Professor Mieczyslaw Chorazy and His Works.

This essay is in memoriam of Professor Mieczyslaw Chorazy (1925 - 2021). Eminent Man, outstanding scientist, soldier of the Warsaw Uprising, moral authority for generations of fellow researchers and an exceptionally warm person. His character and life works are recalled here against the background of the times he lived in.

Memories of Ron Hancock.

This essay is in memoriam of Ronald Hancock (1933 - 2022).

Ron Hancock - a passionate scientist and a Great Man.

This essay is in memoriam of Ronald Hancock (1933 - 2022).

Cracking AlphaFold2: Leveraging the power of artificial intelligence in undergraduate biochemistry curriculums.

AlphaFold2 is an Artificial Intelligence-based program developed to predict the 3D structure of proteins given only their amino acid sequence at atomic resolution. Due to the accuracy and efficiency at which AlphaFold2 can generate 3D structure predictions and its widespread adoption into various aspects of biochemical research, the technique of protein structure prediction should be considered for incorporation into the undergraduate biochemistry curriculum. A module for introducing AlphaFold2 into a senior-level biochemistry laboratory classroom was developed. The module's focus was to have students predict the structures of proteins from the MPOX 22 global outbreak virus isolate genome, which had no structures elucidated at that time. The goal of this study was to both determine the impact the module had on students and to develop a framework for introducing AlphaFold2 into the undergraduate curriculum so that instructors for biochemistry courses, regardless of their background in bioinformatics, could adapt the module into their classrooms.

Self-generating autocatalytic networks: structural results, algorithms and their relevance to early biochemistry.

The concept of an autocatalytic network of reactions that can form and persist, starting from just an available food source, has been formalized by the notion of a reflexively autocatalytic and food-generated (RAF) set. The theory and algorithmic results concerning RAFs have been applied to a range of settings, from metabolic questions arising at the origin of life, to ecological networks, and cognitive models in cultural evolution. In this article, we present new structural and algorithmic results concerning RAF sets, by studying more complex modes of catalysis that allow certain reactions to require multiple catalysts (or to not require catalysis at all), and discuss the differing ways catalysis has been viewed in the literature. We also focus on the structure and analysis of minimal RAFs and derive structural results and polynomial-time algorithms. We then apply these new methods to a large metabolic network to gain insights into possible biochemical scenarios near the origin of life.

Why Should Pharmacy Students Take Biochemistry?

The role of biochemistry in the pharmacy curriculum has recently been questioned based on its relevance to the career of a working pharmacist. This commentary explores the historical background of pharmacy education and the central role of chemistry since the 19th century. Reasons for the importance of biochemistry and other sciences are introduced to demonstrate their role in the practice of pharmacy.

Development and assessment of a virtual escape-room game for teaching industrial bioprocesses.

This article presents a study on the implementation of a virtual escape-room game as a novel teaching methodology in biochemistry education. The game aimed to engage students in producing monoclonal antibodies against SARS-CoV-2 while reinforcing theoretical concepts and fostering teamwork. Three versions of the game were tested, incorporating modifications to address student feedback on and improve the overall experience. The study employed a satisfaction survey to gather insights from students regarding their perception of the game. Results showed that the implementation of answer flexibility using RegEx had a significant positive impact on student satisfaction and motivation. The introduction of RegEx allowed for a more realistic and immersive gaming experience, as students could provide varied answers while still being evaluated correctly. Overall, the findings highlight the effectiveness of the game's design, the suitability of the Google Forms platform for distance learning, and the importance of incorporating answer flexibility through RegEx. These results provide valuable guidance for educators seeking to enhance student engagement and satisfaction through the use of escape-room games in biochemistry education.

Computational approaches to investigate fluoride binding, selectivity and transport across the membrane.

The use of molecular dynamics (MD) simulations to study biomolecular systems has proven reliable in elucidating atomic-level details of structure and function. In this chapter, MD simulations were used to uncover new insights into two phylogenetically unrelated bacterial fluoride (F-) exporters: the CLCF F-/H+ antiporter and the Fluc F- channel. The CLCF antiporter, a member of the broader CLC family, has previously revealed unique stoichiometry, anion-coordinating residues, and the absence of an internal glutamate crucial for proton import in the CLCs. Through MD simulations enhanced with umbrella sampling, we provide insights into the energetics and mechanism of the CLCF transport process, including its selectivity for F- over HF. In contrast, the Fluc F- channel presents a novel architecture as a dual topology dimer, featuring two pores for F- export and a central non-transported sodium ion. Using computational electrophysiology, we simulate the electrochemical gradient necessary for F- export in Fluc and reveal details about the coordination and hydration of both F- and the central sodium ion. The procedures described here delineate the specifics of these advanced techniques and can also be adapted to investigate other membrane protein systems.

Comparative evaluation of open book and conventional assessment methods in medical undergraduate students.

Medical science is a dynamic field of knowledge that is constantly broadening with upcoming clinical research and analysis. Traditional medical education has been focused on textbook-based recall assessments-closed book assessment (CBA). However, the availability of newer technologies has made the accessibility to encyclopedic knowledge expeditious, which demands for a new approach for medical education. As medical professionals, the purpose of learning should be higher cognitive skills such as interpretation and synthesis. So, analyzing students' ability to comprehend the concepts and learning to apply it in a realistic context than merely recalling the facts has come into attention. In this study, we aimed to evaluate and compare the performance of 250 first-year MBBS students at Maulana Azad Medical College, New Delhi, India, between closed book and open book method for biochemistry. Students were divided into two groups, Group A and Group B, based on their average monthly internal assessment marks. CBA was followed by open book assessment (OBA) 1 week apart with similar questionnaire pattern and allotted time. A significant difference in average marks obtained by the two groups was observed in CBA. Group A scored better in CBA, but performance was comparable with Group B in OBA. OBA and CBA can contribute to an assessment program in part because of their complementary pros and cons, and OBA should not be thought of as an alternative to CBA, but their value may be in expanding beyond what is measured by CBA.

Exploring Undergraduate Biochemistry Students' Gesture Production Through an Embodied Framework.

Interpreting three-dimensional models of biological macromolecules is a key skill in biochemistry, closely tied to students' visuospatial abilities. As students interact with these models and explain biochemical concepts, they often use gesture to complement verbal descriptions. Here, we utilize an embodied cognition-based approach to characterize undergraduate students' gesture production as they described and interpreted an augmented reality (AR) model of potassium channel structure and function. Our analysis uncovered two emergent patterns of gesture production employed by students, as well as common sets of gestures linked across categories of biochemistry content. Additionally, we present three cases that highlight changes in gesture production following interaction with a 3D AR visualization. Together, these observations highlight the importance of attending to gesture in learner-centered pedagogies in undergraduate biochemistry education.

Nursing students' experiences with test-enhanced learning in teams: A cross-sectional study.

BACKGROUND: Many nursing students struggle with the disciplines of biosciences, particularly Anatomy, physiology, and biochemistry, which are introduced in the first year. Nursing students' motivation, prior knowledge, and academic performance matter, but teaching methods may also influence students' learning process. Retrieving knowledge through testing has previously proven to enhance learning to a greater extent than time spent on other classroom activities. OBJECTIVE: The aim of this study was to explore nursing students' experiences with test-enhanced learning as a way of enhancing learning in Anatomy, physiology, and biochemistry. DESIGN: The lectures in each topic were followed by testing five days later. The tests were typically multiple-choice tests with short reply-times. The effect was measured in terms of students' self-reported level of satisfaction with test-enhanced learning, and their performance on the final exam in Anatomy, physiology, and biochemistry. The tests were performed in teams to avoid stressful situations that could negatively affect the students' learning process. RESULTS: A key achievement from introducing test-enhanced learning in the Anatomy, physiology, and biochemistry course was a perceived higher learning outcome and increased engagement and motivation among the students, resulting in resulting in more students achieving the highest grades (A and B). However, the students' academic results from upper secondary school also seemed to matter for their achievements on the final exam. CONCLUSION: These results indicated that many students benefited from test-enhanced learning, suggesting that test-enhanced learning can be an important teaching strategy in nursing education, particularly for biosciences.

A simple method to resolve rate constants when the binding mechanism obeys induced fit or conformational selection.

Many interactions involving a ligand and its molecular target are studied by rapid kinetics using a stopped-flow apparatus. Information obtained from these studies is often limited to a single, saturable relaxation that is insufficient to resolve all independent rate constants even for a two-step mechanism of binding obeying induced fit (IF) or conformational selection (CS). We introduce a simple method of general applicability where this limitation is overcome. The method accurately reproduces the rate constants for ligand binding to the serine protease thrombin determined independently from the analysis of multiple relaxations. Application to the inactive zymogen precursor of thrombin, prethrombin-2, resolves all rate constants for a binding mechanism of IF or CS from a single, saturable relaxation. Comparison with thrombin shows that the prethrombin-2 to thrombin conversion enhances ligand binding to the active site not by improving accessibility through the value of kon but by reducing the rate of dissociation koff. The conclusion holds regardless of whether binding is interpreted in terms of IF or CS and has general relevance for the mechanism of zymogen activation of serine proteases. The method also provides a simple test of the validity of IF and CS and indicates when more complex mechanisms of binding should be considered.

Use of interactive mathematical simulations in Fundamentals of Biochemistry, a LibreText online educational resource, to promote understanding of dynamic reactions.

Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to understand. Their interconnections lead to emergent properties such as memory, consciousness, and recognition of self and non-self. To understand how these interconnected reactions lead to cellular life characterized by activation, inhibition, regulation, homeostasis, and adaptation, computational analyses and simulations are essential, a fact recognized by the biological communities. At the same time, students struggle to understand and apply binding and kinetic analyses for the simplest reactions such as the irreversible first-order conversion of a single reactant to a product. This likely results from cognitive difficulties in combining structural, chemical, mathematical, and textual descriptions of binding and catalytic reactions. To help students better understand dynamic reactions and their analyses, we have introduced two kinds of interactive graphs and simulations into the online educational resource, Fundamentals of Biochemistry, a LibreText biochemistry book. One is available for simple binding and kinetic reactions. The other displays progress curves (concentrations vs. time) for simple reactions and complex metabolic and signal transduction pathways. Users can move sliders to change dissociation and kinetic constants as well as initial concentrations and see instantaneous changes in the graphs. They can also export data into a spreadsheet for further processing, such as producing derivative Lineweaver-Burk and traditional Michaelis-Menten graphs of initial velocity (v0) versus substrate concentration.

The quantum mechanics of skincare: A context for the biochemistry curriculum.

Designing a relevant and engaging curriculum for biochemistry undergraduates can be challenging for topics which are at the periphery of the subject. We have used the framework of context-based learning as a means of assessing understanding of quantum theory in a group of students in their junior year. Our context, the role of retinol in skincare, provides a basis for the simple application of quantum mechanical principles to a biological context in an adaptation of the polyene in a box concept. As part of the learner journey, they gain experience of practical computational chemistry, which provided an in silico alternative to traditional laboratory work during the SARS-CoV-19 pandemic. Student feedback was overwhelmingly positive, and this approach is now firmly embedded in the undergraduate curriculum.

When Paul Berg meets Donald Crothers: an achiral connection through protein biosynthesis.

Outliers in scientific observations are often ignored and mostly remain unreported. However, presenting them is always beneficial since they could reflect the actual anomalies that might open new avenues. Here, we describe two examples of the above that came out of the laboratories of two of the pioneers of nucleic acid research in the area of protein biosynthesis, Paul Berg and Donald Crothers. Their work on the identification of D-aminoacyl-tRNA deacylase (DTD) and 'Discriminator hypothesis', respectively, were hugely ahead of their time and were partly against the general paradigm at that time. In both of the above works, the smallest and the only achiral amino acid turned out to be an outlier as DTD can act weakly on glycine charged tRNAs with a unique discriminator base of 'Uracil'. This peculiar nature of glycine remained an enigma for nearly half a century. With a load of available information on the subject by the turn of the century, our work on 'chiral proofreading' mechanisms during protein biosynthesis serendipitously led us to revisit these findings. Here, we describe how we uncovered an unexpected connection between them that has implications for evolution of different eukaryotic life forms.

Volodymyr Oleksiyovych SHLYAKHOVENKO.

With deep sadness, we announce that on December 10, 2023, at the age of 86 passed away an outstanding Ukrainian scientist in the field of oncology, analytical enzymology, and pharmacology, a Laureate of the State Prize of Ukraine for Science and Technology, a member of the Federation of European Biochemical Societies, a member of the State Expert Center of the Ministry of Health of Ukraine, Doctor of Medical Sciences, Professor Volodymyr Oleksiyovych SHLYAKHOVENKO.