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…

Virtual labs have proven to be very versatile and valuable for providing realistic experience for students in STE (Science, Technology, and Engineering) fields. As we progress from delivery of instructional material from classroom to the Internet, there is need to develop laboratory exercises to supplement the theoretical lessons. A Web-based…

Coronavirus (COVID-19) disease is an emerging situation that brought challenges to all sectors, including academia and research. Undergraduate and postgraduate students in biochemistry and molecular biology have been affected significantly due to the recent laboratory closures. Experiments have been suspended for long causing extreme stress to the…

Eleven different laboratory experiments were designed and executed throughout a semester to provide a meaningful research experience for 23 undergraduate biochemistry majors at UTSA. The topic of the semester was based on the idea of exploring new aspects to enhance our understanding of how the human body uses cytochrome P450 enzymes to metabolize…

The recent COVID-19 pandemic has led to widespread lock-down strategies that force universities to perform all educational activities remotely. In this context, laboratory lessons pose a significant challenge. Here, I present an on-line tool that simulates the kinetics of chemical reactions. Enzymatic mechanisms can be easily modeled and followed…

Industrial drug discovery teams encompass scientists from multiple specialties and require participants to communicate effectively across disciplinary boundaries. In this paper, we present an undergraduate or graduate classroom simulation of this environment. Over a series of five workshops, student teams of mixed scientific backgrounds perform…

Augmented/virtual realities (ARs/VRs) promise to revolutionize STEM education. However, most easy-to-use tools are limited to static visualizations, which limits the approachable content, whereas more interactive and dynamic alternatives require costly hardware, preventing large-scale use and evaluation of pedagogical effects. Here, we introduce…

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…

A new program, ECEP2D, for simulating the one-dimensional (1D) and two-dimensional (2D) patterns of the gel electrophoresis of a protein after it has been digested by one or more enzymes is introduced. With ECEP2D, students can gain deeper insights into gel electrophoresis by performing hands-on simulations. For example, students can visualize how…

Virtual laboratory activities are flexible approaches to engage undergraduate students in scientific practices during the COVID-19 pandemic. By utilizing online simulations, students can conduct virtual experiments on important biochemical reactions that occur during photosynthesis. The learning module described here provides students with this…

X-ray crystallography provides structural information of molecules at the atomic level, being a central technique at the forefront of science and technology. However, crystallography teaching is not usually implemented in biochemistry lab classes due to its complex execution by nonexpert users. Here, we report the basic step-by-step workflow…

Facile visualization of biomolecules is an essential component of the undergraduate biochemistry curriculum. In the past, a number of tools have been used to display biomolecules. More recently, the advent of greater accessibility to virtual reality (VR) and augmented reality (AR) programs has created a new mechanism to visualize biomolecules.…

Drug design and development requires collaboration among scientists with diverse expertise. In early-stage drug design, establishment of promising drug candidates requires integration of structure-based molecular design with biopharmaceutics and ADMET (absorption, distribution, metabolism, excretion, and toxicity) principles. Much of this work is…

The commercialization of virtual reality (VR) hardware has enabled the use of VR as an educational tool. We describe how a VR platform was used to create molecular visualizations using standard PDB files with the purpose of delivering biochemistry and cellular biology lessons for undergraduates. Specifically, we describe two new software modules,…

The bacterial cell wall, a structural unit of peptidoglycan polymer comprised of glycan strands consisting of a repeating disaccharide motif [N-acetylglucosamine (NAG) and N-acetylmuramylpentapeptide (NAM pentapeptide)], encases bacteria and provides structural integrity and protection. Lysozymes are enzymes that break down the bacterial cell wall…