and…

Structures of 10 proteins from the Protein Data Bank were 3D printed as part of an undergraduate biochemistry teaching laboratory. All structures were successfully printed in either a space filling surface representation or a cartoon representation that traces the Ca carbon atoms of each amino acid residue. All structures were printed using…

Biology and biochemistry students must learn to visualize and comprehend the complex three-dimensional (3D) structures of macromolecules such as proteins or DNA. However, most tools available for teaching biomolecular structures typically operate in two dimensions. Here, we present protocols and pedagogical approaches for using immersive augmented…