Biochemistry Students Research Articles

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;

Perceptions of self-medication of the population, during the covid-19 pandemic in Peru

Background: Describe characteristics of self-medication of the population, in the context of the COVID 19 pandemic. Material and Methods: We carried out a cross-sectional survey with students in a major public Peruvian university. We measured perception of self-medication of the population, as well as characteristics, consequences, and associated factors. Results: A total of 274 students of Pharmacy and biochemistry filled in the questionnaire, 80.3% of which reported to know someone that self-medicated during the COVID-19 pandemic. 98.9 % of surveyed participants considered that the current pandemic increased self-medication practices in the population and that it occurred more frequently when people have symptoms associated with COVID-19 (65.4%). The medicines most frequently used were ivermectin (79.2%), azithromycin (71.2%) and hydroxychloroquine (38.7%). Conclusion: According to the surveyed participants, self-medication has increased in the general population during the COVID-19 pandemic. Strategies to prevent these practices are needed, as they could delay adequate medical care.

Online team based learning in teaching Biochemistry for first year MBBS students during COVID-19 pandemic.

The emergence of Corona Virus Disease-2019 (COVID-19) pandemic had unprecedented effects on medical education worldwide. Sustaining student engagement in virtual learning is an arduous task. Team based learning (TBL) is a learner-centered approach that can facilitate better student engagement. Adapting TBL to online platform may address the challenges faced in virtual learning. This study was conducted to implement and evaluate online TBL among first year MBBS students in Biochemistry. After obtaining informed consent, three online TBL sessions were planned. The Individual Readiness Assessment Test, Group Readiness Assessment Test, and team application were assigned in Google classroom. The students used online platforms for their team interactions. After submitting their assignments, they joined online discussion with facilitator. Peer evaluation was done via Google forms. At the end of all the sessions, the students' perceptions on the process were collected using a structured anonymous feedback with open comments. Analysis of their feedback showed that the students found the process useful and it helped in fostering their team skills. Five major themes emerged on content analysis of the open comments; 'Enriched team skills', 'Gain in knowledge', 'Impact on attitude', 'Interaction during pandemic', and 'Emotional responses'. Students perceived that the online TBL is effective in improving their engagement, learning, and team skills.

An integrated laboratory experiment for the determination of main components in different food samples.

An integrated laboratory experiment was designed for introducing biochemistry students to basic static biochemistry to deepen their understanding on the properties and analysis of biomolecules such as total carbohydrates, lipid, protein, and protein-constituent amino acids. Food represents a very important source of biomolecules of technological and functional interest; therefore, 15 types of food samples were selected to demonstrate the analysis of basic composition of these biomolecules. In this experiment, students learnt testing the total carbohydrates of all the food samples using 3,5-dinitrosalicylic acid (DNS) method, while performing acid hydrolysis. Then, lipid extraction was done using Soxhlet extraction method in order to determine the crude lipid concentration in different samples. After this, the students learnt testing crude protein content of these samples by using Kjeldahl method, and amino acid analysis was performed using HPLC. From the experiments, students grasped the concept and advantages of these methods and deepened their understanding on compositional analysis of different food samples. This laboratory exercise can be included into any college-level biochemistry courses and gives hands-on experience to the students for conducting scientific research in the field of life sciences, food science, and other bio-related fields.

An ESP Program Based on Cognitive Academic Language Learning Approach for Enhancing Academic Reading and Technical Writing Skills among Microbiology and Biochemistry Students

This study investigated the effectiveness of using An ESP program based on Cognitive Academic Language Learning Approach (CALLA) in developing academic reading and technical writing among Microbiology and Biochemistry first year students at the Faculty of Science, Obourr Campus, Benha University. The study followed a pre-post experimental one group design. The participants were 37 students. The researcher used a needs analysis questionnaire to determine their academic needs. Moreover, the results of the questionnaire indicted their needs to academic reading and technical writing skills. The researcher designed academic reading test and technical writing test. Students were pre-tested, to identify their entry level of academic reading and technical writing skills .Then; they were trained through the ESP CALLA- based program on how to develop their academic reading and technical writing skills. The post-test was applied to the participants to assess the progress in their level of performance in academic reading and technical writing skills. Findings of the study revealed that there was statistically a significant difference at 0.01 in the pre- and post-assessment of academic reading and technical writing skills in favour of the post-assessment. Therefore, the ESP program that based on CALLA was effective in enhancing academic reading and technical writing skills.

Introduction to case-based learning: An attempt to integrate topics in biochemistry

Objectives: Biochemistry is one of the foundation sciences in the medical curriculum, which has immense importance in understanding the future clinical sciences, but it is generally considered to be a subject of just countless biochemical structures, pathways, and reactions. Conventionally, it was taught by means of didactic lectures, tutorials, and practical classes. These days, the education system is changing to a student-centered teaching–learning process with the use of various innovative teaching methods. Case-based learning (CBL) is one such approach which can make learning more effective and interesting. To generate interest of students in Biochemistry by correlating topics and their clinical application. Materials and Methods: After taking permission from the Institutional ethics committee, the students were given didactic lecture on the integration of carbohydrates and lipid metabolisms followed by a test (pre-test). They were then divided into small groups and given case histories which they were to discuss amongst themselves and arrive at a conclusion. These case histories were then discussed one to one with the facilitator. The students were again given a test (post-test). Results: There was a significant difference in the marks obtained in pre and post-test. Majority of the students felt it was an enjoyable and effective way of studying Biochemistry. Faculty also gave an encouraging response. Conclusion: CBL can be an important way of stimulating the students for self-directed learning and integrating topics of Biochemistry so that they are easily conceptualized.

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.

Aiming for the Bullseye: Targeted activities decrease misconceptions related to enzyme function for undergraduate biochemistry students.

Biochemistry curricula present a particular challenge to undergraduate students with abstract concepts which can lead to misconceptions that impede learning. In particular, these students have difficulty understanding enzyme structure and function concepts. Targeted learning activities and three-dimensional (3D) physical models are proposed to help students challenge these misconceptions and increase conceptual understanding. Here we assessed such pedagogical tools using the Enzyme-Substrate Interactions Concept Inventory (ESICI) to measure (mis)conceptual changes from Pre- to Post- time points in a single semester undergraduate biochemistry course. A Control group of students engaged with the active learning activities without the 3D physical models and students in the Intervention group utilized these activities with the 3D physical models. At the Post- time point both groups had higher, yet similar ESICI scores of the same magnitude as the highest scoring group from the national sample. Concomitantly, many misconception markers decreased compared to the national sample, although some of these differed between the Control and Intervention groups. Based on this assessment, both pedagogical approaches successfully increased conceptual understanding and targeted many of the misconceptions measured by the ESICI, however, several misconceptions persisted. Surprisingly, the students who used the 3D physical models did not demonstrate a further decrease in the misconception markers. Additionally, psychometric evaluation of the ESICI with our sample recommends the revision of several questions to improve the validity of this assessment. We also offer suggestions to improve instruction and pedagogical tools with further avenues for research on learning.

Encouraging Biochemistry Students’ Metacognition: Reflecting on How Another Student Might Not Carefully Reflect

Many studies in science education research have found metacognition to be beneficial for undergraduate STEM students. Students do not necessarily know how to employ their metacognition without some training or prompting, and undergraduate chemistry instructors do not always have the capacity to instruct their students on metacognition. Thus, it would be beneficial for instructors and students if metacognition development could be implicitly incorporated into typical classroom activities. In this study, 25 undergraduate students in an upper-division biochemistry course were interviewed via a think-aloud protocol. In the interviews, they were asked to solve two open-ended buffer problems. Before answering the second buffer problem, the students were asked questions designed to target their metacognition. The interview transcripts were qualitatively analyzed through a codebook thematic analysis, with deductive and inductive coding, to understand the types of metacognitive knowledge and metacognitive skills these students demonstrated while solving the buffer problems. The transcripts were also analyzed to understand how these metacognitive prompts may have changed students’ metacognitive approaches to solving the problems. Overall, 20 of the 25 students demonstrated some type of metacognition in response to the metacognitive prompts that they had not demonstrated in the first buffer problem. We discuss how asking students to think how an “unreflective” student would answer a question can prompt students to metacognitively evaluate their thought processes.

Huntingtin Protein Purification and Experimentation: An Innovative Undergraduate Research-Based Biochemistry Experiment

Traditional undergraduate biochemical laboratory curricula are confronted with challenges in improving student-learning outcomes while incorporating exciting and thought-provoking research-based laboratories due to limitations with time, increased student enrollment, and high-cost laboratory resources. However, with specialized biochemical instrumentation being more economically accessible and incorporation of creative approaches to circumvent inflexible undergraduate schedules, it is now possible to overcome some of these challenges. We have designed a unique laboratory experiment intended to mediate some of the limitations common to traditional biochemical experimentation using components of a research-based experience within the confines of a scheduled undergraduate laboratory session. In this experiment, undergraduate biochemistry students investigate the Escherichia coli-based expression and purification of the huntingtin protein with disease length polyglutamine tract using fluorescence-based aggregation assay. Students also investigate a novel area of research exploring the effects of macromolecular crowding agents (Ficoll, Dextran, and polyethylene glycol) on huntingtin protein aggregation

Design of a Didactic Planning Program to strengthen theeducational process of Biochemistry

Biochemistry students find the material complex due to its thematic content, which makes it difficult to understand. Due to this, the objective of this research is to design a Didactic Planning Program applying problem-based learning to strengthen the teaching-learning process in said subject, in the Nursing Career of the Public University of El Alto in Bolivia. The research was developed under a descriptive, non-experimental quantitative approach. The main results highlight that students are satisfied with the teaching guides of the subject, the methodology used in the class; as well as the planning and development of teaching, in addition to the form of learning evaluation. Meanwhile, teachers recognized that the didactic planning program is useful, raises quality levels, enhances students’ theoretical and practical skills, helps discern factors susceptible to modification, and creates a better learning environment. It is concluded that the proposal presented contributes to the teaching process of the subject of Biochemistry by building and integrating knowledge, generating significant learning, allowing more active and autonomous participation of students and allowing them to learn cooperatively, obtaining an effective and innovative solution.

Teaching chemical engineering using Jupyter notebook: Problem generators and lecturing tools

The primary objective of this study is to develop teaching materials for chemical engineering students (or students pursuing other related B.Sc./M.Sc. degrees) that encourage self-learning to facilitate understanding and the development of problem-solving skills. Tools are oriented to support the teaching of “Introduction to Chemical Engineering” courses to 1st year B.Sc. students in Chemical Engineering, 2nd year B.Sc. students in Chemistry, and 3rd year B.Sc. students in Biochemistry at the Universidad Complutense de Madrid (UCM). Problem generators of standard exercises, as an additional complement to the exercises that are used in the lectures, seminars, and assignments to facilitate the learning of the students, have been developed. These generators provide exercises to students with “unlimited” initial values (with certain restrictions). The software that was used to develop these materials was Jupyter Notebook, which runs under the Python 3.6 language. The problem generators can be classified into fixed problem generators, case-based generators, and random problem generators. Additionally, lecturing tools have been developed to support teaching using live/interactive examples. These examples can learning understanding of various topics of the courses.

William "Bill" Joseph Whelan, D.Sc., FRS November 14, 1924 to June 5, 2021.

William "Bill" Joseph Whelan, D.Sc., FRS November 14, 1924 to June 5, 2021.

Training biochemistry students in experimental developmental biology: Induction of cardia bifida formation in the chick embryo.

A high variety of experimental model organisms have been used in developmental biology practical lectures. The work with developing embryos is crucial to make students aware of the multiple biological phenomena underlying normal animal embryogenesis and morphogenesis and represent a unique experimental platform to analyze the impact of molecular signaling in the regulation of all these processes. In particular, Biochemistry undergraduate students enjoy both practical and theoretical lectures on the molecular mechanisms of embryonic development, as that allows them for the integration of crucial molecular concepts (e.g. signaling and signal transduction mechanisms; molecular patterning of development) into the dynamic and progressive context of animal embryonic ontogenesis. Accordingly, it is important to carefully design practical laboratory lectures in developmental biology, as these are a unique pedagogical tools fostering the interests of the students in this subject. This study describes the design, implementation, and evaluation of a two-session laboratory practical activity performed by Biochemistry undergraduate students at University of Málaga (Spain). In this practical activity, which takes advantage of the unique characteristics of the chick embryo, students learn how the vertebrate heart forms from the fusion of two bilateral-symmetric cardiac progenitor pools under the guidance of the underlying endoderm. This cheap and easy practical laboratory activity provides relevant visual information on how experimental manipulations can severely influence anatomical form during organ development, as well as an excellent experimental setting to test molecular regulation of morphogenesis in an ex vivo (ex ovo) context.

Bringing Light to Science Undergraduate Students: A Successful Laboratory Experiment Illustrating the Principles and Applications of Bioluminescence

Although many laboratory experiments are available to illustrate spectrophotometric or fluorometric methods, few of them introduce the use of luminometry to students. Bioluminescence, a subtype of chemiluminescence, is produced when an enzyme-catalyzed chemical reaction gives rise to light emission. Despite the advantages of bioluminescent methods, including sensitivity and specificity, and their increasing use in experimental sciences and biomedical laboratories, their presence in courses is almost nonexistent. The luciferase-catalyzed enzymatic reaction has generated a myriad of practical applications, including those derived from the measurement of the ATP consumed in the reaction. In particular, the measurement of ATP levels in drinking or stored waters directly correlates with their bacteria content, facilitating the development of rapid methods for detecting bacterial contamination. This avoids the long waiting time associated with traditional microbiological methods, based on the growth of the microorganisms in a suitable culture medium. Over the past two years at the University of Malaga, we have implemented a new laboratory experiment for undergraduate chemistry and biochemistry students. In this experiment, students detected bacterial contamination in water by quantifying ATP with the luciferase-catalyzed reaction. The experiment was successfully implemented in two different formats, either as a full project developed by students throughout the entire duration of the academic course, or as a short protocol, carried out in a single laboratory session. Between them, a whole range of intermediate options could be arranged by educators to suit their course requirements and the learning objectives to be achieved by students.

Using Biometric Tools to Investigate How Students Cognitively Process the Structure of Prostaglandin H 2 Synthase

Protein representations such as those found in the Protein Data Bank repository are important for any practicing biochemist to be able to use, interpret, and manipulate; skills commonly referred to as visual literacy in biochemistry. As such, any student enrolled in a biochemistry course should be trained in these skills. However, little is known as to how students navigate these 3-dimensional representations and how to best teach these skills to biochemistry students, especially using virtual 3D modeling software. An additional barrier to learning these skills are that they are associated with the students’ spatial ability. The proposed study uses biometric tools such as eye tracking and electroencephalography (EEG) to investigate how biochemistry students cognitively process and use modeling software UCSF Chimera to explore the structure of Prostaglandin H2 Synthase. Nine biochemistry students were sampled at a metropolitan Midwestern campus in fall 2018 while completing the activity. During the activity, the students’ cognitive processing was captured using EEG while gaze patterns and areas of fixation were captured by Tobii Glasses 2. Additionally, each student completed a series of spatial ability assessments (Hidden Figures Test and Purdue Visualizations of Rotations Test) to capture their level of ability to think visually. This presentation will answer the following research questions: 1) Which combination of electrode channels suggests the most appropriate measurement of cognitive load? 2) How does the cognitive load measurement change when students analyze a quaternary structure versus a tertiary structure of the same protein? and 3) How can we optimize the cognitive load of a 3D virtual modeling activity? The answers to these questions will be used to improve the activity for replication in following years in hopes of decreasing the impact of extraneous factors on cognition and providing the mental space needed for learning the skills associated with visual literacy in biochemistry.

Talking in Circles: Undergraduate Biochemistry Student Conceptions About Biochemical Pathway Regulation

For many undergraduate students, introductory biochemistry courses are difficult because they involve novel abstract concepts that require assimilation of new knowledge with pre-existing notions from biology and chemistry courses. According to cognitive load theory, students use pre-existing schemas to fit this new knowledge onto the framework of what they already know. Extraneous cognitive load can interrupt this process by overwhelming working memory. Misconceptions increase cognitive load and interrupt the mental framework, making it difficult for students to master course material. In the field of biochemistry, little research exists on how students understand and learn about the threshold concept of Biochemical pathway dynamics and regulation. Initially a non-empirical pilot study was conducted with students who had completed an undergraduate biochemistry I course. These participants were interviewed using the three-phase single interview technique (3-PSIT), which probes the student's knowledge by creating cognitive dissonance using visual representations. Preliminary inductive content analysis of the transcribed text from this pilot study identified patterns and categories of (mis)conceptions among students. From this, student responses were collected from assessments informed by the pilot study. These responses were used to further identify patterns of (mis)understanding with regards to pathway regulation. The information gathered here enables development of learning assessments and pedagogical techniques to better teach the complex concepts surrounding biochemical pathway regulation.

Enzyme kinetic parameters estimation: A tricky task?

We are living in the Big Data era, and yet we may have serious troubles when dealing with a handful of kinetic data if we are not properly instructed. The aim of this paper, related to enzyme kinetics, is to illustrate how to determine the Km and Vmax of a michaelian enzyme avoiding the pitfalls in which we often fall. To this end, we will resort to kinetic data obtained by second-year Biochemistry students during a laboratory experiment using β-galactosidase as an enzyme model, assayed at different concentrations of its substrate. When these data were analyzed using conventional linear regression of double-reciprocal plots, the range of Km and Vmax values obtained by different students varied widely. Even worse, some students obtained negative values for the kinetic parameters. Although such a scenario could make us think of a wide inter-student variability regarding their skills to obtain reliable data, the reality was quite different: when properly analyzed (accounting for error propagation) the data obtained by all the students were good enough to allow a correct estimation of the Km (2.8 ± 0.3 mM) and Vmax (179 ± 27 mM/min) with a reduced intergroup standard deviation. A student-accessible discussion of the importance of weighted linear regression in biochemical sciences is provided.

Alternative Assessment to Lab Reports: A Phenomenology Study of Undergraduate Biochemistry Students’ Perceptions of Interview Assessment

Research has begun to explore the undergraduate laboratory in many facets, such as students’ feelings, goals, and instructional approaches to the laboratory. However, research has not explored the experiences of students with summative assessment in the laboratory. This qualitative study investigates the experiences of upper-level undergraduate students’ exposure to lab interviews as an oral summative assessment. A phenomenological approach guided the analysis and interpretation of data gathered from 16 semistructured student interviews. The exploration of the data resulted in the development of an outcome space with three fundamental features and students’ core perceptions about lab interviews. This outcome space explores students’ feelings, performances, and perceived conceptual understandings before, during, and after the interview process. Implications and suggestions for the design and improvement of assessment practices are discussed.

Metabolism in Motion: Engaging Biochemistry Students with Animation

Metabolism, including cellular respiration, encompasses a large component of the topics covered in foundational biochemistry and life science undergraduate courses. The difficulty in instruction and student retention of this topic lies in the conceptualization of the numerous enzymatic reactions involving various substrates/products and their regulation. Learners typically end up focusing on memorizing individual metabolic pathways and their subcomponents (e.g., enzymes, substrates, and products) rather than developing a high-level understanding of the interplay and regulation occurring between pathways and appreciating the real-life application of this knowledge. To address this challenge, we created a 3D animation that introduces students to the fundamental concepts of glucose and fat metabolism, energy production by the citric acid cycle and oxidative phosphorylation, as well as the major points of regulation that emphasize the integration and flux of these metabolic pathways. Survey feedback from cohorts of University of Toronto second-year undergraduate life science students and School of Continuing Studies learners indicated that the animation increased their engagement with the material and confidence in understanding the connectivity between competing pathways and the regulation of metabolism.