Introductory Biochemistry Course Research Articles

Using Student Movement to Improve Understanding of the Pyruvate Dehydrogenase Complex

Students in introductory biochemistry courses often struggle to visualize the structure of large enzyme complexes and understand the mechanisms of the reactions they catalyze. One such complex, the Pyruvate Dehydrogenase Complex (PDC), catalyzes an essential step in glucose catabolism and is comprised of many copies of three enzymes that catalyze five reactions requiring five unique cofactors. To assist students in learning of the PDC reaction and mechanism, students enrolled in in‐person biochemistry participate in a group activity to act out the mechanism of the complex using instructor‐directed student movement. The effect of acting or observing the activity on learning of PDC structure, mechanism, and function is reported using data from IRB‐approved assessment and survey instruments and compared to data from students in virtual biochemistry courses without an activity. Unique course activities involving student movement can improve student learning of complex topics in biochemistry.

Lessons Learned: Active Engagement in a Large‐Enrollment Introductory Biochemistry Course During a Remote Quarter

In the spring of 2020, faculty worldwide were forced to abruptly transition in-person courses to an online format due to the COVID-19 pandemic. To keep students engaged in a large-enrollment introductory biochemistry course, I employed a plethora of techniques from synchronous lectures and active learning via the Zoom platform, to the asynchronous online discussion board Piazza. I also modified the course and assessments in consideration of students’ non-academic struggles relating to the pandemic. Student evaluations at the conclusion of the quarter indicated that they preferred synchronous lectures over asynchronous ones, flipping their pre-course preferences. These techniques and accommodations to the remote learning environment led to an overwhelmingly positive overall experience and promoted student engagement, especially in the face of increasing worldwide social unrest during the remaining two weeks of the quarter.

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.

Design and implementation of active learning strategies to enhance student understanding of foundational concepts in biochemistry.

For many students biochemistry is a demanding course because they are expected to apply previously learned foundational concepts to new biological contexts. These foundational concepts serve as a scaffold onto which to build threshold concepts such as the physical basis of interactions. Unfortunately, many students possess misconceptions or gaps in knowledge of these foundational concepts which hinder their understanding of new information. This paper describes the implementation of an iterative process to improve student foundational concept learning in an introductory biochemistry course. The process includes pre-assessment of foundational concept knowledge, introduction of interventions targeting low performing concepts and re-assessment of student learning gains. Diverse active learning strategies such as problem-based worksheets, tactile learning activities, review activities and learning cycle activities were introduced to target concepts including hydrogen bonding, pH/pKa, bond energy and chemical equilibrium. While all active learning strategies resulted in improved posttest scores compared to pretest scores, no one strategy appears to be more beneficial than another. Survey results suggest students recognized the value of utilizing the various active learning strategies in the classroom to enhance critical thinking skills, engagement during class time, and collaboration skills. The process allows instructors the breadth and flexibility to introduce diverse active learning strategies tailored to their specific student needs in an effort to improve student foundational concept learning.

Reporting Biochemistry to the General Public through a Science Communication Writing Assignment

Students enroll in biochemistry courses for many reasons, whether it be to build a strong foundation in biochemistry content for health science-related careers or to better understand the world around them. Learning is enriched when students can identify the relevance of the content, such as through connecting course content to authentic applications. One way that students can make these connections is by practicing science communication, an increasingly important skill for students to master. Drawing upon the advantages of writing, we designed an assignment that tasked students with writing a summary of a biochemistry-related seminar in which they explained the research and related biochemistry content in the form of a scientific news article targeted for a general audience. In this article, we discuss the design of the assignment and its implementation into an introductory biochemistry course. Results from a feedback survey and our evaluation of student writing assignments suggest that students saw value in communicating science to the general public and reported being able to connect the course content to authentic applications. This assignment is applicable in other chemistry or biology courses as a means to help students develop their skills in science communication and cultivate their appreciation of science content.

A virtual laboratory module exploring photosynthesis during COVID-19.

Virtual laboratory activities are flexible approaches to engage undergraduate students in scientific practices during the COVID‐19 pandemic. By utilizing online simulations, students can conduct virtual experiments on important biochemical reactions that occur during photosynthesis. The learning module described here provides students with this experience and was implemented for first‐year students in a virtual summer bridge program. It introduces new biochemistry majors and nonmajors to the discipline, and it is based on an in‐person photosynthesis laboratory module taught for the summer bridge program before the emergence of COVID‐19. This virtual laboratory module can be readily adapted for use during the academic year in introductory biochemistry courses.

Lessons Learned from Active Engagement in a Large-Enrollment Introductory Biochemistry Course during a Remote Quarter

The combination of the COVID-19 pandemic and social unrest turned education on its head this quarter. To keep students engaged, a plethora of techniques were employed, ranging from synchronous lectures and activities via the Zoom platform to the asynchronous online discussion board Piazza. Consideration of students’ nonacademic struggles also resulted in course modifications. This last method may have been the most effective in promoting student engagement, especially during the remaining 2 weeks of the quarter with increasing worldwide social unrest.

End of the Semester Review of Biochemistry Using a Case Study on Phosphoglucose Isomerase Deficiency

Case study exercises are extensively used as a pedagogical tool not only to deliver the content but also to engage students in problem-solving using real-life scenarios. The transition to the virtual learning platform due to COVID-19 made it even more imperative to implement an inquiry-driven learning exercise that tethers various biochemistry concepts into one activity. Here, I present a case-based activity that was used to review and integrates multiple concepts taught in the introductory biochemistry course. This case study is derived from the clinical data of a newborn, diagnosed with hemolytic anemia pertaining to a defect in the phosphoglucose isomerase enzyme, and laboratory-generated research data comparing the wild type and the mutant proteins. This data-driven case study takes a question-guided approach to review acid–base chemistry, protein structure, protein purification, protein characterization, enzyme kinetics, mechanism, nucleic acids chemistry, carbohydrate chemistry, and metabolism. This activity is conducted over two lecture periods, allowing enough time to implement concepts learned during the entire semester to solve the questions in this activity. Furthermore, the case study helps students to identify some of the challenging concepts and guides them to generate a study list for the cumulative final exam. This activity has been conducted both in a face-to-face classroom setting and in a synchronous virtual classroom using Blackboard Collaborate Ultra. The survey of this activity clearly shows students’ enthusiasm toward participating in case-based learning in both modalities.

Game-based activities targeting visual literacy skills to increase understanding of biomolecule structure and function concepts in undergraduate biochemistry.

Introductory biochemistry courses are often challenging for students because they require the integration of chemistry, biology, physics, math, and physiology knowledge and frameworks to understand and apply a large body of knowledge. This can be complicated by students' persistent misconceptions of fundamental concepts and lack of fluency with the extensive visual and symbolic literacy used in biochemistry. Card sorting tasks and game-based activities have been used to reveal insights into how students are assimilating, organizing, and structuring disciplinary knowledge, and how they are progressing along a continuum from disciplinary novice to expert. In this study, game-based activities and card sorting tasks were used to promote and evaluate students' understanding of fundamental structure-function relationships in biochemistry. Our results suggest that while many markers of expertise increased for both the control and intervention groups over the course of the semester, students involved in the intervention activities tended to move further towards expert-like sorting. This indicates that intentional visual literacy game-based activities have the ability to build underdeveloped skills in undergraduate students.

Examining Curricular Trends in Introductory Biochemistry Courses at Large Universities

Current conversations in chemical education highlight the importance of student‐centered learning approaches and the need to implement such learning approaches in college classrooms. However, commentary and other conversations continue to suggest traditional lectures are predominantly used to teach biochemistry. The goal of this study was to determine curricular trends within introductory biochemistry courses at R1 institutions of higher education. By determining the current state of biochemistry education, strategies can be developed to promote student‐centered learning strategies, particularly in large lecture courses common in biochemistry at the introductory level. The primary focus of this study was to identify common teaching and learning strategies presented in course syllabi. Introductory‐level biochemistry syllabi were collected from 42 R1 institutions. All syllabi were approved by the American Chemical Society (ACS) or counted towards an ACS‐approved degree/program. Syllabi were assessed on course delivery methods, pedagogical strategies used within the course, forms of formative and summative assessment, activities to establish real‐world connections, and major topics presented to students. The results indicate that most courses were presented in a traditional lecture format with few integrating student‐centered strategies such as peer‐led team instruction. Similarly, few syllabi described instructional scaffolds used to construct real‐life connections with biochemistry content. Topics most frequently addressed in the courses included fundamental building blocks, biopolymers, and supramolecular structures. Not surprising was the ubiquitous use of large lecture‐style courses. Lecture has long been shown to be an efficient method of instruction that promote memorization of facts rather than cultivating complex understandings essential in problem‐solving. Results presented demonstrate the need for student‐centered strategies in biochemistry at R1 universities to promote deeper learning, develop critical thinking and problem‐solving skills, and foster connections between content and real‐world applications students could face in their future careers.

Teaching Biochemistry in Context

21st‐century biochemistry and molecular biology (BMB) education has recognized that the breadth of knowledge within the discipline is too expansive to expect students to retain the entirety of BMB content. Instead, BMB education has prioritized a competency‐based approach over a content‐focused curriculum. Examples of such demand include AAAS’s Vision and Change (https://visionandchange.org/) and ASBMB’s Foundational Concepts and Skills (https://www.asbmb.org/education/teachingstrategies/foundationalconcepts/). To meet the demand of a competency‐based curriculum, the sophomore‐level introductory biochemistry course at Juniata College uses as the primary course materials the scientific literature around a central theme (acetylcholine neurotransmission). The curriculum begins with a 16th‐century text and culminates in modern scientific work. Students work in teams to interrogate the 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 scientific papers. Attitudinal assessment of this social constructivist approach to BMB education revealed outcomes consistent with inclusivity and self‐efficacy, including gains in affect with respect to teamwork, curiosity, and scientific literacy. The narrative aspect of the course has led to several collaborative spin‐off projects including the translation of a 19th‐century medical text and an independent science education project. 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.

A Mixed Reality Application To Visualize Amino Acids

This study examines the benefit of using mixed reality to visualize amino acid molecules for students in introductory biochemistry courses at the undergraduate and graduate level. A Novel Microsoft HoloLens application that tests understanding of amino acid structures was developed. The application was made accessible to students by making it compatible with multiple platforms in addition to Universal Windows Platform; these platforms include Android and iOS as well as PC, Mac, and Linux stand‐alone. This was done using Unity3D with coding in C#. The success of application development and implementation in the classroom was tested by students of Biochemistry. The results of student attitude survey regarding the ease and benefit of the application on mixed reality, and any other platforms they choose to use it on, is presented hereinSupport or Funding InformationPRISE, WISER, Flora Stone Mather Center for Women, Case Western Reserve University

Systems thinking in biochemistry: Assessing students’ understanding of metabolic pathway dynamics and regulation

Systems thinking requires consideration of dynamic processes, how parts of a whole interact through causal relationships, and how such systems change over time, often in response to environmental stimuli. A systems thinking approach is essential to understanding the complexities of metabolic pathways, yet few tools exist to probe students’ proficiency in this area. We have developed and used an assessment instrument to measure undergraduate students’ understanding of biochemical pathway dynamics and regulation in a metabolic context. A community of biochemistry educators was involved in an iterative process of designing and testing the instrument and accompanying rubric. The assessment instrument was embedded on final exams in an introductory biochemistry course and student responses were collected over several terms. Analysis of student responses showed that most students were able to interpret visual conventions in an unfamiliar metabolic pathway. Furthermore, many students could make basic predictions about how the system would be expected to respond to changes. However, fewer students generated nuanced responses that accounted for both microscopic changes at the protein level and macroscopic changes in pathway product outputs. Interviews revealed that students struggled to process the volume of complex information provided in prompts and the metabolic pathway diagram. This suggests that supporting information processing skills may be an important part of teaching systems thinking and metabolic logic.Support or Funding InformationNSF‐DUE‐1224868

Rethinking enzyme kinetics: Designing and developing a biomolecular interactive tutorial (BIOMINT) learning tool for undergraduate students.

Enzyme kinetics is the study of enzymatic catalytic rates in biochemical reactions. This topic is commonly taught to life science students in introductory biochemistry courses during their undergraduate education. Unlike most other biochemistry topics, which focus on visual structures of biomolecules and their processes, enzyme kinetics is explained primarily through abstract mathematical and two-dimensional graphical plots. However, these abstract/symbolic representations often make it difficult for students to relate the kinetic parameters to the underlying molecular system that is being described. In this article, we present the design and development of a web-based multimedia interactive learning tool, biomolecular interactive tutorials (BIOMINT) to help students better bridge the relationships between these abstract mathematical models and the molecular behaviors, interactions, and dynamics that produce kinetic phenomena. This learning tool can be accessed at https://bit.ly/biomint. © 2019 International Union of Biochemistry and Molecular Biology, 48(1):74-79, 2020.

Analysis of student reasoning about Michaelis–Menten enzyme kinetics: mixed conceptions of enzyme inhibition

Student understanding regarding topics in upper-division courses, such as biochemistry, is not well represented in the literature. Herein we describe a study that investigated students’ reasoning about Michaelis–Menten enzyme kinetics and enzyme inhibition. Our qualitative study involved semistructured interviews with fourteen second-year students enrolled in an introductory biochemistry course. During the interviews students were provided an enzyme kinetics graph, which they were prompted to describe. Students were asked to look for patterns and trends in the data and interpret the graph to draw conclusions regarding the types of enzyme inhibition observed, providing the opportunity for the students to engage in the science practiceanalyzing and interpreting data. Findings indicate students were able to attend to the relevant parameters (VmaxandKm) in the graph and subsequently associate changes inVmaxandKmto different types of enzyme inhibitors. However, students expressed difficulty explaining why a specific type of inhibition caused the observed change in the kinetic parameters and there was confusion regarding the distinction between noncompetitive and uncompetitive inhibition. Based on our results, we suggest instruction on enzyme kinetics should emphasize qualitative descriptions of the particulate-level mechanisms related to competitive and noncompetitive inhibition, with less emphasis on discussions of uncompetitive and mixed inhibition in introductory biochemistry courses.

Blended Instruction in Introduction to Biochemistry Class

A challenge for biochemistry instructors is dealing with the volume and difficulty of concepts typically taught during semester‐long introductory biochemistry courses. Students struggle to grasp topics because they may not have enough in‐class instruction and practice time to process the new information. Blended learning strategies, such as the flipped classroom approach along with traditional lectures, may offer a solution to this concern. Herein we present the creation of a blended learning introductory biochemistry course. The course used online modules consisting of concept videos tied to active learning problem sets, followed by in‐class sessions of small groups to discuss the application of these concepts. Each topic was covered with a video presentation suited for display on mobile devices that focused on problem solving and an associated active learning project that encouraged practice and application of skills developed in that topic. Students were encouraged to take an online quiz after each set of core topics to assess their readiness in applying the concept. The initial implementation of this module was tested in the Introduction to Biochemistry class and the preliminary data is presented hereinSupport or Funding InformationNord Grant, UCITE, Case Western Reserve UniversityThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Monitoring how changes in pedagogical practices have improved student interest and performance for an introductory biochemistry course.

This study describes feedback on the effects of changes introduced in our teaching practices for an introductory biochemistry course in the Life Sciences curriculum. Students on this course have diverse educational qualifications and are taught in large learning groups, creating challenges for the management of individual learning. We used the constructive alignment principle, refining the learning contract and re‐drafting the teaching program to introduce active learning and an organization of activities that promotes the participation of all the students and helps their understanding. We also created teaching resources available through the university virtual work environment. Our research aimed to measure the effects of those changes on the students’ success. Monitoring of the student performance showed a continuous increase in the percentage of students who passed the course, from 2.13% to 33.5% in 4 years. Analysis of student perceptions highlighted that the teaching methodology was greatly appreciated by the students, whose attendance also improved. The recent introduction of clickers‐questions constituted a complementary leverage. The active involvement of the students and better results for summative assessments are altogether a strong motivation for teaching staff to continue to make improvements.

Individual and Small Groups Assessment – an instructional and evaluative strategy

Assessment is a curricular component that branches out and reaches virtually every aspect of a course. Over time, assessments seem to have lost their wide response characteristics, becoming restricted to measure the amount of knowledge retained by the students. Faced with the scenario of clear expansion of knowledge, it is widely recommended to develop more instructional methods of evaluation, emphasizing the development of skills such as problem solving and critical argumentation. Objective: This study aimed to verify if the use of small groups’ assessment constitute an instrument of instruction as well as of evaluation, which would help the students to learn more solidly and efficiently. Procedures: Seven written tests were applied during an introductory Biochemistry course, one at each end of a module. Students first answer the test individually and then answer the same test in small groups (4-5 students), giving one response per group. Results were treated by Mixed Methods Analysis . Qualitative data were collected through questionnaires and semi-structured interviews; quantitative data were obtained analyzing individual and groups tests performances. Results and discussion: 72,2% of the students (n = 75-159) consider the double assessment procedure an instructional process; 63,7% believe there are benefits with the use of these assessments for Biochemistry learning. Comparing individual and group performances, 71,8% of students who had low individual performance benefit from group assessment. This result gets clear when we consider the student’s average performance in the individual and group assessments: 94,1% of the students improve their grades. In other words, on average the group’s grade is higher than any individual’s grade. Additionally, the questionnaires patterns were confirmed by the interviews analysis. Conclusion: The overall results show that the groups’ assessments can be considered as a good instructional feature, increasing the student’s performance and improving their abilities in problem solving and critical argumentation.

Creating 3D physical models to probe student understanding of macromolecular structure.

The high degree of complexity of macromolecular structure is extremely difficult for students to process. Students struggle to translate the simplified two-dimensional representations commonly used in biochemistry instruction to three-dimensional aspects crucial in understanding structure-property relationships. We designed four different physical models to address student understanding of electrostatics and noncovalent interactions and their relationship to macromolecular structure. In this study, we have tested these models in classroom settings to determine if these models are effective in engaging students at an appropriate level of difficulty and focusing student attention on the principles of electrostatic attractions. This article describes how to create these unique models for four targeted areas related to macromolecular structure: protein secondary structure, protein tertiary structure, membrane protein solubility, and DNA structure. We also provide evidence that merits their use in classroom settings based on the analysis of assembled models and a behavioral assessment of students enrolled in an introductory biochemistry course. By providing students with three-dimensional models that can be physically manipulated, barriers to understanding representations of these complex structures can be lowered and the focus shifted to addressing the foundational concepts behind these properties. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(6):491-500, 2017.

Green Fluorescent Protein-Focused Bioinformatics Laboratory Experiment Suitable for Undergraduates in Biochemistry Courses

An introductory bioinformatics laboratory experiment focused on protein analysis has been developed that is suitable for undergraduate students in introductory biochemistry courses. The laboratory experiment is designed to be potentially used as a “stand-alone” activity in which students are introduced to basic bioinformatics tools and applications after they have covered fundamental aspects concerning the structure and function of proteins within a class. This laboratory experiment explores three different protein bioinformatics tasks using freeware programs available on the National Center for Biotechnology Information Web site. Students first determine the identity of a protein, and its close homologues, to which they have been given an amino acid sequence using the BLASTP search tool. They then perform a multiple alignment of this protein with a given selection of proteins using the COBALT program and analyze and interpret the alignment results to predict the most promising sites for mutagenesis. Last...