Introductory Biochemistry Research Articles

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

Using Edpuzzle as a Method to Improve Student Engagement and Performance in the Introductory Biochemistry Laboratory

Various engagement tools have been commonly used within biochemistry courses to increase student engagement and maximize student exposure to material within the time constraints of a class session. These time constraints also extend to the laboratory component of these courses which often leads to increased levels of anxiety for students. One method that has been used successfully in the past to increase student understanding and performance during laboratory experiments is the utilization of pre‐laboratory video lectures. While the use of pre‐laboratory videos has been shown to be beneficial for students, instructors often have no efficient way of assessing student understanding of the video content prior to the laboratory session. Edpuzzle is a free online service that allows for instructors to upload videos and incorporate questions into videos at various points within the video to assess student understanding. In an effort to increase student performance in an introductory biochemistry laboratory, edpuzzle was adapted to engage students with the material in preparation for the laboratory session. Prior to each laboratory session, students viewed an edpuzzle video and answered questions to assess their understanding of the experimental details and concepts that would be covered in the lab. Surveys were conducted to determine student satisfaction, learning outcomes, and level of anxiety associated with the laboratory as a result of using edpuzzle as a laboratory preparation tool. Students reported high satisfaction rates, increased confidence during laboratory experiments, and decreased anxiety about the laboratory overall. The results suggest that students viewed the edpuzzle application as a valuable component of their laboratory preparation routine. Due to the flexibility of edpuzzle, it can be adapted for use in other chemistry or biology laboratories at various levels. In addition, edpuzzle can also be used as a supplementary tool for expanding lecture content.Support or Funding InformationFlorida Southern College Department of Chemistry, Biochemistry, & Physics

Learning Focus: Scaffolded Primary Literature Curriculum for Improved Student Skills

Essential student skills in the molecular life sciences include the ability to locate relevant chemical literature, to critically analyze and evaluate primary literature, and to communicate scientific understanding in written and oral forms. Often, students have difficulty using primary literature and there is a lack of resources for purposeful development of these skills. To improve undergraduate skills for reading, writing, and critiquing primary literature, a curriculum was developed for an introductory biochemistry lecture to allow students to engage with primary literature in a controlled environment and gradually increase their usage. The curriculum consisted of case studies relating to lecture topics and figure summaries, where students would locate a primary, peer‐reviewed research article and summarize one of the figures from the article. After gaining experience with primary literature in these assignments, students wrote a literature review on a protein’s structure‐function relationship. This scaffolded primary literature curriculum was intended to shift student learning from passive to active engagement by applying their knowledge to reading and critiquing science to improve their confidence. From 2016–2019, the curriculum was assessed using student evaluations, pre‐ and post‐surveys, and student writing samples. Students reported that they felt more comfortable understanding the background necessary to use and critique primary literature, and communicate about that literature in written form. Student performance on these assignments showed that statistical improvement in assignment scores was not achieved until the third case study or figure summary.

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.

Michaelis–Menten Graphs, Lineweaver–Burk Plots, and Reaction Schemes: Investigating Introductory Biochemistry Students’ Conceptions of Representations in Enzyme Kinetics

This work seeks to add to the growing body of chemistry education research that emphasizes the teaching and learning of advanced topics, focusing on students’ understanding of enzyme kinetics. The ...

Developing and Implementing a Free Online Protein Structure and Function Exploration Project To Teach Undergraduate Students Macromolecular Structure–Function Relationships

One of the learning outcomes of any undergraduate biochemistry course should be an appreciation of the relationship between structure and function in biological macromolecules. The availability of state-of-the-art modeling software provides an opportunity to achieve this goal in interesting ways. The Protein Structure and Function Exploration (PSAFE) project was developed at the University of Virginia to introduce undergraduate biochemists to the significance of structure–function relationships and the nuances of scientific writing. The PSAFE project uses the molecular-document capability of the ICM Browser (from Molsoft LLC) to accomplish its goals. Students in introductory biochemistry lecture courses are each assigned a particular protein or nucleic acid to study and characterize throughout the semester. The students progress from learning the basics of protein structure early in the course to a thorough analysis of their proteins and how they achieve their functions, culminating in production of a descriptive narrative by the end of the semester. The student projects are reviewed and edited and then uploaded to an archival website. More than 1100 such projects have now been archived on this site. The majority of the students in these courses report that the PSAFE project was a challenging but highly satisfying experience that greatly enriched their understanding and appreciation of protein structure. PSAFE Online is now available to any interested instructors and students.

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.

Bisubstrate Kinetics of Glutathione S-Transferase: A Colorimetric Experiment for the Introductory Biochemistry Laboratory

Most biochemical transformations involve more than one substrate. Bisubstrate enzymes catalyze multiple chemical reactions in living systems and include members of the transferase, oxidoreductase, and ligase enzyme classes. Working knowledge of bisubstrate enzyme kinetic models is thus of clear importance to the practicing biochemist. However, such models are infrequently explored in the undergraduate biochemistry laboratory. This deficiency suggests the need for well-defined, tractable, and economical methods for characterization of bisubstrate enzyme activity. The application of an established real-time colorimetric assay to investigate kinetic parameters of glutathione transfer by glutathione S-transferase is described. The reported method relies on commercially available materials and uses experimental conditions that are suited to application in the introductory biochemistry laboratory. Investigation of bisubstrate kinetic parameters was performed as part of a three-week laboratory experiment that em...

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.

Execution and assessment of a mindset intervention in an introductory biochemistry class

Academic achievement results from a growth mindset that includes learning to fail, complex thinking and hard work and does not spring simply from intelligence, spontaneity, special skills, offbeat or extremely unusual ideas and behavior, although all of these may, in particular aspects, be involved. Mindset can be cultivated through the targeted use of several interventions that are not disciplinary specific. For this study, the mindset intervention was executed in a first term biochemistry class. The intervention was based on work of Dounas‐Fazer et al and the use of associative learning exercises. Each week students did an associative learning exercise and used a self‐evaluation rubric to reflect on a series of skills important to academic success. The assessment of this intervention was done using the Berkeley Innovation Index and student assessment of learning gains. There was an improvement both in student mindset and learning gains.Support or Funding InformationMellon Foundation

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...

Lowering the activation barrier, not the academic bar: The role of contract grading in decreasing DFW rates in introductory biochemistry

Introductory biochemistry for majors is an upper‐level course that serves students from over three colleges and fifteen different majors with diverse academic backgrounds preparing them for success. As one example, students’ self‐reported chemistry preparation was identified as a factor that, in conjunction with prior GPA and score on the Introductory Molecular and Cell Biology Assessment, predicted 44% of variance in student performance. In this study, we used predictive variables to identify “at risk” students, those at high risk of earning a D or F or withdrawing from biochemistry and offer them a targeted opportunity to develop the higher‐order skills necessary to improve performance. Specifically, we employed a contract grading system; if students fulfilled all aspects of the contract they were guaranteed a C for the course. The contract required students to complete 15 obligations throughout the remainder of the semester, including attending regular help sessions, taking comprehensive notes, creating concept maps, and peer‐reviewing other C contract students’ work. After the first exam, 146 students were identified as “at‐risk”. Seventy‐five students signed the contract; twenty students completed all requirements. We compared student performance on major assessments for at‐risk students who (a) did not opt‐in to the contract, (b) opted in but did not complete the contract, and (c) completed the contract. 95% of students completing the contract earned enough points to achieve at least a C in the course, 45% earned a B or better (as compared to just 24% for students who started the contract but did not complete). Controlling for prior GPA, IMCA score, and self‐report chemistry preparation, we confirmed a statistically significant difference (p<0.01) between students who completed the contract and those who started but did not finish or opted out completely. Course assessments analyzed and a Weighted Bloom's Index for major assessments were calculated. Course assessments were at comparable or higher cognitive skill level than previous control semesters. These data suggest that a contract grading system provides the needed structure to support at‐risk students in developing the skills necessary to improve performance in introductory biochemistry. These data are consistent with previous work examining the role of high‐structure learning environments in supporting low performing students.

A Ten Week, First‐semester Biochemistry Lab Course Studying Bacterial Alkaline Phosphatase

In a traditional introductory biochemistry lab, students are expected to learn a variety of standard biochemical techniques. One of the challenges in designing a lab curriculum is finding a way to engage students in a way where they not only learn the necessary skills, but see how different aspects of biochemistry work together with one another. This work describes a 10 week laboratory project studying wild‐type and mutant bacterial alkaline phosphatase, where students purifying, quantitate, and perform kinetic assays on wild‐type and selected mutants of the enzyme. Additionally, students also perform vector DNA analysis. In addition to simply learning important techniques, students acquire novel biochemical data in their kinetic analysis of mutant enzyme. The experiments are designed to build on student's work from week to week in a way that encourages students to apply quantitative analysis and reasoning skills, reinforcing traditional textbook biochemical concepts. Students are assessed through lab reports focused on journal style writing, quantitative and conceptual question sheets, and traditional exams. Students also are surveyed to obtain data relating to their perception of the efficacy of the course design and in achievement of learning outcomes.Support or Funding InformationThis work was supported by The University of Tampa Dana Foundation Grant; The University of Tampa David Delo Research Professor Grant; The University of Tampa College of Natural and Health Sciences; and The University of Tampa Department of Chemistry, Biochemistry, and Physics.

Exploring the Use of an Online Quiz Game to Provide Formative Feedback in a Large-Enrollment, Introductory Biochemistry Course

Exploring the Use of an Online Quiz Game to Provide Formative Feedback in a Large-Enrollment, Introductory Biochemistry Course

Acceptance of clickers in a large multimodal biochemistry class as determined by student evaluations of teaching: Are they just an annoying distraction for distance students?

A student response system (clickers) was introduced into a second year introductory biochemistry class to improve student engagement and performance. The class was delivered in both internal and distance education (DE) modes, with the DE students receiving recordings of the lectures (including clicker activities). However, there was concern over the use of clickers in internal classes as it may be alienating or distracting to DE students while reviewing the recordings of these lectures. In order to examine students' attitudes toward clickers, closed- and open-ended questions were examined in the student evaluations of teaching (SET). Understanding attitudes of internal and DE students is especially important as differences may exist between these groups due to the different learning environments they experience. Approximately 45% of students completed the surveys, of which 88%-91% provided written comments. Of the written comments, 18% of DE students and 22% of internal students provided unsolicited comments about clickers. Interestingly, no difference was observed in the themes identified in the comments between cohorts. The key themes included 1) clickers were beneficial for learning (and increased knowledge), 2) clickers were engaging/fun, and 3) clickers could have been used more widely. Overall, based on this study, it was believed that clicker usage was not seen as negative activity by DE students and it was worth continuing to use clickers in teaching the large multimodal class studied here. However, there is a need to investigate the potential of new and emerging technologies to provide more interactive experiences for DE students.

Osmotic Stressing, Membrane Leakage, and Fluorescence: An Introductory Biochemistry Demonstration

A fluorescence demonstration is described that incorporates several fundamental aspects of an introductory biochemistry course. A variation of a known leakage assay is utilized to prepare vesicles containing a quenched fluorophore. The vesicles are exposed to several osmotic environments ranging from isotonic to hypotonic. The degree of vesicle swelling, partial rupture or bursting, and subsequent release and dequenching of the encapsulated fluorophore can be observed. This demonstration introduces students to fluorescence, fluorescence quenching, lipid membrane dynamics, membrane permeability, and osmotic pressure. Students are also introduced to the lipid extrusion process and are able to observe the separation of compounds via size exclusion chromatography. This demonstration has the flexibility to be expanded to laboratory experiments that allow students to investigate a variety of membrane properties.