Biochemical Concepts Research Articles

Students’ perceptions on the difficulty of biochemistry concepts covered in Rwandan secondary school biology curriculum

This study explored the Rwandan secondary students’ opinions on learning biochemistry concepts covered in the Rwandan advanced level of secondary school biology curriculum, and the reasons behind the difficulty of the concepts. In this research, sequential exploratory mixed-method designs were adopted. The sample comprised 195 secondary school students, who were purposively selected from the schools in Rwamagana and Kayonza districts of Rwandan Eastern Province. Data were collected using self-administered questionnaires and focus group semi-structured interview guides. Data analysis was carried out using both quantitative and qualitative approaches. Results from this research showed that photosynthesis and respiration are the major units that are challenging to study with the respective percentages of 62.5 and 75.1. On the other hand, the concept of enzymes is the most difficult according to students’ views. The lack of adequate laboratory and learning resources and teachers’ teaching styles were reportedly the reasons behind the difficulty of these units. Therefore, the provision of continuous professional development training on advances in teaching and learning biochemistry to in-service teachers would be one of the strategies to enhance students’ understanding of these concepts.
 
 Keywords: Biochemistry, photosynthesis, enzymes, respiration, secondary school students.

Concept of Biochemistry of Food

Nutritional biochemistry examines the health benefits gained from eating healthy food. It specifically focusses on nutrient chemical components and how they function metabolically, physiologically, and biochemically. The biochemical study gives information about food metabolism and hormones and enzymes participating in this process and describes the process of food intake and how energy is obtained and the way the energy is spent. It is study of nutrition as a science. Nutritional biochemical therapy refers to specific nutritional procedures including assessment and interventions in the treatment of an illness, injury, or disease condition. Studying the biochemistry of food and its metabolism gives us knowledge about effectors of metabolism in positive direction as it is the source of energy, which is the foundation of life. Its negative effect as metabolite can give rise to diabetes mellitus, cardiovascular disease, and cancer.

Case study: Biochemistry without borders: a case study utilising infographics.

The present paper addresses a case study on the implementation of an online learning exercise utilising infographics in undergraduate Biochemistry and General Chemistry courses at the University of Roehampton (UoR) and Hostos Community College (HCC) of the City University of New York (CUNY). Students at UoR were asked to create infographics on topics related to the four major classes of biomolecules: carbohydrates, lipids, proteins and nucleic acids, and these infographics were shared with HCC students in an active learning exercise which incorporated peer evaluation and feedback. We highlight the various teaching and learning strategies, as well as the challenges related to the implementation of digital tools, in the educational process during the COVID-19 pandemic to maintain student engagement and active learning. Student feedback revealed positive learning gains on biochemistry concepts related to the four biomolecules. The exercise was viewed favourably by students, with learners indicating the acquisition of digital skills to effectively represent and visualise their understanding of biochemical concepts and explain these processes to peers.

Teaching the "acid-base" subject in biochemistry via virtual laboratory during the COVID-19 pandemic.

Virtual laboratories have started to be the leading alternative teaching tools during the Covid‐19 pandemic process. The “Acid–Base” subject is among those that form the foundations of biochemistry. Students can learn the “Acid–Base” subject in a secure environment, with remote access through the use of virtual laboratory simulations. Simulation was applied to fourth‐year undergraduate students in Turkey who want to obtain a bachelor's degree in science teaching during the present study. During the application process, the students conducted different experiments on the concepts of strong acid, strong base and pH, which are the basic concepts of biochemistry. In addition, student opinions regarding the application were also obtained. It was thus determined that the majority of the students were able to write hypotheses, test their accuracy and report the test findings correctly; a small number of students started to apply the simulations after examining them in accordance with scientific terminology. At the end of the application, the students also stated that they had fun during the application which also provided effective learning. It is recommended that classroom activity which is integrated with simulation be used in Chemistry, Biochemistry and Science Laboratory Applications courses.

Translating Biochemistry Concepts into Cartoons and Graphic Narratives: Potential and Pitfalls

Simple biochemical concepts can be hard to grasp by non-specialists, even when they are related to practical contexts in industry, day-to-day activities, or well-acknowledged pathological conditions. This is especially important in instances where accurate communication of biochemical aspects for different types of stakeholders may be crucial. Examples include interacting with policymakers to establish guidelines, with patients (and/or caregivers) to identify key concepts in promoting awareness and adherence to therapeutic regimens, or with teachers and students for novel approaches in critical thinking. Focusing on our own work in developing communication tools for different purposes, in this review we will focus on some examples of how biochemical concepts can be effectively translated into illustrations and graphical narratives. For this purpose, engagement with target audiences in developing the materials themselves is key. We also discuss how specific projects can be tailored for different purposes, as well as evidence that comic-book strategies are effective in conveying biochemical and biomedical knowledge.

ELEMENTAL COMPOSITION OF CHAGA MUSHROOM (INONOTUS OBLIQUUS)

Birch chaga Inonotus obliquus is used as a component of many medicines. This is due to the versatile therapeutic effect associated with the content of a large number of biologically active substances of inorganic, organometallic and organic nature, a high content of macro- and microelements both in a free state and in the form of chelate complexes. To establish the qualitative and quantitative elemental composition of birch chaga, highly sensitive physicochemical methods of analysis were used, such as atomic emission spectroscopy (AES), inductively coupled plasma mass spectrometry (ICP-MS), and neutron activation analysis (NAA). The scientific novelty of this study lies in the conduct of a complex physicochemical elemental layer-by-layer analysis of chaga, the analogs of which have not been found in the available literature. The analyzed samples of birch chaga layers contain the following elements: K, Na, Mg, Ca, Zn, Mn, Cu, Fe, Mo, Co, Cr, P, Br, Se, V, Al, Ba, Li, Ag, Au, Rb, Cs, As, Sb, B, Sr, Pb, Ni, Ti, Be, Ta, U, Th, Sc; the concentration of elements is highest in the outer layer of the fungus. It is noted that the content of both biogenic elements (K, Co, Mn) and potentially toxic (Ag, Br, Rb) is significantly higher than the corresponding clarkes in bios. Differences in the content of elements correlate with modern biochemical concepts of the composition of chaga, and in most cases also correlate with the values of clarkes in bios. The value of the detected toxicant elements does not exceed the MPC.

Environmental selection and epistasis in an empirical phenotype-environment-fitness landscape.

Fitness landscapes, mappings of genotype/phenotype to their effects on fitness, are invaluable concepts in evolutionary biochemistry. Although widely discussed, measurements of phenotype-fitness landscapes in proteins remain scarce. Here, we quantify all single mutational effects on fitness and phenotype (EC50) of VIM-2 β-lactamase across a 64-fold range of ampicillin concentrations. We then construct a phenotype-fitness landscape that takes variations in environmental selection pressure into account. We found that a simple, empirical landscape accurately models the ~39,000 mutational data points, suggesting that the evolution of VIM-2 can be predicted on the basis of the selection environment. Our landscape provides new quantitative knowledge on the evolution of the β-lactamases and proteins in general, particularly their evolutionary dynamics under subinhibitory antibiotic concentrations, as well as the mechanisms and environmental dependence of non-specific epistasis.

A novel approach to calculating the kinetically derived maximum dose

The kinetically derived maximal dose (KMD) provides a toxicologically relevant upper range for the determination of chemical safety. Here, we describe a new way of calculating the KMD that is based on sound Bayesian, theoretical, biochemical, and toxicokinetic principles, that avoids the problems of relying upon the area under the curve (AUC) approach that has often been used. Our new, mathematically rigorous approach is based on converting toxicokinetic data to the overall, or system-wide, Michaelis–Menten curve (which is the slope function for the toxicokinetic data) using Bayesian methods and using the “kneedle” algorithm to find the “knee” or “elbow”—the point at which there is diminishing returns in the velocity of the Michaelis–Menten curve (or acceleration of the toxicokinetic curve). Our work fundamentally reshapes the KMD methodology, placing it within the well-established Michaelis–Menten theoretical framework by defining the KMD as the point where the kinetic rate approximates the Michaelis–Menten asymptote at higher concentrations. By putting the KMD within the Michaelis–Menten framework, we leverage existing biochemical and pharmacological concepts such as “saturation” to establish the region where the KMD is likely to exist. The advantage of defining KMD as a region, rather than as an inflection point along the curve, is that a region reflects uncertainty and clarifies that there is no single point where the curve is expected to “break;” rather, there is a region where the curve begins to taper off as it approaches the asymptote (Vmax in the Michaelis–Menten equation).

The effectiveness of the metabolic map in promoting meaningful learning.

Many medical students and practicing physicians view biochemistry, especially its metabolic pathways, as a challenging topic given the depth of material. Medical biochemistry educators aim to help prepare future physicians to apply knowledge of metabolism to disease processes. Research confirms that study tools promote critical thinking and help to connect biochemistry concepts to health and disease processes. To explore whether the Pathways of Human Metabolism Map as a study tool helps to connect basic metabolic pathways to clinical applications. We provided the Pathways of Human Metabolism Map to our first-year osteopathic medical students and conducted a survey to assess their perceptions. Our survey questions aimed to explore the effectiveness of utilizing the metabolic map for connecting the basic metabolic pathways to clinical applications on their studies. Students were surveyed at the end of the course utilizing a Qualtrics survey encompassing Likert scale questions as well as open-ended responses. The results of our comprehensive survey questions revealed the unique perceptions of students. Analysis of our data implicates that study tools like the metabolic map inspire meaningful learning. Our data show that students who utilized the metabolic map in their studies reported that utilizing the map improved their understanding of medical biochemistry. Our research results suggest that providing study aids like the metabolic map encourages students to minimize rote memorization and promotes integration with clinical context. Our results provide a support for study strategies that implement meaningful learning in medical education.

Using Open-Source Bioinformatics and Visualization Tools to Explore the Structure and Function of SARS-CoV-2 Spike Protein

The relationship between protein structure and function is a foundational concept in undergraduate biochemistry. We find this theme is best presented with assignments that encourage exploration and analysis. Here, we share a series of four assignments that use open-source, online molecular visualization and bioinformatics tools to examine the interaction between the SARS-CoV-2 spike protein and the ACE2 receptor. The interaction between these two proteins initiates SARS-CoV-2 infection of human host cells and is the cause of COVID-19. In assignment I, students identify sequences with homology to the SARS-CoV-2 spike protein and use them to build a primary sequence alignment. Students make connections to a linked primary research article as an example of how scientists use molecular and phylogenetic analysis to explore the origins of a novel virus. Assignments II through IV teach students to use an online molecular visualization tool for analysis of secondary, tertiary, and quaternary structure. Emphasis is placed on identification of noncovalent interactions that stabilize the SARS-CoV-2 spike protein and mediate its interaction with ACE2. We assigned this project to upper-level undergraduate biochemistry students at a public university and liberal arts college. Students in our courses completed the project as individual homework assignments. However, we can easily envision implementation of this project during multiple in-class sessions or in a biochemistry laboratory using in-person or remote learning. We share this project as a resource for instructors who aim to teach protein structure and function using inquiry-based molecular visualization activities. <em>Primary image:</em>&nbsp;Exploration of SARS-CoV-2 spike protein: student generated data from assignments I - IV. Includes examples of figures submitted by students, including a sequence alignment and representations of 3D protein structure generated using UCSF Chimera.&nbsp;The primary image includes student generated data and a cartoon from Pixabay, an online repository of copyright free art.&nbsp;

Using student-designed cases to foster creative and critical thinking skills in biochemistry.

In this novel intervention, we have tried to incorporate case-based learning with creative and critical thinking. Creative thinking indulges students to generate and apply new concepts in specific situations, seeing current situations in a new light, identifying alternative theories, and exploring new links that help generate a positive outcome. This may involve combining various hypotheses to form something original, sifting and refining ideas to discover possibilities, constructing new theories, and acting on intuition. This is a quasi-experimental study on educational intervention. First Bachelor of Medicine and Bachelor of Surgery (MBBS) students (N = 80) in their First MBBS students were randomly divided into control (n = 40) and study (n = 40) groups after they had undergone case-based learning in their first semester. The study group was asked to prepare three cases each on type II diabetes mellitus (DM), Fe deficiency anemia, and obstructive jaundice by discussion. Each case was prepared with a) an introduction consisting of presenting complaints, b) body comprising laboratory findings, and c) five questions related to the case. The cases were reviewed by a facilitator and presented to the other groups for discussion. Pretest and posttest questionnaires were collected and analyzed. Based on the pretest scores, students were grouped as low, average, and high performers. Wilcoxon signed rank test was performed, which revealed significant improvement in the posttest scores of all students in the study group. By designing new case histories themselves, students were able to understand the biochemical concepts of common diseases and apply these concepts in causation of diseases. Thus, case-based learning in this setting helped to foster creative and critical thinking skills of first MBBS students.

Team idea mapping method: A brainstorming session for enhancing problem-solving skills in postgraduate medical biochemistry students as assessed by self-efficacy

Objectives: The present study was conducted to evaluate the effect of Team Idea Mapping (TIM) sessions on the problem solving skills of postgraduate (PG) students of Biochemistry, as deduced from retro-pre self-efficacy questionnaire. Materials and Methods: The study was conducted enrolling students pursuing PG-MD course in Medical Biochemistry in a premier medical college. First TIM session was preceded by sensitization of PG students and departmental faculty. In total, four TIM sessions were conducted. Retro-pre self efficacy questionnaire was administered 3 months after the last session. Feedback from the students was collected immediately after last session and satisfaction index was also calculated. Results: The satisfaction index was highest (100) for items stating that TIM sessions promoted interactivity and participatory behaviorand lowest (78) for item stating that TIM sessions promoted reflective behavior respectively. The students expressed enhanced self-efficacy in understanding Biochemistry concepts, clinical application of Biochemistry, problem solving skills in Biochemistry, interpreting laboratory reports, participation in group works and clarifying problems with peers and seniors. However, the sessions were not as effective in instilling technical skills like trouble shooting for analyzer breakdowns. Conclusion: TIM is an effective tool for instilling problem solving skills in medical PG students, additionally fortifying their attitude to work in groups.

Connecting research and teaching introductory cell and molecular biology using an Arabidopsis mutant screen.

A complex research project was translated into a Course-based Undergraduate Research Experience (CURE), which was implemented in sections of an introductory Cell and Molecular Biology laboratory course. The research laboratory generated an engineered plant line producing a growth-inhibiting, lipid-derived plant hormone and mutagenized this line. Students in the CURE cultured the mutagenized plant population and selected and characterized suppressor mutants. They learned to observe phenotypes related to the biosynthesis and perception of the plant hormone and explored the genetic and biochemical basis of these phenotypes. As the students studied the relevant genetic, molecular and biochemical concepts during this CURE, they were able to translate this knowledge into practice and develop scientific arguments. This CURE was a successful collaboration between the teaching lab and the research lab. It benefited both parties as the students had a real-life, deep learning experience in scientific methodology, while the research lab gathered data and materials for further studies.

Details of Laboratory Work for Medical Students

In the modern world of pandemics, a special place is occupied by the problems of education in the fi eld of medicine. In developed countries, medical education remains combined. Practical training of students in the laboratories of the uni-versity is very important. The article describes a biochemistry laboratory class protocol. This protocol is described in order to create an opportunity for students to apply by doing the theoretical concepts underlying biomolecules and vesicles proper-ties, together with the principles of centrifugation and colorimetric methodol-ogies. The aims, objectives, methodology of teaching/learning, and assessment for this laboratory class are indicated. The proposed protocol for a laboratory class described us creates the opportunity for undergraduate students to per-form experiments, to reason, and to discuss some related biochemical concepts, namely protein characterization and properties of specifi c staining reactions; en-zyme quantifi cation by enzymatic reaction; composition and biochemical prop-erties of exovesicles; amphiphilic biomolecules properties; and principles and applications of centrifugation methods. This work was supported by Portuguese Ministry of Science and Higher Education (MCES).

Misconceptions of biology education students in Biochemistry Course during the COVID-19 pandemic

Misconception is one of the main problems in biology education which has the potential to increase when course is packaged in a e-learning. This study aimed to map the level of the biochemistry concept accuracy of students who take online biochemistry lectures. This quantitative research involved Biology Education students, FKIP UMM as research subjects. Online lectures were conducted for ten meetings using ELMU UMM. At the 11st meeting, a concept accuracy test was carried out. The data were then analyzed using descriptive statistics. The result, 64% of students have a low level of concept accuracy, 14% moderate, and 0% good. Therefore, online learning packaging needs to be optimized so that the percentage accuracy of the biochemical concepts of students is maximized.

Merging Biochemical and Analytical Training: a Computational Approach to Chemical Communication

As techniques in biochemistry and neuroscience progress, so is the volume of data generated by advanced technologies. Therefore, there is a need for training young scientists in both fundamental biology and biochemical concepts, but also in the handling, processing, and analysis of large datasets, i.e., Big Data. Two years ago, in the Department of Biochemistry at Virginia Tech, we created a new course entitled “Biochemical Communication,” where senior undergraduate students learn about the biochemical and evolutionary principles guiding chemical communication between organisms. Core components of the course are: 1) Lectures relying on active learning strategies, 2) student-led weekly discussions of the primary literature, and 3) a semester-long project consisting of analyzing large data sets generated in the laboratory of the instructor. Over the past two years, the data sets provided were: electrophysiological recordings from neurons of mosquito antennal lobes (i.e., primary olfactory centers) and gas-chromatography mass-spectrometry data resulting from the collection of plant headspace volatiles. Over the course of the semester (15 weeks), students acquire a working knowledge of data manipulation and visualization techniques, descriptive and inferential statistics, multivariate analysis, and machine learning approaches. These methods are deployed with the programming language R. Students’ training, as well as the approach they elect to employ, are guided by their drive to answer a biological question of their choosing. The work is conducted in groups to promote peer-mentoring. At the end of the semester, each group submits a seven-page long report structured as a scientific publication. The feedback collected after completion of the course indicated that students are receptive and enthusiastic about such hybrid classes where an introduction to biological and biochemical concepts is merged with hands-on learning of programming and data analysis.

Transitioning in‐person Biochemistry and Molecular Biology Research‐based Educational Outreach Programs to Virtual Settings

Scripps Research Education Outreach and Community Engagement (EOCE)programs comprise initiatives for people of all ages including K-12 students and teachers, undergraduates, and the public. Our overarching goals are to promote careers in biomedical research, raise awareness about the importance of scientific research,train the next generation of scientists, and increase diversity in the biomedical research workforce. The Covid-19 pandemic immediately haltedour in-person eventsand presented a new set ofchallenges to reaching our goals. It became necessaryto create a strong online presence to keep connected with our audience and stakeholders. As a leading research institute, Scripps Research is keenly aware of the importance of technology, and we quickly leveraged the use of Zoom and our learning management system (LMS) to facilitate the implementation of online outreach programs. Here we describe three programs that were implemented online. 1) Junior Scientist Training Program (JSTP) is a series of one-week virtual science camps with hands-on science experiments and/or data analysis. What makes JSTP different from other science ‘box’ clubs is that students learn scientific concepts in bioinformatics, microbiology, and biochemistry, and design their own experiments based on the tools provided and their home environment. Results are not ‘pre-determined’ as with traditional laboratory class protocols. This is particularly important because one of the first epiphanies students have with real research is the notion that there is no ‘correct’ answer. 2) Fully Interactive Resources for Students and Teachers (FIRST) is a webinar series featuring scientists discussing their research and career path, advising on how to develop scientific creativity, and giving science demonstrations. This program has been fundamental in supporting thousands of undergraduate students who have been affected by the lack of research opportunities due to the pandemic! 3) SciMet Competition is a Spanish-English bilingual science competition where K-12 students nationwide are invited to demonstrate their scientific curiosity, creativity, and critical thinking skills via drawings (K-5), videos (6-8), and essays (9-12). Projects exceeded our expectations and the bilingual component allowed us to reach into Hispanics and LatinX communities. Gains of moving programs online included increased engagement; increased reach across the USA and the world; higher efficacy in collecting pre- and post-data using integrated surveys and digital applications; successful implementation of inclusive and equitable virtual educational environments; and a significant rise in the number of volunteers due to convenient and accessible online tools for the scientist community. Despite the apprehension of virtual science programs, the benefits prove that some of these elements should be kept in future programming whether in person or not, as we believe that this demonstrates our commitment to our community partners and scientific accessibility for all.

A Narrative Curriculum Using the Primary Literature to Teach Biochemistry

The interdisciplinary field of biochemistry and molecular biology (BMB) is expansive, and the pace of scientific discovery is dizzying. This makes teaching the entirety of BMB - even in three semesters - nearly impossible. Instead, BMB education has moved to competencies over content coverage, as enumerated in ASBMB's Foundational Concepts and Skills and in AAAS's Vision and Change. Focusing on a checklist of competencies can still lead students to learning a collection of disparate facts rather than integrating this knowledge across domains. The second-year Biochemistry course at Juniata College uses acetylcholine neurotransmission as a central narrative from which content is constructed. Beginning with texts from the 1700s, students work in groups to iteratively interrogate primary scientific literature by (i) developing specific questions, (ii) using resources to find answers to those questions, (iii) communicating those answers with the peers in their team, and (iv) using the answers to interpret data and figures. In the process, students teach themselves core biochemical concepts interwoven with mathematics, physiology, chemistry, and physics and set in cultural and historical context. Here, I present evidence that this social constructivist approach leads to gains in inclusivity and self-efficacy with respect to teamwork, curiosity, and scientific literacy. Moreover, the approach has led to several collaborative projects, including translations of 19th-century texts from German and French to English. The design of this course stretches BMB education beyond the limits of traditional content acquisition and into new and exciting ways of engaging students and encouraging them to take control of their own education.

Less (Learning How to Learn) &amp;[prop] More (Learning): Teaching structure‐function with 3D‐printed models in large, undergraduate biochemistry classes

For students to master core biochemical concepts, they must integrate background knowledge from previous courses in biology, chemistry, physics, and math. Students are often inadequately prepared to make the logical jump from chemical structure representations to biochemical macromolecules, leading to multiple misconceptions about structure-function relationships (Villafañe et al., 2011). These misconceptions often lead students to inaccurately describe basic structural details of macromolecules even after their biochemistry education (Harle and Towns, 2013). Biochemistry educators can bridge this gap, and multiple routes have been demonstrated. However, most of these take significant course development. Thus, there is a need for simple, developed structure-function instructional modules scaffolded for students and instructors. Our team of biochemistry educators, 3D-printing experts, and professional assessment designers collectively developed six interactive learning modules teaching structure-function relationships though cheap, 3D-printed macromolecular models. There first three modules cover protein structure, and begin with students connecting amino acids to physically demonstrate phi and psi angles, through secondary, tertiary and quaternary protein structures, and end with the dynamics of product inhibition. The second three modules cover nucleic acids, and ask students to investigate chemical and structural differences between major and minor grooves, transcription-factor/DNA interactions and supercoiling dynamics. Pre- post-module assessments of intervention or control classes show students working with the models made dramatic and significant learning gains over control students. Pre- post-course assessments show the knowledge is retained. We provide all the materials necessary for interested instructors to modify the modules to work in their courses. We also provide an all-virtual module that can be deployed during the pandemic. Harle M, Towns MH (2013) Students' understanding of primary and secondary protein structure: Drawing secondary protein structure reveals student understanding better than simple recognition of structures. Biochemistry and Molecular Biology Education 41: 369-376 Villafañe SM, Bailey CP, Loertscher J, Minderhout V, Lewis JE (2011) Development and analysis of an instrument to assess student understanding of foundational concepts before biochemistry coursework*. Biochemistry and Molecular Biology Education 39: 102-109

Molecular dynamics simulations and analysis for bioinformatics undergraduate students.

A computational biochemistry laboratory, fitted for bioinformatics students, is presented. The molecular dynamics package GROMACS is used to prepare and simulate a solvated protein. Students analyze the trajectory with different available tools (GROMACS and VMD) to probe the structural stability of the protein during the simulation. Students are also required to make use of Python libraries and write their own code to probe non-covalent interactions between the amino acid side chains. Based on these results, students characterize the system in a qualitatively approach but also assess the importance of each specific interaction through time. This work mobilizes biochemical concepts and programming skills, fostering critical thinking and group work and developing presenting skills.