Undergraduate Biochemistry Curriculum Research Articles

Integrating Antiracism, Social Justice, and Equity Themes in a Biochemistry Class

A recent push toward addressing antiracism in science reveals a need to integrate discussions of racism, social justice, and equity into undergraduate STEM classes. Toward this end, in Fall 2020, a theme of “Racism is a Public Health Emergency” was incorporated as an overlay for an existing undergraduate biochemistry curriculum. This theme was used throughout the entire semester and involved discussions of racism, social justice, and equity that were directly integrated with the science content of the course. Students enrolled in the class were surveyed at the end of the semester regarding their perceptions of integrating discussions of racism, social justice, and/or equity into chemistry courses. Students indicated that the inclusion of the overlay increased the relevance of the course material, indicated a high level of understanding of the impact of bias and race on the field of biochemistry, and expressed overwhelmingly positive views regarding future inclusion of similar themes of equity and antiracism in chemistry courses. Additionally, student scores and answers on common final exam questions were compared to previous semesters, revealing that the inclusion of this overlay did not negatively impact coverage of biochemistry content.

Incorporating Anti‐Racism and Equity Themes in a Biochemistry Class

A strategy for addressing racism and promoting social justice was incorporated into an undergraduate biochemistry curriculum. The impetus for this change was to demonstrate solidarity with the Black Lives Matter movement and to support students traditionally excluded from STEM because of their ethnicity or race. At the same time, we hypothesized that inclusion of the theme, Racism is a Public Health Emergency, would make the material more relevant to students, without negatively impacting content coverage and learning. In the Fall 2020 semester, students engaged in seven activities related to the anti-racism overlay, spaced over the course of the semester. While 95% of the students in the course had previously encountered discussions about equity in previous classes, only one of them indicated that the material was covered in a chemistry course. The majority of the students (81%), moreover, agreed or strongly agreed that the inclusion of the anti-racism overlay made the course material more relevant to them. In addition, analysis of answers to final exam questions suggests student achievement of learning outcomes remained similar to previous iterations of the course. The activities detailed here, therefore, addresses an important need in biochemistry curricula to incorporate issues of social justice and could be adapted to a variety of other related fields.

Fast, Simple, Student Generated Augmented Reality Approach for Protein Visualization in the Classroom and Home Study

Facile visualization of biomolecules is an essential component of the undergraduate biochemistry curriculum. In the past, a number of tools have been used to display biomolecules. More recently, the advent of greater accessibility to virtual reality (VR) and augmented reality (AR) programs has created a new mechanism to visualize biomolecules. However, creation of VR and AR programs often requires extensive coding experience. In order to expand the utility of AR programs in visualization of biomolecules, we enabled undergraduate students to create their own AR protein visualization tool using an off-the-shelf program running in multiplatform smartphones or tablets to enhance student inclusivity. Assessment of this program shows that students can create their own biomolecule models, were enthusiastic about doing so, and found that their learning was enhanced when this AR module was inserted into their upper level biochemistry class. This activity could be readily adapted for remote and online learning.

31 P NMR of the pyruvate kinase reaction: An undergraduate experiment in enzyme kinetics.

Understanding how to perform an enzyme assay is a critical learning skill in the undergraduate biochemistry curriculum. Students in biochemistry typically have been exposed to the use of NMR spectroscopy as a tool to determine chemical structure, but rarely are they exposed to the utility of NMR to evaluate enzyme kinetics. Furthermore, coverage of NMR experiments utilizing "alternative nuclei", such as 15 N, 19 F, and 31 P may be neglected. Herein we report a simple 31 P NMR tube experiment that allows students to examine the enzyme kinetics and equilibrium constant of the reaction catalyzed by pyruvate kinase. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(6):509-514, 2017.

Site-Directed Mutagenesis Study of an Antibiotic-Sensing Noncoding RNA Integrated into a One-Semester Project-Based Biochemistry Lab Course

A laboratory sequence is described that is suitable for upper-level biochemistry or molecular biology laboratories that combines project-based and traditional laboratory experiments. In the project-based sequence, the individual laboratory experiments are thematically linked and aim to show how a bacterial antibiotic sensing noncoding RNA (the ykkCD riboswitch) recognizes its target antibiotic, tetracycline. The novelty of the curriculum lies in its extensive coverage of bioinformatics as well as its focus on synthesis, purification, and functional studies of a biologically active RNA. Further advantage of the curriculum is that the model system, the ykkCD riboswitch, regulates expression of a gene that is involved in bacterial antibiotic resistance. Hence, the project makes this important issue part of the undergraduate biochemistry curriculum. The curriculum is available in Open Access format as part of a biochemistry laboratory manual by Gerczei and Pattison. This manuscript summarizes the curriculum and provides suggestions to the instructor regarding its implementation.

Lighten the Load: Scaffolding Visual Literacy in Biochemistry and Molecular Biology.

The development of scientific visual literacy has been identified as critical to the training of tomorrow's scientists and citizens alike. Within the context of the molecular life sciences in particular, visual representations frequently incorporate various components, such as discipline-specific graphical and diagrammatic features, varied levels of abstraction, and spatial arrangements of visual elements to convey information. Visual literacy is achieved when an individual understands the various ways in which a discipline uses these components to represent a particular way of knowing. Owing to the complex nature of visual representations, the activities through which visual literacy is developed have high cognitive load. Cognitive load can be reduced by first helping students to become fluent with the discrete components of visual representations before asking them to simultaneously integrate these components to extract the intended meaning of a representation. We present a taxonomy for characterizing one component of visual representations-the level of abstraction-as a first step in understanding the opportunities afforded students to develop fluency. Further, we demonstrate how our taxonomy can be used to analyze course assessments and spur discussions regarding the extent to which the development of visual literacy skills is supported by instruction within an undergraduate biochemistry curriculum.

Improving undergraduate biochemistry curriculum using threshold concepts: an analysis of student understanding

Threshold concepts (TCs) are concepts that, when mastered, represent a transformed understanding of a discipline without which the learner cannot progress. TCs have been identified in many fields with the goal of redesigning curricula to best benefit the learning of the student. Student data was collected for three of the five biochemistry TCs (steady state, the physical basis of interactions, and the thermodynamics of macromolecular structure formation). Responses were analyzed to determine ubiquitous and nuanced themes in student understanding. Integrative themes including electrostatic properties of molecules, entropic and enthalpic contributions, free‐energy, and kinetics of regulatory systems were investigated due to their importance in biochemistry learning. Our analysis reveals that students often exhibit limited understanding of these concepts, thus they lack the depth of knowledge to fully integrate ideas and apply them to varied biochemical contexts.Support or Funding InformationNSF‐DUE‐1224868

Data‐driven assessment techniques to catalyze student learning (618.19)

As we rearticulate the undergraduate biochemistry curriculum to emphasize deep foundations in core biochemical principles and skills, we must also reconsider the assessment of student learning. Assessment is perhaps an instructor’s most powerful tool for affecting student learning, particularly when it is used to diagnose student understanding and to subsequently adjust activities to address learning difficulties. Yet, in undergraduate science teaching, assessment is largely employed as a summative activity, reducing its effectiveness as a tool for developing student understanding. While extensive research at the K‐12 level provides several insights into best practices for assessment, there is less research at the undergraduate level in general, and undergraduate science in particular.The purpose of the research presented here is to contribute to the growing literature base on effective assessments for undergraduate learning in the molecular life sciences. We designed and tested the efficacy of two formative assessment tools in large‐enrollment, introductory biochemistry courses for majors. Both tools make use of Learning Management Systems (e.g. Desire2Learn, Blackboard, WebCT) to formatively assess and diagnose student understanding and provide responsive feedback for instructors and students to inform learning. Data collected for analysis include: student clickstream data from Learning Management System usage, student open‐response items, student achievement data, and self‐report data. We will present results demonstrating the effectiveness of these tools in terms of (1) ability to uncover the range and extent of student reasoning difficulties, (2) ease and use by instructors, (3) utility to predict student performance and enact early warning systems for at‐risk students, and (4) impact on student learning.Grant Funding Source: Supported by the National Science Foundation, HRD‐0811239

The Introduction of Metagenomics into an Undergraduate Biochemistry Laboratory Course Yielded a Predicted Reductase That Decreases Triclosan Susceptibility in Escherichia coli

Traditional undergraduate science classes often include a laboratory component aimed at enabling the students to experience the classroom topics firsthand. Typically, these experiments are chosen because they have known outcomes that will clearly demonstrate particular aspects of scientific theory. While this approach has its benefits in skill development and concept reinforcement, the lack of novelty inherent in repeating experiments that have been repeated for many years does not accurately convey the feeling of true scientific discovery to the students. In this work, we have designed and implemented a series of experiments into an undergraduate biochemistry curriculum that incorporates the opportunity for scientific discovery, while simultaneously creating an environment for learning routine laboratory techniques. Through this set of experiments, students enrolled in the course were successful in identifying and beginning to characterize an unknown bacterial gene that confers increased tolerance to triclosan on its host.

Incorporation of bioinformatics exercises into the undergraduate biochemistry curriculum

AbstractThe field of bioinformatics is developing faster than most biochemistry textbooks can adapt. Supplementing the undergraduate biochemistry curriculum with data‐mining exercises is an ideal way to expose the students to the common databases and tools that take advantage of this vast repository of biochemical information. An integrated collection of exercises based on pet proteins has been assembled. The exercises described are applicable to either a lecture or laboratory format and require only basic desktop computers, an Internet connection, a current web browser, and the free Chime plug‐in module. In an open‐ended, inquiry‐based format, the assignments ask students to explore concepts such as the relative information content of the different biopolymers, the relationship between primary sequence and tertiary structure, and how sequence conservation can be used to find an enzyme active site.

RasMol and Mage in the Undergraduate Biochemistry Curriculum

Mage and RasMol, free visualization software used to view and manipulate three-dimensional images of proteins and nucleic acids, have been incorporated extensively in the undergraduate biochemistry courses at several institutions in the University System of Georgia. Some teaching and learning activities using RasMol and Mage, and new educational resources, including the GLACTONE Web site and a CD-ROM, are described. The results of a survey of students enrolled in undergraduate biochemistry courses at five institutions in the University System of Georgia indicate that an overwhelming majority of students felt strongly that using Mage and RasMol increased their understanding of biochemistry. The survey also indicates that the majority of students used RasMol or Mage outside of the classroom either on campus or at home. The majority of the students surveyed recommend that RasMol or Mage be used in freshman chemistry and high school. We have trained high school teachers and faculty at two-year colleges throughout Georgia to use RasMol and have demonstrated its possible applications in lower-level chemistry and biology courses.

Seminar experience in an undergraduate biochemistry curriculum

Seminar experience in an undergraduate biochemistry curriculum