Biochemistry Laboratory Course Research Articles

Bridging the biochemistry lecture and laboratory courses: Construction and application of the "Innovative Experimental Design" module.

Both lecture and laboratory courses of biochemistry are important professional courses for undergraduates with biology related majors. Course optimization and update is crucial but challenging, especially for the laboratory course. Although taught separately, here we showed a strategy to bridge the two courses and promote the improvement of both. In addition to knowledge teaching, we implanted the "Innovative Experimental Design" module in the lecture course in which students were required to design and present their own experimental ideas. After evaluation by the faculty group, the best idea was supported for further experimental test. Here we described the preliminary experiments and optimization procedures about the idea of microbial fuel cells. This experiment is ready to be included into the laboratory course program in spring 2023.

Comparing Learning Outcomes and Student and Instructor Perceptions of a Simultaneous Online versus In-Person Biochemistry Laboratory Course.

This article compares the learning outcomes and student perceptions of a one semester undergraduate biochemistry laboratory course that was taught using either a fully online or a fully in-person teaching modality. The semester long biochemistry laboratory mimicked the work sequence a researcher would encounter when transforming a plasmid containing a gene for a recombinant protein (superfolder green fluorescent protein, sf-GFP) and then purifying, identifying, and characterizing that protein. The two modalities of the course were completed in the same semester, by the same instructor, in which students self-selected into which modality they preferred at the beginning of the semester. Students in the in-person section reported enjoying the laboratory course more than the online cohort of students and found it to be less time-consuming. Additionally, a survey of biochemistry laboratory instructors from across the United States, who had experience teaching both online and in-person biochemistry laboratories, indicated that the majority of instructors that responded to the survey preferred the in-person modality: believing them to be more effective and engaging for the students, more enjoyable, and less time-consuming for the instructor. Statistical analysis of formative and summative assessments indicated no significant difference in non-hands-on student learning objective and learning goal scores between the two groups, but the small number of students and instructors in this study limits the generalizability of these results.

Use of OneNote class notebook as a combined electronic laboratory notebook and content delivery tool in an introductory biochemistry laboratory course.

The COVID-19 pandemic has forced a shift in thinking regarding the safe delivery of wet laboratory courses. While we were fortunate to have the capacity to continue delivering wet laboratory experiments with physical distancing and other measures in place, modifications to the mechanisms of delivery within courses were necessary to minimize risk to students and teaching staff. One such modification was introduced in BCH370H, an introductory biochemistry laboratory course, where a OneNote Class Notebook (ONCN) was used as an electronic laboratory notebook (ELN) in place of the traditional hardbound paper laboratory notebook (PLN) used prior to the pandemic. The initial reasoning for switching to an ELN was around safety-allowing course staff and students to maintain physical distancing whenever possible and eliminating the need for teaching assistants to handle student notebooks; however, the benefits of the ONCN proved to be significantly more. OneNote acted not only as a place for students to record notes but the Class Notebook's unique features allowed easy integration of other important aspects of the course, including delivery of laboratory manuals, posting of student results, notetaking feedback, sharing of instructional materials with teaching assistants, and more. Student and teacher experiences with the ONCN as used within a fully in person biochemistry laboratory course, as well as learned best practices, are reviewed.

A project-oriented biochemistry laboratory for protein engineering and structure-function using small laccase enzyme from Streptomyces coelicolor.

An understanding of structure-function relationships in proteins is essential for modern biochemical studies. The integration of common freely accessible bioinformatics tools available online with the knowledge of protein-engineering tools provide a fundamental understanding of the application of protein structure-function for biochemical research. In order for students to apply their prior knowledge of recombinant protein technology into the understanding of protein structure-function relationships, we developed a semester-long project-oriented biochemistry laboratory experience that is the second laboratory course of a series. For easier integration of knowledge and application, we organized this course into four sequential modules: protein structure visualization/modification, mutagenesis target identification, site-directed mutagenesis, and mutant protein expression, purification, and characterization. These tasks were performed on the protein small laccase (SLAC) that was cloned and characterized by students in the previous semester during the first biochemistry laboratory course of the series. This goal-oriented project-based approach helped students apply their prior knowledge to newly introduced techniques to understand protein structure-function relationships in this research-like laboratory setting. A student assessment before and after the course demonstrated an overall increase in learning and enthusiasm for this topic.

Expression, Purification and Characterization of RecJ Nuclease -An Integrated Biochemistry Laboratory Course for Undergraduates

Expression, Purification and Characterization of RecJ Nuclease -An Integrated Biochemistry Laboratory Course for Undergraduates

Harnessing the Topics of Cytochrome P450 Enzymology and Artemisinin to Teach a Semester-Long Biochemistry Laboratory Course

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 artemisinin, an endoperoxide-containing plant natural product used to treat malaria. Biochemical techniques introduced to the students included computational (dry lab) techniques: the use of bioinformatics tools to design plasmids for protein expression, software to analyze the 3-dimensional structure of proteins, metabolomics software to analyze enzyme-catalyzed reaction extracts by mass spectrometry, and docking software to dock ligands into the active site of proteins. In addition, students performed experimental (wet lab) techniques including: a transformation experiment to incorporate plasmid DNA into bacteria, an extraction of plasmid DNA from bacterial cells, performing enzymatic incubations and preparing samples for analysis by mass spectrometry, and running an SDS protein gel electrophoresis. The semester ended with the use of a web-based program to allow students to visualize the proteins they were studying throughout the semester with a virtual reality headset. This course was taught for the first time at the university, so this manuscript should inspire ideas for future biochemistry laboratory courses taught in the course based undergraduate research experiences (CUREs) format.

Imagining, designing, and interpreting experiments: Using quantitative assessment to improve instruction in scientific reasoning

Effectively teaching scientific reasoning requires an understanding of the challenges students face when learning these skills. We designed an assessment that measures undergraduate student abilities to form hypotheses, design experiments, and interpret data from experiments in cellular and molecular biology. The assessment uses intermediate-constraint free-response questions with a defined rubric to facilitate use with large classes, while identifying common reasoning errors that may prevent students from becoming proficient at designing and interpreting experiments. The assessment measured a statistically significant improvement in a senior-level biochemistry laboratory course, and a larger improvement between the biochemistry lab students and a separate cohort in a first-year introductory biology lab course. Two common errors were identified for forming hypotheses and using experimental controls. Students frequently constructed a hypothesis that was a restatement of the observation it was supposed to explain. They also often made comparisons to control conditions not included in an experiment. Both errors were most frequent among first-year students, and decreased in frequency as students completed the senior-level biochemistry lab. Further investigation of the absent controls error indicated that difficulties with reasoning about experimental controls may be widespread in undergraduate students. The assessment was a useful instrument for measuring improvement in scientific reasoning at different levels of instruction, and identified errors that can be targeted to improve instruction in the process of science.

Thinking more wisely: using the Socratic method to develop critical thinking skills amongst healthcare students

BackgroundIn medicine, critical thinking is required for managing and tolerating medical uncertainty, as well as solving professional problems and treating diseases. However, the core of Confucianism, teacher-centered and exam-oriented settings in middle and high school education may pose challenges to developing critical thinking in Han Chinese or Taiwanese students. Students may be adversely affected by these pedagogies since student-centered settings were more effective in stimulating their critical and reflective thinking, as well as a sense of responsibility, in the ever-changing world. Therefore, guiding students with less stable foundations of critical thinking might require a different approach. A review article highlighted the potential utility of the Socratic method as a tool for teaching critical thinking in the healthcare field. The method involves posing a series of questions to students. More importantly, medical students and residents in clinical teaching are familiar with the method. Almost all healthcare students must complete a biochemistry laboratory course as part of their basic science training. Thus, we aimed to train students to develop critical thinking in the biochemistry laboratory course by using learning sheets and teacher guidance based on the Socratic method and questioning.MethodWe recruited second-year students from a medical school, of whom 32 had medical science and biotechnology majors (MSB), 27 had pharmaceutical science majors (PS), and 85 were medical undergraduate (MU) students. An exercise in critical thinking was conducted during a biochemistry laboratory course, which consisted of five different biochemical experiments, along with learning sheets that contained three or four critical thinking questions. Then, the teacher evaluated the students’ ability to think critically based on nine intellectual dimensions (clarity, accuracy, precision, relevance, depth, breadth, logic, fairness, and significance) based on the universal intellectual standards developed by Prof. Linda Elder and Richard Paul. In the following analysis, regression models and multivariate analysis were used to determine how students improved over time, and trajectory analysis were carried out in order to observe the trends in students’ critical thinking skills construction.ResultsClarity and logic dimensions were identified as the key elements to facilitate the development of critical thinking skills through learning sheets and teacher guidance in students across all three different healthcare majors. The results showed that metacognitive monitoring via Socratic questioning learning sheets have demonstrated potential encourage students to develop critical thinking skills in all dimensions. Another unique contribution of current study was present the heterogeneous learning patterns and progress trajectories of clarity and logic dimensions within classes.ConclusionUsing the Socratic learning model could effectively develop students’ critical thinking skills so they can more effectively care for their patients.

Effective Creation and Usage of Simplified Virtual Curation Lab Using Google Sites: Implementation for Principles of Biochemistry Laboratory Course

Effective Creation and Usage of Simplified Virtual Curation Lab Using Google Sites: Implementation for Principles of Biochemistry Laboratory Course

Mushroom Tyrosinase Assay is used to Teach Enzyme Kinetics and Inhibition Studies in an Undergraduate Biochemistry Course

A spectrophotometric mushroom tyrosinase assay was optimized for use in the undergraduate biochemistry laboratory course at Virginia Tech. The laboratory exercise is designed to teach students about enzyme kinetics and tyrosinase‐inhibitor interactions. The tyrosinase protein structure was first studied using the python based molecular visualization software PyMOL and a PDB ID from the Protein Data Bank. The PDB ID that was used was PY9W and displays a H(2) L(2) tetramer. The H subunits of the complex contain a copper binding site that is coordinated by 3 histidine residues. The structure/function relationship was further studied using an immersive modeling hypercube. The assay uses white button mushrooms as the source of the tyrosinase enzyme, l‐3,4 dihydroxyphenylalanine (L‐DOPA) as the substrate, and kojic acid as the inhibitor. The optimal amounts of enzyme, substrate, and inhibitor are first determined, then a series of experiments are conducted which test varying concentrations of L‐DOPA against varying concentrations of kojic acid. Change in absorbance is measured at 475 nm in a spectrophotometer and the data is plotted to determine the kinetic constants and type of inhibition. Experimental kinetic constants are then compared to previously reported values. Further protein concentration in the tyrosinase extract is determined using Bradford assays. The incorporation of this exercise into the undergraduate biochemistry laboratory course at Virginia Tech will allow students to explore enzyme kinetics and tyrosinase‐inhibitor interactions.

Engaging an Undergraduate Researcher to Develop a Mushroom Tyrosinase Assay as a Summative Assessment Device for an Upper‐level Biochemistry Laboratory Course

Working with an undergraduate enrolled in 2‐credits of independent research a mushroom tyrosinase enzyme assay was researched, piloted, and optimized during the fall 2021 semester. The assay included crude mushroom extract from Agaricus bisporus, commonly known as white button mushrooms mixed with l‐3,4 dihydroxyphenylalanine (l‐DOPA) as a substrate. Change in absorbance was measured at 475 nm in a spectrophotometer. A version of this assay was then used to write and administer a summative assessment (a lab practical) in three sections of a 6‐credit capstone laboratory course for biochemistry majors. The practical evaluated students’ ability to measure enzyme reaction rates, make accurate dilutions, apply knowledge of Michaelis‐Menten kinetics to determine the Km and the Vmax of an enzyme of which they had little or no prior knowledge, and finally to gauge ability to determine the inhibition constant (Ki) of a provided inhibitor (kojic acid). While researching and optimizing this assay the undergraduate researcher gained hands‐on experience troubleshooting, preparing stock buffer solutions, realizing the limitations of certain substrate solubility, and observing the time constraints of an assay in which measurable products autocatalyze to form products that are not measurable by a spectrophotometer. The development of this assay and practical exam were both extremely student‐centered as the student gained practice judging the quality and feasibility of assays by searching and reading biochemistry and molecular biology education literature and communicating both via email and in‐person with corresponding authors. Generating new course content in a large lab courses with multiple sections is a challenge, especially in courses that have been taught for many years. Providing search parameters to an independent undergraduate researcher and suggesting journals to begin looking for feasible published protocols led to the implementation of an assay that piqued the interest of the student and lab instructors while also being useful as a tool for biochemistry laboratory assessment.

An Approach to Transitioning Undergraduate Biochemistry Laboratory Courses Online

An Approach to Transitioning Undergraduate Biochemistry Laboratory Courses Online

BASIL: A biochemistry laboratory CURE with flexibility across learning modalities

Since 2015, a collaboration of instructors at a diverse range of institutions have developed a biochemistry laboratory curriculum known as BASIL (Biochemistry Authentic Scientific Inquiry Laboratory). Scientific objectives of BASIL focus on characterizing biochemical activities of proteins with known structure and unknown function. BASIL curriculum (freely available on GitHub https://basilbiochem.github.io/basil/) includes modules on computational predictions of protein function, protein purification, and analysis of biochemical activity and kinetics. Three main challenges for our implementation included 1) scaling of research training from the “apprentice” model to the classroom, 2) alignment of course learning objectives, activities and assessments with research goals to create optimal conditions for productive struggle, 3) student buy-in. To understand if/how students in our course develop laboratory research skills, we began assessing anticipated learning outcomes, focusing on students’ evaluation of protein purification experiments. Initial assessment results revealed learning difficulties and led to modifications in instructional activities, including use of simulated experiments. The BASIL curriculum was intentionally designed to provide flexibility in its use in terms of sequencing and scope of experiments, content, and focus to meet desired course learning objectives. This flexibility proved beneficial in maintaining learning objectives when switching from the traditional lab format to online or hybrid delivery necessitated during the COVID-19 pandemic. Using a combination of lecture and video based explanations students were able to investigate their protein of interest completely online. Students working in this format reported gains in knowledge, experience and confidence. We did find that these gains were more pronounced in the bioinformatic experiments and concepts than about their wet-lab counterparts. In order to address these gaps in understanding interactive online resources are under current development by the BASIL team. In addition to addressing the short-term need for a set of coordinated electronic materials for biochemistry laboratory courses, this adaptation of the BASIL curriculum provides a meaningful distance-learning alternative in future years and may serve as a platform to broaden access to quality STEM education to more diverse student populations well after the pandemic has past.

Redesign of an Advanced Biochemistry Laboratory into a Course‐Based Undergraduate Research Experience

In recent years, more efforts have been made to integrate authentic research experiences into undergraduate laboratory courses to improve student learning and broaden access to scientific research. However, traditional expository and limited inquiry-based laboratory courses continue to exist at the undergraduate level depriving students of the opportunity to fully engage in authentic scientific practices. Described herein is the redesign of a limited inquiry-based Advanced Biochemistry Laboratory course at a public small liberal arts college into a course-based undergraduate research experience (CURE) that enhances the research skills of students. By piloting course changes in a low-enrollment elective course over 3 years, the instructor was able to improve the laboratory infrastructure of the department with the purchase of two new advanced instruments to support laboratory courses and faculty research. Within this intentionally redesigned course, students created a research plan, conducted oral and poster presentations, produced a manuscript-styled laboratory report, and developed a curriculum vitae. Students also gained working knowledge of 1-3 advanced instruments during structure-function studies of a model protein.

Analysis of Amylase in the Kitchen: An At-Home Biochemistry Experiment for the COVID-19 Pandemic

During the COVID-19 pandemic, an at-home enzyme assay was developed for a biochemistry laboratory course at Arizona State University. The experiment was designed to use items that could be easily obtained and safe to use. The experiment focused on the analysis of salivary amylase using starch from food as a substrate, black tea as an inhibitor, and tincture of iodine to quantify the amount of starch present. In this article, we describe the design of the experiment and an analysis of the student performance with specific mention of the common problems that the students experienced. While this experiment was specifically designed as an at-home experiment, it could easily be adapted to use in a typical undergraduate biochemistry laboratory.

Pivoting an Upper-Level, Project-Based Biochemistry Laboratory Class to Online Learning During COVID-19: Enhancing Research Skills and Using Community Outreach to Engage Undergraduate Students

Closing the university due to the COVID-19 pandemic resulted in a sudden shift from independent research projects in biochemistry to a virtual learning experience focused on essential research skills and an added community outreach activity. Here, pedagogical strategies and lessons learned on restructuring this upper-level biochemistry laboratory course to a remote format are described.

Activities and assessment solutions for students in advanced molecular genetics and biochemistry to direct and engage with public communication in an online environment.

Apart from classroom presentations to their instructors and peer groups, STEM students have limited opportunities or encouragement to engage in guided communication of scientific concepts to others (family, friends, or the general public). A critical need exists for accurate, comprehensible science to be disseminated to these groups. To develop student proficiency in communication of complex biomolecular concepts impacting diverse audiences, I introduce learning approaches and assessments easily adapted to fit the needs of individual instructors and any molecular biology or biochemistry laboratory or lecture course in a remote/online environment. To help students develop an appreciation of the needs of different audiences and the nuanced drivers of clear communication, I provided them the choice of projects of similar length: Option (1) Create a scientific news release and short podcast or video clip newscast describing a recent advancement in understanding the molecular/biochemical basis of a disease; or Option (2) Create a lesson plan and mini-video designed to teach a simple biochemical or molecular mechanism of disease with learning objectives, a brief activity, and appropriate assessment mechanisms. Students who chose the scientific news release/newscast activity distilled complex biomolecular concepts using the 5 W's of journalism-who, what, where, why, when-and learned to accurately communicate the relevance of advanced scientific discoveries and recent events for a broader audience. Students who chose the lesson plan designed activities centered on biomolecular science concepts that build upon what their audience already knows, revealing possibilities for undergraduates to contribute to educational outreach to secondary school teachers and classes.

Re‐designing Biochemistry Laboratory to Implement BASIL CURE: from Structure to Function, from Student to Researcher

Course‐based undergraduate research experiences (CUREs) have recently emerged as an alternative to traditional science laboratory instruction. Cross‐institutional faculty communities help crowd‐source curricular design and assessment, as well as facilitate data sharing and trouble‐shooting. As participants in the Biochemistry Authentic Scientific Inquiry Laboratory (BASIL) community, we re‐designed our upper level biochemistry laboratory course to incorporate CURE. Scientific objectives of BASIL focus on characterizing biochemical activities of proteins with known structure and unknown function. BASIL curriculum (freely available on GitHub https://basilbiochem.github.io/basil/) includes modules on computational predictions of protein function, protein purification, and analysis of biochemical activity and kinetics.Over the course of four years, our implementation has evolved to accommodate local needs and constraints and to address technical, logistical and pedagogical challenges we encountered along the way. We discuss this evolution in light of recommendations for CURE course design (Kloser et al., 2011) and the five dimensions of CURE (scientific practices, discovery, relevance, collaboration, and iteration; Auchincloss et al., 2014). Three main challenges for our implementation included 1) scaling of research training from the “apprentice” model to the classroom, 2) alignment of course learning objectives, activities and assessments with research goals to create optimal conditions for productive struggle, 3) student buy‐in.CURE implementation presents challenges with timing of research experiments in a scheduled course, availability of equipment, management of reagent requests and hazardous waste. Instructional support staff (AML) was critical for overcoming a number of logistical, technical and pedagogical challenges. In addition, undergraduate students pursuing research projects outside of class contributed to the CURE by developing new protocols, testing new proteins or generating computational predictions using tools that were outside the scope of the course. To understand if/how students in our course develop laboratory research skills, we began assessing anticipated learning outcomes previously defined by Irby et al. (2018), focusing on students’ evaluation of protein purification experiments. Initial assessment results revealed learning difficulties and led to modifications in instructional activities, including use of simulated experiments. To gauge student frustration and to help students improve their metacognitive skills, we asked students to reflect on their experiences in short weekly structured journal entries. Students’ negative perceptions of failed experiments, potentially, rooted in fixed mindset, require additional intervention.Support or Funding InformationSupported by NSF‐IUSE #1503676 to ALG, #1710538 to ALG and EMJ; 1503811 and 1709170 PAC.

Many hands make light work, or too many cooks spoil the soup? Lessons from the development of the BASIL biochemistry laboratory curriculum through a diverse multi‐institutional collaboration.

The BASIL (Biochemistry Authentic Scientific Investigation Laboratory) curriculum is driven by a consortium of biochemistry and computational instructors. BASIL is a protein biochemistry Course‐based Undergraduate Research Experience (CURE) in which students discover enzymatic function of previously uncharacterized proteins. It combines computational and wet‐lab protein science to deliver foundational concepts within the undergraduate biochemistry teaching lab. BASIL came together in 2015 as instructors sought to integrate genuine research into the biochemistry laboratory course to broaden the impact of teaching through research.In order to maximize impact, BASIL has been intentionally developed as a collaborative effort across institutions diverse in type, size, and location nationwide. This presentation summarizes lessons learned from building this collaboration, including the following aspects. (1) Establishing the group: Participants were identified and recruited for the most part at national meetings such as Experimental Biology/ASBMB and others. (2) Funding: Development of the BASIL curriculum was supported by NSF IUSE as a collaborative research proposal. (3) Communication: Group members interact through videoconferencing on a weekly basis, and at national/regional meetings. (4) Teaching resources: The BASIL curriculum has been published as a free and open‐source resource, supplemented by online teaching suggestions. (5) Assessment: The effectiveness of this curriculum has been assessed through student surveys shared across campuses and surveys of faculty to monitor success of (and obstacles to) implementation at each home campus. (7) Dissemination and recruitment: Availability of the BASIL resources has been published, and additional faculty/campuses continue to join as BASIL implementors.These are presented with the goal of sharing successful (and not‐so‐successful) strategies for collaborating across campuses as a way to stimulate effective student learning while promoting faculty development and well‐being through this team model.Support or Funding InformationNSF IUSE 1709278

Hands-On Electrospray Ionization Mass Spectrometry for Undergraduate Biochemistry Students: Peptide Identification by Ladder Sequencing

Mass spectrometers are ever-increasingly powerful, user-friendly, and affordable. Thus, the addition of mass spectrometry experiments into the undergraduate laboratory curriculum is now both feasible and an effective tool to introduce students to relevant instrumentation. Here an experiment demonstrating the use of a high-resolution electrospray ionization mass spectrometer (ESI-HRMS) for the identification of peptide sequences and the differentiation of isomeric peptides was developed and implemented in a biochemistry laboratory course for third-year chemistry major undergraduate students. This lab activity was a first introduction to mass spectrometry for undergraduate biochemistry students. As a prelab assignment, students were tasked to predict the mass-to-charge ratios and the fragmentation patterns for six given peptides using an online fragmentation prediction tool (Protein Prospector’s MS-Product tool). Students then analyzed two unknown peptides using ESI-HRMS. The theoretical and experimental results were compared to reveal the identity of the two unknown peptides. The student success rate of recognizing the unknown peptide sequences was 87.5%. This laboratory experiment provided students with hands-on experience using a research-grade ESI-HRMS instrument to solve a bioanalytical problem—specifically, the identification of the primary structure of a peptide of unknown sequence. Learning outcomes were evaluated for this experiment, which showed student understanding of peptide sequencing using mass spectrometry.